Cigna Genetic Testing for Hereditary and Multifactorial Conditions - (0052) Form

The following Coverage Policy applies to health benefit plans administered by Cigna Companies. Certain Cigna Companies and/or lines of business only provide utilization review services to clients and do not make coverage determinations. References to standard benefit plan language and coverage determinations do not apply to those clients. Coverage Policies are intended to provide guidance in interpreting certain standard benefit plans administered by Cigna Companies. Please note, the terms of a customer’s particular benefit plan document [Group Service Agreement, Evidence of Coverage, Certificate of Coverage, Summary Plan Description (SPD) or similar plan document] may differ significantly from the standard benefit plans upon which these Coverage Policies are based. For example, a customer’s benefit plan document may contain a specific exclusion related to a topic addressed in a Coverage Policy. In the event of a conflict, a customer’s benefit plan document always supersedes the information in the Coverage Policies. In the absence Medical Coverage Policy: 0052 of a controlling federal or state coverage mandate, benefits are ultimately determined by the terms of the applicable benefit plan document. Coverage determinations in each specific instance require consideration of 1) the terms of the applicable benefit plan document in effect on the date of service; 2) any applicable laws/regulations; 3) any relevant collateral source materials including Coverage Policies and; 4) the specific facts of the particular situation. Each coverage request should be reviewed on its own merits. Medical directors are expected to exercise clinical judgment where appropriate and have discretion in making individual coverage determinations. Where coverage for care or services does not depend on specific circumstances, reimbursement will only be provided if a requested service(s) is submitted in accordance with the relevant criteria outlined in the applicable Coverage Policy, including covered diagnosis and/or procedure code(s). Reimbursement is not allowed for services when billed for conditions or diagnoses that are not covered under this Coverage Policy (see “Coding Information” below). When billing, providers must use the most appropriate codes as of the effective date of the submission. Claims submitted for services that are not accompanied by covered code(s) under the applicable Coverage Policy will be denied as not covered. Coverage Policies relate exclusively to the administration of health benefit plans. Coverage Policies are not recommendations for treatment and should never be used as treatment guidelines. In certain markets, delegated vendor guidelines may be used to support medical necessity and other coverage determinations. This Coverage Policy addresses testing for harmful or likely harmful changes in the genetic information of cells that occur in the egg or sperm cell at conception. These changes, also called variants are inherited or passed down through generations by blood relatives. The changes may increase a person’s risk or tendency to have a certain disease or disorder. When a combination of gene changes and other factors influence whether or not a condition results in a trait or health condition, it is known as multifactorial. Examples of factors other than genes are lifestyle, smoking and the environment. Several types of testing are discussed in this Coverage Policy, including testing for a single change in a gene or part of a gene and testing for multiple changes in a gene or genes. Also discussed are tests that measure how a gene is turned on or off, which is referred to as gene expression. Test results can help determine how advanced a disease is and the chance of it coming back. Results can also help decide on a treatment and how well the condition may, or is responding to treatment. Whole exome or whole genome sequencing for hereditary and multifactorial conditions is not included within the scope of this Coverage Policy. Please see CP 0519 Whole Exome Sequencing and Whole Genome Sequencing for Non-Cancer Indications for criteria related to whole exome and whole genome sequencing. Coverage Policy Many benefit plans limit coverage of laboratory tests, genetic counseling and genetic testing. Please refer to the applicable benefit plan language to determine benefit availability and terms, conditions and limitations of coverage for the services discussed in this Coverage Policy. Note: Whole exome or whole genome sequencing for hereditary and multifactorial conditions is not included within the scope of this Coverage Policy. Please see CP 0519 Medical Coverage Policy: 0052 Whole Exome Sequencing and Whole Genome Sequencing for Non-Cancer Indications for criteria related to whole exome and whole genome sequencing. If coverage for laboratory tests, genetic counseling and genetic testing is available and disease- or condition-specific criteria for genetic testing or genetic counseling are not outlined in a related Cigna Coverage Policy, the following criteria apply. Laboratory Testing Laboratory testing, including genetic testing (proprietary or non-proprietary, individual test or panel) is considered medically necessary when ALL of the following criteria are met: The proposed test or each proposed test in a panel is Food and Drug Administration (FDA)-approved and/or performed in a Clinical Laboratory Improvement Amendments (CLIA)-accredited laboratory. The proposed test or each proposed test in a panel is medically necessary for the diagnosis(es)/indication(s) listed. Results of the proposed test or each proposed test in a panel will directly impact clinical decision making. For an out-of-network request to be covered at an in-network benefit level, the proposed test or each proposed test in a panel must not be available from an in-network laboratory for the indication(s) or diagnoses listed. ------------------------------------------------------------------------------------------- Genetic Counseling Pre- and post-test genetic counseling is recommended for any individual undergoing genetic testing for any indication. Pre-and post-test genetic counseling is considered medically necessary for EITHER of the following: an individual undergoing genetic testing • an individual who is a potential candidate for genetic testing by ANY of the following: an independent Board-Certified or Board-Eligible Medical Geneticist • an American Board of Medical Genetics and Genomics or American Board of Genetic Counseling-certified Genetic Counselor not employed by a commercial genetic testing laboratory (Genetic counselors are not excluded if they are employed by or contracted with a laboratory that is part of an Integrated Health System which routinely delivers health care services beyond just the laboratory test itself). ➢ a genetic nurse credentialed as either a Clinical Genomics Nurse (CGN) or an Advanced Clinical Genomics Nurse (ACGN) by the Nurse Portfolio Credentialing Commission, Inc. OR a genetic nurse with an Advanced Genetics Nursing Certification (AGN-BC) renewed by the American Nurses Credentialing Center (ANCC) who is not employed by a commercial genetic testing laboratory (Genetic nurses are not excluded if they are employed by or Medical Coverage Policy: 0052 contracted with a laboratory that is part of an Integrated Health System which routinely delivers health care services beyond just the laboratory test itself). ------------------------------------------------------------------------------------------- Single Gene Genetic Testing for Germline Conditions Single gene genetic testing for a heritable disorder is considered medically necessary when EITHER of the following criteria is met: • Individual demonstrates signs/symptoms of a genetically-linked heritable disease. Individual or fetus has a direct risk factor (e.g., based on family history or pedigree analysis) for the development of a genetically-linked heritable disease. And ALL of the following criteria are met: Results will directly impact clinical decision-making and/or clinical outcome for the individual being tested. Testing methodology targeting deoxyribonucleic acid (DNA) and/or ribonucleic acid (RNA) is considered scientifically valid for identification of a genetically-linked heritable disease and is the most appropriate method unless technical limitations (e.g., poor quality sample) necessitate the need for alternate testing strategies. If testing guidelines exist, the clinical scenario falls within those recommendations. • The clinical benefit of testing outweighs the potential risk of psychological or medical harm to the individual being tested. Single gene genetic testing is considered medically necessary when the above criteria are met for ALL of the following conditions including but not limited to: Alpha-1 antitrypsin disease Alpha and beta thalassemia Canavan disease Cystic fibrosis DFNB1 nonsyndromic hearing loss and deafness Familial hypercholesterolemia (homozygous and heterozygous) Fragile X syndrome Gaucher disease Muscular dystrophies (DMD, BMD, EDMD, DM1, DM2, SM) Niemann-Pick disease Nuclear mitochondrial genes Rett syndrome Sickle cell disease Tay-Sachs disease 21-hydroxylase deficiency Familial amyotrophic lateral sclerosis (FALS) ------------------------------------------------------------------------------------------------------------- Genetic testing is not covered or reimbursable for the screening, diagnosis or management of ANY of the following conditions: genetic variants:  MTHFR  ACE Medical Coverage Policy: 0052  AGT  Apolipoprotein E (APOE)  APP  Presenilin 1 (PSEN1)  Presenilin 2 (PSEN2)  Interleukin 6-174 variant  Chromosome 9 (9p21)  Kinesin-like protein 6  rs3798220 allele-lipoprotein A variant Genetic testing or gene mapping in the general population is not covered or reimbursable. ------------------------------------------------------------------------------------------------------------- Multi-Gene Genetic Testing Panels Genetic testing for hereditary conditions using a multigene sequencing panel is considered medically necessary when ALL of the following criteria are met: • • phenotype warrants testing of multiple genes and a relevant differential diagnosis list is documented test results may preclude the need for multiple and/or invasive procedures or tests, follow- up, or screening that would be recommended in the absence of panel testing criteria for multi-gene panel testing is not described elsewhere in this Coverage Policy. results will directly impact medical management of the individual being tested clinical presentation is consistent with a genetic etiology Genetic testing for nonsyndromic forms of hearing loss using a multigene sequencing panel as recommended by the American College of Medical Genetics is considered medically necessary when ALL of the following criteria are met: • medical and birth histories are not suggestive of an environmental (i.e., non-genetic) cause of hearing loss, including but not limited to: individual lacks physical findings suggestive of a known genetic syndrome  otitis media  tympanic membrane perforation  temporal bone fractures  auditory tumors  congenital rubella  congenital syphilis  congenital toxoplasmosis  congenital malformations of the inner ear  congenital cytomegalovirus (CMV) infection  prematurity Genetic testing for global developmental delay or intellectual disability using a multigene sequencing panel is considered medically necessary when EITHER of the following criteria is met: individual is diagnosed with global developmental delay* following formal assessment by a developmental pediatrician or neurologist Medical Coverage Policy: 0052 individual is diagnosed with moderate/severe/profound intellectual disability** following formal assessment by a developmental pediatrician or neurologist Global developmental delay is defined as significant delay in younger children, under age five years, in at least two of the major developmental domains: gross or fine motor; speech and language; cognition; social and personal development; and activities of daily living. **Moderate/severe/profound intellectual disability as defined by Diagnostic and Statistical Manual of Mental Disorders (DSM-5) criteria, diagnosed by 18 years of age. Genetic testing for multifactorial diseases using panels, gene expression classifiers, or polygenic risk scores is considered medically necessary when EITHER of the following conditions is met: • individual demonstrates signs/symptoms of a multifactorial disease individual has a direct risk factor (e.g., based on family history or pedigree analysis) for the development of a multifactorial disease And ALL of the following are met: • the test has been shown to improve clinical outcomes results will directly impact clinical decision-making and clinical outcome for the individual being tested presence of genetic variant(s) is highly predictive for the development of the multifactorial condition Genetic screening in the general population is not covered or reimbursable. ---------------------------------------------------------------------------------------------------------- Genetic Testing for Mitochondrial Disorders Genetic testing for mitochondrial disorders using ANY of the following types of testing is considered medically necessary: • • multi-gene nuclear DNA panels when ANY of the following criteria are met: targeted analysis when a specific mitochondrial disorder is suspected full sequencing and deletion/duplication analysis of mitochondrial DNA  an individual has documented unexplained lactic acidosis (e.g., in the absence of sepsis, heart failure)  an individual has multisystem involvement suggested by exhibiting at least two of the following:  myopathy  abnormal electromyography (EMG)  motor developmental delay  neurological developmental delay or intellectual disability  speech delay  dystonia  ataxia  presence of gastrointestinal tract (e.g., dysphagia, vomiting, gastroparesis), immune or endocrine disease Medical Coverage Policy: 0052  disorders of hearing (e.g., sensorineural hearing loss)  disorders of vision (e.g., optic atrophy)  growth delay or failure to thrive  elevated lactate  exercise intolerance and cardiomyopathy  ptosis  external opthalmoplegia  renal tubular acidosis  encephalopathy  seizures  migraine  stroke-like episodes  peripheral neuropathy  sensorineural hearing loss  spasticity  elevated alanine  elevation of Krebs’ cycle intermediates   imaging /other Leigh disease lactate peak on MRS Leukoencephalopathy with brainstem and spinal cord involvement  cavitating leukoencephalopathy   deep cerebral white matter involvement and corpus callosum agenesis leucoencephalopathy with thalamus involvement --------------------------------------------------------------------------------------------------------- Genetic Testing for Connective Tissue Disorders and Thoracic Aortic Aneurysm (TAA) and Dissection (TAD) Single gene or targeted multi-gene panel testing is considered medically necessary for an individual with ANY of the following indications: Thoracic aortic dissection (TAD)  <70 years, with hypertension  Any age, without hypertension Thoracic aortic aneurysm (TAA), when aortic z-score reported on echocardiogram meets ANY of the following criteria:  Any age: >3.5  >70 years: 2.5-3.5, in the absence of hypertension  <70 years: 2.5-3.5  <20 years: >2 and other systemic features are present or aortic z-score progression is documented Presence of TAD or TAA not meeting criteria above and one additional affected first- or second-degree relative When a first degree relative who meets criteria for TAA or TAD is unavailable for testing • Presence of syndromic features suggestive of a connective tissue disorder (e.g., Marfan syndrome, Loeys-Dietz syndrome, Ehlers Danlos syndrome Single site genetic testing for the relevant gene when there is a known familial pathogenic or likely pathogenic variant in a first- or second-degree relative Medical Coverage Policy: 0052 Genetic testing for hereditary connective tissue disorders is considered not medically necessary in an individual with isolated or non-syndromic generalized joint hypermobility or hypermobile Ehlers Danlos syndrome (hEDS). -------------------------------------------------------------------------------------------------------- Newborn Screening Cigna covers newborn screening for genetic disorders (e.g., screening for metabolic, endocrine, hemoglobin and other disorders) performed in accordance with state mandates. General Background Laboratory Testing Some general principles apply to reimbursement of all laboratory tests. The testing method being used must be scientifically validated for each indication for which the test or panel is being proposed. Due to the high complexity of genetic tests, the proposed test or each proposed test in a panel must be Food and Drug Administration (FDA)-approved and/or performed in a Clinical Laboratory Improvement Amendments (CLIA)-accredited laboratory. There are several important advantages to a test being CLIA certified, including the test having a higher degree of precision and performance by trained laboratory professionals. Tests performed in CLIA-accredited laboratories must meet regulatory CLIA standards. The results of each individual test or each test in a panel must be clinically useful for the diagnoses or indications for which the test is being performed. Further, outcomes must be meaningful, that is, they must directly impact clinical decision making and result in improved outcomes for the individual being tested. Genetic Counseling Genetic counseling is the process of helping individuals understand and adapt to the medical, psychological, and familial indications of genetic contributions to disease. Genetic counseling services span the life cycle from preconception counseling to infertility evaluation, prenatal genetic screening and diagnosis, and include predisposition evaluation and genetic diagnosis. Genetic counseling is recommended both pre-and post-genetic test to interpret family and medical histories to assess the chance of disease occurrence and recurrence, educate regarding inheritance, testing, management prevention and resources, and counsel to promote informed choices and adaptation to risk or condition. Germline and somatic genetic testing may identify secondary and incidental findings unrelated to the primary testing indication. Pre-test genetic counseling can elicit patient preferences regarding these findings, and assist in formulating a plan for returning such results before testing occurs (National Society of Genetic Counselors [NSGC], 2020). A variety of genetics professionals provide these services: board-certified or board-eligible medical geneticists, an American Board of Medical Genetics and Genomics or American Board of Genetic Counseling-certified Genetic Counselor, and genetic nurses credentialed as either Clinical Genomics Nurse (CGN) or an Advanced Clinical Genomics Nurse (ACGN) by the Nurse Portfolio Credentialing Commission, Inc. or a genetic nurse with an Advanced Genetics Nursing Certification (AGN-BC) renewed by the American Nurses Credentialing Center (ANCC). Genetic Testing Medical Coverage Policy: 0052 Disease can result when there is an alteration or pathogenic variant in a DNA sequence which causes the cell to produce the wrong protein, or too much or too little of the correct protein. When the pathogenic variant occurs in an egg or sperm it is referred to as a germline variant. Germline gene variants are inherited; that is, passed down in families by blood relatives. Some conditions, such as sickle cell disease, are caused by a single germline pathogenic variant. Other conditions, such as diabetes and heart disease, are more complex. These complex conditions are referred to as multifactorial conditions. Multifactorial conditions are also inherited, but may be caused by more than one germline pathogenic variant. The presence of a pathogenic variant(s) may increase an individual's risk of developing one of these conditions; however, a combination of genetic and environmental factors such as nutrition, exercise, weight, smoking, drinking alcohol, and medication use may influence the observable characteristics of the condition. Genetic testing involves the analysis of human deoxyribonucleic acid (DNA), ribonucleic acid (RNA), chromosomes, proteins, and certain metabolites in order to detect alterations or changes related to an inherited disorder. Types of genetic testing used to identify germline pathogenic variant(s) that cause hereditary and multifactorial conditions include single gene testing, targeted analysis, and multigene sequencing panels. The test must have clinical utility. Clinical utility refers to the usefulness of the test to impact health outcomes and treatment. The National Human Genome Research Institute Task Force on Genetic Testing (NHGRI) recommended the following underlying principles to ensure the safety and effectiveness of genetic tests (Holtzman and Watson, 1998): The genotypes to be detected by a genetic test must be shown by scientifically valid methods to be associated with the occurrence of a disease, independently replicated and subject to peer review. Analytical sensitivity and specificity of a genetic test must be determined before it is made available in clinical practice. Data to establish the clinical validity of genetic tests (clinical sensitivity, specificity, and predictive value) must be collected under investigative protocols. In clinical validation, the study sample must be drawn from a group of subjects representative of the population for whom the test is intended. Formal validation for each intended use of a genetic test is needed. Before a genetic test can be generally accepted in clinical practice, data must be collected to demonstrate the benefits and risks that accrue from both positive and negative results. Genetic testing may be