Genetic Testing for Reproductive Carrier Screening and Prenatal Diagnosis - (0514) 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 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

Medical Coverage Policy: 0514 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 genetic testing for germline variant reproductive carrier screening and prenatal diagnosis. Germline gene variants occur in the egg and sperm cells, also known as the germ cells. These variants are inherited, that is, passed down in families by blood relatives. Reproductive carrier screening and prenatal diagnosis refer to testing for the presence of certain germline gene variants that are associated with disease or a risk of disease in an individual’s offspring and descendants, before or after pregnancy has occurred. This type of testing allows for reproductive planning.

Coverage Policy Many benefit plans limit coverage of genetic testing, genetic counseling and infertility services. 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. For additional information regarding coverage for specific genetic tests, please refer to the Genetic Testing Collateral File.

GENETIC COUNSELING 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 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 Genetic Clinical Nurse (GCN) or an Advanced Practice Nurse in Genetics (APNG) by either the Genetic Nursing Credentialing Commission (GNCC) or 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 contracted with a laboratory that is part of an Integrated Health System which routinely delivers health care services beyond just the laboratory test)

Medical Coverage Policy: 0514

GERMLINE CARRIER TESTING FOR FAMILIAL DISEASE Preconception or prenatal carrier testing for an individual who has the capacity and intention to reproduce is considered medically necessary when ANY of the following criteria is met: There is an identified pathogenic or likely pathogenic variant in a blood relative • EITHER of the following criteria is met:  an individual’s reproductive partner is a known carrier of a disease-causing pathogenic or likely pathogenic variant in a recessively inherited condition  a genetic diagnosis has been confirmed in an affected relative, AND the affected relative has not had genetic testing and is unavailable for testing When ANY of the above criteria is met, preconception or prenatal carrier testing is considered medically necessary for the following indications (list may not be all inclusive): Nuclear mitochondrial genes Muscular dystrophies (DMD, BMD, EDMD, DM1, DM2, SM) Fragile X syndrome Rett syndrome PTEN-related disorders Von Hippel-Lindau disease Long QT syndrome

Retinoblastoma 21-hydroxylase deficiency

Sickle cell disease Alpha and beta thalassemia Gaucher disease Niemann-Pick disease Canavan disease Tay-Sachs disease DFNB1 nonsyndromic hearing loss and deafness Huntington disease Cystic fibrosis Preconception or prenatal genetic testing of a prospective biologic female parent for Fragile X (i.e., FMR1) gene mutations is considered medically necessary for EITHER of the following indications:

family history of unexplained intellectual disability or developmental delay, or autism in a blood relative personal or family history of premature ovarian insufficiency Preconception or prenatal carrier testing for spinal muscular atrophy by SMN1 gene variant analysis (CPT code 81329) for the purpose of reproductive screening is considered medically necessary when the individual has the capacity and intention to reproduce and testing has not been previously performed. Preconception or prenatal carrier testing for cystic fibrosis (CF) with targeted variant analysis of CFTR gene variants (CPT code 81220) as described by the American College of Medical Genetics (ACMG) is considered medically necessary for a prospective biologic parent with the capacity and intention to reproduce and testing has not previously been performed. Preconception or prenatal carrier testing for hemoglobinopathies (i.e., thalassemias, sickle cell disease) (CPT codes 81257, 81361) is considered medically necessary when

Medical Coverage Policy: 0514 the individual has the capacity and intention to reproduce and testing has not been previously performed. Preconception or prenatal carrier testing for a prospective biologic parent of Ashkenazi Jewish (AJ) descent is considered medically necessary for the conditions specified by the American College of Medical Genetics, including but not limited to the following: • Tay-Sachs disease (CPT code 81255) • Canavan disease (CPT code 81200) • Fanconi anemia group C (CPT code 81242) • Niemann-Pick disease, type A (CPT code 81330) • Bloom syndrome (CPT code 81209) • Mucolipidosis IV (CPT code 81290) • Gaucher disease, type 1 (CPT code 81251) •

familial dysautonomia (CPT code 81260) targeted panel testing for variants found in an individual of AJ descent Reproductive carrier screening based on the general population risk, other than conditions noted above, is considered not medically necessary. Reproductive carrier screening for nonmedical traits (e.g., eye color, hair color) is considered not medically necessary. A multigene reproductive carrier screening panel with ≥ 15 genes to predict the risk of severe inherited disease is not covered or reimbursable.

PREIMPLANTATION GENETIC TESTING OF AN EMBRYO When the specific criteria noted below are met, Cigna will cover the embryo biopsy procedure to obtain the cell and genetic testing associated with preimplantation genetic testing (PGT) under the core medical benefits of the plan. The embryo biopsy procedure, genetic test and pre-and post-test genetic counseling associated with PGT (PGT for monogenic disorders [PGT-M] or PGT for chromosomal structural rearrangements [PGT-SR]) are considered medically necessary when ALL of the following criteria are met: •

the genetic condition is associated with severe disability or has a lethal natural history the proposed test is medically necessary for the diagnosis(es)/indication(s) listed and there is sufficient evidence to demonstrate improved health outcomes the results of the genetic test will impact clinical decision-making and clinical outcome when ANY of the following criteria is met:  both biologic parents are carriers of a single gene autosomal recessively-inherited

disorder  one biologic parent is a known carrier of a single gene autosomal dominantly- inherited disorder or a single x-linked disorder  one biologic parent is a translocation carrier When the above criteria are met, PGT is considered medically necessary for the following indications (list may not be all inclusive):

Nuclear mitochondrial genes Muscular dystrophies (DMD, BMD, EDMD, DM1, DM2, SM)

Sickle cell disease Alpha and beta thalassemia

Medical Coverage Policy: 0514 Fragile X syndrome Rett syndrome PTEN-related disorders Von Hippel-Lindau disease Long QT syndrome

Retinoblastoma 21-hydroxylase deficiency Gaucher disease Niemann-Pick disease Canavan disease Tay-Sachs disease DFNB1 nonsyndromic hearing loss and deafness Huntington disease Cystic fibrosis PGT for any other indication, including but not limited to the following, is considered experimental, investigational or unproven: human leukocyte antigen (HLA) typing of an embryo to identify a future suitable stem-cell tissue or organ transplantation donor testing solely to determine if an embryo is a carrier of an autosomal recessively-inherited disorder testing for a multifactorial condition testing for variants of unknown significance

• PGT for testing of an embryo for nonmedical gender selection or nonmedical traits is considered not medically necessary. PGT-P (polygenic risks scores) is considered not medically necessary. PREIMPLANTATION GENETIC TESTING FOR ANEUPLOIDY (PGT-A) Preimplantation genetic testing for aneuploidy (PGT-A) by any testing methodology (e.g., comparative genetic hybridization [CGH], fluorescence in situ hybridization [FISH], gene sequencing) for any indication, including but not limited to the following indications, is considered not medically necessary: advanced maternal age (i.e., ≥ age 35 years) • repeated in vitro fertilization (IVF) failures • recurrent spontaneous abortions

PRENATAL GENETIC SCREENING AND TESTING OF A FETUS Pre- and post-test genetic counseling is recommended for an individual who is considering genetic screening for fetal aneuploidy. SEQUENCING-BASED NON-INVASIVE PRENATAL TESTING (NIPT) Sequencing-based non-invasive prenatal testing (NIPT) (CPT® codes 81420, 81507, 0327U) to screen for fetal trisomy 13, 18 and 21 is considered medically necessary in a viable single or twin gestation pregnancy ≥ 10 weeks gestation when testing has not already been performed. In-network coverage of sequencing-based NIPT screening tests for fetal trisomy 13, 18 and 21 performed in an out of network laboratory is considered not medically necessary since these are available at an in-network laboratory.

Medical Coverage Policy: 0514 Molecular analysis of intact fetal cells (i.e., fetal trophoblast[s] in a maternal sample) is considered experimental, investigational or unproven. Sequencing-based non-invasive prenatal testing for any other indication, including but not limited to the following, is not covered or reimbursable: higher order multiple gestations (e.g. triplets and higher) • • vanishing twin syndrome • • • • • when used to determine genetic cause of miscarriage (e.g., missed abortion, incomplete twin zygosity screening for trisomy 7, 9, 16, 22 or other rare autosomal trisomies (RATs) screening for microdeletions single-gene disorders abortion) screening for nonmedical traits (e.g., biologic sex) screening for a sex-chromosome aneuploidy

INVASIVE PRENATAL TESTING OF A FETUS Invasive prenatal testing of a fetus for a familial variant is considered medically necessary when the results of genetic testing will impact clinical decision-making and clinical outcome and ANY of the following criteria are met: • both biologic parents are carriers of an autosomal recessively-inherited disorder OR the mother is a known carrier of an autosomal recessively-inherited disorder and the father’s status is unknown and unavailable the mother is a carrier of an X-linked condition one parent is the carrier of an autosomal dominantly–inherited disorder Prenatal testing of a fetus is considered medically necessary when abnormal findings have been identified on ultrasound. Prenatal reproductive evaluation of a fetus is considered medically necessary using EITHER of the following tests:

comparative genomic hybridization (CGH) testing (chromosomal microarray analysis) (CPT code 81228, 81229) genome wide copy number variant analysis/low pass WGS (81349)

for ANY of the following indications: a woman is undergoing invasive prenatal genetic testing • • intrauterine fetal loss at ≥ 20 weeks or stillbirth intrauterine fetal loss with a documented structural anomaly at any gestation age Prenatal molecular testing of a fetus for familial variants of unknown significance (VUS) is not covered or reimbursable.

