Medical Policy: 02.04.50 

Original Effective Date: April 2015 

Reviewed: March 2019 

Revised: March 2019 

 

Benefit Application:

Benefit determinations are based on the applicable contract language in effect at the time the services were rendered. Exclusions, limitations or exceptions may apply. Benefits may vary based on contract, and individual member benefits must be verified. Wellmark determines medical necessity only if the benefit exists and no contract exclusions are applicable. This medical policy may not apply to FEP. Benefits are determined by the Federal Employee Program.

 

This Medical Policy document describes the status of medical technology at the time the document was developed. Since that time, new technology may have emerged or new medical literature may have been published. This Medical Policy will be reviewed regularly and be updated as scientific and medical literature becomes available.

 

Description:

Whole Exome Sequencing (WES)

Whole exome sequencing (WES) sequences consists of analysis of the protein-coding regions of the human genome, either DNA or RNA. This comprises <2% of the genome and involves the areas currently beli eved to be the most likely to include mutations that result in clinical phenotypes and disease. Such large-scale genomic sequencing has been proposed for use in scenarios suggesting a single genetic etiology but lacking a clear diagnostic testing path and in which stepwise testing can result in costly and prolonged diagnostic odyssey.

 

A potential major indication for use is molecular diagnosis of individuals with a phenotype that is suspicious for a genetic disorder or for individuals with known genetic disorders that have a large degree of genetic heterogeneity involving substantial gene complexity. Such individuals may be left without a clinical diagnosis of their disorder, despite a lengthy diagnostic work-up involving a variety of traditional molecular and other types of conventional diagnostic tests. For some of these individuals, WES, after initial conventional testing has failed to make the diagnosis, may return a likely pathogenic variant.

 

Given the variety of disorders and management approaches, there are a variety of potential health outcomes from a definitive diagnosis. In general, the outcomes of a molecular genetic diagnosis include 1) impacting the search for diagnosis, 2) informing follow-up that can benefit a child by reducing morbidity, and 3) affecting reproductive planning for parents and potentially the affected patient.

 

The standard diagnostic work-up for patients with suspected Mendelian (genetic disease which follows simple mendelian patterns of inheritance) may include combinations of radiographic, electrophysiologic, biochemical, biopsy, and targeted genetic evaluations. The search for a diagnosis may become a time consuming and expensive process.

 

Whole Genome Sequencing (WGS)

Whole genome sequencing (WGS)/rapid whole genome sequencing, also known as full genome sequencing, complete genome sequencing or entire genome sequencing, is a laboratory procedure which seeks to determine an individual’s entire DNA sequence, specifying the order of every base pair within the genome at a single time. WGS allows researchers to study 98% of the genome that does not generally contain protein coding genes. The clinical role of WGS has yet to be established. Research is still being done to determine if WGS can be used to accurately identify the presence of a disease, predict the development of a particular disease in asymptomatic individuals as well as how an individual might respond to pharmacological therapy. It has been theorized that WGS might eventually improve clinical outcomes by preventing the development of disease.

 

Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS) Technology

WES or WGS/rapid whole genome sequencing using next-generation sequencing technology can facilitate obtaining a genetic diagnosis in patients. WES is limited to most of the protein-coding sequence of an individual (85%), is composed of about 20,000 genes and 180,000 exons (protein-coding segments of a gene), and constitutes approximately 1% of the genome. It is believed that the exome contains about 85% of heritable disease-causing mutations. WES has the advantage of speed and efficiency relative to Sanger sequencing of multiple genes. WES shares some limitations with Sanger sequencing. For example, it will not identify the following: intronic sequences or gene regulatory regions; chromosomal changes; large deletions; duplications; or rearrangements within genes, nucleotide repeats, or epigenetic changes. WGS uses techniques similar to WES, but includes noncoding regions. WGS has greater ability to detect large deletions or duplications in protein-coding regions compared with WES, but requires greater data analytics. Technical aspects of WES and WGS are evolving, including the development of databases such as the National Institutes of Health’s ClinVar database to catalog variants, uneven sequencing coverage, gaps in exon capture before sequencing, and difficulties with narrowing the large initial number of variants to manageable numbers without losing likely candidate mutations. The variability contributed by the different platforms and procedures used by different clinical laboratories offering exome sequencing as a clinical service is unknown.

 

American College of Medical Genetics and Genomics issued a policy statement regarding the use of genomic testing that recommends testing be considered in phenotypically affected individual when:

  • The phenotype or family history data strongly implicates a genetic etiology, but the phenotype does not correspond with a specific disorder for which a genetic test targeting a specific gene is available on a clinical basis.
  • A patient presents with a defined genetic disorder that demonstrates a high degree of genetic heterogeneity, making WES or WGS analysis of multiple genes simultaneously a more practical approach.
  • A patient presents with a likely genetic disorder in which specific genetic tests available for that phenotype have failed to arrive at a diagnosis.

 

One of the most complex issues surrounding whole exome and whole genomic testing is the risk of incidental or secondary finding, where mutations unrelated to the clinical phenotype or variants of uncertain significance are identified. While incidental identification of clinically significant mutations pose issues of informed consent, these findings often have medical management recommendations. However, even among the 56 genes recommended for the reporting of incidental findings by the ACMG, there are challenges in determining phenotype consequences of variants identified. Experts agree that the involvement of trained genetics professionals in consulting with patients and families are essential prior to and after ordering and completing genetic testing.

 

Whole Exome Sequencing (WES) in Patients with Multiple Congenital Anomalies and Neurodevelopmental Disorders

Clinical Content and Test Purpose

The purpose of whole exome sequencing (WES) in patients who have multiple unexplained congenital anomalies or a neurodevelopmental disorder is to establish a molecular diagnosis. The criteria under which diagnostic testing for a genetic or heritable disorder may be considered clinically useful are as follows:

  • A definitive diagnosis cannot be made based on history, physical examination, pedigree analysis, and/or standard diagnostic studies or tests;
  • The clinical utility of a diagnosis has been established (e.g. by demonstrating that a definitive diagnosis will lead to changes in clinical management of the condition, changes in surveillance, or changes in reproductive decision making, and these changes will lead to improved health outcomes); and
  • Establishing the diagnosis by genetic testing will end the clinical work-up for other disorders.

 

Patients

The relevant population of interest is patients presenting with multiple unexplained congenital anomalies or neurodevelopmental disorder that are suspected to have a genetic basis but are not explained by standard clinical workup.

 

Comparators

The following practice is currently being used to diagnose multiple unexplained congenital anomalies or a neurodevelopmental disorder: standard clinical workup without WES.

 

Outcomes

The general outcomes of interest are accuracy of next-generation sequencing (NGS) compared with Sanger sequencing, the sensitivity and specificity and positive and negative predictive value for the clinical condition, and improvement in health outcomes. Heath outcomes include a reduction in morbidity due to appropriate treatment and surveillance, the end of the diagnostic odyssey, and effects on reproductive planning for parents and potentially the affected patient.

 

False-positive test results can lead to misdiagnosis and inappropriate clinical management. False-negative test results can lead to a lack of genetic diagnosis and continuation of the diagnostic odyssey.

 

Timing

The timing of the diagnostic accuracy outcomes of interest is time to diagnosis.

 

Setting

WES tests are offered commercially through various manufacturers.

 

Clinically Valid

A test must detect the presence or absence of a condition, the risk of developing a condition in the future, or treatment response (beneficial or adverse).

 

A number of studies have reported on the use of whole exome sequencing (WES) in clinical practice. Typically, the populations included in these studies have suspected rare genetic disorders, although the specific populations vary.

 

The largest reason for referral to a tertiary care center was an unexplained neurodevelopmental disorder. Many patients have been through a standard clinical workup and testing without identification of a genetic variant to explain their condition. Diagnostic yield in these studies is defined as the proportion of tested patients with clinically relevant genomic abnormalities. Testing parent-child trios has been reported to increase diagnostic yield, to identify an inherited variant from an unaffected parent and be considered benign, or to identify a de novo variant not present in an unaffected parent. Because there is no reference standard for the diagnosis of patients who have exhausted alternative testing strategies, clinical confirmation may be the only method for determining false-positive and false-negative rates. No reports were identified of incorrect diagnoses, and how often they might occur is unclear.

 

The below table outlines the diagnostic yields of whole exome sequencing (WES) for congenital anomalies or a neurodevelopmental disorder.

