Noninvasive prenatal screening (NIPS) for fetal chromosome abnormalities in a general-risk population: An evidence-based clinical guideline of the American College of Medical Genetics and Genomics (ACMG).

PURPOSE: This workgroup aimed to develop an evidence-based clinical practice guideline for the use of noninvasive prenatal screening (NIPS) for pregnant individuals at general risk for fetal trisomy 21, trisomy 18, or trisomy 13 and to evaluate the utility of NIPS for other chromosomal disorders. METHODS: The NIPS Evidence-Based Guideline Work Group (n = 7) relied on the results from the recent American College of Medical Genetics and Genomics (ACMG) systematic review to form the evidentiary basis of this guideline. Workgroup members used the Grading of Recommendations Assessment, Development, and Evaluation Evidence to Decision framework to draft recommendations. The guideline underwent extensive internal and external peer review with a public comment period before approval by the ACMG Board of Directors. RESULTS: Evidence consistently demonstrated improved accuracy of NIPS compared with traditional screening methods for trisomies 21, 18, and 13 in singleton and twin gestations. Identification of rare autosomal trisomies and other microdeletion syndromes with NIPS is an emerging area of interest. CONCLUSION: ACMG strongly recommends NIPS over traditional screening methods for all pregnant patients with singleton and twin gestations for fetal trisomies 21, 18, and 13 and strongly recommends NIPS be offered to patients to screen for fetal sex chromosome aneuploidy.

Management of individuals with germline pathogenic/likely pathogenic variants in CHEK2: A clinical practice resource of the American College of Medical Genetics and Genomics (ACMG).

PURPOSE: Although the role of CHEK2 germline pathogenic variants in cancer predisposition is well known, resources for managing CHEK2 heterozygotes in clinical practice are limited. METHODS: An international workgroup developed guidance on clinical management of CHEK2 heterozygotes informed by peer-reviewed publications from PubMed. RESULTS: Although CHEK2 is considered a moderate penetrance gene, cancer risks may be considered as a continuous variable, which are influenced by family history and other modifiers. Consequently, early cancer detection and prevention for CHEK2 heterozygotes should be guided by personalized risk estimates. Such estimates may result in both downgrading lifetime breast cancer risks to those similar to the general population or upgrading lifetime risk to a level at which CHEK2 heterozygotes are offered high-risk breast surveillance according to country-specific guidelines. Risk-reducing mastectomy should be guided by personalized risk estimates and shared decision making. Colorectal and prostate cancer surveillance should be considered based on assessment of family history. For CHEK2 heterozygotes who develop cancer, no specific targeted medical treatment is recommended at this time. CONCLUSION: Systematic prospective data collection is needed to establish the spectrum of CHEK2-associated cancer risks and to determine yet-unanswered questions, such as the outcomes of surveillance, response to cancer treatment, and survival after cancer diagnosis.

Noninvasive Prenatal Screening for Single-Gene Disorders.

Single-gene disorders (SGDs), also known as monogenic disorders, are caused by pathogenic variants at individual loci. Prenatal cell-free DNA screening for SGDs has been investigated for decades. Detecting paternal and de novo variants may be somewhat straightforward, whereas detecting maternally inherited variants poses a significant challenge. Although commercially available in both high-risk and low-risk patients, many limitations exist. The use of SGDs is not supported by professional medical societies.

The training of future clinical geneticists: Evaluation and reflection on the ACMG Foundation for Genetic and Genomic Medicine Summer Genetics Scholars Program.

PURPOSE: The purpose of the Summer Genetics Scholars Program of the ACMG Foundation for Genetic and Genomic Medicine is to expose medical students to medical genetics and genomics early during school with the aim of increasing the number of physicians pursuing a career in this field. This survey study evaluated the Summer Genetics Scholars Program on the achievement of its goals. METHODS: Former Summer Genetics Scholars who had completed medical school were sent a 13-question survey aimed at evaluating the program and obtaining feedback about their experiences. RESULTS: Of 125 former scholars, 55 completed the survey with 2 additional participants partially completing the survey. The vast majority of former participants report either being very satisfied or satisfied with their experience (96%). CONCLUSION: Whereas most participants found their experience to be beneficial, evaluation of the initial 6 years of the program did not show an increase in the number of students entering residencies in medical genetics and genomics. It likely is too early to assess the program's true influence on entry into the field because data were only available for the first 6 years of the Summer Genetics Scholars Program, and many residents typically choose to complete another primary specialty before medical genetics and genomics.