used to aid in diagnosis or confirmation of a disorder in a symptomatic individual (i.e., diagnostic or confirmatory testing), to predict risk of future disease in an asymptomatic individual (i.e., predictive testing), to allow reproductive planning (i.e., reproductive carrier testing), prenatal testing of a fetus, preimplantation genetic diagnosis, and newborn screening. The scope of this policy includes diagnostic and confirmatory, single or multigene testing for hereditary and multifactorial conditions. Single Gene Genetic Testing for Germline Conditions Single gene germline genetic testing is frequently performed to diagnose or confirm the presence of a disease-causing pathogenic or likely pathogenic variant and may be appropriate if an individual demonstrates characteristics of a genetically-linked heritable disease or has a direct risk factor for the development of the specific disease in question. Diagnostic testing may also be performed to help determine the course of a disease or choice of treatment. Genetic testing for a number of genetically linked heritable conditions is supported by various professional society guidelines. Medical Coverage Policy: 0052 Methylenetetrahydrofolate Reductase (NAD(P)H) (MTHFR) Gene Variants Polymorphisms in the MTHFR gene have been associated with an increased risk of homocystinuria, and studied as a possible risk factor for a number of other conditions such as heart disease, stroke, preeclampsia, glaucoma, cleft palate, and certain psychiatric conditions. Increased levels of homocysteine have also been associated with an increased risk of thromboembolism (Genetics Home Reference [GHR], 2019). Although MTHFR has been associated with increased risk of homocystinuria; genetic testing is not indicated because these variants are not associated with thromboembolism (Hickey, et al., 2013). MTHFR variants have also been associated with an increased risk of neural tube defects, such as anencephaly or spina bifida. The 677C>T variant is the most commonly studied. This involves a change in a single deoxyribonucleic acid (DNA) nucleotide in the MTHFR gene, which produces a form of MTHFR that has reduced activity at higher temperatures (i.e., thermolabile). Individuals with the thermolabile form of the enzyme have increased blood levels of homocysteine. It is estimated that over 25% of individuals of Hispanic origin and 10-15% of North American Caucasians are homozygous for this variant (Hickey, et al., 2013). U.S. Food and Drug Administration (FDA): The FDA has granted 510(k) approval to several genomic DNA in vitro diagnostic tests for MTHFR mutation, including Invader MTHFR 677 and Invader MTHFR 1298 (Hologic, Inc., 2011, Marlborough, MA), eSensor MTHFR Genotyping Test (Osmetech Molecular Diagnostics, 2010, Pasadena, CA), and Verigene MTHFR Nucleic Acid Test (Nanosphere, Inc., 2007, Northbrook, IL). Literature Review: Although there are a number of observational studies in the published peer- reviewed scientific literature regarding the association of MTHFR variants and increased risk of homocystinuria, neural tube defects and other conditions, randomized control data are limited. Evidence to demonstrate the impact of genotyping on improved health outcomes, including disease management, is also limited. Several variants of the MTHFR gene have been associated with increased risk of developing a number of conditions; however, its role in these conditions has not been established (GHR, 2019; Hickey, et al., 2013). There is insufficient evidence in the published peer-reviewed scientific literature to determine the clinical utility of MTHFR genetic testing and its impact on net health outcomes. Professional society consensus support for MTHFR genotyping is limited. At this time the role of genetic testing for MTHFR has not been established. Tsai et al. (2009) reported results of a longitudinal cohort analysis of participants (n=1434) of the CARDIA study. DNA was extracted from the peripheral leukocytes of blood collected from each participant. MTHFR 677C.T genotype was determined using selective amplification. The mean of serum B vitamins and tHcy concentrations and the prevalence of folate deficiency and moderate hyperhomocysteinemia were compared in 844 Caucasian and 587 African American participants before folic acid fortification (year zero and year seven) and after fortification (year 15). Mandatory folic acid fortification as initiated by the U.S. government in 1998 improved the nutritional status of folate in both Caucasians and African Americans, with an approximate three- fold increase in folate concentrations at year 15 compared with year zero. The authors used the sensitivity and specificity of MTHFR 677C.T genotyping to predict elevated tHcy concentrations using various tHcy cutoffs to define hyperhomocysteinemia. The authors concluded that after folic acid fortification in the U.S., measurement of tHcy rather than genotyping of MTHFR 677TT should be used as the primary assay for the diagnosis and monitoring of moderate hyperhomocysteinemia. ACE and AGT Gene Variants Medical Coverage Policy: 0052 ACE Gene: The ACE gene (i.e., angiotensin I converting enzyme [peptidyl-dipeptidase A] 1) is part of the renin-angiotensin system (GHR, 2013a). ACE is a relatively nonspecific peptidase and one of the most polymorphic genes, thought to affect a number of physiologic processes including blood pressure control, hematopoiesis, reproduction, renal development and function, and immune response. Specifically, variants in the ACE gene have been identified as the most common cause of renal tubular dysgenesis; at least 33 variants have been found in affected individuals. A variation in the ACE gene, called the ACE I (insertion)/D (deletion) type, is a focus of ongoing research. Individuals may have two I alleles (II), two D alleles (DD), or one of each (ID). The DD type has been associated with increased levels of angiotensin-converting enzyme compared to the other types. Researchers propose that individuals with the DD type have an increased risk of stroke. It is also thought that individuals with this type who have diabetes mellitus have an increased risk of nephropathy. The contribution of other genetic and environmental influences on these risk factors is unknown (GHR, 2013a). Angiotensinogen (AGT) Gene Variants: Individuals with an inherited variant in the AGT gene are more likely to become hypertensive and to experience more severe forms of the disease earlier in life. AGT polymorphism may be associated with increased risk of cardiovascular disease and increased responsiveness to angiotensin converting enzyme (ACE) inhibitor therapy, salt restriction, and weight loss. Analysis of the gene may have potential to help individualize therapy by determining the patient’s responsiveness to certain types of antihypertensive interventions. Evidence in the peer-reviewed, published scientific literature is insufficient to support the clinical utility of this testing and does not support that the detection of AGT leads to improvement of clinical outcomes in patient management. The AGTR1 gene (i.e., angiotensin II receptor type 1 [AT1 receptor]) is also part of the renin- angiotensin system. Like variants associated with the ACE gene, AGTR1 gene variations have also been linked to renal tubular dysgenesis. Other variants, including the 1166A>C variant have been associated with several conditions including an increased risk for the development of essential hypertension, heart disease, and nephropathy (GHR, 2013b). Although it has been suggested that the presence of ACE and AGTR1 gene variants increase risk and susceptibility for a number of conditions, the influence of environmental factors and other variables on the development of these conditions is unknown. There are limited data in the published peer-reviewed scientific literature to inform improved health outcomes using the results of this testing. Established strategies for genetic testing of this gene are lacking. Genetic testing for ACE and AGTR1 gene variants remains a continued focus of research; however, the role of such testing to inform clinical practice and improve health outcomes has not yet been established. Literature Review: Randomized controlled trial data to inform on the ability of ACE and AGT gene variant testing to improve health outcomes are lacking. Evidence in the published peer- reviewed scientific literature regarding genetic testing for ACE and AGTR1 gene variants is primarily limited to association studies and uncontrolled trials related to conditions for which increased risk has been proposed. There are scarce data regarding testing strategies and the outcomes of genetic testing on the diagnosis and management of these conditions. Apolipoprotein E (APOE) Gene Variants Genetic testing for apolipoprotein-E epsilon (APOE) testing has been proposed as a means to provide additional risk information for those patients currently identified as low- or intermediate- risk for cardiovascular disease by standard lipoprotein testing and risk factor assessment. APOE controls the metabolism of the highly atherogenic apolipoprotein B (apo B) containing lipoproteins. It is a protein constituent of VLDL and chylomicrons. The APOE gene provides instructions for making Apo E; Apo E binds to the cell surface receptors to form molecules called lipoproteins. However, there is no uniform standard for analyzing the relationship of APOE genotypes or Medical Coverage Policy: 0052 phenotypes to cardiovascular disease (CVD) risk. At this time, genotype-phenotype correlations are incompletely understood (Bird, 2018). Genetic testing for APOE has also has been proposed as a means to diagnose or predict susceptibility to early- and late-onset Alzheimer's disease (AD). At least three different alleles of APOE epsilon have been identified: APOE epsilon-2 (APOE e2), APOE epsilon-3 (APOE e3) and APOE epsilon-4 (APOE e4). APOE is a susceptibility polymorphism; the presence of one or two e4 alleles increases the risk but does not guarantee that someone will develop AD. Neuropathologic findings of beta-amyloid plaques and intraneuronal neurofibrillary tangles on autopsy examination remain the gold standard for diagnosis of AD (Bird, 2018). Clinical diagnosis prior to autopsy confirmation is made by use of diagnostic testing. Recommendations by the National Institute of Neurological and Communicative Diseases and Stroke and the Alzheimer’s Disease and Related Disorders Association ([NINCDS-ADRDA]) criteria were published by McKhann et al. (2011), on behalf of the National Institute on Aging and the Alzheimer’s Association. These criteria correctly diagnose the disease 80%-90% of the time. The role of APOE in late-onset AD is a topic of research interest. The APOE e4 genotype is found in many elderly persons without dementia and about 42% of persons with late-onset AD do not have an apolipoprotein-E (APOE) epsilon-4 allele. The absence of this allele does not rule out the diagnosis of Alzheimer’s