GERMLINE MUTATION REPRODUCTIVE GENETIC TESTING FOR RECURRENT PREGNANCY LOSS The following genetic tests are considered medically necessary for the evaluation of recurrent pregnancy loss (i.e., two or more pregnancy losses):

Medical Coverage Policy: 0514 peripheral-blood karyotyping of the biologic parents to detect balanced chromosomal abnormalities

karyotyping or comparative genomic hybridization (CGH) testing (chromosomal microarray analysis) (CPT code 81228, 81229) of the products of conception at the time of the second loss EITHER of the following genetic tests for recurrent pregnancy loss is considered not medically necessary: molecular testing for highly skewed X-inactivation patterns • molecular cytogenetic testing using comparative genomic hybridization (CGH) testing for chromosomal analysis (e.g., parental blood) Methylene tetrahydrofolate reductase (MTHFR) testing for recurrent pregnancy loss is not covered or reimbursable. Single gene mutation analysis, including for ANY of the following genes is considered not medically necessary in the evaluation of recurrent pregnancy loss: F7 (coagulation factor VII [serum prothrombin conversion accelerator] R353Q variant) • F13B (coagulation factor XIII, B polypeptide, V34L variant) • PAI-1 gene testing

GERMLINE MUTATION REPRODUCTIVE GENETIC TESTING FOR INFERTILITY The following services are considered medically necessary when performed solely to establish the underlying etiology of infertility: genetic testing for cystic fibrosis in males with either congenital bilateral absence of vas deferens or azoospermia or severe oligospermia (i.e., < five million sperm/millimeter) with palpable vas deferens

karyotyping for chromosomal abnormalities in males with nonobstructive azoospermia or severe oligospermia

Y-chromosome microdeletion testing in males with nonobstructive azoospermia or severe oligospermia

Sperm penetration assay (hamster penetration test, zona free hamster oocyte test) for those with male factor infertility, who are considering in vitro fertility (IVF) cycles and intracytoplasmic sperm (ICSI) In the absence of a diagnosis of infertility, Cigna considers IVF services associated with preimplantation genetic diagnosis to be not medically necessary. The following tests are not covered or reimbursable:

sperm DNA integrity testing (e.g., Sperm Chromatin Structure assay [SCSA], TUNEL assay, Comet assay, Human Sperm Activation Assay [HSAA], Sperm DNA Decondensation™)

General Background

Genetic Counseling

Medical Coverage Policy: 0514 Genetic counseling is defined as 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 (National Society of Genetic Counselors [NSGC]; Edwards, 2010). 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 (NSGC). A variety of genetics professionals provide these services: Board- Certified or Board-Eligible Medical Geneticists, an American Board of Medical Genetics or American Board of Genetic Counseling-certified Genetic Counselor, and genetic nurses credentialed as either a Genetic Clinical Nurse (GCN) or an Advanced Practice Nurse in Genetics (APNG) by either the Genetic Nursing Credentialing Commission (GNCC) or the American Nurses Credentialing Center (ANCC). Individuals should not be employed by a commercial genetic testing laboratory, although counseling services by these individuals 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. Germline Carrier Testing for Familial Disease A genetic test is defined as the analysis of human deoxyribonucleic acid (DNA), ribonucleic acid (RNA), chromosomes, proteins, and certain metabolites in order to detect mutations or alterations related to an inherited disorder; that is, one passed down by blood relatives. Genetic tests are often performed for the purpose of reproductive carrier screening and prenatal diagnosis to allow for reproductive planning. These terms refer to a search for certain genotypes that are already associated with disease or predisposition which may lead to disease in an individual’s offspring and descendants, or may produce other variations not known to be associated with disease. Genetic testing for reproductive carrier screening and prenatal diagnosis may be appropriate in certain clinical scenarios, including carrier testing for familial disease, ethnic carrier screening, preimplantation genetic diagnostic testing of an embryo, prenatal testing and screening, recurrent pregnancy loss and infertility. Preconception or prenatal testing of a fetus allows for informed reproductive choices. Certain principles apply to genetic testing to determine the presence of gene mutations known to cause heritable disease within a blood-related family. It is generally appropriate to utilize a stepwise process for preconception and prenatal carrier testing unless timing of the testing will limit reproductive choice because of gestational age. Published consensus guidelines from the American College of Medical Genetics and Genomics (ACMG, 2006) and the American Congress of Obstetricians and Gynecologists (ACOG, 2017) support carrier testing for familial disease. Carrier testing, including testing for a known familial mutation, targeted mutation analysis, gene sequencing, duplication/deletion testing or gene dose analysis methods is established as a means to improve health outcomes in selected individuals with risk of a familial disease. Such testing allows prospective parents to make informed reproductive choices. Disorders for which preconception carrier testing may be appropriate include, but are not limited to the following: Nuclear mitochondrial genes Muscular dystrophies (DMB, BMD, EDMD, DM1, DM2, SM) Fragile X syndrome Rett syndrome PTEN-related disorders Von Hippel-Lindau disease

21-hydroxylase deficiency Sickle cell disease

Alpha and beta Thalassemia Gaucher disease Niemann-Pick disease Canavan disease

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Long QT syndrome Retinoblastoma

Huntington disease Spinal Muscular Atrophy (SMA)

Tay-Sachs disease DFNB1 nonsyndromic hearing loss and deafness Cystic fibrosis Genetic testing for non-medical traits such as hair and eye color does not result in improved health outcomes and such testing is not considered to have clinical utility for these indications. Certain disorders are known to occur with greater frequency in defined ethnic populations compared to frequency in the general population. The ACMG (2008) and ACOG (2017) published guidelines to support preconception and prenatal carrier screening for these indications. Genetic testing using targeted mutation panels is considered the standard of care for the following disorders: • Tay-Sachs disease (CPT code 81255) • Canavan disease (CPT code 81200) • Fanconi anemia group C (CPT code 81242) • Niemann-Pick disease, type A (CPT code 81330) • Bloom syndrome (CPT code 81209) • Mucolipidosis IV (CPT code 81290) • Gaucher disease, type 1 (CPT code 81251)

familial dysautonomia (CPT code 81260) Such testing is considered standard of care in clinical practice for certain defined germline disorders; however, in the absence of clinical features which would suggest one of these disorders, the clinical utility of gene sequencing as a testing approach has not been established. Large pan-ethnic expanded carrier screening panels are now available which may include hundreds of genes, and are intended to be used for general population carrier screening. There are no standard guidelines regarding which disease genes and pathogenic or likely pathogenic variants to include on an expanded carrier screening panel of this size. These panels often include diseases that are present with increased frequency in specific populations, as well as a large number of diseases for which the carrier frequency in the general population is low in the absence of a known family history. Multiple professional societies have called for guidelines to be developed that would limit genes on these panels based on standard criteria, such as only including severe, childhood-onset genetic diseases, and only genes for which pathogenic or likely pathogenic variant frequencies are known and prognosis can be predicted based on genotype (Edwards, et al., 2015; Grody, et al., 2013). There is insufficient evidence to support improved health and/or pregnancy outcomes with the use of large multigene reproductive carrier screening panels to predict the risk of severe inherited disease. ACMG (2020) published consensus guidelines to support targeted mutation analysis of 23 CFTR mutations for testing of individuals for whom the risk of cystic fibrosis is a concern. In an effort to standardize the laboratory approach to screening, the Subcommittee on Cystic Fibrosis Screening, the American College of Medical Genetics and Genomics (ACMG) recommends the use of a pan- ethnic panel that includes all mutations with an allele frequency ≥ 0.1% in the general United States (U.S.) population. Initially, 25 mutations were included in the standard core mutation analysis of the CFTR gene; however, a 2004 update to the ACMG cystic fibrosis carrier screening statement recommended no additions and two deletions (I148T, 1078delT). The ACMG mutation