StudyPatient PopulationNStudy DesignYield, n (%)Additional Information
Wright et. al. 2018 Children with severe undiagnosed neurodevelopmental disorders, and/or congenital anomalies, abnormal growth parameters, dysmorphic features and unusual behavioral phenotypes 1,133 Reanalyzed existing data using improved variant calling methodologies, novel variant detection algorithms, updated variant annotation, evidence-based filtering strategies, and newly discovered disease-associated genes Able to diagnose an additional 182 individuals, taking the overall diagnostic yield to 454 out of 1,133 (40%); another 43 (4%) had a finding of uncertain clinical significance This study highlights the importance of coupling large scale research with clinical practice
Nambot et. al. (2018) Children with congenital anomalies and intellectual disability with a negative prior diagnostic work-up 416 Retrospective study examined 416 consecutive tests performed over 3 years to demonstrate the effectiveness of periodically reanalyzing whole exome sequencing (WES) data. Out of the 416 patients included, data for 156 without a diagnosis were reanalyzed. Obtained 24 additional diagnoses, the final yield of positive results was 27.9% through strict diagnostic approach and 2.9% through an additional research strategy This study highlights the effectiveness of periodically combining diagnostic reinterpretation of clinical whole exome sequencing (WES) data with translational research involving data sharing for candidate genes
Evers et. al. (2017) Children with undiagnosed neurodevelopment disorders (NDD), neurometabolic disorders and dystonias 72 Prospective study, referral and selection unclear Overall all 35%; in 36% of patients with NDD, 43% of patients with neurometabolic disorders, and 25% of patients with dystonias Clinical implications included management changes in 8 cases and impact on family planning in 20 families
Vissers et. al. (2017) Children with complex neurologic disorders of suspected genetic origin 150 Prospective comparative study. All patients received both the standard diagnostic work-up (e.g. cerebral imaging, muscle biopsies or lumbar punctures, and sequential gene-by-gene-based testing) and whole exome sequencing (WES) simultaneously Whole exome sequencing (WES) identified 29.3% compared with the standard pathway 7.3% Data supports the use in whole exome sequencing (WES) in pediatric neurology for disorders or presumed genetic origin
Rossi et. al. (2017) Individuals with autism spectrum disorder or autistic features referred for whole exome sequencing 163 Selected from 1200 consecutive retrospective samples from commercial lab 25.8% (42 of 163) for positive or likely positive findings 66.3% of patients already had a clinician reported autism diagnosis
Nolan et. al. (2016) Children with unexplained neurodevelopment disorders (NDD) 53 Retrospective chart review of patients evaluated in the University of Michigan Pediatric Neurology Clinic Whole exome sequencing (WES) improved the presumptive diagnostic rate in patient cohort from 25% to 48% Clinical implications included family planning, medication selection, and systematic investigation. Compared to current second tier testing, whole exome sequencing (WES) can result in lower long-term charges and more timely diagnosis
Stark et. al. (2016) Infants with suspected monogenic disorders 80 Prospectively evaluate the diagnostic and clinical utility of singleton whole exome sequencing (WES) compared with standard investigation including single or multigene panel sequencing when clinically indicated 46 infants received a molecular genetic diagnosis through singleton WES (57.5%) compared with 11 (13.75%) who underwent standard investigations in the same patient group Clinical management changed following exome diagnosis in 15 of 46 diagnosed participants (32.6%). Twelve relatives received a genetic diagnosis following cascade testing, and 28 couples were identified as being at high risk of recurrence in future pregnancies. This prospective study providers strong evidence for increased diagnostic and clinical utility of singleton whole exome sequencing (WES) as a first tier sequencing test for infants with suspected monogenic disorder
Tarailo-Graovac et. al. (2016) Exome sequencing in patients with intellectual developmental disorder and unexplained metabolic phenotypes 41 Consecutively enrolled patients referred to a single center A diagnosis was obtained in 28 of 41 (68%) who were evaluated A change in treatment beyond genetic counseling in 44% of patients with whole exome sequencing (WES)
Farwell et. al. (2015) Families with undiagnosed genetic conditions 500 Referred to a clinical laboratory for diagnostic exome sequencing A positive or likely positive result was identified in 30% of patients (152/500); a novel gene finding was identified in 7.5% of patients (31/416); the highest diagnostic rates were observed among patients with ataxia, multiple congenital anomalies and epilepsy (44, 36 and 35% respectively). This data demonstrated the utility of family based exome sequencing and analysis to obtain the highest reported detection rate in an unselected cohort, illustrating the utility of diagnostic exome sequencing for the molecular diagnosis of genetic disease
Wright et. al. (2015) Children with undiagnosed developmental disorders and their parents 1133 Deciphering Developmental Disorders (DDD) study developed a UK wide patient recruitment network involving over 180 clinicians across all 24 regional genetic services, performing genome-wide microarray and whole exome sequencing Achieved a diagnostic yield of 27% Implementation of a robust translational genomics workflow is achievable within a large scale rare disease research study to allow feedback of potentially diagnostic findings to clinicians and research participants
Yang et. al. (2014) Individuals with suspected genetic disorders 2000 (primarily pediatric 1756 88%) Whole-exome sequencing (WES) tests were performed at a clinical genetics laboratory in the United States and results were reported by clinical molecular geneticists certified by the American Board of Medical Genetics and Genomics A molecular diagnosis was reported in 504 patients (25.2%) with 58% of the diagnostic mutations not previously reported Whole exome sequencing (WES) provided a potential molecular diagnosis for 25% of a large cohort of patients referred for evaluation of suspected genetic conditions
Lee et. al. (2014) Children with suspected rare Mendelian disorders 814 Consecutive patients with undiagnosed genetic conditions at the University of California, Los Angeles, Clinical Genomics Center. Clinical exome sequencing was conducted as trio-CES (both parents and their affected child sequenced simultaneously) or as proband CES only on the affected individual when parental samples were not available Of the 814 cases, the overall molecular diagnosis rate was 26%. The molecular diagnosis rate for trio-CES was 31% and 22% for proband-CES In this sample of patients with undiagnosed, suspected genetic conditions, trio-CES was associated with higher molecular diagnostic yield than proband-CES or traditional molecular diagnostic methods
Iglesias et. al. (2014) Common indications for testing were birth defects and developmental delay 115 (78.9% were children) Usefulness of whole-exome sequencing (WES) in routine clinical practice Out of 115 patients a definitive diagnosis was made in 37 patients (32.2%) Establishing a diagnosis led to discontinuation of additional planned testing in all patients, screening for additional manifestations in eight, altered management in fourteen, novel therapy in two, identification of other familial mutation carriers in five and reproductive planning in six
Soden et. al. (2014) Children with unexplained neurodevelopmental disorders (NDD) 119 children (100 families) Effectiveness of exome and genome sequencing in the diagnosis of neurodevelopmental disorders, single center database 45% received molecular diagnosis A change in clinical care or impression of the pathophysiology was reported in 49% of families
Srivastava et. al. (2014) Children with various neurodevelopmental disabilities 78 Retrospective cohort study analyzing patients in a pediatric neurogenetics clinic who underwent whole exome sequencing (WES) The overall presumptive diagnostic rate 41% The high diagnostic yield of whole exome sequencing (WES) supports its use in pediatric neurology practice
Yang et. al. (2013) Suspected genetic disorders 250 (80% were children) Consecutive patients at single center 25% molecular diagnostic rate Whole exome sequencing (WES) identified the underlying genetic defect in 25% of consecutive patients referred for evaluation of a possible genetic condition

 

Clinically Useful

A test is clinically useful if the use of the results informs management decisions that improve the net health outcome of care. The net health outcome can be improved if patients receive correct therapy, or more effective therapy, or avoid unnecessary therapy, or avoid unnecessary testing.

 

Direct evidence of clinical utility is provided by studies that have compared health outcomes for patients managed with and without the test. Because these are intervention studies, the preferred evidence would be from randomized controlled trials (RCTs).

 

Indirect evidence on clinical utility rests on clinical validity. If the evidence is insufficient to demonstrate test performance, no inferences can be made about clinical utility.

 

Cohort studies following children from presentation to outcomes have not been reported. There are considerable challenges conducting studies of sufficient size given the underlying genetic heterogeneity, and including follow-up adequate to observe final health outcomes. Studies addressing clinical utility have reported mainly diagnostic yield and management changes. Thus, it is difficult to quantify lower or upper bounds for any potential improvement in the net health outcome owing in part to the heterogeneity of disorders, rarity, and outcome importance that may differ according to identified pathogenic variants. Actionable items following testing in the reviewed studies included family planning, change in management, change or avoidance of additional testing, surveillance for associated morbidities, prognosis, and ending the diagnostic odyssey.

 

The evidence reviewed supports a perspective that identifying a pathogenic variant can (1) impact the search for a diagnosis, (2) inform follow-up that can benefit a child by reducing morbidity and rarely potential mortality, and (3) affect reproductive planning for parents and later potentially the affected child. When recurrence risk can be estimated for an identified variant (e.g. by including parent testing), future reproductive decisions can be affected. Early use of WES can reduce the time to diagnosis and reduce the financial and psychological burdens associated with prolonged investigation.

 

Summary

For individuals who have multiple unexplained congenital anomalies or a neurodevelopment phenotype who receive whole exome sequencing (WES), the evidence includes case series. Patients who have multiple congenital anomalies or a neurodevelopment disorder with a suspected genetic etiology, but the specific alteration is unclear or unidentified by a standard clinical workup (chromosomal microarray analysis, chromosomal karyotype, fluorescence in situ hybridization (FISH), metabolic testing, imaging, single gene tests, referrals to other specialists), may be left without a clinical diagnosis of their disorder, despite a lengthy clinical workup. These case series have reported diagnostic yields of WES ranging from 25% to 68%, depending on the individual’s age, phenotype, and previous workup. Comparative studies have reported an increase in diagnostic yield compared with standard testing strategies. Thus, for individuals who have a suspected genetic etiology but for whom the specific genetic alteration is unclear or unidentified by standard clinical work-up, WES may return a likely pathogenic variant. A genetic diagnosis for these patients is reported to change management, including medication changes, discontinuation of or additional testing, ending the diagnostic odyssey and family planning. The evidence is sufficient to determine that this testing results in meaningful improvement in the net health outcome for multiple congenital anomalies and neurodevelopmental disorders.

 

Whole Exome Sequencing (WES) for Epilepsy and Seizure Disorders

Epilepsy is a common neurological disorder affecting 1-1.5% of the world’s population and is more commonly diagnosed in children than adults. Epilepsy is often accompanied by cognitive and developmental delay. A detailed family history is mandatory as a family history of seizures may suggest a dominantly inherited epileptic disorder. If a genetic disorder is suspected as the cause of epilepsy or seizure disorder a timely diagnosis may reduce overall cost, limit the diagnostic odyssey, improve prognostication and lead to targeted therapy. Genetic counseling should be available to these patients, and the genetic evaluation should be undertaken at a tertiary level of care. Generally, genetic testing is not recommended in drug responsive epilepsy/seizure disorder or at epilepsy/seizure onset, although genomic hybridization (CHG – karyotype, FISH, CMA) and single gene sequencing can be used as first tier evaluation of patients with global developmental delay, which is a population that is at higher risk of epilepsy/seizure disorders.

 

Patients who have seizure or epilepsy disorder with a suspected genetic etiology, which is unclear or unidentified by standard clinical workup, may be left without a clinical diagnosis of their disorder and for a portion of these patients, whole exome sequencing (WES) may return a likely pathogenic variant.

 

Farwell et. al. (2015) reported on results from the first 500 probands referred to a clinical laboratory for diagnostic exome sequencing in families with undiagnosed genetic conditions. Family-based exome sequencing included whole-exome sequencing followed by family inheritance-based model filtering, comprehensive medical review, familial cosegregation analysis, and analysis of novel genes. A positive or likely positive result in a characterized gene was identified in 30% of patients (152/500). A novel gene finding was identified in 7.5% of patients (31/416). The highest diagnostic rates were observed among patients with ataxia, multiple congenital anomalies, and epilepsy (44, 36, and 35%, respectively). Twenty-three percent of positive findings were within genes characterized within the past 2 years. The diagnostic rate was significantly higher among families undergoing a trio (37%) as compared with a singleton (21%) whole-exome testing strategy. The authors concluded, the data demonstrates the utility of family-based exome sequencing and analysis to obtain the highest reported detection rate in an unselected clinical cohort, illustrating the utility of diagnostic exome sequencing as a transformative technology for the molecular diagnosis of genetic disease.

 

In 2016, Allen et. al. in a single-center study investigated a cohort of 50 children with unexplained early onset epileptic encephalopathy (EOEE) using whole exome sequencing (WES). They characterized all phenotypes in detail and classified children according to known electroclinical syndromes where possible. Infants with previous genetic diagnoses, causative brain malformations, or inborn errors of metabolism were excluded. They identified disease-causing variants in 11 children (22%) in the following genes: STXBP1 (n = 3), KCNB1 (n = 2), KCNT1, SCN1A, SCN2A, GRIN2A, DNM1, and KCNA2. They also identified two further variants (in GRIA3 and CPA6) in two children requiring further investigation. Eleven variants were de novo, and in one paternal testing was not possible. Phenotypes were broadened for some variants identified. The authors concluded, this study demonstrates that WES is a clinically useful screening tool for previously investigated unexplained EOEE and allows for reanalysis of data as new genes are being discovered. Detailed phenotyping allows for expansion of specific gene disorders leading to epileptic encephalopathy and emerging sub-phenotypes.

 

Tsuchida et. al. (2018) reported on the detection of copy number variations (CNV) in epilepsy using exome data. Epilepsies are common neurological disorders and genetic factors contribute to their pathogenesis. Copy number variations (CNVs) are increasingly recognized as an important etiology of many human diseases including epilepsy. Whole-exome sequencing (WES) is becoming a standard tool for detecting pathogenic mutations and has recently been applied to detecting CNVs. They analyzed 294 families with epilepsy using WES, and focused on 168 families with no causative single nucleotide variants in known epilepsy-associated genes to further validate CNVs using 2 different CNV detection tools using WES data. They confirmed 18 pathogenic CNVs, and 2 deletions and 2 duplications at chr15q11.2 of clinically unknown significance. Of note, they were able to identify small CNVs less than 10 kb in size, which might be difficult to detect by conventional microarray. We revealed 2 cases with pathogenic CNVs that one of the 2 CNV detection tools failed to find, suggesting that using different CNV tools is recommended to increase diagnostic yield. Considering a relatively high discovery rate of CNVs (18 out of 168 families, 10.7%) and successful detection of CNV with <10 kb in size, CNV detection by WES may be able to surrogate, or at least complement, conventional microarray analysis.