Cancer Risk C (CR-C), a functional genomics test is a sensitive and rapid test for germline mismatch repair deficiency.

PURPOSE: Heritable pathogenic variants in the DNA mismatch repair (MMR) pathway cause Lynch syndrome, a condition that significantly increases risk of colorectal and other cancers. At least half of individuals tested using gene panel sequencing have a variant of uncertain significance or no variant identified leading to no diagnosis. To fill this diagnostic gap, we developed Cancer Risk C (CR-C), a flow variant assay test. METHODS: In response to treatment with an alkylating agent, individual assays of the nuclear translocation of MLH1, MSH2, BARD1, PMS2, and BRCA2 proteins and the nuclear phosphorylation of the ATM and ATR proteins distinguished pathogenic/likely pathogenic (P/LP) from benign/likely benign variants in MMR genes. RESULTS: A risk classification score based on MLH1, MSH2, and ATR assays was 100% sensitive and 98% specific. Causality of MMR P/LP variants was shown through gene editing and rescue. In individuals with suspected Lynch syndrome but no P/LP, CR-C identified most (73%) as having germline MMR defects. Direct comparison of CR-C on matched blood samples and lymphoblastoid cell lines yielded comparable results (r2 > 0.9). CONCLUSION: For identifying germline MMR defects, CR-C provides augmentation to traditional panel sequencing through greater accuracy, shorter turnaround time (48 hours), and performance on blood with minimal sample handling.

Cell-free DNA screening for trisomies 21, 18, and 13 in pregnancies at low and high risk for aneuploidy with genetic confirmation.

BACKGROUND: Cell-free DNA noninvasive prenatal screening for trisomies 21, 18, and 13 has been rapidly adopted into clinical practice. However, previous studies are limited by a lack of follow-up genetic testing to confirm the outcomes and accurately assess test performance, particularly in women at a low risk for aneuploidy. OBJECTIVE: To measure and compare the performance of cell-free DNA screening for trisomies 21, 18, and 13 between women at a low and high risk for aneuploidy in a large, prospective cohort with genetic confirmation of results STUDY DESIGN: This was a multicenter prospective observational study at 21 centers in 6 countries. Women who had single-nucleotide-polymorphism-based cell-free DNA screening for trisomies 21, 18, and 13 were enrolled. Genetic confirmation was obtained from prenatal or newborn DNA samples. The test performance and test failure (no-call) rates were assessed for the cohort, and women with low and high previous risks for aneuploidy were compared. An updated cell-free DNA algorithm blinded to the pregnancy outcome was also assessed. RESULTS: A total of 20,194 women were enrolled at a median gestational age of 12.6 weeks (interquartile range, 11.6-13.9). The genetic outcomes were confirmed in 17,851 cases (88.4%): 13,043 (73.1%) low-risk and 4808 (26.9%) high-risk cases for aneuploidy. Overall, 133 trisomies were diagnosed (100 trisomy 21; 18 trisomy 18; 15 trisomy 13). The cell-free DNA screen positive rate was lower in the low-risk vs the high-risk group (0.27% vs 2.2%; P<.0001). The sensitivity and specificity were similar between the groups. The positive predictive value for the low- and high-risk groups was 85.7% vs 97.5%; P=.058 for trisomy 21; 50.0% vs 81.3%; P=.283 for trisomy 18; and 62.5% vs 83.3; P=.58 for trisomy 13, respectively. Overall, 602 (3.4%) patients had no-call result after the first draw and 287 (1.61%) after including cases with a second draw. The trisomy rate was higher in the 287 cases with no-call results than patients with a result on a first draw (2.8% vs 0.7%; P=.001). The updated algorithm showed similar sensitivity and specificity to the study algorithm with a lower no-call rate. CONCLUSION: In women at a low risk for aneuploidy, single-nucleotide-polymorphism-based cell-free DNA has high sensitivity and specificity, positive predictive value of 85.7% for trisomy 21 and 74.3% for the 3 common trisomies. Patients who receive a no-call result are at an increased risk of aneuploidy and require additional investigation.