Medical Coverage Policy: 0514 panel is considered the standard test for population-based carrier testing and is performed in Clinical Laboratory Improvement Amendments (CLIA)-certified laboratories. Targeted mutation analysis for common deletion or gene variants (i.e., HBB, HBA1, HBA2) for thalassemia and sickle cell disease is supported by published professional society guidelines and peer-reviewed evidence. Gene sequencing and deletion/duplication studies may be appropriate to identify mutations if results of targeted mutation studies are negative or use of a stepwise approach limits reproductive options due to gestational age. Consensus support for screening for all heritable conditions in the general population is lacking. According to the ACMG (2019), the approach to genetic counseling and testing for the different phenotypes has not yet been addressed on a population screening level. Except where identified as clinically useful elsewhere in this Coverage Policy, carrier screening in the general population in the absence of definitive clinical features does not impact clinical decision-making or improve health outcomes. Therefore, clinical utility for this indication has not been established. Professional Societies/Organizations For a summary of professional society recommendations/guidelines (including Use Outside of the US) regarding germline carrier testing for familial disease, please see Appendix. Preimplantation Genetic Testing of an Embryo Preimplantation genetic diagnosis (PGD), now referred to as preimplantation genetic testing (PGT) is clinically useful when a genetic disorder is associated with a severe disability or has a lethal natural history PGT would be appropriate when reproductive partners are carriers of a single gene autosomal recessively-inherited disorder or one partner is a known carrier of an autosomal dominant or x-linked heritable disorder and the results will impact clinical decision-making. PGD may be appropriate for the following indications (this list may not be all-inclusive): Nuclear mitochondrial genes Muscular dystrophies (DMD, BMD, EDMD, DM1, DM2, SM Fragile X syndrome Rett syndrome PTEN-related disorders Von Hippel-Lindau disease Long QT syndrome Retinoblastoma 21-hydroxylase deficiency

Sickle cell disease Alpha and beta thalassemia Gaucher disease Niemann-Pick disease Canavan disease Tay-Sachs disease DFNB1 nonsyndromic hearing loss and deafness Huntington disease Cystic fibrosis Use of PGD in multifactorial conditions and for testing for variants of unknown significance does not result in improved health outcomes. The clinical utility of PGD has not been established for these indications. PGD used solely to determine if an embryo is a carrier of an autosomal recessively inherited disorder is not supported in published professional society/organization guidelines. PGD used solely to identify potential suitable stem-cell tissue or solid organ transplantation donor is not considered standard of care for this indication. PGD has also been proposed as a means to detect chromosomal rearrangements (e.g., translocations) in order to decrease the rate of spontaneous abortions. However, at this time there are insufficient data to support preimplantation genetic screening for unexplained recurrent miscarriage.

Medical Coverage Policy: 0514 Although testing for a known familial mutation is an accepted testing strategy for PGD, the role of gene sequencing has not been established in the published peer reviewed scientific literature. Testing of an embryo for nonmedical gender selection or nonmedical traits, such as hair and eye color does not result in improved health outcomes and clinical utility for this indication has not been established. A polygenic risk score is an estimate of an individual’s genetic risk for a specific polygenic phenotype that is derived from weights of alleles from hundreds to thousands of loci. A polygenic risk score informs about an individual’s relative risk compared to the remainder of the population. Published peer-reviewed scientific literature for polygenic risk scores is lacking and insufficient to support coverage. Professional Societies/Organizations For a summary of professional society recommendations/guidelines (including Use Outside of the US) regarding preimplantation genetic testing of an embryo, please see Appendix. Preimplantation Genetic Screening for Aneuploidy PGD has been used for the screening of embryos for common aneuploidies in couples undergoing IVF procedures for infertility with a history of recurrent pregnancy loss, repeated IVF failures and/or advanced maternal age. When PGD is performed for any of these indications, it has been referred to as PGD-A, or as preimplantation genetic screening (PGS). Outcome measures used in PGD-A include pregnancy rates (e.g., for recurrent pregnancy loss, and live birth rates). The error rate of aneuploidy detection has been reported to be as high as 15%. This use of PGD is a screening procedure to detect those aneuploidies most commonly observed after birth or in miscarriages (e.g., involving detection of chromosomes X, Y, 13, 16, 18, 21, and 22). Together, these chromosomes account for 95% of all chromosomal abnormalities. Additional well-designed, multicenter studies are needed before the role of preimplantation genetic screening (PGS) for aneuploidy can be established. There is insufficient evidence and professional guidance in the published, peer-reviewed scientific literature to support PGD for: human leukocyte antigen (HLA) - matching, screening of common aneuploidy or chromosomal translocations as a method to improve live birth rates, to reduce the risk of pregnancy loss in women of advanced maternal age, or for late-onset disorders. The clinical treatment utility of PGD for late-onset conditions has not been clearly delineated. Published consensus guidelines from ACOG (2009) do not support PGS as a genetic screening test for common aneuploidy. The clinical utility for this indication has not been established. Literature Review Studies evaluating the effectiveness of PGS include prospective nonrandomized and randomized controlled trials. In general study results have suggested that PGS does not improve pregnancy outcomes for young women with recurrent implantation failure or those of advanced maternal age (Rubio, et al., 2013; DeBrock, et al., 2010; Meyer, et al., 2009; Hardarson, et al., 2008; Yakin, et al., 2008; Mastenbroek, et al., 2007; Staessen, et al., 2004). Professional Societies/Organizations For a summary of professional society recommendations/guidelines (including Use Outside of the US) regarding preimplantation genetic screening for common aneuploidy, please see Appendix. Prenatal Genetic Screening and Testing of a Fetus Discussion of prenatal genetic screening and testing in this Coverage Policy refers to sequencing- based noninvasive prenatal tests (NIPT) (i.e., cell-free deoxyribonucleic acid [DNA] screening) and invasive prenatal tests such as chorionic villus sampling [CVS] and amniocentesis. These tests are performed in early pregnancy and used to test for germline mutation genetic disorders.

Medical Coverage Policy: 0514 Sequencing-Based Non-Invasive Prenatal Testing (NIPT) Sequencing-based genomic testing, a type of NIPT has been proposed for use as an advanced screening test to assess whether a pregnant woman is at increased risk of having a fetus affected by a genetic disorder (American College of Obstetricians and Gynecologists [ACOG], 2016). One benefit of such screening is the potential decrease in the number of invasive procedures, and therefore, the decrease in the potential for miscarriage as a complication of invasive testing. As a screening test for genetic disorders, sequencing-based NIPT may also allow for reproductive options. Sequencing-based testing evaluates short segments of relies on the presence of circulating fetal or cell-free deoxyribonucleic acid (DNA) in the maternal plasma during pregnancy. The clinical utility of sequencing-based NIPT has been established as a means to detect fetal trisomy 13, 18 and 22 in the published, peer-reviewed scientific literature for a woman at ≥ 10 weeks gestation with a viable, singleton pregnancy. No specific test has been established to be significantly different than the others for this purpose. The sensitivity and specificity of cell-free DNA screening in a singleton gestation has been reported to be uniformly high, ranging from 99.1%-100% and 99.7%-100%, respectively, primarily for trisomy 21. Negative predictive values have been reported to be near, or at 100%, with positive predictive values of 83% and 55% for high- and average-risk populations, respectively. Laboratories variably report screening results as positive, negative or ‘no call’, a category to describe indeterminate or uninterpretable results. No-call results comprise approximately 4–8% of screened pregnancies and may occur secondary to assay failure, high assay variance or low fetal fraction. Low fetal fraction, defined as below 4%, confers significantly higher risk for fetal aneuploidy. Counseling before screening should include the possibility of results in this category (Dasche, 2016). Confirmatory CVS or amniocentesis is still needed in pregnancies with a positive result. According to the American College of Obstetricians and Gynecologists (2020), women with a positive screening test result should be counseled regarding their higher risk of aneuploidy and offered the option of diagnostic testing. Those who have a negative test result should be counseled regarding their lower adjusted and residual risk. Women with a negative screening result should not be offered additional screening tests for aneuploidy because this will increase their potential for a false-positive test result. According to the American Congress of Obstetrics and Gynecologists (2020), cell free DNA screening can be performed in twin gestations. Sensitivity for trisomy 21 using cell free DNA for twin pregnancy is similar to singleton pregnancy although test failure may be higher. Because each fetus in a single pregnancy contribute different amounts of cell free DNA into the maternal circulation it is possible that an aneuploidy fetus would contribute less fetal DNA, masking the aneuploid test result. Nonetheless, noninvasive prenatal testing using cell-free DNA is considered an appropriate noninvasive prenatal screening option. A number of sequencing-based NIPTs have been developed that utilize cell free DNA to detect fetal aneuploidy. Trisomies 13, 18 and 21 are detected with high accuracy. Many tests offer detection of one or more other syndromes, but detection of other aneuploidies has not have been determined to be clinically beneficial. Luna Prenatal Test is a cell-based prenatal genetic test which isolates pure fetal DNA from rare fetal trophoblast cells circulating in maternal blood. This test in noninvasive, only requires a maternal blood sample and can be performed early in pregnancy, from 8 to 22 weeks of gestation. Currently, there is insufficient evidence in published, peer-reviewed scientific literature and lack of professional society to support this testing method.