 

Summary

Patients who have seizure or epilepsy disorder with a suspected genetic etiology, which is unclear or unidentified by standard clinical workup, may be left without a clinical diagnosis of their disorder and for a portion of these patients, WES may return a likely pathogenic variant. Based on review of the peer reviewed medical literature which consists of case series, these case series have reported diagnostic yields of WES of 35%.  A genetic diagnosis for these patients is reported to change management, including medication changes, discontinuation of or additional testing, ending the diagnostic odyssey and family planning.  The evidence is sufficient to determine that this testing results in meaningful improvement in the net health outcome for epilepsy/seizure disorders.

 

Whole Exome Sequencing (WES) for a Suspected Genetic Disorder Other Than Multiple Congenital Anomalies, Neurodevelopmental Disorders or Epilepsy/Seizure Disorders

Clinical Context and Test Purpose

Most of the literature on whole exome sequencing (WES) is on neurodevelopmental disorders in children; however, other potential indications for WES have been reported. These include limb-girdle muscular dystrophy, inherited retinal disease, and other disorders including mitochondrial, endocrine, and immunologic disorders. The yield for unexplained limb-girdle muscular dystrophy and retinal disease is high, but a limited number of patients have been studied to date.

 

The purpose of WES in patients who have a suspected genetic disorder other than multiple unexplained congenital anomalies, a neurodevelopmental disorder or epilepsy/seizure disorders is to establish a molecular diagnosis. The criteria under which diagnostic testing for a genetic or heritable disorder may be considered clinically useful are as above.

 

Comparators

The following practice is currently being used to diagnose a suspected genetic disorder other than multiple unexplained congenital anomalies or a neurodevelopmental disorder: standard clinical workup without WES. 

 

Outcomes

The general outcomes of interest are the accuracy of next generation sequencing (NGS) compared with Sanger sequencing, the sensitivity and specificity and positive and negative value for the clinical condition, and clinical health outcomes. Health outcomes include a reduction in morbidity due to appropriate treatment and surveillance, the end of the diagnostic odyssey, and effects on reproductive planning for parents and potentially the affected patient.

 

Timing

The test is performed when standard clinical workup has failed to arrive at a diagnosis.

 

Setting

Whole exome sequencing (WES) tests are offered commercially through various manufacturers.

 

Clinically Valid

A test must detect the presence of absence of a condition, the risk of developing a condition in the future, or treatment response (beneficial or adverse).

 

Studies have assessed whole exome sequencing (WES) for a broad spectrum of disorders. Some studies used a virtual gene panel that is restricted to genes that are associated with the phenotype, while others have examined the whole exome, either initially or sequentially. An advantage of WES over individual gene or gene panel testing is that the stored data allows reanalysis as new genes are linked to the patient phenotype. WES has also been reported to be beneficial in patients with atypical presentations.

 

The following outlines the diagnostic yields of whole exome sequencing (WES) for conditions other than multiple congenital anomalies, neurodevelopmental disorders or epilepsy/seizure disorders:

 

StudyPatient PopulationNDesignYield, n (%)Additional Information / Study Gaps
Hauer et. al. (2018) Short stature in whom common non-genetic causes has been excluded 200 Randomly selected from a consecutive series of patients referred for work-up; trio testing performed Whole exome sequencing allows identification of the underlying cause of short stature in at least 33% of cases Enables physicians to improve diagnosis, treatment and genetic counseling.
Gaps include: variants of uncertain significance (VUS) not reported; and no description of indeterminate samples
Walsh et. al. (2017) Peripheral neuropathy in patients ranging from 2-68 years with uninformative results underwent expanded analysis of whole exome sequencing 38 out of 50 remained undiagnosed Prospective research study at tertiary pediatric and adult centers to explore diagnostic utility and cost effectiveness of whole exome sequencing 7 out of 36 achieved a diagnosis following expanded whole exome sequencing analysis Initial targeted analysis with virtual gene panel, followed by WES
Gaps include: Proband testing only; variants of uncertain significance (VUS) not reported
Miller et. al. (2017) Craniosynostosis in patients who tested negative on targeted genetic testing 40 Research study of referred patients Identified likely associated mutations in 15 patients (37.5%) Altered management and reproductive decision making
Gaps included: variants of uncertain significance (VUS) not reported; selection not random or consecutive; and no description of indeterminate samples
Ghaoui et.al. (2015) Unexplained limb-girdle muscular dystrophy 60 families Prospectivestudy of patients identified from specimen bank 27 of 60 families Achieved a diagnostic success rate of 45.0% in their difficult-to-diagnose cohort of patients.
Gaps included: variants of uncertain significance (VUS) not reported; and no description of indeterminate samples
Wortmann et. al. (2015) Suspected mitochondrial disorder 109 Single clinical practice A molecular diagnosis was achieved in 39% Gaps included: proband testing only; variants of uncertain significance (VUS) not reported; unclear how patients were selected from those eligible; and no description of indeterminate samples
Neveling et. al. (2013) Unexplained disorders: blindness, deafness, movement disorders, mitochondrial disorders, and colorectal cancer 186 Outpatient
Genetic clinical; post hoc comparison with Sanger sequencing
3% - 52% Whole exome sequencing had a much higher diagnostic yield than Sanger sequencing for deafness, blindness, mitochondrial disease and movement disorders. For colorectal cancer this as low under both strategies
Gaps included: Included highly heterogenous diseases; proband testing only; variants of uncertain significance (VUS) not reported; unclear how patients were selected from those referred; and no description of indeterminate samples

 

Clinically Useful

A test is clinically useful if the use of the results informs management decisions that improve the net health outcome of care. The net health outcome can be improved if patients receive correct therapy, or more effective therapy, or avoid unnecessary therapy, or avoid unnecessary testing.

 

Direct evidence of clinical utility is provided by studies that have compared health outcomes for patients managed with and without the test. Because these are intervention studies, the preferred evidence would be from randomized controlled trials (RCTs).

 

Indirect evidence on clinical utility rests on clinical validity. If the evidence is insufficient to demonstrate test performance, no inferences can be made about clinical utility.

 

A genetic diagnosis for an unexplained disorder can alter management in several ways: such a diagnosis may lead to including genetic counseling and ending the diagnostic odyssey and may affect reproductive decision making.

 

Because clinical validity of whole exome sequencing (WES) for this indication has not been established, a chain of evidence cannot be constructed.

 

In 2015, Valencia et. al. performed a retrospective review of 40 clinical cases to determine the clinical utility of their hospital’s clinical whole exome sequencing (WES) in a pediatric setting for unexplained genetic disorders (congenital anomalies, mitochondrial, endocrine and immunodeficiencies) calculating the diagnostic yield, and detailing the patients for whom clinical management was altered. Moreover, they examined the potential cost-effectiveness of WES by examining the cost burden of diagnostic workups. Of the first 40 clinical cases, they identified genetic defects in 12 (30%) patients, of which 47% of the mutations were previously unreported in the literature. Among the 12 patients with positive findings, seven have autosomal dominant disease and five have autosomal recessive disease. Ninety percent of the cohort opted to receive secondary findings and of those, secondary medical actionable results were returned in three cases. Among these positive cases, there are a number of novel mutations that are being reported here. The diagnostic workup included a significant number of genetic tests with microarray and single-gene sequencing being the most popular tests. Significantly, genetic diagnosis from WES led to altered patient medical management in positive cases. The authors concluded, the use of WES to analyze 40 consecutive clinical cases yielded a diagnosis in 30% of these cases, which demonstrates the utility of this technology as a diagnostic test for pediatric patients with a wide variety of disease presentations. Positive WES results allowed clinicians to complete the genetic workup, end the diagnostic odyssey and provide appropriate medical management and more informative genetic counseling to families. Importantly, a number of novel mutations are being reported here. The cost-effectiveness of WES testing is evident by the reduction of time to diagnosis and cost of other testing and in some cases WES may be warranted as a first-tier test. Although there are technical challenges with next generation sequencing (NGS), WES provides a unique glimpse into the complexity of genetic disorders as well as the challenges in diagnosing them. However, healthcare system integration and routine adoption of WES need more careful consideration and future research.

 

Summary

There is an increasing number of reports assessing use of whole exome sequencing (WES) to identify a molecular basis for disorders other than multiple congenital anomalies, neurodevelopmental disorders or epilepsy/seizure disorders. The diagnostic yield in these studies range from as low as 3% to 52%. One concern with WES is the possibility of incidental findings. Some studies have reported on the use of a virtual gene panel with restricted analysis of disease-associated genes, and the authors noted that WES data allows reanalysis as new genes are linked to the patient phenotype. Overall, there are a limited number of patients that have been studied for any specific disorder, and clinical use of WES in these disorders is at an early stage. Further studies are needed to evaluate the clinical validity and clinical utility of whole exome sequencing for disorders other than multiple congenital anomalies, neurodevelopmental disorders or epilepsy/seizure disorders. The evidence is insufficient to determine the effects of the technology on net health outcomes.

 

Whole Genome Sequencing for a Suspected Genetic Disorder

Clinical Context and Test Purpose

The purpose of whole genome sequencing (WGS) in patients who have a suspected genetic disorder is to establish a molecular diagnosis from either the coding or noncoding regions of the genome.

 

Patients

The relevant population of interest is patients presenting with any of a variety of disorders and anomalies suspected to have a genetic basis but not explained by a standard work-up.

 

Comparators

The following practice is currently being used to diagnose a suspected genetic disorder: standard clinical work-up without WGS.

 

Outcomes

Outcome of interest are as described above for use of WES in patients with multiple congenital anomalies or a neurodevelopmental disorder.

 

Setting

Whole genome sequencing (WGS) tests are offered commercially through various manufacturers.

 

Clinically Valid

A test must detect the presence of absence of a condition, the risk of developing a condition in the future, or treatment response (beneficial or adverse).

 

Studies have shown that WGS can detect more pathogenic variants than WES, due to an improvement in detecting copy number variants, insertions and deletions, intronic single-nucleotide variants, and exonic single-nucleotide variants in regions with poor coverage on WES. In some studies the genes examined were those that had previously been associated with the phenotype, while other studies were research-based and conducted more exploratory analysis. It has been noted that genomes that have been sequenced with WGS are available for future review when new variants associated with clinical diseases are discovered.

 

Soden et al. (2014) reported on one hundred families with 119 children affected by neurodevelopmental disorders (NDD) who had whole genome sequencing (WGS), whole exome sequencing (WES), or WES followed by WGS of parent-child trios, with the sequencing approach guided by acuity of illness. Forty-five percent received molecular diagnoses. An accelerated sequencing modality, rapid WGS, yielded diagnoses in 73% of families with acutely ill children (11 of 15). Forty percent of families with children with non-acute NDD, followed in ambulatory care clinics (34 of 85), received diagnoses: 33 by WES and 1 by staged WES then WGS. A change in clinical care or impression of the pathophysiology was reported in 49% of newly diagnosed families. According to the authors, if WES or WGS had been performed at symptom onset, genomic diagnoses may have been made 77 months earlier. It is suggested that initial diagnostic evaluation of children with NDD should include trio WGS or WES, with extension of accelerated sequencing modalities to high-acuity patients. According to the authors, this study had several limitations. It was retrospective and lacked a control group. Clinical data were collected principally through chart review, which may have led to under- or overestimates of changes in clinical management. The authors did not ascertain information about long-term consequences of diagnosis, such as the impact of genetic counseling. Comparisons of costs of genomic and conventional diagnostic testing excluded associated costs of testing, such as outpatient visits, and may have included tests that would nevertheless have been performed, irrespective of diagnosis. The acuity-based approach to expedited WGS and non-expedited WES was a patient care–driven approach and was not designed to facilitate direct comparisons between the two methods.

