High positive predictive value 22q11.2 microdeletion screening by prenatal cell-free DNA testing that incorporates fetal fraction amplification.

OBJECTIVE: 22q11.2 deletion syndrome (DS) is a serious condition with a range of features. The small microdeletion causing 22q11.2DS makes it technically challenging to detect using standard prenatal cfDNA screening. Here, we assess 22q11.2 microdeletion clinical performance by a prenatal cfDNA screen that incorporates fetal fraction (FF) amplification. METHODS: The study cohort consisted of patients who received Prequel (Myriad Genetics, Inc.), a prenatal cfDNA screening that incorporates FF amplification, and met additional eligibility criteria. Pregnancy outcomes were obtained via a routine process for continuous quality improvement. Samples with diagnostic testing results were used to calculate positive predictive value (PPV). RESULTS: 379,428 patients met study eligibility criteria, 76 of whom were screen-positive for a de novo 22q11.2 microdeletion. 22 (29.7%) had diagnostic testing results available, and all 22 cases were confirmed as true positives, for a PPV of 100% (95% CI 84.6%-100%). This performance was based on cases that ranged broadly across FF (5.9%-41.1%, mean 23.0%), body mass index (22.3-44.8, mean 29.9), and gestational age at testing (10.0w-34.6w, median 12.7w). Ultrasound findings in screen-positive pregnancies were consistent with those known to be associated with 22q11.2DS. CONCLUSION: 22q11.2 microdeletion screening that incorporates FF amplification demonstrated high PPV across both general and high-risk population cohorts.

Expanded carrier screening: What conditions should we screen for?

Carrier screening tests reproductive couples for their risk of having children affected by serious monogenic conditions. Carrier screening has historically been offered for certain conditions in high-risk populations. However, more recent evidence has shown that offering carrier screening to all patients, regardless of their ethnicity, more effectively and equitably identifies at-risk couples. Coupled with technology that enables screening for a nearly unlimited number of conditions, this expanded carrier screening (ECS) approach is now supported by professional society guidelines. Despite recent recommendations by the American College of Medical Genetics and Genomics to screen all patients who are pregnant or considering pregnancy for 113 conditions, questions remain about what conditions should be included on a core ECS panel. Here, we briefly review the history of carrier screening and guidelines on criteria for panel design. We then suggest which of these criteria are most critical, as well as thresholds to identify which conditions meet these criteria. Based on these interpretations, we recommend a core panel of 64 conditions that would identify the vast majority of at-risk couples. Widespread adoption of a core panel such as this would result in a marked improvement in the number of patients currently receiving comprehensive carrier screening.

A guidelines-consistent carrier screening panel that supports equity across diverse populations.

PURPOSE: The American College of Obstetricians and Gynecologists (ACOG) and the American College of Medical Genetics and Genomics (ACMG) suggest carrier screening panel design criteria intended to ensure meaningful results. This study used a data-driven approach to interpret the criteria to identify guidelines-consistent panels. METHODS: Carrier frequencies in >460,000 individuals across 11 races/ethnicities were used to assess carrier frequency. Other criteria were interpreted on the basis of published data. A total of 176 conditions were then evaluated. Stringency thresholds were set as suggested by ACOG and/or ACMG or by evaluating conditions already recommended by ACOG and ACMG. RESULTS: Forty and 75 conditions had carrier frequencies of ≥1 in 100 and ≥1 in 200, respectively; 175 had a well-defined phenotype; and 165 met at least 1 severity criterion and had an onset early in life. Thirty-seven conditions met conservative thresholds, including a carrier frequency of ≥1 in 100, and 74 conditions met permissive thresholds, including a carrier frequency of ≥1 in 200; thus, both were identified as guidelines-consistent panels. CONCLUSION: Clear panel design criteria are needed to ensure quality and consistency among carrier screening panels. Evidence-based analyses of criteria resulted in the identification of guidelines-consistent panels of 37 and 74 conditions.

Evaluating the efficacy of three carrier screening workflows designed to identify at-risk carrier couples.

OBJECTIVE: To evaluate the efficacy of three different carrier screening workflows designed to identify couples at risk for having offspring with autosomal recessive conditions. METHODS: Partner testing compliance, unnecessary testing, turnaround time, and ability to identify at-risk couples (ARCs) were measured across all three screening strategies (sequential, tandem, or tandem reflex). RESULTS: A total of 314,100 individuals who underwent carrier screening were analyzed. Sequential, tandem, and tandem reflex screening yielded compliance frequencies of 25.8%, 100%, and 95.9%, respectively. Among 14,595 couples tested in tandem, 42.2% of females were screen-negative, resulting in unnecessary testing of the male partner. In contrast, less than 1% of tandem reflex couples included unnecessary male testing. The median turnaround times were 29.2 days (sequential), 8 days (tandem), and 13.3 days (tandem reflex). The proportion of ARCs detected per total number of individual screens were 0.5% for sequential testing and 1.3% for both tandem and tandem reflex testing. CONCLUSION: The tandem reflex strategy simplifies a potentially complex clinical scenario by providing a mechanism by which providers can maximize partner compliance and the detection of at-risk couples while minimizing workflow burden and unnecessary testing and is more efficacious than both sequential and tandem screening strategies.