Medical Coverage Policy: 0514 Depending on the testing methodology used for each individual test, sequencing-based NIPTs may also detect various other fetal genetic disorders including: trisomy 7, 9, 16, 22 or other rare autosomal trisomies (RATs); sex-chromosome aneuploidy (e.g., Klinefelter syndrome, Turner syndrome, Jacob syndrome); vanishing twin syndrome; twin zygosity; fetal sex; microdeletions; single-gene disorders; and genetic cause of miscarriage. However, data are very limited in the published, peer-reviewed scientific literature regarding the predictive value of any of these tests to detect these additional fetal abnormalities, and whether maternal outcomes are improved if further invasive testing is required is unknown. Professional society support for these indications in the form of published consensus guidelines is also lacking. The clinical utility of sequencing-based NIPT to detect trisomies 7, 9, 16 and 22 is also unknown; there is insufficient evidence in the published peer-reviewed scientific literature to establish whether pregnancy outcomes are improved by detection of these additional chromosomal abnormalities. Validation data regarding the predictive value of any NIPT to detect these trisomies are lacking in the published, peer-reviewed scientific literature. Several laboratory methods allow for detection of microdeletions; however, data are lacking regarding the predictive value of NIPT for this indication and the impact on pregnancy outcomes is unknown. Such testing is not supported in the form of recommendations by ACMG (2013), the European Society of Human Genetics/American Society of Human Genetics and the Society for Maternal-Fetal Medicine. Validation data are limited regarding the role of NIPT for use as a screening tool in average-risk pregnancies or in a woman with a multiple gestation pregnancy and professional society support is lacking. At present, the role of NIPT for these indications has not been established. The clinical utility for NIPT to detect fetal sex is lacking in the scientific literature; professional society consensus guideline support is also lacking for this indication. There are limited data in the published peer-reviewed scientific literature regarding the use of next generation sequencing performed via NIPT to identify single gene (monogenetic) disorders (Dan, et al., 2016; Verhoef, et al., 2016; Chitty, et al., 2015). However, unanswered questions about mosaicism and false positives raise concerns for harm and whether such testing requires confirmatory testing by invasive methods is not yet known (Jenkins, et al., 2017). The clinical utility of NIPT to identify single gene disorders is currently unknown given the limited published peer reviewed scientific evidence. Published professional society support in the form of consensus guidelines is also lacking. Literature Review Trisomies 13, 18, 21: The role of sequencing-based cell-free DNA testing to detect trisomy 13, 18 and 21 has been investigated in a number of prospective clinical trials, systematic reviews and technology assessments to determine if there are improved clinical outcomes as a result of such testing (Gil, et al., 2015; Zhang, et al., 2015; Norton, et al., 2012). Zhang et al. (2015) reported results of the clinical performance of massively parallel sequencing- based NIPT in detecting trisomies 21, 18 and 13 in 147,314 clinical samples in low-risk and high- risk pregnancies in a prospective, multicenter observational study. Eligibility for NIPT included participants of at least 18 years old with a singleton or twin pregnancy at nine weeks’ gestation or beyond. Individuals were considered high-risk for aneuploidy for any of the following: advanced maternal age (>35 years), a positive conventional Down syndrome screening test, abnormal sonographic markers, family history of aneuploidy or a previous pregnancy with a trisomic fetus. Individuals with none of the high-risk factors were defined as low risk for aneuploidy. NIPT performance in the detection of trisomy 21 in these two groups was compared using karyotyping or follow-up results as gold standard. There were a small number of cases positive for trisomies 18 and 13 in the low-risk group and NIPT performance for these two trisomies was not compared between risk groups. Results were obtained in 146,958 samples and outcome data were available

Medical Coverage Policy: 0514 in 112,669 (76.7%). Repeat sampling was required in 3,213 cases; 145 had test failure. Overall sensitivity of NIPT was 99.17%, 98.24% and 100% for trisomies 21, 18 and 13, respectively. Specificity was 99.95%, 99.95% and 99.96% for trisomies 21, 18 and 13, respectively. There was no significant difference in test performance between high-risk and low-risk subjects (sensitivity, 99.21% vs 98.97% (p=0.82); specificity, 99.95% vs 99.95% (p=0.98)). Data suggest that sequencing-based NIPT to detect trisomy 21 has high sensitivity and specificity in high and low- risk populations. Gil et al. (2015) updated results of a previously published meta-analysis to include 37 studies published up to January 4, 2015. The inclusion criteria were prospective and retrospective peer- reviewed studies reporting clinical validation or implementation of maternal cell-free DNA (cfDNA) testing in screening for aneuploidies, in which data on pregnancy outcome were provided for more than 85% of the study population. Twenty-four studies reported on the performance of screening by cfDNA analysis for trisomy 21. Pooled weighted DNA testing and detection rates (DR) 99.2% and 0.09%, respectively. Twenty-one studies reported on the performance of screening by cfDNA analysis for trisomy 18. Pooled weighted DR and FPR were 96.3% and 0.13%, respectively. A total of 18 studies reported on the performance of screening by cfDNA analysis for trisomy 13. Pooled weighted DR and FPR were 91.0% and 0.13%, respectively. The performance of cfDNA analysis of maternal blood in the identification of singleton pregnancies with trisomy 18 or 13, with respective DRs of 96% and 91%, and a combined FPR of 0.26%, is worse than is the performance of screening for trisomy 21. DR and FPR for monosomy X were 90.3% and 0.23%, respectively, and 93.0% and 0.14%, respective for sex chromosome aneuploidies other than monosomy X. For twin pregnancies, the DR for trisomy 21 was 93.7% and the FPR was 0.23. The authors note there are no advocates of screening for fetal trisomies 18 and 13 independently from screening for trisomy 21. Data from this systematic review and metaanalysis suggest a high detection rate and low false positive rate when testing for fetal trisomy 21. There is sufficient evidence in the published, peer-reviewed scientific literature to establish the clinical validity of NIPT as a method to screen for these indications. Further, such testing is supported by published professional society consensus guidelines. Norton et al. (2015) reported results of a prospective, multicenter trial comparing standard screening (i.e., measurement of nuchal translucency and biochemical analysis) and cell-free DNA (cfDNA) testing in pregnant women >18 years presenting for aneuploidy screening at 10-14 weeks of gestation. Study participants underwent both standard screening and cfDNA testing. Patients were ineligible if they were outside the gestational-age window, had no standard screening result, had known maternal aneuploidy or cancer, had conceived with the use of donor oocytes, or had a twin pregnancy or an empty gestational sac that was identified on ultrasonography. The primary outcome was the area under the receiver-operating-characteristic curve (AUC) for trisomy 21. The risk of trisomy 18 and 13 was also assessed. Lab personnel performing cfDNA analysis were blinded to all other clinical data, including results of ultrasonographic and standard screening. Using the maternal age of enrolled participants mid- trial, the estimate of the prevalence of trisomy 21 was adjusted to 1 in 500, and the required sample size reduced to 18,700. Of 18,955 women who were enrolled, results from 15,841 were available for analysis, with 1489 lost to follow-up. Sixty-eight chromosomal abnormalities were identified (1 in 236 pregnancies). Of these, 38 were trisomy 21. The AUC for trisomy 21 was 0.999 for cfDNA testing and 0.958 for standard screening (p=0.001). Sensitivity to detect Trisomy 21 was 100% and 78.9% in the cfDNA and standard screening groups, respectively (p=0.008). False positive rates were 0.06% and 5.4% in the cfDNA and standard screening group, respectively (p<0.001). The positive predictive value for cfDNA testing was 80.9% compared with 3.4% for standard screening (P<0.001). Approximately 3% of cfDNA tests did not yield a result because of assay variation or a low fetal fraction.