 

Willig et al. (2015) performed a retrospective comparison of rapid whole-genome sequencing (STATseq) and standard genetic testing in a case series from the neonatal and pediatric intensive care units (NICU and PICU) of a large children's hospital. The participants were families with an infant younger than 4 months with an acute illness of suspected genetic cause. The intervention was STATseq of trios (both parents and their affected infant). The main measures were the diagnostic rate, time to diagnosis, and rate of change in management after standard genetic testing and STATseq. Twenty (57%) of 35 infants were diagnosed with a genetic disease by use of STATseq and three (9%) of 32 by use of standard genetic testing. Median time to genome analysis was 5 days (range 3-153) and median time to STATseq report was 23 days. Thirteen (65%) of 20 STATseq diagnoses were associated with de-novo mutations. Impact on clinical management was noted in 13 (65%) of 20 infants with a STATseq diagnosis, four (20%) had diagnoses that led to a clinical intervention and six (30%) were started on palliative care. The 120-day mortality was 57% (12 of 21) in infants with a genetic diagnosis. According to the authors, in selected acutely ill infants, STATseq had a high rate of diagnosis of genetic disorders. The authors indicated that while having a genetic diagnosis altered the management of infants in the NICU or PICU in this single institution; additional studies with a higher patient population are needed to validate the clinical utility of  whole genome sequencing (WGS) in this patient population.

 

Taylor et al. (2015) conducted a study to assess factors influencing the success of WGS to obtain a genetic diagnosis across a broad range of clinical conditions with no previously identified causal mutation. They sequenced 217 individuals from 156 independent cases or families across a broad spectrum of disorders in which previous screening had identified no pathogenic variants. The investigators quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritization. They found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, the investigators identified disease-causing variants in 21% of cases, with the proportion increasing to 34% (23/68) for Mendelian disorders and 57% (8/14) in family trios. They also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, although only 4 were ultimately considered reportable. According to the investigators, their results demonstrate the value of genome sequencing for but also highlight many outstanding challenges, including the challenges of interpreting unrelated variants.

 

Bodian et al. (2016) assessed the potential of whole genome sequencing (WGS) to replicate and augment results from conventional blood-based newborn screening (NBS). Research-generated WGS data from an ancestrally diverse cohort of 1,696 infants and both parents of each infant were analyzed for variants in 163 genes involved in disorders included or under discussion for inclusion in US NBS programs. WGS results were compared with results from state NBS and related follow-up testing. NBS genes are generally well covered by WGS. There is a median of one (range: 0-6) database-annotated pathogenic variant in the NBS genes per infant. Results of WGS and NBS in detecting 28 state-screened disorders and four hemoglobin traits were concordant for 88.6% of true positives (n = 35) and 98.9% of true negatives (n = 45,757). Of the five infants affected with a state-screened disorder, WGS identified two whereas NBS detected four. WGS yielded fewer false positives than NBS (0.037 vs. 0.17%) but more results of uncertain significance (0.90 vs. 0.013%). The authors concluded that WGS may help rule in and rule out NBS disorders, pinpoint molecular diagnoses, and detect conditions not amenable to current NBS assays. There is a need for additional studies that compare WGS with traditional NBS methods and evaluate the change in patient management resulting from WGS for newborn screening

 

In a prospective study, Stavropoulos et al. (2016) utilized whole genome sequencing (WGS) and comprehensive medical annotation (CMA) to assess 100 patients referred to a pediatric genetics service, and compared the diagnostic yield versus standard genetic testing. WGS identified genetic variants meeting clinical diagnostic criteria in 34% of cases, representing a fourfold increase in diagnostic rate over CMA alone and more than twofold increase in CMA plus targeted gene sequencing. WGS identified all rare clinically significant copy number variants (CNVs) that were detected by CMA. In 26 patients, WGS revealed indel and missense mutations presenting in a dominant (63%) or a recessive (37%) manner. The investigators found four subjects with mutations in at least two genes associated with distinct genetic disorders, including two cases harboring a pathogenic CNV and single nucleotide variants (SNV). In the authors’ opinion, when considering medically actionable secondary findings in addition to primary WGS findings, 38% of patients would benefit from genetic counselling. While promising, additional studies of WGS as a primary test in comparison to conventional genetic testing and whole exome sequencing (WES) are needed.

 

Bowling et al. (2017) report results of whole exome sequencing (WES) or whole genome sequencing (WGS) on 371 individuals with developmental delay or intellectual disabilities enrolled in the Clinical Sequencing Exploratory Research (CSER) consortium (WES for 127 and WGS for 244) A total of 284 participating families were enrolled with both biological parents and 35 affected individuals had one parent included. Mean age of study participants was 11 years and 58% were male. Affected individuals displayed symptoms described by 333 unique Human Phenotype Ontology terms with over 90% of individuals displaying intellectual disability, 69% with speech delay, 45% with seizures, and 20% with microcephaly or macrocephaly; 18% had an abnormal brain magnetic resonance imaging (MRI) result and 81% had been subjected to prior genetic testing. Pathogenic or likely pathogenic variants were found in 100 individuals (27%), with variants of uncertain significance in an additional 42 (11%). The pathogenic or likely pathogenic identification rate was not significantly different between WES or WGS (p = 0.30) for single nucleotide variants or small insertions or deletions; although WGS can also identify copy number variants.

 

Petrikin et al. (2018) conducted a partially blinded randomized control trial on the clinical utility of rapid whole genome sequencing (rWGS) in neonatal intensive care unit/pediatric intensive care unit patients from October 2014 to June 2016. Eligible patients were <4 months old and had illnesses suggestive of a genetic disease, but were of unknown etiology. The studied intervention was trio rWGS, meaning whole genome sequencing (WGS) testing was completed in about 2 days, and was performed on the infant and parents. rWGS results were confirmed by another testing method prior to clinical reporting unless a situation arose where life-threatening progression was likely. There were 129 infants in the study period that were potential candidates, and 65 (50%) were ultimately enrolled. Thirty-two infants were randomized to rWGS plus standard genetic testing, and the remaining 33 had standard genetic testing alone. Standard genetic testing was defined as any genetic test considered standard of care, and therefore available to order through the electronic medical record. During the study period, non-rapid WGS became available, and was considered a standard test. The baseline characteristics of the infants in both groups were similar. The most common indications were congenital anomalies and neurological disorders. In the control group, only 6% of the infants had cardiovascular findings compared to the rWGS group (28%), and this may have impacted the likelihood of genetic disease. Other than newborn screening, the average age at first test order was 14 days. In those that had standard genetic testing, a diagnosis was identified by the test in 23% (7) of test cases, and 24% (8) of controls. The diagnostic rate by type of test included 6% by chromosome microarray, 18% by targeted panel testing, 33% by whole exome sequencing (WES), and 13% by methylation testing. In this group, it is noted that rWGS would not identify 33%, or five of fifteen diagnoses, as four were structural variants and one was a change in DNA methylation not identifiable at the time of this study by rWGS. The median time from test order to diagnosis was 64 days. In the test group, rWGS identified a diagnosis in 31% (10) cases, with a median time to diagnosis of 14 days, which included confirmatory testing. After un-blinding the randomization after 10 days of enrollment, it was requested by participating physicians to allow 7 of the 33 controls to participate in rWGS. It was declined for two patients as they were not acutely ill and about to be discharged. The remaining 5 had rWGS, and 2 received a diagnosis by rWGS that was later confirmed by standard genetic testing that was already being performed. Overall, infants receiving trio rWGS had a higher rate of diagnosis and shorter time to diagnosis than infants receiving standard tests alone. The ability of this study to understand the clinical utility of rWGS was hampered by the cross-over requests after 10 days of enrollment un-blinding, and the increasing availability of targeted panel tests, WES and WGS during the study period as standard tests, which ultimately caused the study to end early. The authors concluded that rWGS trended toward earlier diagnosis in the NICU, prior to discharge, but more studies are needed to determine if a shorter time to diagnosis improves clinical utility, outcomes, or healthcare utilization.

 

In another review of rapid whole genome sequencing (rWGS) in acutely ill infants, Farnaes et al. (2018) provides a retrospective review of inpatients from July 2016 to March 2017. A total of 42 families received rWGS plus standard of care genetic testing for the purpose of diagnosing genetic disorders. Trio testing was performed on 29 cases, 1 quad (parents plus two affected children), 9 duos (mother-infant) and three infants only. The majority of infants in the study were Hispanic/Latino (59%), and were in a neonatal intensive care unit (NICU), pediatric intensive care unit (PICU) or cardiovascular care unit (71%), on respiratory support (76%), and inotropic support (40%). The most common clinical indication was multiple congenital anomalies (29%). There was little consanguinity (2%). In examining the standard genetic testing results, the authors note that 4 infants received a diagnosis from these results. The most common standard test was chromosome microarray, but routine chromosome analysis, fluorescent in situ hybridization, and various biochemical tests were also utilized. One infant had a change in care as a result of the diagnosis. rWGS provided a diagnosis in 18 infants. All findings were confirmed through standard genetic tests. Thirteen children had a change in care as a result which included starting new medications (5), discontinuing medications (2), surgical procedures were changed (4). Palliative care was planned for one infant. Overall, the authors concluded that the availability of the rWGS results allowed changes in care that prevented morbidities in 11 of the infants and significant risk reduction in acute mortality in 1 from a medication change. In summary, the authors found that the diagnostic sensitivity in this cohort was 43% for rWGS and 10% for standard genetic testing, and concluded that rWGS may benefit acutely ill inpatient infants as a first tier test, but further studies are needed.

 

Clinically Useful

A test is clinically useful if the use of the results informs management decisions that improve the net health outcome of care. The net health outcome can be improved if patients receive correct therapy, or more effective therapy, or avoid unnecessary therapy or avoid unnecessary testing.

 

Direct evidence of clinical utility is provided by studies that have compared health outcomes for patients managed with and without the test. Because these are intervention studies, the preferred evidence would be from randomized controlled trials (RTCs).

 

Indirect evidence on clinical utility rests on clinical validity. If the evidence is insufficient to demonstrate test performance, no inferences can be made about clinical utility.

 

Dewey et al. (2014) conducted a pilot study to determine the resources required to identify and interpret clinically relevant genetic variation using whole genome sequencing (WGS) technologies and to evaluate clinical action prompted by WGS findings. An exploratory study of WGS was conducted in 12 adult participants at Stanford University Medical Center between November 2011 and March 2012. A multidisciplinary team reviewed all potentially reportable genetic findings. Five physicians proposed initial clinical follow-up based on the genetic findings. Depending on sequencing platform, 10% to 19% of inherited disease genes were not covered to accepted standards for single nucleotide variant discovery. Genotype concordance was high for previously described single nucleotide genetic variants (99%-100%) but low for small insertion/deletion variants (53%-59%). Curation of 90 to 127 genetic variants in each participant required a median of 54 minutes per genetic variant, resulted in moderate classification agreement between professionals, and reclassified 69% of genetic variants cataloged as disease causing in mutation databases to variants of uncertain or lesser significance. Two to 6 personal disease-risk findings were discovered in each participant, including 1 frameshift deletion in the BRCA1 gene implicated in hereditary breast and ovarian cancer. Physician review of sequencing findings prompted consideration of a median of 1 to 3 initial diagnostic tests and referrals per participant, with fair interrater agreement about the suitability of WGS findings for clinical follow-up. The authors concluded that in this exploratory study of 12 volunteer adults, the use of WGS was associated with incomplete coverage of inherited disease genes, low reproducibility of detection of genetic variation with the highest potential clinical effects, and uncertainty about clinically reportable findings.