disease, however the association of the APOE e4 allele with AD is significant. Nevertheless, APOE genotyping is neither fully specific nor sensitive. Additional genes and loci under investigation include ABCA7, AKAP9, BIN1, CASS4, CD2AP, CD33, CLU, EPHA1, FERMT2, HLA-DRB5/DRB1, INPP5D, MEF2C, MS4A6A/MS4A4E, PICALM, PLD3, PTK2B, SORL1, and UNC5C (Bird, 2018). There is insufficient evidence in the peer-reviewed, scientific literature to support the use of APOE testing for the screening, diagnosis or management of cardiovascular disease or Alzheimer’s disease (AD). APOE genotyping does not reduce the risk of developing Alzheimer’s disease, change the clinical treatment, or substantially modify disease progression in individuals with Alzheimer’s disease. U.S. Food and Drug Administration (FDA): In 2020, the FDA granted 510(k) approval for the over-the-counter, direct-to-consumer Helix Genetic Health Risk App for Late-Onset Alzheimer’s Disease (Helix OpCo, LLC, 2020, Toronto, Canada). The manufacturer claims that the test reports the lifetime risk of developing Alzheimer’s disease at or above age 65 years based on six genotypes of the APOE gene. The predicate test for this approval was the 23andMe PGS Genetic Health Risk Report for Late-onset Alzheimer’s Disease (23andMe, 2017, Sunnyvale, CA), which reported on the e4 variant only. Potential users of either test are advised that the tests are not diagnostic, do not detect all genetic variants associated with late-onset Alzheimer’s disease, and that an individual’s race, ethnicity, age, and/or sex may affect result interpretation. Literature Review: The Agency for Healthcare Research and Quality (AHRQ) identified 15 cohort studies involving 8509 subjects that examined the association between APOE and the risk of cognitive decline. Various studies reported that APOE epsilon-4 (e4) was associated with greater decline on some, but not all, cognitive measures. Presence of an APOE e4 allele was not, however, significantly different in those who maintained cognitive performance compared to those with minor declines (Williams, et al., 2010). Tsuang et al. (1999) prospectively evaluated APOE testing for AD in a community-based case series of 132 persons with no previous diagnosis of dementia. Clinical diagnosis yielded a sensitivity of 84%, specificity of 50%, and positive and negative predictive values of 81% and 56%, respectively. Neuropathologic AD was confirmed in 94 of 132 patients, with a prevalence of 71%. The presence of an APOE epsilon-4 allele was associated with an estimated sensitivity of Medical Coverage Policy: 0052 59%, specificity of 71%, and positive and negative predictive values of 83% and 41%, respectively. The authors noted that findings do not support the use of APOE genotyping alone in the diagnosis of AD in the general medical community. In a neuropathologically confirmed series, the addition of APOE testing increased the positive predictive value of a diagnosis of AD from 90% to 94%. In those patients with a clinical diagnosis of non-Alzheimer’s dementia the absence of an APOE e4 allele increased the negative predictive value from 64% to 72% (Waldemar, 2007). Amyloid Precursor Protein (APP), Protein Presenilin 1 (PSEN1), and Protein Presenilin 2 (PSEN2) Early onset familial Alzheimer disease (EOFAD) is diagnosed in families with multiple affected individuals with mean age of onset before 65 years and/or with a documented pathogenic variant in one of the genes known to be associated with this disorder. Although clinically indistinguishable by phenotype, three subtypes have been recognized, based on differences in the causative gene variant: Alzheimer disease type 1 (AD1), caused by pathogenic variant of APP (10%-15% of EOFAD); Alzheimer disease type 3 (AD3), caused by pathogenic variant of PSEN1, (30%-70% of EOFAD); and Alzheimer disease type 4 (AD4), caused by pathogenic variant of PSEN2 (<5% of EOFAD). Kindreds with autosomal dominant EOFAD with no identifiable pathogenic variants in PSEN1, PSEN2, or APP have been described; thus, it is likely that variants in additional genes are causative (Bird, 2018). Genetic testing of at-risk asymptomatic adults for early-onset familial Alzheimer’s disease is clinically available for PSEN1, PSEN2 and APP variants. However, genetic testing is not helpful in predicting age of onset, severity, type of symptoms, or rate of progression in asymptomatic individuals. At this time genotyping for PSEN1, PSEN2, and APP variants does not reduce the risk of developing Alzheimer’s disease, change the clinical treatment, or substantially modify disease progression in individuals with early-onset disease. Literature Review: The clinical utility of genetic testing for APP, PSEN1 and PSEN2 to diagnose or manage early-onset familial Alzheimer disease in at-risk individuals or as a screening tool in the general population has not yet been established. At this time there is insufficient evidence in the published, peer-review scientific literature to demonstrate improved health outcomes with such testing. Cardiac Disease – Risk Factors Interleukin 6–174 Variant: Interleukin 6 is an inflammatory cytokine that is believed to play a role in the acute phase response and inflammatory cascade similar to C-reactive protein. One polymorphism, –174, has been reported to be of specific importance (Lieb, et al., 2004). However, evidence regarding the relationship between interleukin 6–174 and cardiovascular disease has not been consistently demonstrated in the peer-reviewed, published scientific literature. The results of some studies show an association between plasma levels and cardiovascular disease (Reichert, 2016; Bermudez, et al., 2002) and, in other studies, authors have reported it is not a suitable marker for coronary heart disease and that significant associations have not been found (Sukhija, et al., 2007; Sie, et al., 2006; Lieb et al., 2004). A 2021 systematic review and meta-analysis demonstrated an overall association between interleukin 6–174 polymorphism and coronary artery disease in Asian and Asian Indian ancestral subgroups, while other ancestries failed to show any meaningful association (Rai, et al., 2021). The limitations of the overall body of published evidence preclude the ability to draw strong conclusions on the clinical utility of interleukin 6–174 testing at this time. Kinesin-like protein 6 (KIF6): Kinesin-like protein 6 is a protein involved in intracellular transport expressed in many tissues and cell types. Theoretically, variants of KIF6 (719Arg allele) may be a risk factor associated with cardiovascular disease (CVD), in particular with myocardial infarction. While the role of KIF6 in CVD is not clearly established in the peer-reviewed scientific Medical Coverage Policy: 0052 literature, there are a few studies that support an association with CVD (Shiffman, et al., 2008a; Shiffman, et al., 2008b; Iakoubova, et al., 2008; Bare, et al., 2007). Early evidence suggested that high dose statin therapy compared with standard dose reduced the risk of death or major cardiovascular events in patients who were carriers of the gene (Iakoubova, et al., 2008). However, more recent evidence in the form of large randomized controlled trials and a meta- analysis of prospective case-control studies found that the KIF6 genotype had no significant impact on CVD or response to statin therapy (Akao, et al., 2012; Hopewell, et al., 2011a; Assimes, et al., 2010). Further studies are needed to clearly define the functional effect of the gene, the affect KIF6 has on CVD, and to determine how testing impacts medical management strategies and improves clinical outcomes. Chromosome 9 Polymorphism 9p21: Genomic profiling (evaluating multiple genes) has been evaluated as a method of improving cardiac risk determination compared to traditional cardiac risk factors. The Genomic Applications in Practice and Prevention (EGAPP) Working Group (launched by the Centers for Disease Control and Prevention) sought indirect evidence to support that genomic profiling has an impact on cardiac risk estimation and that improvement in risk determination would result in management changes that improved clinical outcomes. EGAPP acknowledged direct evidence is lacking. Overall, 29 gene candidates were evaluated with 58 different gene variant associations. Only one marker, chromosome 9p21 SNPs (single nucleotide polymorphisms), had strong credibility; other combinations were moderate or weak (Palomaki, et al., 2010). Based on the published recommendations (EGAPP, 2010) there was insufficient evidence to support testing in the general population for the 9p21 variant or for any of the 57 other variants found in 28 genes. As a result, the magnitude of health benefit for these was tests were found to be insignificant. A 2019 meta-analysis of 49 case-control and prospective cohort studies showed no clear association between variation at chromosome 9p21 and risk of subsequent myocardial infarction or coronary heart disease-related death (Patel, et al., 2019). The extent to which genomic profiling alters cardiac risk estimation remains unknown and genomic testing cannot be recommended until evidence supports improved clinical outcomes. rs3798220 allele-lipoprotein A (LPA) variant: Genetic variants of the Lp(a) gene have been investigated to evaluate the influence of the variants on Lp(a) levels and associated cardiac risk. One single nucleotide polymorphism (LPA rs3798220) has been identified in the LPA gene as being associated with both elevated levels of lipoprotein(a) and an increased risk of thrombosis. Theoretically, patients with a positive test for the LPA genetic variant rs3798220 may derive more benefit from the anti-thrombotic properties of aspirin due to the increased risk for thrombosis, thereby reducing cardiac disease risk. As a result, testing for the rs3798220 variant has been proposed as a method of stratifying benefit from aspirin treatment. The U.S. Preventive Services Task Force (USPSTF) guidelines do support aspirin therapy for a specific subset of individuals for reducing the risk of stroke or myocardial infarction. Aspirin therapy is a well-established therapy but may be associated with gastrointestinal bleeding. Authors contend that testing for the LPA genetic variant may help to better define the risk/benefit ratio of aspirin therapy when the Lp(a) level is elevated. Evidence in the published, peer-reviewed scientific literature evaluating the association of lipoprotein A variants and elevated Lp(a) is limited, with mixed outcomes being reported (Li, et al., 2014; Anderson, et al , 2013; Koch, et al., 2013; Hopewell, et al., 2011b; Chasman, et al., 2009; Clarke, et al., 2009; Shiffman, et al., 2008a; Shiffman, et al., 2008b). Currently the evidence does not lend support that testing offers any additional prognostic value compared to Lp(a). There remain concerns regarding clinical validity, including a lack of assay standardization and the absence of universal guidelines