Medical Coverage Policy: 0514 Limitations noted by the authors include that the study only made a comparison between cfDNA testing and standard first-trimester screening and that the study was powered to compare only the detection of trisomy 21 in the two study groups. The authors also note the rate of detection for trisomy 21 using standard screening methods was lower than the 82%-87% seen in other studies. Whether results of this test impacted clinical management or improved pregnancy outcomes is unknown. While cfDNA has been validated as a method to detect trisomy 21, maternal serum and nuchal translucency screening can identify the risk for a broad array of abnormalities that are not detectable on cfDNA testing. The role of this test in screening for aneuploidy in woman without increased risk remains uncertain; and clinical utility has not been established. Sex-Chromosome Aneuploidy: Data are also limited in the published peer-reviewed scientific literature regarding the ability of NIPTs to detect sex-chromosome aneuploidies. In a validation study by Mazloom et al. (2013), massively parallel sequencing was performed on cfDNA isolated from the plasma of 1564 pregnant women with known fetal karyotype. Another study of 411 maternal samples from women with blinded-to-laboratory fetal karyotypes was then performed to determine the accuracy of the classification algorithm. The blinded validation yielded a detection rate of 96.2%, a false positive rate of 0.3% and a nonreportable rate of 5%. Although a high detection rate and low false positive rate was reported in this single study there is insufficient evidence to establish the effectiveness of NIPT to detect sex chromosome aneuploidy, and the impact of such results on treatment planning. Further, support for use of NIPT as a method to detect sex-chromosome aneuploidy is lacking in the form of professional society consensus guidelines. At this time the role of NIPT for this indication has not been established. Microdeletions: Guidelines from the American College of Medical Genetics and Genomics (2013) and jointly published recommendations from the European Society of Human Genetics/American Society of Human Genetics (2015) as well as the Publications Committee of the Society for Maternal-Fetal Medicine (2015) note that use of NIPT to test for microdeletions is not recommended. Clinical validation studies relative to use of NIPTs to detect microdeletion syndromes are very limited in the published, peer-reviewed scientific literature. Wapner et al. (2015) reported on a test with a primary purpose of estimating the performance of a single- nucleotide polymorphism (SNP)-based noninvasive prenatal test for five microdeletion syndromes in 469 samples (358 plasma samples from pregnant women, 111 artificial plasma mixtures). These were amplified with the use of a massively multiplexed polymerase chain reaction, sequenced, and analyzed for the presence or absence of deletions of 22q11.2, 1p36, distal 5p, and the Prader-Willi/Angelman region. Detection rates were 97.8% for a 22q11.2 deletion, 100% for Prader-Willi, Angelman, 1p36 deletion, and cri-du-chat syndromes (24/24). False-positive rates were 0.76% for 22q11.2 deletion syndrome and 0.24% for cri-du-chat syndrome. No false positives occurred for Prader-Willi, Angelman or 1p36 deletion syndromes. SNP-based noninvasive prenatal microdeletion screening was accurate in this single study; however, additional validation studies are needed before such testing is useful in routine clinical practice. Srinivasan et al. (2013) published results of a study involving 11 pregnant women. This small study was designed to determine the deep sequencing and analytic conditions needed to detect fetal subchromosome abnormalities across the genome from a maternal blood sample. Seven of seven cases of microdeletions, duplications, translocations, and one trisomy 20 were detected blindly by massively parallel sequencing. Small study numbers limit the ability to translate these results to routine clinical practice.

Professional Societies/Organizations

Medical Coverage Policy: 0514 For a summary of professional society recommendations/guidelines regarding sequencing-based non-invasive prenatal testing, please see Appendix. Invasive Prenatal Testing of a Fetus Other prenatal genetic testing of a fetus for which clinical utility has been established includes testing when the results of testing will impact clinical decision-making and clinical outcome and the mother is a carrier of an X-linked condition, when both biologic parents are carriers of an autosomal recessively-inherited disorder or the mother is a known carrier of an autosomal recessively-inherited disorder and the father’s status is unknown and unavailable and when one parent is the carrier of an autosomal dominantly–inherited disorder. Additionally, prenatal testing using targeted mutation analysis (CPT code 81220) for cystic fibrosis when fetal echogenic bowel has been identified on ultrasound is considered a standard of care based on professional society consensus guidelines. Prenatal reproductive comparative genomic hybridization (CGH) testing (chromosomal microarray analysis) (CPT code 81228, 81297) is also supported by guidelines published by ACOG (when a woman is undergoing invasive prenatal genetic testing or in the case of intrauterine fetal demise or stillbirth. Literature Review A number of prospective cohort and case series studies, systematic review and a meta-analysis have reported on the diagnostic accuracy for CGH/CMA compared with conventional karyotyping in greater than 13,000 prenatal samples (Dhillon, et al., 2014; Hillman, et al., 2013; Armengol, et al., 2012; Lee, et al., 2012; Reddy, et al., 2012; Shaffer, et al., 2012; Wapner, et al., 2012; Fiorentino, et al., 2011). Indications for testing include abnormal ultrasound, advanced maternal age, abnormal maternal serum screening, positive family history, parental anxiety and other or nonspecific. Overall, the data suggest microarray analysis provides significantly improved detection of clinically significant genomic abnormalities compared to those found with conventional karyotyping. Professional Societies/Organizations For a summary of professional society recommendations/guidelines (including Use Outside of the US) regarding invasive prenatal testing of a fetus, please click Appendix. Germline Mutation Reproductive Genetic Testing for Recurrent Pregnancy Loss Chromosomal analysis tests and cytogenetic testing: Published professional society consensus guidelines support the clinical usefulness of chromosomal analysis, such as karyotyping of peripheral blood and products of conception in the case of two or more pregnancy losses. There is also consensus support for molecular cytogenetic testing when karyotyping of the products of conception is not possible because of a lack of tissue sample or poor culture growth. Microarray Analysis: Evidence in the published peer-reviewed scientific literature, including textbook and reproductive health society positions, evaluating the utility of microarray analysis such as CGH and SNP for recurrent pregnancy loss is lacking and strong evidence-based conclusions cannot be made regarding clinical utility, estimated recurrence rates, and impact on patient management and patient clinical outcomes. In a recent systematic review and meta-analysis involving nine published studies comparing CMA testing on the products of conception with conventional karyotyping, Dhillon et al. (2014) reported that CMA testing resulted in a higher detection rate of abnormalities compared to karyotyping. The authors reported there was agreement between CMA and karyotyping in 86% of cases, CMA detected an additional 13% abnormalities versus karyotyping, and karyotyping detected 3% over CMA. The incidence of a variant of unknown significance was 2%. Unless uncertain findings were proven to be benign the authors included them as pathogenic. Overall, the authors acknowledged

Medical Coverage Policy: 0514 “additional prospective research is needed in this area using a large cohort, with a representative, prospective population undergoing both a recognized reproducible array and karyotyping.” Testing for X-linked Recessive Traits: Genetic mutations such as X-linked recessive traits (e.g., highly skewed X-inactivation patterns) have also been investigated as a cause of RSA; however, data are limited. Some authors have reported that there is no correlation between skewed X-inactivation and RSA (Warburton, et al., 2009; Kaare, et al., 2008; Pasquier, et al., 2007; Hogge, et al., 2007). Moreover, recommendations of the National Society of Genetic Counselors (Laurino, et al., 2005) indicate that an association between X-inactivation patterns and pregnancy outcome has not been clearly established and further investigation should be conducted. Additionally, according to the ACOG practice bulletin (2001), commercially available testing for this and other related molecular genetic abnormalities is not widely available. At present, testing for highly skewed X-inactivation patterns as a cause of RSA is not well-supported in the literature. Single Gene Mutation Analysis Single gene mutation analysis is not indicated in the work-up of recurrent pregnancy loss. There is insufficient evidence in the published, peer-reviewed scientific literature to demonstrate clinical usefulness and it has not been established as a standard of care in clinical practice. To date, professional society support in the form of published consensus guidelines is lacking. Genetic Testing for Other Gene Mutations (i.e., F7 [serum prothrombin conversion accelerator] gene mutation R353Q, F13B polypeptide gene mutation V34L, and PAI-1): Genetic testing has been proposed for these gene variants; however, data are lacking regarding the clinical utility of these tests to inform health outcomes in an individual with an hereditary hypercoagulability disorder. Literature Review High quality controlled clinical trial data are lacking regarding the ability of genetic testing to inform improved health outcomes, including the prevention of venous thromboembolic events in individuals with F7 R353Q variant, F13B polypeptide V34L variant, and PAI-1. Professional Societies/Organizations For a summary of professional society recommendations/guidelines (including Use Outside of the US) regarding germline mutation reproductive genetic testing for recurrent pregnancy loss, please see Appendix. Germline Mutation Reproductive Genetic Testing for Infertility Infertility is defined as the failure to achieve pregnancy after 12 months of regular unprotected intercourse (Agency for Healthcare Research and Quality [AHRQ], 2008; American Society of Reproductive Medicine [ASRM], 2013). The etiology of infertility may have a genetic basis such as cystic fibrosis in a male with congenital bilateral absence of vas deferens, azoospermia or severe oligospermia. Genetic testing with targeted mutation analysis of the 23 CFTR mutations as described by the ACMG and ACOG is considered clinically useful. Karyotyping, Y-chromosome microdeletion testing in males with nonobstructive azoospermia or severe oligospermia, and sperm penetration assays may also be considered appropriate. According to the American Urological Association (Schlegel, et al., 2021a), detection of certain genetic causes of male infertility allows couples to be informed about the potential to transmit genetic abnormalities that may affect the health of offspring. Thus, an appropriate male evaluation may allow the couple to better understand the basis of their infertility and to obtain genetic counseling when appropriate. The clinical utility of sperm DNA integrity testing has not been established in the published, peer- reviewed scientific literature. This test has been proposed to identify a male factor contributing to