 

Cirino et al. (2014) examined the validity of whole genome sequencing (WGS) in 41 patients with hypertrophic cardiomyopathy (HCM) who had undergone a HCM targeted next generation sequencing panel test. Twenty of the participants had pathogenic variants identified by targeted sequencing, and WGS detected 19 of them. Three additional variants were found in genes associated with HCM, but these genes are not typically included in HCM targeted sequencing panels. Additionally 84 secondary (incidental) findings were uncovered. The authors concluded that WGS may provide advantages in being able to interrogate more genes, and give the opportunity for re-analysis over time, but noted that expertise in genomic interpretation is required to incorporate into care.

 

Ellingford et al. (2016) compared the use of next generation gene targeted next generation sequencing (NGS) with whole genome sequencing (WGS) in a nested cohort of 46 (of 562) people with inherited retinal disease (IRD). Targeted sequencing and WGS were found to have a similar sensitivity and specificity, but WGS identified an additional 14 clinically relevant variants. If applied to the whole cohort of 562, the authors hypothesized that WGS would provide an overall 29% (95% confidence interval, 15-45) uplift in diagnostic yield. They also noted, however, that creating a more targeted NGS panel would have a similar result.

 

Alfares et al. (2018) examined the clinical utility of whole genome sequencing (WGS) compare to re-analysis of whole exome sequencing (WES). All cases that underwent CAP accredited CLIA lab WES and WGS in the genetics clinic of King Abdulaziz Medical City between 2013-2017 were examined, regardless of phenotype. WES was performed on either an Illumina NextSeq or HiSeq, or on an Ion Proton system. The average coverage depth was 95X. WGS was performed on a HiSeq 4000. The average coverage depth was 30X. Variant call files (VCF) were obtained for each case, and raw data analysis was performed in cases where the final results showed discrepancies. Discrepancies were classified into three categories; due to the time interval between tests, new discoveries could explain the discrepancy, intronic or large copy number variants may not have been seen due to WES limitations, and finally, the type of sequencing system could have created the discrepancy. Overall, 154 patients were included in the study and had negative comparative genome array results, and had negative or inconclusive WES results. Most were male (56%), pediatric (91%) and consanguineous (70%). Forty six were eventually excluded because WGS results were incomplete, additional testing was required, or WES VCF were not available from prior testing. The remaining 108 patients had complete clinical information and final WES and WGS results available. Of these, 10 patients had positive WGS results with prior negative WES results, and 5 had inconclusive results. The remaining 93 had negative WGS results. The average time between WES testing and WGS testing was only 5 months, and in that time no new clinical information was collected on the 10 positive WGS patients. However, in 3 cases, variants were found in WES, but not reported, because the data that demonstrated their pathogenicity was published after the initial WES was completed. In addition, four cases that had WES performed by the Ion Proton system missed variants that were anticipated to be found by WES. Original raw data files were not available from this lab to determine if the variants were present but filtered out, or if the genes were not adequately covered. Additional WES analysis using the Illumina system in these patients detected these four variants. Overall, only 3 cases were positive by WGS that were completely unidentifiable by WES. The authors concluded that in the final 108 patients, if they had re-analyzed the original WES data, they would have identified 30% of the positive cases, and that WGS only achieved a 7% higher detection rate. It was concluded that for this population re-analysis of WES data before, or in lieu of WGS, may have better clinical utility. Limitations of this study include the small sample size and the high rate of consanguinity, which may have resulted in a disproportionate number of positives on the initial WES test, which could in general limit the utility of WGS in the study population.

 

Another study that reviewed the utility of whole exome sequencing (WES) and whole genome sequencing (WGS) was conducted by Carss et. al. (2017). The authors studied a cohort of 722 individuals with inherited retinal disease (IRD) who had WES (n=72), WGS (n=605) or both (n=45) as part of the NIHR-BioResource Rare Diseases research study. The diagnoses included in the cohort included retinitis pigmentosa (n = 311), retinal dystrophy (n = 101), cone-rod dystrophy (n = 53), Stargardt disease (n = 45), macular dystrophy (n = 37), and Usher syndrome (n = 37). In the 117 individuals who had WES, 59 (50%) had pathogenic variants identified. Forty five individuals with a negative WES had subsequent WGS, and an additional 14 pathogenic variants were found. In three of these, the variant location was absent from the WES hybrid capture kit. Three individuals had large copy number variants that could not be called by WES, and three others had variants that were found in the WES results, but the quality was poor and they were not called. In the remaining 5 individuals, the variants were also found in WES, but the mode of inheritance was unexpected so WGS was used to exclude other possible causes of the disease. The detection rate varied by phenotype, ranging from 84% in individuals with Usher syndrome to 29% in those with cone dystrophy. Ethnicity also impacted the detection rate. Only 30% of individuals with African ancestry had cases solved, compared to 55% of European ancestry or 57% of South Asian ancestry. The authors further reviewed benefits of WGS. They noted that 3 individuals had pathogenic, non-coding variants that would not be detected by WES. They compared the IRD genes that were high or low in GC content in their WGS data set to the same genes in the WES ExAC database and concluded that the WGS dataset had consistent coverage whereas the WES data did not. They also noted that in their data set, WGS was better at detecting synonymous variants and variants in regulatory regions compared to WES. Overall the detection rate for WGS was 56% in this cohort. Factors that may influence this study compare to others is the technology used, phenotype screening and phenotypes used. They observed that the subset of people tested who had no prescreening had a higher pathogenic call rate, suggesting that the cohort may have been enriched for difficult cases, and the detection rate for WGS could be higher if used as a first line test. The authors noted that their WES coverage rate was 43X, compared to the >80X recommended for a commercial lab, and that might have influenced the results.

 

Summary

The limited clinical experience with whole genome sequencing (WGS)/rapid whole genome sequencing causes gaps in interpreting variants of uncertain significance or other incidental findings. As a result, the benefits and risks of WGS testing are poorly defined and the role of WGS in the clinical setting has not yet been established. Although WGS/rapid whole genome sequencing has the potential to identify causal variants for a wide variety of conditions that may be missed with other technologies, as well as to identify predictive biomarkers, the information derived from WGS has not yet been translated into improved outcomes and changed medical management.  Further studies are needed to establish clinical utility of WGS/rapid whole genome sequencing. The evidence is insufficient to determine the effects of the technology on net health outcomes.

 

Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS) for Cancer

Cancer is a complex biological process. Historically, cancers have been classified according to their anatomic site of origin (e.g. lung, breast, liver, colon), but within these groupings there are multiple subtypes with differences in response to treatment and overall behavior. Currently there are a number of DNA sequence based tests that are used in cancer medicine, ranging from single gene tests for mutations to more expensive panels which might include hundreds of defined cancer genes and mutations “hot spots”. Technologic advances have now brought the possibility of more extensive interrogation of the genome through whole exome and whole genome sequencing for cancer.

 

Cancers are caused by the accumulation of genetic alterations that may lead to the dysfunction of regulation cell growth, resulting in the development of tumors. In recent years, whole exome sequencing (WES), which allows detection of 85% of disease causing variants, has been used to compare tumor and normal DNA to allow the identification of variants specific to the tumor. Genetic changes in cancer are increasingly used for diagnosis and may guide treatment decisions. In 2014, Malhotra et. al. explored whether there is evidence that WES improves outcomes for patients with cancer. The published evidence was evaluated using a methodology that combines the analytic validity, clinical validity, clinical utility, and ethical, legal and social implications (ACCE) model for genetic test evaluations and internationally accepted health technology assessment methodology. Conclusions were based on peer reviewed published studies of > 10 patients, with ≥ 3 studies for a given phenotype. WES has been conducted most extensively (seven studies to date) in breast cancer patients, with fewer studies of other types of cancers (e.g. leukemia, prostate cancer, and ovarian cancer). Studies evaluating somatic alterations showed high intratumor and intertumor heterogeneity. In addition, both novel and previously implicated variants were identified. However, only three studies with > 10 individuals have shown potential for clinical utility of WES; whereby, variants identified through WES may determine response to drug treatment. The authors concluded despite evidence for clinical validity of WES in cancers, clinical utility is very limited and needs to be further evaluated in larger clinical studies.

 

In 2015, Laskin et. al. reviewed the findings of a Personalized OncoGenomics (POG) study. This study sought to establish a process to integrate data from whole genome sequencing (WGS) into routine cancer care. In this POG program study, medical oncologists recruited patients from their general oncology clinics with the intention of sampling a variety of cancer histologies, Between June 2012 and August 2014, 100 adult patients with incurable cancers consented to participate. Fresh tumor and blood samples were obtained and used for whole genome and RNA sequencing. Computational approaches were used to identify candidate driver mutations, genes, and pathways. Diagnostic and drug information were then sought based on these candidate “drivers.” Reports were generated and discussed weekly in a multidisciplinary team setting. Other multidisciplinary working groups were assembled to establish guidelines on the interpretation, communication, and integration of individual genomic findings into patient care. Of 78 patients for whom WGS was possible, results were considered actionable in 55 cases. In 23 of these 55 cases, the patients received treatments motivated by WGS. The authors indicated that a multidisciplinary team of clinicians and scientists can implement a paradigm in which WGA is integrated into the care of late stage cancer patients to inform systemic therapy decisions. In this study it was noted that a limitation of using whole genome sequencing is the lengthy turnaround times for the production and analysis of whole genome data, which hampers its clinical application in cancer where rapid treatment decisions are frequently required.

 

Zhang et al. (2015) studied the prevalence of cancer pre-disposition germline mutations in children and adolescents with cancer in 1,120 patients under the age of 20. Whole exomes were sequenced in 456 patients and whole genomes were sequenced in 595, or both in 69. Results were analyzed in 565 genes, including 60 that are associated with autosomal dominant cancer syndromes. Genetic variant pathogenicity was determined by a team of experts who relied on peer reviewed literature, cancer and locus specific databases, computational predictions, and second hits identified in the participant tumor genome. This same variant calling approach was used to analyze data on 966 controls from the 1000 Genomes Projects who were not known to have cancer and data from 733 children from an autism study. Overall, germline mutations were found in 95 children with cancer (8.5%), as compared to only 1.1% of 1000 Genome Project and 0.6% of autism study controls. The mutations were most commonly found in TP53, APC, BRCA2, NF1, PMS2, RB1 and RUNX3. Eighteen patients also have variants in tumor suppressor genes. Of the 58 patients who had family history information available and a mutation in a predisposing dominant cancer gene, 40% had a significant family history of cancer.

 

Patients with metastatic and treatment-resistant cancer were prospectively enrolled at a single academic center for paired metastatic tumor and normal tissue whole exome sequencing (WES) during a 19-month period (Beltran et al., 2015). A comprehensive computational pipeline was used to detect point mutations, indels, and copy number alterations. Mutations were categorized as category 1, 2, or 3 on the basis of level of potential action; clinical reports were generated and discussed in precision tumor board. Patients (n=97, with 154 tumor pairs) were observed for 7 to 25 months for correlation of molecular information with clinical response. Results showed that more than 90% of patients harbored actionable or biologically informative alterations, although treatment was guided by the information in only 5% of cases. This study highlights opportunities for future clinical trials regarding whole-exome sequencing in precision medicine.