Impact of introducing cell-free DNA screening into clinical care on first trimester ultrasound.

OBJECTIVE: First-trimester ultrasound is an important component of prenatal care. We investigated the impact of introducing cell-free DNA (cfDNA) aneuploidy screening into routine care, on performance of first-trimester ultrasound. METHODS: Retrospective study of patients who had prenatal care at a tertiary referral center. We compared the performance of any first-trimester ultrasound between three different aneuploidy screening protocols, used consecutively during the study period: (1) combined first-trimester screening (FTS); (2) FTS and cfDNA offered together; (3) patients requested to choose between FTS and cfDNA. Secondary outcomes included performance of nuchal translucency (NT), aneuploidy screens and diagnostic genetic procedures. RESULTS: The number of patients undergoing first-trimester ultrasound remained similar with the second protocol but decreased in the third (68.7% vs. 40.9%, OR 0.32, 95% CI 0.25-0.4, p < 0.001). Diagnostic procedures decreased between protocol 1 and 2 (7.6% vs. 4.4%, OR 0.59, 95% CI 0.37-0.93, p = 0.02) while NT scans decreased between protocol 2 and 3 (6.8% vs. 1.3%, OR 0.18, 95% CI 0.09-0.4, p < 0.001). The rate of FTS decreased over the study period and less women had cfDNA when they had to choose one method (p < 0.001). CONCLUSIONS: Introducing cfDNA screening as an alternative to FTS, resulted in fewer patients receiving ultrasound in the first-trimester.

Screening for autosomal recessive and X-linked conditions during pregnancy and preconception: a practice resource of the American College of Medical Genetics and Genomics (ACMG).

Carrier screening began 50 years ago with screening for conditions that have a high prevalence in defined racial/ethnic groups (e.g., Tay-Sachs disease in the Ashkenazi Jewish population; sickle cell disease in Black individuals). Cystic fibrosis was the first medical condition for which panethnic screening was recommended, followed by spinal muscular atrophy. Next-generation sequencing allows low cost and high throughput identification of sequence variants across many genes simultaneously. Since the phrase "expanded carrier screening" is nonspecific, there is a need to define carrier screening processes in a way that will allow equitable opportunity for patients to learn their reproductive risks using next-generation sequencing technology. An improved understanding of this risk allows patients to make informed reproductive decisions. Reproductive decision making is the established metric for clinical utility of population-based carrier screening. Furthermore, standardization of the screening approach will facilitate testing consistency. This practice resource reviews the current status of carrier screening, provides answers to some of the emerging questions, and recommends a consistent and equitable approach for offering carrier screening to all individuals during pregnancy or preconception.

Patient attitudes toward prenatal diagnostic testing during antenatal care in an urban population.

OBJECTIVE: Investigate factors that influence the decision to accept or decline diagnostic testing for pregnant women referred for genetic counseling. METHODS: Cross sectional anonymous survey of pregnant women undergoing genetic counseling at a tertiary care referral center. Subjects' perceived risk of procedure related loss and fetal chromosomal problem were obtained via survey where patients rated risk from 0 (no risk) to 10 (highest risk). RESULTS: There were no differences in sociodemographic factors between women undergoing a diagnostic procedure compared to those not undergoing a procedure. As the perceived risk for having a baby with genetic problem increased by one point, the estimated odds of having the diagnostic procedure increased by 43% controlling for the perceived risk of procedure related loss (p < .0001). Similarly, as the perceived risk of miscarriage increased by one point, the odds of having the diagnostic procedure decreased by 40%, controlling for the perceived risk of having a baby with a genetic problem (p < .0001). The main reason women cited for not undergoing a procedure was fear of procedure related loss. CONCLUSIONS: Pregnant women that decline diagnostic testing have a higher perceived risk of procedure related loss and lower perceived risk of fetal chromosomal abnormality than those who accept.