Medical Coverage Policy: 0514 unexplained infertility or in the treatment of infertility to direct interventions. Several tests for sperm DNA integrity are now available (e.g., Sperm Chromatin Structure Assay [SCSA], TUNEL assay, Comet assay). Another test to assess sperm DNA is the Sperm DNA Decondensation test (e.g., Human Sperm Activation Assay [HSAA], SDD™). The AUA (2011) reported that the assays demonstrate low sensitivity and high specificity; there is insufficient evidence to support the routine use of DNA integrity testing in the evaluation and management of male factor infertility. Professional Societies/Organizations For a summary of professional society/organization recommendations/guidelines regarding germline mutation reproductive genetic testing for infertility, please see Appendix. Include what the comparators are and what the standard of care is we need to understand what the alternative(s) are—what testing, treatment or device would or could be used instead? What is the gold standard/standard of care, and other approaches that may be considered,

Appendix

Professional Societies/Organizations Recommendations/Guidelines Germline Carrier Testing for Familial Disease American College of Medical Genetics and Genomics (ACMG): The ACMG (Gregg, et al., 2021) published a practice resource for screening of autosomal recessive and X-linked conditions during pregnancy and preconception recommending carrier screening paradigms should be ethnic and population neutral and more inclusive of diverse populations to promote equity and inclusion. Their recommended approach to this involves a tiered system based on carrier frequency: Tier one includes the recommendations previously adopted by ACMG and ACOG adopting an ethic and population neutral approach when screening for cystic fibrosis and spinal muscular atrophy. It also includes additional carrier screening determined after risk assessment (i.e., personal medical history, family history, labs, and imaging). • Tier two is based on an ACOG recommendation for conditions that have a severe or moderate phenotype and a carrier frequency of at least 1/100.

Tier three is carrier screening for conditions with a carrier frequency ≥ 1/200. • Tier four includes less common genes with no lower limit carrier screening frequency. ACMG recommends all pregnant patients and those planning a pregnancy should be offered tier three carrier screening and not solely tier one and/or tier two as these do not provide equitable evaluation of all racial/ethnic groups. In a policy statement regarding prenatal/preconception expanded carrier screening, ACMG (2013) notes: Disorders should be of a nature that most at-risk patients and their partners identified in the screening program would consider having a prenatal diagnosis to facilitate making decisions surrounding reproduction.

The inclusion of disorders characterized by variable expressivity or incomplete penetrance and those known to be associated with a mild phenotype should be optional and made transparent when using these technologies for screening.

For each disorder, the causative gene(s), mutations, and mutation frequencies should be known in the population being tested, so that meaningful residual risk in individuals who test negative can be assessed.

Medical Coverage Policy: 0514 The calculation of residual risk requires knowledge of two factors: one is the carrier frequency within a population, the other is the proportion of disease-causing alleles detected using the specific testing platform. Laboratories using multiplex platforms often have limited knowledge of one or both factors.

There must be validated clinical association between the mutation(s) detected and the severity of the disorder. In a policy statement regarding carrier screening for SMA (2008, reaffirmed 2013), ACMG notes: A negative screening test for one or both partners reduces but does not eliminate the possibility of an affected offspring, because the test sensitivity is <100% (~90% detection rate).

Carrier testing should be offered to all couples regardless of race or ethnicity • Carrier testing should be offered to asymptomatic individuals with a confirmed or suspected family history of SMA.

A prerequisite for prenatal testing is the previous identification of the homozygous deletion in the proband or positive carrier status in the parents.

Regarding screening for Fragile X, ACMG notes (2004): Population carrier screening is not recommended at this time except as part of a well- defined clinical research protocol.

DNA testing for permutation size alleles should be considered if a woman has ovarian failure before the age of 40, as part of the infertility evaluation and prior to in vitro fertilization. The ACMG practice guidelines for carrier screening in individuals of Ashkenazi Jewish descent include the following recommendations regarding genetic testing (Gross, et al., 2008, reaffirmed 2013): Carrier screening should be offered to all individuals of Ashkenazi Jewish descent who are pregnant or considering pregnancy.

Carrier screening for these disorders should include testing for the specific mutations related to the conditions, which will result in a carrier detection rate 95% for most disorders.

The offering of such testing should ideally take place before pregnancy, thereby giving individuals time to make appropriate reproductive decisions based on their own personal choices and cultural backgrounds. Currently, the majority of testing takes place in the primary care obstetrical setting and not in the medical genetic specialty environment. However, regardless of the clinical setting, adequate counseling should be provided to anyone considering testing so that choices are informed. If only one member of a couple is of Ashkenazi Jewish background, then testing should still be offered with the individual of Ashkenazi Jewish descent being tested first

In a policy statement regarding laboratory standards and guidelines for population-based cystic fibrosis carrier screening, ACMG (2001) notes the following: CF carrier screening should be offered to all individuals regardless of ethnicity • preconception testing be encouraged whenever possible, although testing will often occur in the prenatal setting

Couple-based testing is recommended for Caucasian couples of Northern European and Ashkenazi Jewish descent, particularly when concurrently testing for other common genetic disorders in the latter population.

Medical Coverage Policy: 0514 a pan-ethnic mutation panel that includes all CF-causing mutations with an allele frequency of ≥0.1% in the general U.S. population is recommended. ACMG (2011) states that an extended panel is not recommended for routine carrier screening of reproductive couples. The ACMG (2011) indications for CF genetic testing with the ACMG panel of 23 mutations include: • • • • • • preimplantation testing • prenatal diagnostic testing, positive family history or for couples having a CF mutation in both partners carrier testing, partners of individuals with positive family history of CF carrier testing, partners of males with CBAVD carrier testing, general population of reproductive couples carrier testing, premarital population, to assist in selection of mate carrier testing, positive family history carrier testing, gamete donors prenatal diagnostic testing, echogenic bowel fetus during second trimester American College of Obstetricians and Gynecologists (ACOG): A Committee Opinion on carrier screening for genetic conditions included the following recommendations (ACOG, 2017): General Recommendations  Information about genetic carrier screening should be provided to every pregnant woman. After counseling, a patient may decline any or all screening.  Carrier screening and counseling ideally should be performed before pregnancy.  If an individual is found to be a carrier for a specific condition, the individual’s reproductive partner should be offered testing in order to receive informed genetic counseling about potential reproductive outcomes.  Concurrent screening of the patient and her partner is suggested if there are time

constraints for decisions about prenatal diagnostic evaluation.  Carrier screening for a particular condition generally should be performed only once in a person’s lifetime and the results should be documented in the patient’s health record. Because of the rapid evolution of genetic testing, additional mutations may be included in newer screening panels. The decision to rescreen a patient should be undertaken only with the guidance of a genetics professional who can best assess the incremental benefit of repeat testing for additional mutations. Spinal Muscular Atrophy  Screening for spinal muscular atrophy should be offered to all women who are considering pregnancy or are currently pregnant.  In patients with a family history of spinal muscular atrophy, molecular testing reports of the affected individual and carrier testing of the related parent should be reviewed, if possible before testing. If reports are not available, SMN1 deletion testing should be recommended for the low-risk partner Cystic Fibrosis  Carrier screening should be offered to all women who are considering pregnancy or are currently pregnant  Complete analysis of the CFTR gene by DNA sequencing is not appropriate for routine carrier screening  If a woman’s reproductive partner has cystic fibrosis or apparently isolated congenital bilateral absence of the vas deferens, the couple should be provided follow-up genetic counseling by an obstetrician–gynecologist or other health care provider with expertise in genetics for mutation analysis and consultation. Fragile X Syndrome

Medical Coverage Policy: 0514  Fragile X premutation carrier screening is recommended for women with a family history of fragile X-related disorders or intellectual disability suggestive of fragile X syndrome and who are considering pregnancy or are currently pregnant.  If a woman has unexplained ovarian insufficiency or failure or an elevated follicle- stimulating hormone level before age 40 years, fragile X carrier screening is recommended to determine whether she has an FMR1 premutation.  All identified individuals with intermediate results and carriers of a fragile X premutation or full mutation should be provided follow-up genetic counseling to discuss the risk to their offspring of inheriting an expanded full-mutation fragile X allele and to discuss fragile X-associated disorders (premature ovarian insufficiency and fragile X tremor/ataxia syndrome).  Prenatal diagnostic testing for fragile X syndrome should be offered to known

carriers of the fragile X premutation or full mutation.

 DNA-based molecular analysis (e.g., Southern blot analysis and polymerase chain reaction) is the preferred method of diagnosis of fragile X syndrome and of determining FMR1 triplet repeat number (e.g., premutations). In rare cases, the size of the triplet repeat and the methylation status do not correlate, which makes it difficult to predict the clinical phenotype. In cases of this discordance, the patient should be referred to a genetics professional. Genetic Conditions in Individuals of Eastern and Central European Jewish Descent  When only one partner is of Ashkenazi Jewish descent, that individual should be offered screening first. If it is determined that this individual is a carrier, the other partner should be offered screening.