 

The results of the German pilot study called ‘Individualized Therapy for Relapsed Malignancies in Childhood’ (INFORM) was reported on by Worst et al. in 2016. This was a precision medicine study utilizing tumor and blood whole-exome, low-coverage whole-genome, and RNA sequencing, complemented with methylation and expression microarray analyses. The goal was to identify individualized therapies for children and adolescents diagnosed with a high risk relapsed/refractory cancer. Fifty-seven patients from 20 centers were prospectively tested, and diagnoses included sarcomas (n = 25), brain tumors (n = 23), and other (n = 9).

 

Parsons et al. (2016) conducted a study to determine the prevalence of somatic and germline mutations in children with solid tumors. From August 2012 through June 2014, children with newly diagnosed and previously untreated central nervous system (CNS) and non-CNS solid tumors were prospectively enrolled in the study at a large academic children’s hospital. Blood and tumor samples underwent whole exome sequencing (WES) in a certified clinical laboratory with genetic results categorized by clinical relevance. A total of 150 children participated, with a mean age of 7 years, with 80 boys and 70 girls. Tumor samples were available for WES in 121 patients. In this group, somatic mutations with established clinical utility were found in 4 patients, and mutations with possible clinical utility were found in 29. CTNNB1 had the most mutations, followed by KIT, TSC2, BRAF, KRAS, and NRAS. Diagnostic germline mutations related to the child’s clinical presentation was found in 150 patients and included 13 dominant mutations in known cancer susceptibility genes, including TP53, VHL, and BRCA1. One recessive liver disorder with liver cancer was identified in TJP2 and one renal cancer, CLCN5. Incidental findings were found in 8 patients. Nearly all patients (98%) had variants of unknown significance in known cancer genes, drug response genes, and genes known to be associated with recessive disorders.

 

The clinical impact of molecular profiling on pediatric tumors in children with refractory cancer was studied by Østrup et al. (2018) based on experiences in 2015 at the Center for Genomic Medicine, Rigshospitalet (Copenhagen, Denmark). Forty six tumor samples, two bone marrow aspirates, three cerebral spinal fluid samples, and one archived tumor DNA from 48 children were analyzed by whole exome sequencing (WES), RNA sequencing, transcriptome arrays, and single nucleotide polymorphism (SNP) arrays for mutation burden and to determine if actionable results could be found. Twenty patients had extracranial solid tumors and 25 had CNS tumors. Three patients were diagnosed with a hematological malignancy. Eleven of the 25 CNS tumors underwent additional DNA methylation profiling to obtain a second opinion on the diagnosis. At the time of the study, six patients were deceased. In 33 patients, actionable findings were identified which included 18 findings that helped make a final diagnosis, and 22 that allowed identification of potential treatment targets. Eleven findings had both a diagnostic and a treatment impact. Nine of the 33 findings were already known by prior histopathology tests. The highest yield for actionable findings was from WES (39%), followed by SNP array (37%) and RNA sequencing (21%). Clinical interventions based on these results were implemented in 11 of 44 patients, including 8 patients who received therapy based on the molecular profile. Six patients experienced direct benefit with improved response or stable disease. Four received compassionate use therapy. The authors commented that although 60% of the reports that went back to clinicians contained actionable findings, the clinicians encountered barriers to obtaining available or approved treatments which limited the utility of the advanced diagnostics. There are clinical trials available based on advanced molecular profiling, but the authors note that not all facilities have the infrastructure in place to provide comprehensive molecular profiling.

 

Nicolson et. al. (2018) used whole exome sequencing (WES) to identify the genetic variants found in follicular thyroid cancer (FTC). They analyzed 39 tumors that were classified by subtype; 12 were minimally invasive (miFTC), 17 were encapsulated angioinvasive (eaFTC), and 10 were widely invasive (wiFTC). Samples were collected between 2002 and 2013. All samples were reviewed by a minimum of two independent pathologists to histopathological confirmation using the World Health Organization (WHO) 2017 guidelines. Hurthle cells were included, although differentiated by the WHO 2017 guidelines, because both Hurthle and conventional FTCs can exhibit invasive behavior. Samples underwent exome sequencing for a minimum 20X coverage, copy number variation analysis, and 13 of the samples were able to be tested for three common gene fusions found in FTC: PAX8-PPARγ, RET-PTC1, and RET-PTC3. Matched normal samples were collected from adjacent normal tissue or from white blood cell DNA. SciClone was used to detect clonal populations of tumor cells in each sample. Age, gender, tumor size (by largest diameter), and American Joint Committee on Cancer (AJCC) stage (7th and 8th editions), and genetic test results were assessed for association with invasive status. Most patients were female (67%) and the mean age was 55 years old. The medial tumor diameter was 3.6 cm and 92% had Stage I or Stage II disease. After surgery, patients were followed for disease progression for a median 5.8 years. The overall recurrence and disease progression rate was 15%. Overall, mutations in the RAS gene family were found in 20% of samples. TSHR mutations were identified in 4 tumors. DICER1, EIF1AX, KDM5C, NF1, PRDM1, PTEN, and TP53 were recurrently mutated in 2 samples each. The range of mutation burden in the tumors ranged from 1-44 variants per tumor. There were no statistically significant differences in mutation burden between subtypes. There were 55 germline variants found in potential cancer-associated genes, but none had been previously catalogued as a thyroid susceptibility gene. In general, the FTCs in this study had a general copy number gain. The most common gains were of 5q, 7p, and 12q. In the 13 samples that underwent fusion gene analysis, 1 was found to have the PAX8-PPARγ fusion. When results were analyzed in the context of outcome, the total mutation burden, cancer driver burden, FTC driver burden and AJCC stage were all associated with worse prognosis. The authors’ statistical analysis suggests that the genetic profile may be a strong prognostic factor independent of histopathology. More research is needed to determine if similar results could be obtained on less invasive biopsy specimens.

 

Summary

Oncologists are becoming rapidly educated about the range of genomic platforms that exist in the treatment of cancer, and technologic advances have brought the possibility of more extensive interrogation of the genome through whole exome sequencing (WES) and whole genome sequencing (WGS) where the variants identified may determine response to drug treatment and improve outcomes for patients with cancer. One of the limitations of this testing is the lengthy turnaround times for the production and analysis of whole genome data, which hampers its clinical application in cancer, where rapid treatment decisions are frequently required. While studies may show promising results, at present, there is limited data on the clinical use of WES and WGS in the treatment of cancer. The clinical utility is very limited and needs to be further evaluated in large clinical studies to include larger patient populations in a variety of cancer histologies. The evidence is insufficient to determine the effects of the technology on net health outcomes.

 

Prenatal and Preimplantation Whole Exome and Whole Genome Sequencing

Prenatal diagnosis by genomics (i.e. next generation whole exome or whole genome) sequencing has significant limitations. The current technology does not support short turnaround times which are often expected in the prenatal setting. There are high false positive, false negative, and variants of unknown clinical significance rates. These rates can be expected to be significantly higher than seen when array comparative genomic hybridization is used in prenatal diagnosis. Published literature on the use of next generation whole exome and whole genome testing in the invasive prenatal setting is lacking. The evidence is insufficient to determine the effects of this testing on net health outcomes.

 

Preimplantation genetic testing involves analysis of biopsied cells as part of an assisted reproductive procedure. It is generally considered to be divided into two categories.  Preimplantation genetic diagnosis (PGD) is used to detect a specific inherited disorder and aims to prevent the birth of affected children to couples at high risk of transmitting a disorder. Preimplantation genetic screening (PGS) involves testing for potential genetic abnormalities in conjunction with in vitro fertilization for couples without a specific known inherited disorder.

 

The biopsy material can be analyzed in variety of ways:

  • Polymerase chain reaction or other amplification techniques can be used to amplify the harvested DNA with subsequent analysis for single genetic defects. This technique is most commonly used when the embryo is at risk for a specific genetic disorder such as Tay-Sachs disease or cystic fibrosis.
  • Fluorescent in situ hybridization (FISH) is a technique that allows visualization of specific (but not all) chromosomes to determine the number or absence of chromosomes. This technique is most commonly used to screen for aneuploidy, sex determination, or to identify chromosomal translocations. FISH cannot be used to diagnose single genetic defect disorders. However, molecular techniques can be applied with FISH (e.g. microdeletions, duplications) and, thus single gene defects can be recognized with this technique. Another approach becoming more common is array comparative genome hybridization testing at either the 8-cell or, more often, the blastocyst stage. Unlike FISH analysis, this allows for 24 chromosome aneuploidy screening, as well as more detailed screening for unbalanced translocations and inversions and other types of abnormal gains and losses of chromosomal material.
  • Next generation sequencing to include whole exome and whole genome sequencing has potential applications, but these techniques are being actively studied and is in a relatively early stage of development compared with other methods of analyzing biopsied material. Further well conducted randomized clinical trials are needed before conclusions can be drawn about the impact on the net health benefit. The evidence is insufficient to determine the effects of this testing on net health outcomes.

 

There are limited data on whole exome sequencing (WES) in prenatal genetic diagnostic testing. Fu et. al. (2017) did sequential analysis involving karyotype, chromosome microarray analysis (CMA), and then WES in a cohort of 3949 structurally abnormal fetuses. Eighteen percent (720) fetuses had abnormal karyotype. CMA analysis was performed on those with a normal karyotype (1680) and 8% (168) had a pathogenic copy number variant. Of these with a normal karyotype and CMA analysis, 196 underwent WES, and 47 (24%) had a pathogenic variant identified that could potentially explain the phenotype; additionally, the incidence of variants of unknown significance (VUS) and secondary findings was 12% and 6%, respectively.

 

Aarabi et. al. (2018) conducted a study of the utility of the whole exome sequencing (WES) in prenatal cases with structural birth defects. Twenty fetuses with structural abnormalities with normal karyotype and chromosome microarray analysis (CMA) results underwent WES, as did their parents. Initial results using only prenatal findings die not identify any pathogenic or likely pathogenic variants. WES results were later re-evaluated utilizing prenatal and post-natal phenotypes. Inclusion of the post-natal phenotypes results in identifying pathogenic variants in 20% of cases including PORCN gene in a fetus with split-hand/foot malformation, as well as reportable variants of uncertain significance in fetuses with postnatal muscle weakness and Adams-Oliver syndrome. In one patient, post-natal magnetic resonance imaging (MRI) identified the presence of holoprosencephaly. The case was referred for Sanger sequencing of related genes, and a 47 bp deletion was found in ZIC2 that was missed by WES. The authors suggested that incomplete fetal phenotyping limits the utility of WES, and if prenatal WES is undertaken, re-analysis of data with additional post-natal phenotype information can be useful.

 

Further studies are needed to establish the clinical validity and clinical utility of WES in this setting.