Gain-of-function pathogenic variants in SMAD4 are associated with neoplasia in Myhre syndrome.

Myhre syndrome is an increasingly diagnosed rare syndrome that is caused by one of two specific heterozygous gain-of-function pathogenic variants in SMAD4. The phenotype includes short stature, characteristic facial appearance, hearing loss, laryngotracheal stenosis, arthritis, skeletal abnormalities, learning and social challenges, distinctive cardiovascular defects, and a striking fibroproliferative response in the ear canals, airways, and serosal cavities (peritoneum, pleura, pericardium). Confirmation of the clinical diagnosis is usually prompted by the characteristic appearance with developmental delay and autistic-like behavior using targeted gene sequencing or by whole exome sequencing. We describe six patients (two not previously reported) with molecularly confirmed Myhre syndrome and neoplasia. Loss-of-function pathogenic variants in SMAD4 cause juvenile polyposis syndrome and we hypothesize that the gain-of-function pathogenic variants observed in Myhre syndrome may contribute to neoplasia in the patients reported herein. The frequency of neoplasia (9.8%, 6/61) in this series (two new, four reported patients) and endometrial cancer (8.8%, 3/34, mean age 40 years) in patients with Myhre syndrome, raises the possibility of cancer susceptibility in these patients. We alert clinicians to the possibility of detecting this syndrome when cancer screening panels are used. We propose that patients with Myhre syndrome are more susceptible to neoplasia, encourage increased awareness, and suggest enhanced clinical monitoring.

Adherence of cell-free DNA noninvasive prenatal screens to ACMG recommendations.

PURPOSE: Noninvasive prenatal screening (NIPS) for fetal aneuploidy via cell-free DNA has been commercially available in the United States since 2011. In 2016, the American College of Medical Genetics and Genomics (ACMG) issued a position statement with specific recommendations for testing laboratories. We sought to evaluate adherence to these recommendations. METHODS: We focused on commercial laboratories performing NIPS testing in the United States as of 1 January 2018. Sample laboratory reports and other materials were scored for compliance with ACMG recommendations. Variables scored for common and sex chromosome aneuploidy detection included detection rate, specificity, positive and negative predictive value, and fetal fraction. Labs that performed analysis of copy-number variants and results for aneuploidies other than those commonly reported were identified. Available patient education materials were similarly evaluated. RESULTS: Nine of 10 companies reported fetal fraction in their reports, and 8 of 10 did not offer screening for autosomal aneuploidies beyond trisomy 13, 18, and 21. There was inconsistency in the application and reporting of other measures recommended by ACMG. CONCLUSIONS: Laboratories varied in the degree to which they met ACMG position statement recommendations. No company adhered to all laboratory guidance.

Counseling patients on reproductive aging and elective fertility preservation-a survey of obstetricians and gynecologists' experience, approach, and knowledge.

PURPOSE: What are the experience, approach, and knowledge of US Obstetricians and Gynecologists' (ob-gyn) towards counseling patients on reproductive aging (RA) and elective fertility preservation (EFP). METHODS: A cross-sectional survey emailed by the American College of Obstetricians and Gynecologists (ACOG) to 5000 ACOG fellows consisting of 9 demographic and 28 questions relating to counseling patients on RA and EFP. RESULTS: Seven hundred and eighty-four responders completed the survey. Although 82.8% agreed that conversations relating to RA should take place with patients desiring future childbearing and delaying due to social reasons, only 27.6% stated that they frequently counsel these women aged 18-34 years old, compared to 75.8% aged 35-44 years old (P < 0.01). Limited time (75.8%) and limited knowledge (41.4%) were amongst the most frequent reported barriers towards counseling patients on RA. Fifty-eight percent stated that they have been asked about EFP by patients. Although 74.8% agreed that conversations should take place related to EFP in women desiring future childbearing and delaying due to social reasons, only 27.6% stated that they frequently counsel these patients on EFP (P < 0.01). Limited time (75%) and limited knowledge (59.9%) were amongst the most frequent barriers towards counseling on EFP. CONCLUSIONS: In the USA, methods to improve patient counseling and provider knowledge on RA and EFP are warranted and further studies are needed to address optimal methods to improve counseling and knowledge related to these topics.