for screening and subsequent risk assessment of high Lp(a) levels; studies on clinical validity and utility are needed (CDC, 2022). Medical Coverage Policy: 0052 Gene Expression Profiling for Cardiovascular Disease Risk: Gene expression is a process by which a gene's coded information is translated into the structures present and operating in the cell and has been investigated as a diagnostic tool for evaluating individuals with cardiovascular disease. U.S. Food and Drug Administration (FDA): While many genetic and genomic tests are regulated by the FDA, laboratory developed tests (i.e., in vitro diagnostic tests that are designed, manufactured and used within a single laboratory) go to market without independent analysis. One such example was the Corus CAD Assay from CardioDx Inc. (Palo Alto, CA), which was proposed as a quantitative gene expression test intended to rule out coronary artery disease (CAD) in stable, nondiabetic individuals. However in 2019, a Medicare Local Coverage Decision of non-coverage was issued, stating “the manufacturer has failed to demonstrate that testing resulted in improved patient outcomes or that testing changed physician management to result in improved patient outcomes”, (CMS, 2021). The test is no longer commercially available. Literature Review: Although there are some data in the published, peer-reviewed scientific literature evaluating risk factors as a method of assessing cardiovascular disease, the added value beyond that associated with traditional testing has not been firmly established. Consensus support from professional societies/organizations in the form of published guidelines is lacking. The impact of genetic testing on meaningful clinical outcomes such as morbidity and mortality has not yet been clearly defined. Evidence in the published peer-reviewed scientific literature evaluating gene expression testing for determining cardiovascular disease risk (e.g., Corus CAD) is limited to prospective validation studies and case control studies (Filsoof, et al., 2015; Ladapo, et al., 2015; Daniels, et al., 2014; McPherson, et al., 2013; Thomas, et al., 2013; Vargas, et al., 2013; Lansky, et al., 2012; Rosenberg, et al., 2012; Elashoff, et al., 2011; Rosenberg, et al., 2010; Wingrove, et al., 2008). Wingrove et al. (2008) and Elashoff et al. (2011) evaluated genes associated with CAD as part of the development of the gene expression assay algorithm for assessing CAD in nondiabetic patients. Herman et al. (2014) published the results of a prospective clinical trial (n=261) to evaluate the impact of GES testing on reduction of diagnostic uncertainty in the evaluation of subjects presenting with symptoms suggestive of obstructive CAD. The trial is referred to as the “Primary Care Providers Use of a Gene Expression Test in Coronary Artery Disease Diagnosis (IMPACT- PCP)" trial. Subjects were nondiabetic patients presenting with stable, nonacute typical and atypical symptoms of obstructive CAD. Ten subjects were excluded, primarily due to GES exclusion criteria. Preliminary clinical decisions without GES results were made by the primary care physician and compared to final decisions made with the GES results. Primary outcomes included the change in patient management between preliminary and final decisions; secondary outcomes included assessment of the pattern of change for each patient, including the effect the change had on patient outcomes. The average pretest probability of obstructive CAD was 28 ± 17%. There was a change in diagnostic plan in 145 subjects with 93 having a reduction in intensity of testing (p<0.001). GES was not associated with untoward outcomes within the first 30 days follow-up; one major adverse cardiac event occurred within the 30 day period. GES testing in this study group allowed physicians to reclassify subjects for subsequent testing. Limitations of the study included sample population of nondiabetic subjects, and short-term follow-up of 30 days for monitoring of adverse events. Ladapo et al. (2014) published the results of the REGISTRY trial which was a prospective, multicenter observation registry of data collected regarding utilization of health care services for subjects who underwent GES testing at seven primary care sites. Following GES testing, medical assessments of the subjects were followed for 45 days to determine how clinicians managed the Medical Coverage Policy: 0052 subjects (e.g., cardiology referrals, cardiac stress tests, angiography). Primary outcomes included the 45 day assessment outcomes, in addition to six-month follow up for evaluating major cardiac adverse events. The GES showed statistically significant relationships with patterns of cardiac referrals; subjects with a low GES had 94% decreased odds of referral versus subjects with an elevated GES. The overall major adverse cardiac event rate was 5/339 during the follow-up period. Ladapo and colleagues concluded GES had an effect on patient management that was clinically relevant, and the test was safe as evidenced by a low major cardiac adverse cardiac event rate. The study was limited by lack of a control group. McPherson et al. (2013) evaluated the impact of gene expression testing on disease management by a group of cardiology specialists. The results of this study (n=88) demonstrated that subjects with low gene expression scores (i.e., ≤ 15) were more likely to have a decrease in the intensity of diagnostic testing. In addition, patients with elevated levels were more likely to undergo additional testing for the evaluation of obstructive CAD. Limitations of this study include small sample population, evaluation of short term outcomes (six months), and inclusion criteria of low risk individuals. Thomas et al. (2013) reported the results of a prospective, multicenter, double blind trial evaluating gene expression as a method to assess obstructive CAD (n=431) (COMPASS study). The study population consisted of a cohort of subjects referred for diagnostic myocardial perfusion imaging (MPI) stress testing with angina or angina equivalent symptoms. The subjects had blood samples for gene expression obtained prior to MPI and based on MPI results were referred for either invasive coronary angiography or CT angiography. The subjects were followed for six months with a study end point of a major adverse cardiac event. Angiography results were compared to GES and MPI results. GES was significantly correlated with maximum percent stenosis (≥ 50). Negative predictive value, sensitivity and specificity were reported at 96%, 89% and 52%, respectively. In the authors’ opinion gene expression scoring was more predictive of obstructive CAD compared to MPI and other clinical factors. Limitations noted by the authors included potentially lower disease prevalence in the subjects due to inclusion/exclusion criteria, and lack of comparison of GES scores to other noninvasive imaging modalities. Rosenberg and colleagues published results of the PREDICT trial (Personalized Risk Evaluation and Diagnosis in the Coronary Tree) in 2010, a trial designed to validate the diagnostic accuracy of gene expression, and reported sensitivity and specificity were 85% and 43% respectively. The authors noted the algorithm score was moderately correlated with maximum percent stenosis (p<0.001). As a follow-up to the 2010 trial, Rosenberg and associates (2012) reported on the relation of gene expression testing to major adverse cardiovascular events and revascularization procedures. The study group involved an extended cohort of the PREDICT trial which included the validation cohort (n=526) as well as the algorithm development cohort (n=640). Subjects underwent angiography and gene expression testing and were followed for one year post angiography. The study endpoint was major adverse cardiac event or procedures. At one year the endpoint rate was 25% overall for all subjects. The gene expression score (GES) was associated with composite overall endpoint of both major events and procedures at one year (p<0.001) and at 12 months the sensitivity and specificity were 86% and 41% respectively. Elevated GES scores (>15) trended towards an increased rate of adverse events and procedures. The authors noted study limitations included limited follow-up period post index angiography, and exclusion of individuals with high risk unstable angina and low risk asymptomatic subjects. Further studies with larger cohorts and evaluation of longer term outcomes are needed. Multi-Gene Germline Genetic Testing Panels Medical Coverage Policy: 0052 Overall, the clinical utility of genetic testing is dependent upon the particular phenotype or observable characteristics of a disease and set of genes being tested. Similar to genetic testing for single genes, smaller, more targeted panels to assess for a particular disorder may have clinical utility when used to aid in diagnosis of heterogeneous genetic conditions. As with single gene testing, results of testing should directly impact clinical management and improve clinical outcomes for the individual being tested. Test results may preclude the need for additional tests, follow up or screening that would be recommended if panel testing is not performed. Additional advantages of panel testing include possible time and cost effectiveness as compared with the time and cost of analyzing each gene separately. The role of panel testing has not been established when treatment is largely supportive and/or results of testing will not result in a direct change in clinical management of the individual or lead to an improvement in clinical outcomes. Most multi-gene panels use next-generation sequencing (NGS) methodology, but some still use Sanger sequencing. Next generation sequencing technology allows large amounts DNA to be sequenced rapidly at a much lower price than prior sequencing methods. The evolution of this technology has spurred the development of tests that sequence multiple genes simultaneously. Such testing is expected to enable widespread evaluation of patients’ genomes in the clinical setting (Taber, et al., 2014). Multigene test panels range from small to large numbers of genes. For testing of multifactorial conditions, testing panels may include gene expression classifier and polygenic risk score tests. A polygenic risk score (PRS) is an assessment of a person’s risk of developing a specific condition based on the collective influence of many genetic variants. A PRS may only explain a person’s relative (not absolute) risk for a disease, as the data used for generating a PRS comes from large- scale genomic studies. Approximately 79% of participants in genome-wide association studies are of European descent, despite comprising only 16% of the global population. Thus, there may not be adequate data about genomic variants from other populations to calculate a PRS in those populations. There is currently limited generalizability of genetic risk scores across diverse populations (NHGRI, 2020; Martin, et al., 2019). The American