 Tay–Sachs Disease o Screening for Tay–Sachs disease should be offered when considering pregnancy or during pregnancy if either member of a couple is of Ashkenazi Jewish, French–Canadian, or Cajun descent. Those with a family history consistent with Tay–Sachs disease also should be offered screening. o When one member of a couple is at high risk (i.e., of Ashkenazi Jewish,

o French–Canadian, or Cajun descent or has a family history consistent with Tay–Sachs disease) but the other partner is not, the high-risk partner should be offered screening. If the high-risk partner is found to be a carrier, the other partner also should be offered screening. If Tay–Sachs disease screening is performed as part of pan-ethnic expanded carrier screening, it is important to recognize the limitations of the mutations screened in detecting carriers in the general population. In the presence of a family history of Tay–Sachs disease, expanded carrier screening panels are not the best approach to screening unless the familial mutation is included on the panel.

o Referral to an obstetrician–gynecologist or other health care provider with genetics expertise may be helpful in instances of inconclusive enzyme testing results or in discussion of carrier testing of an individual with non-Ashkenazi Jewish ethnicity whose reproductive partner is a known carrier of Tay–Sachs disease. Regarding expanded carrier screening, ACOG Committee Opinion (2017, reaffirmed 2020) notes the following: Ethnic-specific, panethnic, and expanded carrier screening are acceptable strategies for prepregnancy and prenatal carrier screening.

All patients who are considering pregnancy or are already pregnant, regardless of screening strategy and ethnicity, should be offered carrier screening for cystic fibrosis and

Medical Coverage Policy: 0514

spinal muscular atrophy, as well as a complete blood count and screening for thalassemias and hemoglobinopathies. If a woman is found to be a carrier for a specific condition, her reproductive partner should be offered screening to provide accurate genetic counseling for the couple with regard to the risk of having an affected child. Individuals with a family history of a genetic disorder may benefit from the identification of the specific familial mutation or mutations rather than carrier screening. Given the multitude of conditions that can be included in expanded carrier screening panels, the disorders selected for inclusion should meet several of the following consensus- determined criteria: have a carrier frequency of 1 in 100 or greater, have a well-defined phenotype, have a detrimental effect on quality of life, cause cognitive or physical impairment, require surgical or medical intervention, or have an onset early in life. Additionally, screened conditions should be able to be diagnosed prenatally and may afford opportunities for antenatal intervention to improve perinatal outcomes, changes to delivery management to optimize newborn and infant outcomes, and education of the parents about special care needs after birth.

Carrier screening panels should not include conditions primarily associated with a disease of adult onset. ACOG addresses hemoglobinopathies in pregnancy in Practice Bulletin No. 78 published in 2007. The updated Practice Advisory published in 2022 states, “Previous recommendations for hemoglobinopathy testing have used a race/ethnicity-based strategy. However, race and self- identified ethnicity are poor proxies for genetics since self-identification with a specific race/ethnicity may be incompatible with genetic ancestry. Given that approximately 1 in 66 people in the United States have a hemoglobinopathy trait, ACOG recommends offering universal hemoglobinopathy testing to persons planning pregnancy or at the initial prenatal visit if no prior testing results are available for interpretation. This helps ensure that at-risk individuals receive counseling about genetic risks; learn their reproductive options, which include preimplantation genetic testing and prenatal diagnosis; and make informed decisions. Hemoglobinopathy testing may be performed using hemoglobin electrophoresis or molecular genetic testing (eg, expanded carrier screening that includes sickle cell disease [SCD] and other hemoglobinopathies). The use of noninvasive prenatal diagnosis for SCD with cell-free fetal DNA is still experimental and currently not recommended.” Genetics Committee of the Society of Obstetricians and Gynaecologists of Canada (SOGC) and the Prenatal Diagnosis Committee of the Canadian College of Medical Geneticists (CCMG): Clinical practice guidelines for carrier screening for thalassemia and hemoglobinopathies in Canada include the following recommendations (Langlois, et al., 2008):

If both partners are found to be carriers of thalassemia or an Hb variant, or of a combination of thalassemia and a hemoglobin variant, they should be referred for genetic counselling- ideally prior to conception, or as early as possible in the pregnancy. Additional molecular studies may be required to clarify the carrier status of the parents and thus the risk to the fetus. Prenatal diagnosis should be offered to the pregnant woman/couple at risk for having a fetus affected with a clinically significant thalassemia or hemoglobinopathy. The International Myotonic Dystrophy Consortium (IDMC, 2000): Published his society published genetic testing guidelines for DM1. Regarding reproductive carrier screening the Guidelines note that prenatal testing may be appropriate if: a parent has already been diagnosed with DM1, prenatal testing can be used to assess fetal risk

Medical Coverage Policy: 0514 a parent is at 50% risk and asymptomatic, the best approach is a two-step process by which the at-risk parent is tested first and prenatal testing done subsequently (if still necessary) Preimplantation Genetic Testing of an Embryo American Society for Reproductive Medicine and the Society for Assisted Reproductive Technology (2007): Recommendations for preimplantation genetic diagnosis (PGD) include: Before PGD is performed, genetic counseling must be provided. • PGD can reduce the risk for conceiving a child with a genetic abnormality carried by one or both parents if that abnormality can be identified with tests performed on a single cell. • Prenatal diagnostic testing to confirm the results of PGD is encouraged strongly because PGD has technical limitations that include the possibility of false negatives. Preimplantation Genetic Testing for Aneuploidy (PGT-A) American Society for Reproductive Medicine and the Society for Assisted Reproductive Technology (2007): Recommendations for PGD: Before PGD is performed, thorough education and counseling must be performed to ensure the patient understands the limitations of the technique, risk of error, and lack of evidence that PGD improves outcomes.

Available evidence does not support the use of PGD as currently performed to improve live- birth rates in patients with advanced maternal age.

Available evidence does not support the use of PGD as currently performed to improve live- birth rates in patients with previous implantation failure.

Due to the high prevalence of aneuploidy in patients with recurrent implantation failure, decisions concerning future treatments should not be based on the results of PGD in one or more cycles.

Available evidence does not support the use of PGD as currently performed to improve live- birth rates in patients with recurrent pregnancy loss.

Available evidence does not support the use of PGD as currently performed to reduce miscarriage rates in patients with recurrent pregnancy loss related to aneuploidy. Sequencing-Based Non-Invasive Prenatal Testing (NIPT) American Congress of Obstetricians and Gynecologists (ACOG; 2020): Practice Bulletin 226 (2020, replaces Practice Bulletin 162) from ACOG includes the following information regarding screening for fetal chromosomal abnormalities: Screening and diagnostic testing for chromosomal abnormalities should be offered to all patients early in pregnancy regardless of maternal age or risk for chromosomal abnormality.

Cell-free DNA is the most sensitive and specific screening test for the common fetal aneuploidies (trisomies 21, 13 and 18) and can be performed any time after 9-10 weeks gestation. If a patient chooses screening for aneuploidy only one screening approach should be used.

• Cell-free DNA screening can be performed in twin gestations. • Sensitivity for trisomy 21 using cell free DNA for twin pregnancy is similar to singleton pregnancy although test failure may be higher. In a Committee Opinion by ACOG/SMFM on microarrays and next-generation sequencing technologies (2016) the Committee notes that cell-free whole genome DNA screening is not recommended.

Medical Coverage Policy: 0514 American College of Medical Genetics and Genomics ([ACMG], 2013): On behalf of the ACMG Gregg et al. published guidelines regarding noninvasive prenatal screening for aneuploidy. The Guidelines note: NIPS is not able to distinguish specific forms of aneuploidy. Identification of the mechanism of aneuploidy is important for recurrence risk counseling and emphasizes the importance of diagnostic testing following NIPS.

NIPS does not screen for single-gene mutations. • Uninformative test results due to insufficient isolation of cell-free fetal DNA could lead to a delay in diagnosis or eliminate the availability of information for risk assessment.

NIPS does not screen for open neural tube defects. • NIPS does not replace the utility of a first-trimester ultrasound examination • Limited data are currently available on the use of NIPS in twins and higher-order pregnancies.

NIPS has no role in predicting late-pregnancy complications. European Society of Human Genetics (ESHG) and the American Society of Human Genetics (ASHG): On behalf of the ESHG/ASHG, Dondorp et al. (2015) published recommendations regarding NIPTs. The recommendations note the following: NIPT offers improved accuracy when testing for common autosomal aneuploidies compared with existing tests such as cFTS. However, a positive NIPT result should not be regarded as a final diagnosis

Expanding NIPT-based prenatal screening to also report on sex chromosomal abnormalities and microdeletions not only raises ethical concerns related to information and counseling challenges but also risks reversing the important reduction in invasive testing achieved with implementation of NIPT for aneuploidy, and is therefore currently not recommended. Society for Maternal-Fetal Medicine Publications Committee (2015): In publication #36 the Committee notes the following: The presence of a second gestational sac has been associated with false-positive cfDNA results; therefore, this test is not a good option for women with a “vanishing twin” or empty second sac. At this time, the data are too limited to recommend routine cfDNA aneuploidy screening in women with multifetal gestations. It is important for providers to recognize that a positive result for any of these aneuploidies confers a chance that the fetus is affected, which is usually far <99%, particularly in lower risk patients.