 

Summary

Prenatal and preimplantation for screening or diagnosis by genomics i.e. next generation whole exome or whole genome sequencing has significant limitations. The current technology does not support short turnaround times which impacts prenatal diagnosis and reproductive decision making. There are high false positive, false negative, and variants of unknown clinical significance rates (incidental findings that may cause anxiety). Based on the peer reviewed medical literature the evidence is insufficient in proving the clinical utility of this technology in the use of prenatal and preimplantation genetics. Current society guidelines do not recommend the routine use of whole genome and whole exome sequencing for prenatal and preimplantation screening or diagnosis outside the context of clinical trials until sufficient peer reviewed data and validation studies are published. Further studies are needed to establish the clinical validity and clinical utility of whole exome sequencing (WES) and whole genome sequencing (WGS). The evidence is insufficient to determine the effects of the technology on net health outcomes.

 

Genetic Counseling

Due to the likelihood of the discovery of a variant of uncertain significance or other incidental findings, pre-and-post genetic counseling for any individual undergoing WES is required. This recommendation is consistently and widely published by multiple professional societies and experts. Genetic counseling by an independent provider can reduce unnecessary use of this test.

 

Genetic counseling is defined as the process of helping an individual understand and adapt to the medical, psychological and familial indications of genetic contributions to disease. Genetic counseling is recommended in both pre-and-post genetic testing to interpret family and medical histories to assess the change of disease occurrence and recurrence, educate regarding inheritance, testing, management prevention and resources and counsel to promote informed choices and adaption to risk or condition.

 

A variety of genetics professionals provide these services: Board-Certified or Board-Eligible Medical Geneticists, and American Board of Medical Genetics or American Board of Genetic Counseling-certified Genetic Counselor, and genetic nurses credentialed as either a Geneteic Clinical Nurse (GCN) or an Advanced-Practice Nurse in Genetics (APGN) by either the Genetic Nursing Credentialing Commission (GCNN) or the American Nurses Credentialing Center (ANCC). Individuals should not be employed by a commercial genetic testing laboratory unless they are employed by or contracted with a laboratory that is part of an integral Health System which routinely delivers health care services beyond just the laboratory test itself.

 

Practice Guidelines and Position Statements

American Society of Reproductive Medicine (ASRM)

In 2007, the American Society for Reproductive Medicine (ASRM) issued a practice committee opinion that concluded that available evidence did not support the use of preimplantation genetic screening (PGS) as currently performed to improve live birth rates in patients with advanced maternal age, previous implantation failure, or recurrent pregnancy loss, or to reduce miscarriage rates in patients with recurrent pregnancy loss related to aneuploidy.

 

American College of Obstetricians and Gynecologists

In 2016, the American College of Obstetricians and Gynecologists issued a joint committee opinion (Number 682) with the Society for Maternal-Fetal Medicine, regarding microarrays and next-generation sequencing technology: the use of advanced genetic diagnostic tools in obstetrics and gynecology that states: Routine use of whole genome or whole exome sequencing for prenatal diagnosis in not recommended outside the context of clinical trials until sufficient peer reviewed data and validation studies are published.

 

American Academy of Neurology

In 2015, the American Academy of Neurology issued an evidence based guideline regarding the evaluation, diagnosis, and management of congenital muscular dystrophy (CMD) that states:

  • In individuals with CMD who either do not have a mutation identified in one of the commonly associated genes or have a phenotype whose genetic origins have not been well characterized, physicians might order whole exome or whole genome sequencing when those technologies become more accessible and affordable for routine use. (Level C)

 

The American College of Medical Genetics and Genomics (ACMG)

In 2012, The American College of Medical Genetics and Genomics (ACMG) issued a policy statement, Points to Consider in the Clinical Applications of Genomic Sequencing, which states that diagnostic testing with WES/WGS should be considered in the clinical diagnostic assessment of phenotypically affected individual when:

  • The phenotype or family history data strongly implicate a genetic etiology, but the phenotype does not correspond with a specified disorder for which a genetic test targeting a specific gene is available on a clinical basis.
  • A patient presents with a defined genetic disorder that demonstrates a high degree of genetic heterogeneity, making WES or WGS analysis of multiple genes simultaneously a more practical approach.
  • A patient presents with a likely genetic disorder but specific genetic tests available for that phenotype have failed to arrive at a diagnosis.
  • A fetus with a likely genetic disorder in which specific genetic tests, including targeted sequencing tests, available for that phenotype have failed to arrive at a diagnosis.
    • Prenatal diagnosis by genomic (i.e. next generation whole exome or whole genome) sequencing has significant limitations. The current technology does not support short turn around times which are often expected in the prenatal setting. There are high false positive, false negative, and variants of unknown clinical significance rates. These can be expected to be significantly higher than seen when array CGH is used in prenatal diagnosis.

 

Pre-Test Considerations
  • Pre-test counseling should be done by a medical geneticist or an affiliated genetic counselor and should include a formal consent process.

 

Post-Test Consideration
  • Genetic services and other appropriate specialist interventions associated with clinically relevant results should be available and accessible to those tested.

 

Genetic Screening
  • WES/WGS should not be used at this time as an approach to prenatal screening.
  • WES/WGS should not be used as a first-tier approach for newborn screening.
  • WES/WGS may be considered in preconception carrier screening, using a strategy to focus on genetic variants known to be associated with significant phenotypes in homozygous and hemizygous progeny. In view of the long turnaround times and interpretive complexities currently associated with this technology, preconception carrier screening is strongly favored over post-conception screening.
  • Asymptomatic individuals interested in WES/WGS for purposes of health screening should receive both pre-test and post-test counseling from a trained medical geneticist and/or affiliated genetic counselor. They should be informed of the potential risks and benefits of such testing and the virtual certainty of finding variants of uncertain significance. The threshold for determining which results should be returned to individuals seeking screening should be set significantly higher than that set for diagnostic testing due to the much lower a priori chance of disease in such individuals.

 

In 2015, ACMG issued a position statement on the clinical utility of genetic and genomic services which states: “We submit that the clinical utility of genetic testing should take into account effects on diagnostic or therapeutic management, implications for prognosis, health and psychological benefits to patients and their relatives. We believe that clinical utility must also take into account the value a diagnosis can bring to the individual, the family and society in general".

 

“ACMG believes there is great clinical value in arriving at a precise medical diagnosis, enabling, among other things, identification of a disorder’s cause and prognosis, as well as frequently informing preventative and treatment modalities. ACMG considers the following to be important clinical utilities related to genetic/genomic information”.

 

Clinical Utility for Individual Patients
  • Situations in which definitive diagnosis specifically informs causality, prognosis, and treatment.
  • Newborn screening for conditions recommended by the Secretary’s Discretionary Advisory Committee on Heritable Disorders of Newborns and Children.
  • The discovery of medically actionable secondary findings in the course of genomic testing that have associated treatments that improve/affect outcome.

 

Clinical Utility for Families
  • Enables at-risk family members to obtain testing to determine whether they carry a causative mutation, offering the possibility for early intervention. This clinical utility is independent of whether the affected family member has benefited directly from this diagnosis.
  • Enables specific and informed reproductive decision making and family planning.
  • Brings resolution to the costly (in terms of both psychosocial and financial contexts) and wasteful (for the medical system at large) diagnostic odyssey that is often pursued in a quest to establish a diagnosis. There are countless examples of economic and psychological costs to the health-care system and to patients and families during the quest to obtain a diagnosis.
  • Enables involvement in disease support groups and other types of social support groups and other types of social support for families.

 

“Not only can genetic testing inform genetic risks in other family members, but testing of other family members can sometimes/often inform the interpretation of results in a patient. For example, information regarding whether a candidate variant is de novo or inherited provides powerful evidence of its potential pathogenicity, thereby giving the finding utility in other family members. Genome-scale testing of parents and patient (trio testing) also reduces the number of variants that have to be considered as causative, thereby facilitating better interpretation of testing results and minimizing reporting of costly (in terms of both patient well-being and economic terms) false-positive results.”

 

In 2016, the American College of Medical Genetics and Genomics (ACMG) released an updated policy statement on recommendations for reporting secondary findings in clinical exome and genome sequencing. This is an update of their 2013 policy statement. The policy statement states: “We have continued to focus primarily on secondary findings (SFs) related to monogenic disorders for which there is evidence of clinical utility. Additionally, we have attempted to standardize the evaluation of current and prospective genes by adopting a process that includes a semiquantitative metric for determining actionability that is consistent with the goals of ClinGen Actionability Working Group. We continue to support the reporting of known or expected pathogenic variants, but we do not recommend reporting variants of uncertain significance as secondary findings (SFs).”

 

Regulatory Status

Clinical laboratories may develop and validate tests in-house and market them as a laboratory service; laboratory developed tests (LDTs) must meet the general regulatory standards of the Clinical Laboratory Improvement Amendments (CLIA). Exome or genome sequencing tests as a clinical service are available under the auspices of CLIA. Laboratories that offer LDTs must be licensed by CLIA for high complexity testing. To date, the U.S. Food and Drug Administration (FDA) has chosen not to require any regulatory review of this test.

 

Prior Approval:

Not applicable.

 

Policy:

See also medical policy 02.04.38 Noninvasive Prenatal Screening for Fetal Aneuploidies Using Cell - Free Fetal DNA in Maternal Plasma

 

Whole Exome Sequencing for the Evaluation of Unexplained Neurodevelopmental Disorders, or Multiple Congenital Anomalies, or Epilepsy/Seizure Disorder(81415, 81416)

Whole exome sequencing (WES) may be considered medically necessary for the evaluation of unexplained neurodevelopmental disorders, or multiple congenital anomalies, or epilepsy/seizure disorder in children when ALL of the following criteria are met:

  • Patient is 17 years or less of age: AND
  • A genetic etiology is considered the most likely explanation for the phenotype despite previous genetic testing (e.g. comparative genomic hybridization (CGH) chromosomal microarray analysis (CMA); karyotyping analysis; FISH (fluorescence in-situ hybridization) analysis; and targeted single gene testing) that failed to yield a diagnosis; OR
  • When previous genetic testing has failed to yield a diagnosis, and the affected individual is faced with invasive procedures or testing as the next diagnostic step (e.g. muscle biopsy); AND
  • There is a predicted impact on health outcomes including:
    • Application of specific treatments; or
    • Withholding of contraindicated treatments; or
    • Surveillance for later-onset comorbidities; or Initiation of palliative care; or
    • Withdrawl of care; AND
  • The test is ordered by a board certified genetic counselor or board certified medical geneticist or other board certified physician with expertise in clinical genetics; AND
  • The individual and family history has been evaluated by a board certified genetic counselor or board certified medical geneticist or other board certified physician with expertise in clinical genetics with specific expertise in the conditions and relevant genetics for which testing is being considered; AND
  • Genetic counseling has been completed by a board certified genetic counselor or board certified medical geneticist or other board certified physician with expertise in clinical genetics; AND
  • A clinical letter detailing the evaluation by a board certified genetic counselor or board certified medical geneticist or other board certified physician with expertise in clinical genetics which includes ALL of the following information:
    • Differential diagnosis; and
    • Testing algorithm; and
    • Previous tests performed and results; and
    • A genetic etiology is the most likely explanation; and
    • Recommendation that whole exome sequencing is the most appropriate test; and
    • Predicted impact on the patient’s plan of care; AND 
  • Alternate etiologies have been considered and ruled out when possible (e.g. environmental exposures, injury, infection).

 

Required documentation: The individual’s medical records must reflect the medical necessity for the care provided. The medical record should include, but are not limited to: records from health care professionals office, test reports to include all prior genetic testing and results as indicated above, how the testing will directly impact clinical decision making and clinical outcome for the individual being tested, the results will preclude the further need for multiple and/or invasive testing and the records support the individual(s) being tested have received genetic counseling, to include that they have also been evaluated and the test was ordered by a board certified genetic counselor or board certified medical geneticist or other board certified physician with expertise in clinical genetics.