College of Medical Genetics and Genomics (ACMG) cautions the use of these tests, noting that genetic studies on complex traits and disease susceptibility is an "inexact science" (ACMG, 2021). Mitochondrial Disorders Mitochondrial disorders have significant genetic heterogeneity involving numerous variants in nuclear DNA or mitochondrial DNA (mtDNA)), clinical variability and variation in disease onset with many nonspecific symptoms which may be common in the general population. No specific sign, symptom or biochemical marker may be specifically characteristic or indicative of a particular disease or condition. Recommendations for testing are available by several professional societies, including the Mitochondrial Medical Society, the Association for Clinical Genomic Science and the European Academy of Neurology, National Institute of Neurological Disorders and Stroke. Witters et al. (2018). reassessed mitochondrial diagnostic criteria in the genomics era emphasizing its utility in the diagnostic workup and interpretation of molecular testing results; however, they emphasized the importance of molecular analysis for individuals with lower scores (≥2). LOE: 5. DNA testing for mitochondrial disease through next-generation sequencing (NGS) has emerged as the new gold standard methodology for mtDNA genome sequencing based on improved reliability and sensitivity (Parikh et al., 2015). NGS should be considered as first-line testing for analysis of the mitochondrial genome in blood or urine. Additionally, individuals who had negative mtDNA testing in blood but still have a high clinical suspicion for the condition should have mtDNA assessed in another tissue (Parikh, 2015). Nearly 300 nuclear genes have been associated with mitochondrial disease (Craven et al., 2017). Thus, two approaches to molecular testing have emerged for individuals with clinical Medical Coverage Policy: 0052 suspicion for mitochondrial disease due to multisystem involvement: targeted mtDNA and/or nDNA testing, with additional follow-up testing if negative; or broader testing via whole exome sequencing (WES) or whole genome sequencing (WGS) (Mavraki et al., 2023; Parikh et al., 2015). Targeted testing may be particularly useful when the differential diagnosis is clear based on phenotype and/or biochemical testing, while WES or WGS may be especially considered for more complex phenotypes (Mavraki et al., 2023). Given that mitochondrial diseases may be due to variants in mtDNA or nuclear DNA, simultaneous mtDNA and nDNA testing may be prudent when possible (Mavraki et al., 2023). Genetic testing is not recommended for an individual with hypermobile Erlos Danos syndrome alone. U. S. Food and Drug Administration (FDA) Laboratory tests are available for mitochondrial disease, the majority many of which are proprietary laboratory-developed tests. These are not approved, cleared or otherwise regulated by the FDA. Tests must be Clinical Laboratory Improvement Amendments (CLIA) approved or waived. Connective Tissue Disorders and Thoracic Aortic Aneurysm and Dissection Up to 25% of individuals with thoracic aortic disease harbor an underlying Mendelian pathogenic variant (Renard, 2018). Molecular testing is often employed to confirm a suspected diagnosis given the wide phenotypic variability. If a patient’s clinical features are suspicious for a single type of connective tissue disorder, then it is most appropriate to pursue targeted genetic testing for that condition. However, given the overlap in clinical features across syndromic connective tissue disorders, it can be difficult to establish a targeted differential diagnosis in many cases and testing using a multi-gene panel may be appropriate. Criteria using Z score results from echocardiogram to determine the appropriate indication for genetic testing for heritable thoracic aortic diseases genetic diseases are based on published recommendations of the Heritable Thoracic Aortic Diseases (HTAD) Rare Diseases working group of the European Reference Network on rare multisystemic vascular diseases (VASCERN) (Caruana, 2023).HTAD recommendations represent expert opinion providing a pathway to improve patient care by diminishing time to diagnosis, facilitating the establishment of a correct diagnosis using molecular genetics when possible, excluding the diagnosis in unaffected persons through appropriate family screening and avoiding overuse of resources (2023). Multigene Panel Testing for Nonsyndromic Hearing Loss Hearing loss is the most common sensory deficit in humans, affecting up to 1 in 500 newborns. About 1.2 in every 1,000 children is severely or profoundly deaf at three years old. In developed countries, approximately 80% of congenital hearing loss is due to genetic causes and the remainder to environmental causes. Approximately 80% of prelingual deafness is genetic, most often autosomal recessive and non-syndromic (ClinGen, 2022). Genetic forms are diagnosed by otologic, audiological, ancillary (i.e., computed tomography [CT] examination of the temporal bone), and DNA-based testing, as well as by physical examination and family history. Molecular testing of gene GJB2 (which encodes the protein connexin 26) and GJB6 should be considered in the evaluation of individuals with congenital nonsyndromic sensorineural hearing loss consistent with autosomal recessive inheritance or in families with apparent "pseudodominant" inheritance of DFNB1 (Smith and Jones, 2016). Approximately 98% of individuals with DFNB1 have two identifiable GJB2 variants. Approximately 2% of individuals with DFNB1 have one identifiable GJB2 variant and one of two large deletions that include a portion of GJB6. Diagnosis depends upon molecular genetic testing to identify deafness-causing variants in the genes GJB2 and GJB6. GJB2 gene is the major gene responsible for nonsyndromic, recessive deafness and variants in GJB2 gene and GJB6 gene together account for 50% of autosomal recessive nonsyndromic hearing loss. Medical Coverage Policy: 0052 Multigene testing or screening with a panel of genetic tests has been proposed to test for many causes of hearing loss. The extreme genetic heterogeneity and the frequent lack of phenotypic variability make genetic diagnosis of nonsyndromic hearing loss (NSHL) difficult using single-gene screening techniques—for this reason, multigene screening panels for NSHL have been developed. Indeed, next generation sequencing-based large gene panels have become the testing method of choice for hearing loss. For some syndromic forms of hearing loss, such as Usher syndrome or Pendred syndrome, the nonauditory features can be subtle, especially in early childhood, and certain environmental or nongenetic factors play a major etiologic role in hearing loss. Literature Review: Evidence in the peer-reviewed published literature supports the use of multigene panel testing for nonsyndromic hearing loss (NSHL) for select individuals. There is significant genetic heterogeneity in NSHL, with more than 6,000 causative variants having been found in over 110 genes; multigene panels have therefore overtaken single-gene testing as the preferred approach to testing (Shearer, et al., 2017). Sloan-Heggen et al. (2016) completed targeted genomic enrichment and massively parallel sequencing (TGE + MPS) testing on patients referred for genetic testing for hearing loss (n=1119). Using a custom-developed panel of up to 89 genes, researchers identified a genetic cause of hearing loss in 440 patients (39%). The analysis identified 5,900 variants, 14% of which were deemed causally related to the hearing loss phenotype and reported as pathogenic or likely pathogenic. The four genes most frequently involved were GJB2 (22%), STRC (16%), SLC26A4 (7%), and TECTA (5%). Variants in GJB2 were the most common cause of severe-to-profound hearing loss (20%), and STRC accounted for 30% of diagnoses in subjects with mild-to-moderate hearing loss. Of note, ethnicity impacted the diagnostic rate (p<0.005). The diagnostic rate for Caucasian subjects was 38%, and in cohorts self-identified as Asian and Middle Eastern the diagnostic rate was 63 and 72%, respectively (p<0.005). The diagnostic rate was lowest in African Americans at 26% (p<0.05). The authors noted that a thorough history and physical was essential in guiding the comprehensive genetic testing and making an appropriate diagnosis. Shearer and Smith (2015) noted similar diagnostic rates in their retrospective review of 20 studies of comprehensive genetic testing for hearing loss (n=603 subjects). There were significant differences in the number and type of genes included and whether copy number variations were examined. The overall diagnostic rate was 41% (ranging from 10% to 83% depending on the panel). The authors noted that disease-specific comprehensive (panel) testing provided a better overall diagnostic rate across varying ethnicities than single gene testing, which must be tailored to the phenotype and population being studied. For example, mutations in the gene GJB2 are the cause of between 15–40% of autosomal recessive NSHL in Caucasian individuals but mutations in this same gene very rarely cause genetic hearing loss in other populations; panel testing negated the need for possibly inappropriate sequential single gene testing. Multigene Panel Testing in Global Developmental Delay and Intellectual Disability Developmental delay, intellectual disability, and related phenotypes affect 1–2% of children and may pose medical, financial, and psychological challenges for the individual and family. Standard clinical genetic testing for developmental delay and intellectual disability includes karyotype, microarray, Fragile X, single gene, gene panel, and/or mitochondrial DNA testing (Bowling, et al., 2017; Mithyantha, et al., 2017; Moeschler, et al., 2014). Global developmental delay (GDD) is significant delay affecting children under five years of age, in at least two or more of the major developmental domains: gross or fine motor; speech/language; cognition; social/personal development; and activities of daily living. Children with GDD present with delays in achieving developmental milestones at the anticipated age. This implies deficits in Medical Coverage Policy: 0052 learning and adaptation, which in turn suggests that the delays are significant and may predict future intellectual disability (Moeschler, et al., 2014). Intellectual disability (ID) is a neurodevelopmental disorder that begins in childhood and is characterized by intellectual difficulties as well as difficulties in conceptual, social, and practical areas of living. The Diagnostic and Statistical Manual of Mental Disorders (DSM-5), published by the American Psychiatric Association, requires three criteria for a diagnosis of ID: deficits in intellectual functioning (reasoning, problem solving, planning, abstract thinking, judgment, academic learning, and learning from experience), confirmed by clinical evaluation and individualized standard intelligence testing