When testing for rare conditions (such as aneuploidy in younger women), the positive predictive value is much lower than when testing for more common conditions (such as trisomy 21 in older women). More false-positive results are expected in women who are at low risk or when screening is done for very rare conditions. The PPV for trisomy 21 has been reported as varying from 45% in low-risk patients to ≥96% in the highest risk patients. In one study of diagnostic testing after abnormal cfDNA screens, aneuploidy was confirmed in 93% of trisomy 21 cases, in 64% of trisomy 18 cases, in 44% of trisomy 13 cases, and in 38% of sex chromosomal abnormalities.

Testing for microdeletions using free cell DNA has not been validated in clinical trials; rather, proof-of-principle studies have included the mixing of normal and abnormal DNA in laboratory samples at ratios thought to represent typical fetal fraction. Even with very high sensitivity and specificity, at such low prevalence, the PPV of such testing is likely very low, and the clinical utility is unclear. At this time, routine screening for microdeletions with cfDNA is not recommended.

Medical Coverage Policy: 0514 Invasive Prenatal Testing of a Fetus American Congress of Obstetricians and Gynecologists (ACOG)/Maternal and the Society for Maternal-Fetal Medicine (SMFM): In an update of the 2013 committee opinion, ACOG/SMFM published a document regarding the use of chromosomal microarray analysis in prenatal diagnosis (2016). ACOG made the following recommendations:

In patients with a fetus with one or more major structural abnormalities identified on ultrasonographic examination and who are undergoing invasive prenatal diagnosis, chromosomal microarray analysis is recommended. This test replaces the need for fetal karyotype. In patients with a structurally normal fetus undergoing invasive prenatal diagnostic testing, either fetal karyotyping or a chromosomal microarray analysis can be performed. Most genetic mutations identified by chromosomal microarray analysis are not associated with increasing maternal age; therefore, the use of this test for prenatal diagnosis can be considered for all women, regardless of age. In cases of intrauterine fetal demise or stillbirth when further cytogenetic analysis is desired, chromosomal microarray analysis on fetal tissue (i.e., amniotic fluid, placenta, or products of conception) is recommended because of its increased likelihood of obtaining results and improved detection of causative abnormalities.

Limited data are available on the clinical utility of chromosomal microarray analysis to evaluate first-trimester and second-trimester pregnancy losses; therefore, this is not recommended at this time.

Comprehensive patient pretest and posttest genetic counseling from qualified personnel such as a genetic counselor or geneticist regarding the benefits, limitations, and results of chromosomal microarray analysis is essential. Germline Mutation Reproductive Genetic Testing for Recurrent Pregnancy Loss American College of Medical Genetics and Genomics (ACMG, 2013): On behalf of the ACMG, Hickey et al. published guidelines regarding MTHFR polymorphism testing. The guideline notes that MTHFR polymorphism genotyping should not be ordered as part of the clinical evaluation for thrombophilia or recurrent pregnancy loss. American Congress of Obstetricians and Gynecologists (Practice Bulletin regarding thromboembolism in pregnancy (ACOG, 2016) notes women who have a history of thrombosis who have not had a complete evaluation of underlying etiologies should be tested for antiphospholipid antibodies and inherited thrombophilias. A Practice Bulletin regarding inherited thrombophilias in pregnancy (ACOG, 2018) notes: Screening for inherited thrombophilias is useful only when results will impact management decisions. It is not useful when treatment is indicated for other risk factors.

Screening is not recommended for women with a history of fetal loss or adverse pregnancy outcomes (e.g., abruption, preeclampsia, fetal growth restriction).

Screening with MTHFR mutation analysis or fasting homocysteine level is not recommended. ACOG/The Society for Maternal Fetal Medicine: ACOG/SMFM (2016) published a Committee Opinion regarding chromosomal microarray (CMA) and next generation sequencing for prenatal diagnosis. The Committee notes that CMA of fetal tissue (i.e., amniotic fluid, placenta, products of conception) is recommended in the evaluation of intrauterine death or stillbirth when further cytogenetic analysis is desired. The Opinion also noted that whole exome and whole genome sequencing for prenatal diagnosis is not recommended outside the context of clinical trials. Cell- free DNA screening is not recommended.

Medical Coverage Policy: 0514 American Society of Reproductive Medicine ([ASRM], 2012): ASRM published the following recommendations for the evaluation and treatment of recurrent pregnancy loss: assessment of RSA focuses on screening for genetic factors and antiphospholipid syndrome, assessment of uterine anomaly, hormonal and metabolic factors, and lifestyle variables. These may include the following genetic tests:  peripheral karyotypic analysis of parents  karyotypic analysis of products of conception in the setting of ongoing therapy for

RSA ASRM notes if a remediable cause of recurrent pregnancy loss is identified cytogenetic analysis of subsequent losses can be employed to determine whether the event was random and not a treatment failure per se. If a 46 XX karyotype is revealed by cytogenetic analysis, reflex DNA extraction and analysis of maternal serum by microsatellite analysis may permit differentiation between a fetal source versus a maternal source. National Society for Genetic Counselors ([NSGC], 2005, reaffirmed 2010): on behalf of the NSGC, Laurino, et al. published guidelines noting a referral to a genetics specialist is indicated when prior evaluations for RSA have been normal and when the pregnancy, medical and family history evaluation indicate a possible genetic cause for RSA. Other NSGC genetic evaluation and testing recommendations include the following: when possible, chromosomal analysis on fetal tissue • • • routine karyotyping of each partner testing for factor V Leiden and prothrombin G20210A should be considered testing for less common thrombophilias (anticoagulant protein C, protein S, antithrombin III) should be reserved for those women with a personal and/or family history of venous thromboembolism testing for thermolabile C677T methylenetetrahydrofolate reductase mutation (MTHFR) is not justified (associated with some hereditary thrombophilia patterns such as hyperhomocysteinemia) testing for alpha thalassemia for Southeast Asian and Mediterranean ancestry is recommended (with or without a personal family history of fetal hydrops) specialized chromosomal studies such as comparative genome hybridization, subtelomeric studies, interphase studies on sperm, and assays for skewed X-inactivation patterns are not warranted (the clinical utility has yet to be proven)

The NSGC reaffirmed that the use of specialized chromosomal studies such as comparative genome hybridization, subtelomeric studies, interphase studies on sperm and assays for skewed X-inactivation patterns are not warranted at this time, as their clinical utility has yet to be determined. Pregnancy and Thrombosis Working Group: On behalf of this association, Duhl et al. (2007) published a consensus report and recommendations for prevention and treatment of VTE and adverse pregnancy outcome. The authors acknowledged that no clear conclusions can be drawn from the studies they reviewed regarding an association between inherited thrombophilias and adverse pregnancy outcomes-some studies show a positive relationship, and other studies show no relationship. According to Duhl, most of the research demonstrated that FVL is not typically associated with pregnancy loss prior to 10 weeks’ gestation. More evidence exists suggesting that a loss after 10 weeks’ gestation may be associated with these disorders.

Medical Coverage Policy: 0514 Germline Mutation Reproductive Genetic Testing for Infertility American Society of Reproductive Medicine (ASRM; 2013): The Practice Committee of the ASRM (2013) noted there is insufficient evidence to recommend the routine use of sperm DNA integrity tests in the evaluation and treatment of the infertile couple. American Urological Association (AUA) (Schlegel, et al., 2021): Regarding guidelines statements directed to genetic testing for male infertility, the AUA notes: Karyotype and Y-chromosome microdeletion analysis should be recommended for men with primary infertility and azoospermia or severe oligozoospermia (<5 million sperm/mL) with elevated FSH or testicular atrophy or a presumed diagnosis of impaired sperm production as the cause of azoospermia. (Expert Opinion)

Clinicians should recommend Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) mutation carrier testing (including assessment of the 5T allele) in men with vasal agenesis or idiopathic obstructive azoospermia. (Expert Opinion)

Sperm DNA fragmentation analysis is not recommended in the initial evaluation of the infertile couple. (Moderate Recommendation; Evidence Level Grade: C)

For couples with recurrent pregnancy loss, men should be evaluated with karyotype (Expert Opinion) and sperm DNA fragmentation. (Moderate Recommendation; Evidence Level Grade: C) Body of evidence strength Grade C in support of a Moderate Recommendation indicates that the statement can be applied to most patients in most circumstances but that better evidence is likely to change confidence.