 

Whole Exome Sequencing (WES) for All Other Indications (81415, 81416, 81417, 0036U)

Whole exome sequencing (WES) is considered investigational for all other indications, including but not limited to the following as the evidence is insufficient to determine the effects of the technology on net health outcomes:

  • Screening and evaluating disorders in individuals when the above criteria is not met.
  • Screening asymptomatic individuals for genetic disorders.
  • Molecular profiling of tumors for the diagnosis, prognosis or management of cancer.

 

Whole Exome Reanalysis (81417)

Reanalysis of previously obtained whole exome sequence for one of the above medically necessary indications (i.e. unexplained neurodevelopmental disorders, or multiple congenital anomalies, or epilepsy/seizure disorder in children), may be considered medically necessary when one of the following criteria is met:

  • There has been an onset of additional symptoms that broadens the phenotype assessed during the original exome evaluation; or
  • There has been the birth or diagnosis of a similarly affected first-degree relative that has expanded the clinical picture.

 

Reanalysis or repeat testing for whole exome sequencing (WES) not meeting one the above indications is considered not medically necessary.

 

Whole Genome Sequencing (81425, 81426, 81427, 0012U, 0013U, 0014U, 0094U)

Whole genome sequencing (WGS)/rapid whole genome sequencing is considered investigational for all indications, including but not limited to the following:

  • For screening and evaluating any genetic disorder.
  • Screening asymptomatic individuals for genetic disorders.
  • Molecular profiling of tumors for the diagnosis, prognosis or management of cancer.

 

Although whole genome sequencing (WGS)/rapid whole genome sequencing has the potential to identify causal variants for a wide variety of condition that may be missed with other technologies, as well as to identify predictive biomarkers, the information derived from whole genome sequencing (WGS)/rapid whole genome sequencing has not yet been translated into improved outcomes and changed medical management. Further studies are needed to establish the clinical utility of whole genome sequencing (WGS)/rapid whole genome sequencing. The evidence is insufficient to determine the effects of the technology on net health outcomes.

 

Prenatal and Preimplantation Testing Whole Exome and Whole Genome Sequencing (81415, 81416, 81417, 81425, 81426, 81427, 81479, 0012U)

Whole exome sequencing (WES) and whole genome sequencing (WGS) for prenatal diagnosis or preimplantation testing of an embryo for the screening or diagnosis of genetic disorders is considered investigational.

 

Prenatal and preimplantation diagnosis and screening by genomics (i.e. next generation whole exome or whole genome) sequencing has significant limitations. The current technology does not support short turnaround times which impacts prenatal diagnosis and reproductive decision making. There are also false positive, false negative and variants of unknown clinical significance (incidental findings that may cause anxiety). Based on the peer reviewed medical literature the evidence is insufficient in proving the clinical utility of this technology in the use of prenatal and preimplantation genetics. Further validation studies are needed regarding the clinical utility and therefore, the evidence is insufficient to determine the effects of the technology on net health outcomes.

 

Policy Guidelines and Definitions

Genetic Counseling

Genetic counseling is primarily aimed at patients who are at risk for inherited disorders, and experts recommend formal genetic counseling in most cases when getting testing for inherited conditions is considered. The interpretation of results of genetic tests and understanding of risk factors can be very difficult and complex. Therefore, genetic counseling will assist individuals in understanding the possible benefits and harms of genetic testing, including the possible impact of the information on the individual’s family. Genetic counseling may alter the utilization of genetic testing substantially and may reduce inappropriate testing. Genetic counseling should be performed by an individual with experience and expertise in genetic medicine and genetic testing methods.

 

A variety of genetics professionals provide these services: Board-Certified or Board-Eligible Medical Geneticists, and American Board of Medical Genetics or American Board of Genetic Counseling-certified Genetic Counselor, and genetic nurses credentialed as either a Geneteic Clinical Nurse (GCN) or an Advanced-Practice Nurse in Genetics (APGN) by either the Genetic Nursing Credentialing Commission (GCNN) or the American Nurses Credentialing Center (ANCC).

 

Trio Testing

Analysis of the individual’s exome with comparative evaluation of the exons of two close relatives – typically both parents.

 

Neurodevelopmental Disorders

Is responsible for childhood onset brain dysfunction. It may result in developmental differences manifested as cognitive dysfunction, behavioral problems, and/or motor dysfunction.

 

Congenital Disorder

Congenital disorder is also known as birth defects, congenital anomalies or congenital malformations. Congenital disorder can be defined as structural or functional anomalies that occur during intrauterine life and can be identified prenatally, at birth or sometimes may only be detected later in infancy.

 

Screening Genetic Testing

Systematic program offered to a specified population of asymptomatic individuals to make a risk estimate regarding an inherited predisposition to disease, to detect an inherited disease at an early stage, or make a risk estimate regarding the possibility of transmitting a disease to offspring, for the purpose of disease prevention, early treatment or family planning.

 

Diagnostic Genetic Testing

Performed in symptomatic individuals and the genetic testing may be the method used to identify, confirm or rule out a condition in conjunction with clinical signs and symptoms. The confirmatory evidence should then assist with therapeutic interventions.

 

Chromosomal Microarray Analysis (CMA)

Allows for identification of very small deletions or duplications of chromosomes.

 

Comparative Genomic Hybridization (CGH)

Is a technique that allows the detection of losses and gains of DNA copy number across the entire genome.

 

Karyotype

Is a laboratory technique that produces an image of an individual’s chromosomes. The karyotype is used to look for abnormal numbers or structures of chromosomes.

 

Fluorescence In-Situ Hybridization (FISH)

FISH is a test that maps the genetic material in human cells, including specific genes of portion of genes. FISH uses a protein, called a probe, to “stick” to known sequence of DNA (usually a known mutation). If that sequence is present in a patient’s sample, the probe will bind to it and light up under a fluorescent microscope. FISH also can be used to detect chromosome rearrangements, marker chromosomes (extra pieces of unidentified chromosomal material), and duplications or deletions of large pieces of DNA.

 

First-Degree Relative

A first-degree relative is defined as a close blood relative which includes the individual’s parents, full siblings or children.

 

Procedure Codes and Billing Guidelines:

To report provider services, use appropriate CPT* codes, Alpha Numeric (HCPCS level 2) codes, Revenue codes, and/or diagnosis codes.

  • 81415 Exome (eg, unexplained constitutional or heritable disorder or syndrome); sequence analysis
  • 81416 Sequence analysis, each comparator exome (eg parents, siblings) (list separately in addition to code for primary procedure)
  • 81417 Re-evaluation of previously obtained exome sequence (eg updated knowledge or unrelated condition/syndrome)
  • 81425 Genome (eg unexplained constitutional or heritable disorder or syndrome) sequence analysis
  • 81426 Sequence analysis, each comparator genome (eg, parents, siblings) (list separately in addition to code for primary procedure)
  • 81427 Re-evaluation of previously obtained genome sequencing (eg updated knowledge or unrelated condition/syndrome)
  • 81479 Unlisted molecular pathology  (when utilized for next generation genome or exome sequencing for prenatal and preimplantation genetic testing)
  • 0012U Germline disorders, gene rearrangement detection by whole genome next generation sequencing, DNA, whole blood report of specific gene arrangement(s)
  • 0013U Oncology (solid organ neoplasia), gene rearrangement detection by whole genome next generation sequencing, DNA, fresh or frozen tissue or cells, report of specific gene rearrangement(s)
  • 0014U Hematology (hematolymphoid neoplasia) gene rearrangement detection by whole genome next generation sequencing, DNA whole blood or bone marrow report of specific gene rearrangement(s)
  • 0036U Exome (i.e. somatic mutations) paired formalin-fixed paraffin embedded tumor tissue and normal specimen sequence analysis
  • 0094U Genome (e.g. unexplained constitutional or heritable disorder or syndrome), rapid sequence analysis

 

Selected References:

  • Blue Cross and Blue Shield Association Technology Evaluation Center (TEC). Special Report: Exome Sequencing for Clinical Diagnosis of Patients with Suspected Genetic Disorders. Volume 28, Tab 3.
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  • Ayuso C, Millan JM, Mancheno M, et al. Informed consent for whole-genome sequencing studies in the clinical setting. Proposed recommendations on essential content and process. Eur J Hum Genet. Oct 2013;21(10):1054-1059
  • Biesecker LG. Opportunities and challenges for the integration of massively parallel genomic sequencing into clinical practice: lessons from the ClinSeq project. Genet Med. Apr 2012;14(4):393-398
  • De Ligt J, Boone PM, Pfundt R, et al. Detection of clinically relevant copy number variants with whole exome sequencing. Hum Mutat. Oct 2013;34(10):1439-1448
  • Dewey FE, Grove ME, Pan C, et al. Clinical interpretation and implications of whole genome sequencing. JAMA Mar 12 2014;311(10):1035-1045
  • Green RC, Berg JS, Grody WW, et al. ACMG Recommendations for Reporting of Incidental Findings in Clinical Exome and Genome Sequencing, Genet Med Jul 2013;15(7):565-574
  • American College of Medical Genetics and Genomics (ACMG) Policy Statement: Points to Consider in the Clinical Application of Genomic Sequencing. May 15, 2012
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  • Yang Y, Muzny DM, Reid JG, et al. Clinical whole exome sequencing for the diagnosis of mendelian disorders N Engl J Med. Oct 17 2013;369(16):1502-1511
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  • Richards S, Aziz N, Bale Sherri, et.al. Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendations of the American College of Medical Genetics and Genomics and Association of Molecular Pathology, Genet Med. 2015 May 17(5): 405-424
  • Dewey F, Grove M, Cuiping P, et. al. Clinical Interpretation and Implications of Whole Genome Sequencing. JAMA 2014 March 12; 311(10): 1035-1045
  • Rehm H, Bale Sherri, Bayrak-Toydemir P, et.al. ACMG Clinical Laboratory Standards for Next Generation Sequencing. Genet Med 2013 September; 15(9): 733-747
  • Allen NM, Conroy J, Shahwan A, et. al. Unexplained early onset epileptic encephalopathy: Exome screening and phenotype expansion. Epilepsia Jan 2016;57(1):e12-17. PMID 26648591
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  • Ellingford JM, Barton S, Bhaskar S, et. al. Whole genome sequencing increases molecular diagnostic yield compared with current diagnostic testing for inherited retinal disease. Ophthalmology May 2016;123(5):1143-1150. PMID 26872967
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  • UpToDate. Birth Defects: Approach to Evaluation. Carlos A. Bacino M.D., FACMG. Topic last updated December 19, 2016.
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Policy History:

  • March 2019 - Annual Review, Policy Revised
  • March 2018 - Annual Review, Policy Revised
  • March 2017 - Annual Review, Policy Revised
  • March 2016 - Annual Review, Policy Renewed
  • April 2015 - New Policy

Wellmark medical policies address the complex issue of technology assessment of new and emerging treatments, devices, drugs, etc.   They are developed to assist in administering plan benefits and constitute neither offers of coverage nor medical advice. Wellmark medical policies contain only a partial, general description of plan or program benefits and do not constitute a contract. Wellmark does not provide health care services and, therefore, cannot guarantee any results or outcomes. Participating providers are independent contractors in private practice and are neither employees nor agents of Wellmark or its affiliates. Treating providers are solely responsible for medical advice and treatment of members. Our medical policies may be updated and therefore are subject to change without notice.

 

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