deficits in adaptive functioning that significantly hamper conforming to developmental and sociocultural standards for the individual's independence and ability to meet their social responsibility onset of these deficits during childhood ID may be further classified as mild, moderate, severe, or profound. The designation depends upon the degree of impairment in an individual’s daily living skills, conceptual developmental, and social development; and level of support needed (National Academies of Sciences, Engineering, and Medicine, 2015). Characteristics of each classification may include (Badesch, 2021): Mild: Able to live independently with minimum levels of support; difficulties in learning academic skills; impaired abstract thinking, executive functioning, and short-term memory; concrete approach to problems and solutions; immature in social interactions; possible difficulty in regulating emotion; limited understanding of risk in social situations Moderate: Independent living may be achieved with moderate levels of support, such as those available in group homes; conceptual skills markedly delayed; needs daily assistance to complete conceptual tasks of day-to-day life; needs support for all use of academic skills; decision-making abilities are limited, needs caregivers to assist with personal life decisions; may misinterpret social cues; marked differences from peers in social and communicative behavior Severe: Requires daily assistance with self-care activities and safety supervision; caregivers provide extensive support for problem-solving; attainment of conceptual skills is limited; poor understanding of written language and/or certain concepts involving numbers, time, quantity; limited spoken vocabulary and grammar; simple speech; possible speech augmentive device; understands simple speech and gestural communication • Profound: Requires 24-hour care and close supervision with self-care activities; often will have congenital syndromes; sensory and physical impairments may limit social activities; very limited communication, largely nonverbal; may understand some simple instructions or gestures; conceptual skills involve the physical world; very limited understanding of symbolic communication; may use objects purposefully; may obtain some visuospatial skills In 2021, the American College of Medical Genetics and Genomics (ACMG) published a practice guideline for exome and genome sequencing for pediatric patients with congenital anomalies or intellectual disability. The guideline recommended whole exome sequencing as a first- or second- tier test for children with congenital anomalies, developmental delay, and/or ID. Additionally, ACMG noted that panel testing for a specific phenotype is often considered as an alternative to exome testing. Isolated autism (i.e., autism without intellectual disability or congenital malformation) was out of scope for the ACMG recommendation (Manickam, et al., 2021). For discussion of whole exome sequencing in the diagnosis of global developmental delay and intellectual disability, please see Cigna Coverage Policy 0519 Whole Exome and Whole Genome Sequencing. Medical Coverage Policy: 0052 Newborn Screening Newborn screening is performed to limit the morbidity and mortality attributable to selected inherited diseases (American Academy of Pediatrics ([AAP], 2013). Newborn screening programs are organized through state governments and are generally mandated. According to the March of Dimes (2020), screening is available for disorders in which accurate diagnosis and early treatment of the disorder can improve health outcomes. Some genetic screening tests are not DNA- or chromosome-based tests but use biochemical markers or phenotypic features. Each year, over four million infants in the U.S. undergo screening, and approximately 12,900 infants are diagnosed with one of the 35 core conditions included in the panel. The most prevalent disorders are hearing loss, primary congenital hypothyroidism, sickle cell disease, and cystic fibrosis (Sontag, et al., 2020). Professional Societies/Organizations Genetic Testing for Alzheimer’s Disease: APOE, APP, PSEN1 and PSEN2 Gene Variants American Academy of Neurology (AAN): The Quality Standards Subcommittee of the AAN updated an earlier practice parameter for the diagnosis of dementia in the elderly. Regarding Alzheimer’s disease (AD), this evidence-based review concluded that there are no laboratory tests, including APOE genotyping or other genetic markers or biomarkers, which are appropriate for routine use in the clinical evaluation of patients with suspected AD. However, genotyping and biomarkers, as well as imaging, are promising avenues that are being pursued (Knopman, et al., 2004). American Psychiatric Association (APA): The 2007 practice guidelines for the treatment of patients with Alzheimer’s disease and other dementias noted that a definitive diagnosis of AD requires both the clinical syndrome and microscopic examination of the brain at autopsy, at which time the characteristic plaques and neurofibrillary tangles widely distributed in the cerebral cortex will be seen. A careful clinical diagnosis of disease conforms to the pathological diagnosis 70%– 90% of the time. Further, the guideline noted that, although genes involved in a variety of dementia syndromes have been identified and family members of patients with dementia are often concerned about their risk of developing dementia, genetic testing is generally not part of the evaluation of patients with dementia except in very specific instances. In particular, testing for apolipoprotein E4 (APOE4) is not recommended for use in diagnosis. The presence of an APOE4 allele does not change the need for a thorough workup and does not add substantially to diagnostic confidence. National Institute on Aging (NIA): In 2019, the NIA published a fact sheet noting that although a blood test can identify which APOE alleles a person has, it cannot predict who will or will not develop Alzheimer’s disease. Per the NIA, it is unlikely that genetic testing will ever be able to predict the disease with 100% accuracy because too many other factors may influence its development and progression. Further, the NIA noted APOE testing is used in research settings to identify study participants who may have an increased risk of developing Alzheimer’s. National Institute on Aging/Alzheimer’s Association: The NIA/AA issued consensus recommendations regarding the diagnosis of AD. For probable AD dementia in a carrier of a causative genetic mutation the recommendations note that in persons who meet the core clinical criteria for probable AD dementia, evidence of a causative genetic mutation (in APP, PSEN1, or PSEN2), increases the certainty that the condition is caused by AD pathology. Carriage of the 3/4 allele of the apolipoprotein E gene is not sufficiently specific to be considered in this category (McKhann, et al., 2011). Medical Coverage Policy: 0052 National Society of Genetic Counselors (NSGC)/American College of Medical Genetics and Genomics (ACMG): On behalf of the NSGC/ACMG, Goldman et al. (2018) published consensus practice guidelines for genetic counseling and testing for AD. The Guidelines recommend that pediatric testing for AD should not occur. Additionally, the Societies stated that direct-to-consumer APOE testing is not advised. The Guidelines noted that a risk assessment should be performed by pedigree analysis to determine whether the family history is consistent with early-onset Alzheimer’s disease (EOAD) or late-onset Alzheimer’s disease (LOAD) and with autosomal dominant (with or without complete penetrance), familial, or sporadic inheritance. Patients should be informed that currently there are no proven pharmacologic or lifestyle choices that reduce the risk of developing AD or stop its progression. The Guidelines also noted: For families in which an autosomal dominant AD gene mutation is a possibility: Testing for genes associated with early- onset autosomal dominant AD should be offered in the following situations:  a symptomatic individual with EOAD in the setting of a family history of dementia or in the setting of an unknown family history (e.g., adoption)  autosomal dominant family history of dementia with one or more cases of EOAD  a relative with a mutation consistent with EOAD (currently PSEN1/2 or APP)  Ideally, an affected family member should be tested first. If no affected family member is available for testing and an asymptomatic individual remains interested in testing despite counseling about the low likelihood of an informative result (a positive result for a pathogenic mutation), he/she should be counseled according to the recommended protocol. If the affected relative, or their next of kin, is uninterested in pursuing tested, the option of deoxyribonucleic acid (DNA) banking should be discussed. For families in which autosomal dominant AD is unlikely: Genetic testing for susceptibility loci (e.g., apolipoprotein-E [APOE]) is not clinically recommended due to limited clinical utility and poor predictive value. Genetic Testing for Cardiac Disease Risk American Academy of Family Physicians (AAFP): The AAFP recommends against genomics profiling to assess risk for cardiovascular disease, stating “the net health benefit from the use of any genomic tests for the assessment of cardiovascular disease risk is negligible and there is no evidence that they lead to improved patient management or increased risk reduction” (AAFP, 2012). American College of Cardiology Foundation (ACCF) /American Heart Association (AHA) Task Force on Practice Guidelines: Greenland et al. (2010) published guidelines which note that genotype testing for CHD risk assessment in asymptomatic adults is not recommended. The task force noted that there is currently no proven benefit in risk assessment when genomic testing is added to the basic global risk assessment, such as Framingham. There is no data to support results of genotype testing alter management and improve clinical outcomes. The task force conducted a systematic review of the scientific evidence (March 2008 – April 2010) and used evidence based methodologies to weigh the evidence which was reviewed. Level A evidence represented data from multiple randomized controlled trials or meta-analyses, level B evidence was data from a single RCT or nonrandomized trial, and level C evidence represented Medical Coverage Policy: 0052 consensus opinion, case studies or standard of care. The recommendations were approved and endorsed by the ACCF, AHA, American Society of Echocardiography, American Society of Nuclear Cardiology, Society of Atherosclerosis Imaging and Prevention, Society of Cardiovascular Computed Tomography, and Society for Cardiovascular Magnetic Resonance. The American College of Cardiology Foundation (ACCF) and the American Heart Association (AHA) published guidelines for assessment of cardiovascular risk in asymptomatic individuals (i.e., apparently healthy adult) (Greenland, et