Experiences from a pilot program bringing BRCA1/2 genetic screening to theUS Ashkenazi Jewish population.

PURPOSE: The notion of offering population-based screening to the Ashkenazi Jewish (AJ) population for the BRCA1/2 founder mutations continues to gain support. A program called the BRCAcommunity initiative was designed to identify the benefits and barriers associated with implementing this screening in a clinical setting. METHODS: Interested AJ individuals were stratified into high-risk (HR) and low-risk (LR) groups based on self-reported cancer histories. Those at HR were offered traditional genetic counseling/testing; those at LR were offered group genetic counseling and subsidized AJ BRCA founder mutation testing. RESULTS: During the pilot year, 62% of initial registrants and 53% of ultimate study participants were classified into the HR group. Among the 101 HR and 88 LR study participants, 8 and 2 BRCA carriers were identified, respectively. The LR carriers would have been missed by current mechanisms. Survey responses provided insight into the motivations and fears associated with pursuing testing, the efficacy of the initiative design, and challenges that exist on multiple levels, including the community, health-care providers, and insurance coverage. CONCLUSION: Although the medical value of identifying presymptomatic BRCA carriers in Ashkenazi Jews is evident, further measures need to be taken before this effort can be accomplished on a large scale.Genet Med advance online publication 13 October 2016.

Prediction of breast cancer risk based on flow-variant analysis of circulating peripheral blood B cells.

PURPOSE: Identifying women at high risk for breast cancer can trigger a personal program of annual mammograms and magnetic resonance imaging scans for early detection, prophylactic surgery, or chemoprevention to reduce the risk of cancer. Yet, current strategies to identify high-risk mutations based on sequencing panels of genes have significant false-positive and false-negative results, suggesting the need for alternative approaches. METHODS: Flow-variant assays (FVAs) that assess the effects of mutations in the double-strand break (DSB) repair genetic pathway in lymphoblastoid cells in response to treatment with radiomimetic agents were assessed for sensitivity, specificity, and accuracy both alone and as part of a logistic regression classification score. In turn, these assays were validated in circulating B cells and applied to individuals with personal and/or family history of breast and/or ovarian cancer. RESULTS: A three-FVA classification score based on logistic regression had 95% accuracy. Individuals from a breast cancer-positive cohort with affected family members had high-risk FVA classification scores. CONCLUSION: Application of a classification score based on multiple FVAs could represent an alternative to panel sequencing for identifying women at high risk for cancer.Genet Med advance online publication 16 March 2017.

Patient Perspectives on Intimate Partner Violence Discussion during Genetic Counseling Sessions.

Intimate partner violence (IPV) is a major health concern in the United States (ACOG 2013). The World Health Organization (WHO) describes IPV as any physical, sexual, psychological harm by a current or former intimate partner (WHO 2016). Due to the psychosocial depth and nature of discussions within genetic counseling sessions, patients may disclose and/or discuss IPV as it relates to sexual well-being, reproductive and overall health. This study aims to assess the role for IPV screening, counseling and intervention in genetic counseling practice by investigating the incidence, experiences and attitudes about IPV among genetic counseling patients. Patients receiving genetic counseling at an urban metropolitan hospital were anonymously surveyed about experiences and perspectives on IPV as a topic of discussion during genetic counseling sessions. Among 60 eligible patients, 50 completed the survey (49 females, 1 male, of which, 5 identified as LGBT) ages 20 to 66. The incidence of IPV in this group was 16.0 % (n = 8). Majority of participants had never been asked about IPV by a healthcare provider (n = 32; 64.0%), would have felt comfortable answering questions about IPV by their healthcare provider (n = 34; 68.0%), and would have felt comfortable answering questions about IPV by their genetic counselor (n = 39; 78.0%). Perspectives from all participants, notably those with IPV history, provided insights to the role of genetic counselors in areas for IPV screening and counseling training.