al., 2010). The guidelines did not support genotype testing (level B evidence) or measurement of lipid parameters such as lipoproteins, apolipoproteins, particle size and density, beyond the standard fasting lipid profile (level C evidence), or natriuretic peptide testing (level B evidence). Updated ACC/AHA guidelines on the assessment of cardiovascular risk (Goff, 2013) do not address genetic testing to determine cardiovascular risk. Evaluation of Genomic Applications in Practice and Prevention (EGAPP, 2010): The working group concluded there was insufficient evidence to determine analytic validity, clinical validity, or clinical utility for gene expression testing for determining cardiovascular risk. Genetic Testing for Methylenetetrahydrofolate Reductase (NAD(P)H) (MTHFR) Polymorphisms American College of Medical Genetics and Genomics (ACMG): The reaffirmed ACMG practice guideline on the lack of evidence for MTHFR polymorphism testing noted (Bashford, et al., 2020): MTHFR polymorphism genotyping should not be ordered as part of the clinical evaluation for thrombophilia or recurrent pregnancy loss MTHFR polymorphism genotyping should not be ordered for at-risk family members American College of Obstetricians and Gynecologists (ACOG): ACOG (2018) does not endorse testing for MTHFR polymorphisms for routine risk assessment, evaluation of thrombosis risk, or recurrent pregnancy loss. Genetic Testing for Mitochondrial Disease Mitochondrial Medical Society, (2015): The Mitochondrial Medicine Society published the following consensus recommendations on genetic testing for mitochondrial disorders: Massively parallel sequencing/NGS of the mtDNA genome is the preferred methodology when testing mtDNA and should be performed in cases of suspected mitochondrial disease instead of testing for a limited number of pathogenic point mutations. Patients with a strong likelihood of mitochondrial disease because of a mtDNA mutation and negative testing in blood, should have mtDNA assessed in another tissue to avoid the possibility of missing tissue-specific mutations or low levels of heteroplasmy in blood • Heteroplasmy analysis in urine can selectively be more informative and accurate than testing in blood alone, especially in cases of MELAS due to the common m. 3243A>G mutation. mtDNA deletion and duplication testing should be performed in cases of suspected mitochondrial disease via NGS of the mtDNA genome, especially in all patients undergoing a diagnostic tissue biopsy.  If a single small deletion is identified using polymerase chain reaction– based analysis, then one should be cautious in associating these findings with a primary mitochondrial disorder.  When multiple mtDNA deletions are noted, sequencing of nuclear genes involved in mtDNA biosynthesis is recommended. Medical Coverage Policy: 0052 When a tissue specimen is obtained for mitochondrial studies, mtDNA content (copy number) testing via real-time quantitative polymerase chain reaction should strongly be considered for mtDNA depletion analysis because mtDNA depletion may not be detected in blood. When considering nuclear gene testing in patients with likely primary mitochondrial disease, NGS methodologies providing complete coverage of known mitochondrial disease genes is preferred. Single-gene testing should usually be avoided because mutations in different genes can produce the same phenotype. If no known mutation is identified via known NGS gene panels, then whole exome sequencing should be considered The Mitochondrial Medicine Society also commented on mtDNA depletion syndromes, which are characterized by a significant reduction in mtDNA copy number in affected tissues. Diagnosis requires quantification of mtDNA content, typically in affected tissue, with identification of a significant decrease below the mean of normal age, gender, and tissue- specific control when normalized to nDNA tissue content. mtDNA content is not assessed by NGS of the mtDNA genome and must be assayed by a separate quantitative real-time polymerase chain reaction. Association for Clinical Genomic Science ([ACGS], 2020): The ACGS published guidelines for the genetic testing strategies for diagnostic and familial testing, variant interpretation and reporting, and prenatal diagnosis and reproductive options. The systematic analysis of the entire mtDNA by NGS is quicker and facilitates accurate heteroplasmy assessment thus improving sensitivity and increasing diagnostic yield. Moreover, the use of whole exome The application of NGS and other emerging “omics” tools including RNA-seq has also greatly assisted the identification of novel candidate disease genes involved in mitochondrial function. Genetic Testing for Connective Tissue Disorders and Thoracic Aortic Aneurysm (TAA) and Dissection (TAD) Heritable Thoracic Aortic Diseases (HTAD) Rare Diseases working group of the VASCERN European Reference Network (2023): The HTAD working group published a strategy for diagnostic work-up of individuals with suspected heritable aortic thoracic diseases. According to the recommendations, patients are referred to an expert center for further evaluation if they meet at least one of the following criteria: thoracic aortic dissection (TAD)  3.5: all adults  Z score 2.5–3.5: if non-hypertensive or hypertensive and <60 years children  Z score >3: all children family history of HTAD with/without a pathogenic variant in a gene linked to HTAD • ectopia lentis without other obvious explanation • • Genetic testing should be considered in those with a high suspicion of underlying genetic systemic score of >5 in adults and >3 in children. aortopathy. Though panels vary among centers, for patients with thoracic aortic aneurysm or dissection or systemic features these should include genes with a definitive or strong association to HTAD. Genetic cascade screening and serial aortic imaging should be considered for family screening and follow-up. Medical Coverage Policy: 0052 Multigene Panel Testing for Nonsyndromic Hearing Loss American College of Medical Genetics and Genomics (ACMG): The ACMG practice resource for the clinical evaluation and etiologic diagnosis of hearing loss included the following recommendations specific to genetic testing for nonsyndromic hearing loss (HL): For individuals lacking physical findings suggestive of a known syndrome a tiered diagnostic approach should be implemented:  Unless clinical and/or family history suggests a specific genetic etiology, comprehensive HL gene panel testing should be initiated. If panel testing is negative, genome-wide testing, such as exome sequencing or genome sequencing, may be considered. However, issues related to genomic testing, such as the likelihood of incidental or secondary findings, will have to be addressed.  The HL panel should include the genes recommended by the HL Gene Curation Expert Panel. Because of the existing variations in gene number and content among currently available HL gene panels, clinicians must be aware of the genes included in the test (panel) chosen and the performance characteristics of the platform chosen, including coverage, analytic sensitivity, and what types of variants will be detected. Additional testing strategies may need to be adopted to address the technical challenges caused by highly homologous regions, including pseudogenes. It should be noted that the cost of these new genetic sequencing technologies is decreasing so rapidly that the use of large sequencing panels targeted toward HL- related genes as the initial test, may, in many cases, already be more cost-effective in the evaluation of HL.  If genetic testing reveals variant(s) in an HL–related gene, gene-specific genetic counseling should be provided, followed by appropriate medical evaluations and referrals.  If genetic testing fails to identify an etiology for a patient’s hearing loss, the possibility of a genetic etiology remains. This point must be emphasized because it can be misunderstood by clinicians and by patients and their families. For interested patients and families, further genetic testing may be pursued on a research basis. • Regardless of whether genetic test results are positive, negative, or inconclusive, results should be communicated through the process of genetic counseling and potential risks to other family members should be conveyed (Li, et al., 2022). American Academy of Audiology/Joint Committee on Infant Hearing (JCIH): In its 2019 position statement on principles and guidelines for early hearing detection and intervention programs, the Joint Committee on Infant Hearing endorsed genetic counseling and testing for children with confirmed hearing loss, in accordance with the American College of Medical Genetics and Genomics (ACMG) recommendations (JCIH, 2019). Newborn Screening American Academy of Pediatrics (AAP)/American College of Medical Genetics and Genomics (ACMG): In a joint statement on ethical and policy issues in genetic testing, the AAP and ACMG expressed support for the mandatory offering of newborn screening for all children. The joint statement noted “After education and counseling about the substantial benefits of newborn screening, its remote risks, and the next steps in the event of a positive screening result, parents should have the option of refusing the procedure, and an informed refusal should be respected” (AAP, 2018). Additionally, the ACMG has developed numerous ACT (action) sheets to aid providers in determining the appropriate steps if an infant has screened positive, and related algorithms that provide an overview of the basic steps involved in determining a final diagnosis in the infant. Polygenic Risk Scores Medical Coverage Policy: 0052 American College of Medical Genetics and Genomics (ACMG, 2023): The ACMG notes the following regarding polygentic risk scores (PRS): PRS test results do not provide a diagnosis, instead they provide a statistical prediction of increased clinical risk. A low PRS does not rule out significant risk for the disease or condition in question. • If the risk prediction of a PRS is derived from a population that is different from the patient being tested, then the results may have a poor predictive value for the patient. Isolated PRS testing is not the appropriate test for clinical scenarios in which monogenic etiology is known or suspected. Before testing, a patient and provider should discuss the indications for the PRS test, and the patient should be informed how the PRS results will be used to guide medical management. PRS-based medical management should be evidence-based; however, there is currently limited evidence to support the use of PRS to guide medical management. Clinical follow-up for PRS should be consistent with best practices outlined by professional societies with appropriate expertise in instances when and where evidence-based practice guidelines exist. The ACMG’s position is that preimplantation PRS testing is not yet appropriate for clinical use and should not be offered at this time.