Clinical validity of expanded carrier screening: Evaluating the gene-disease relationship in more than 200 conditions.

Clinical guidelines consider expanded carrier screening (ECS) to be an acceptable method of carrier screening. However, broader guideline support and payer adoption require evidence for associations between the genes on ECS panels and the conditions for which they aim to identify carriers. We applied a standardized framework for evaluation of gene-disease association to assess the clinical validity of conditions screened by ECS panels. The Clinical Genome Resource (ClinGen) gene curation framework was used to assess genetic and experimental evidence of associations between 208 genes and conditions screened on two commercial ECS panels. Twenty-one conditions were previously classified by ClinGen, and the remaining 187 were evaluated by curation teams at two laboratories. To ensure consistent application of the framework across the laboratories, concordance was evaluated on a subset of conditions. All 208 evaluated conditions met the evidence threshold for supporting a gene-disease association. Furthermore, 203 of 208 (98%) achieved the strongest ("Definitive") level of gene-disease association. All conditions evaluated by both commercial laboratories were similarly classified. Assessment using the ClinGen standardized framework revealed strong evidence of gene-disease association for conditions on two ECS panels. This result establishes the disease-level clinical validity of the panels considered herein.

Clinical utility of hereditary cancer panel testing: Impact of PALB2, ATM, CHEK2, NBN, BRIP1, RAD51C, and RAD51D results on patient management and adherence to provider recommendations.

BACKGROUND: Although management guidelines exist for several genes associated with a 2-fold to 5-fold increase in the relative risk for certain cancers, the value of testing for them remains controversial. METHODS: De-identified personal and family history data for 654 individuals with pathogenic variants (PVs) in PALB2, ATM, CHEK2, NBN, BRIP1, RAD51C, and/or RAD51D were analyzed for pretest and post-test candidacy for guideline-recommended management of cancer risk. These individuals were invited to complete a survey about provider recommendations and their adherence. RESULTS: Twenty-four percent of CHEK2, ATM, PALB2, or NBN PV carriers were appropriate for consideration of annual breast magnetic resonance imaging screening before genetic testing, with the remaining 76% appropriate only after testing. No BRIP1, RAD51C, or RAD51D PV carriers were appropriate for consideration of risk-reducing salpingo-oophorectomy before genetic testing; 100% were appropriate only after testing. Seventeen percent of CHEK2 PV carriers were appropriate for earlier and more frequent colonoscopy before genetic testing, with the remaining 83% appropriate only after testing. Provider recommendations for annual breast magnetic resonance imaging, consideration of risk-reducing salpingo-oophorectomy, and earlier and more frequent colonoscopy were reported by 42%, 26%, and 66% of breast, ovarian, and colorectal cancer risk PV carriers, respectively, before genetic testing, versus 82%, 79%, and 81%, respectively, after testing. Nearly all respondents had planned or undertaken provider-recommended management. CONCLUSIONS: Testing for PALB2, ATM, CHEK2, NBN, BRIP1, RAD51C, and RAD51D changed management for those carrying PVs. Provider recommendations were aligned with guidelines, and patients adhered to recommendations, both of which are critical for reducing both long-term cancer morbidity and mortality.

Evaluation and classification of severity for 176 genes on an expanded carrier screening panel.

BACKGROUND: Disease severity is important when considering genes for inclusion on reproductive expanded carrier screening (ECS) panels. We applied a validated and previously published algorithm that classifies diseases into four severity categories (mild, moderate, severe, and profound) to 176 genes screened by ECS. Disease traits defining severity categories in the algorithm were then mapped to four severity-related ECS panel design criteria cited by the American College of Obstetricians and Gynecologists (ACOG). METHODS: Eight genetic counselors (GCs) and four medical geneticists (MDs) applied the severity algorithm to subsets of 176 genes. MDs and GCs then determined by group consensus how each of these disease traits mapped to ACOG severity criteria, enabling determination of the number of ACOG severity criteria met by each gene. RESULTS: Upon consensus GC and MD application of the severity algorithm, 68 (39%) genes were classified as profound, 71 (40%) as severe, 36 (20%) as moderate, and one (1%) as mild. After mapping of disease traits to ACOG severity criteria, 170 out of 176 genes (96.6%) were found to meet at least one of the four criteria, 129 genes (73.3%) met at least two, 73 genes (41.5%) met at least three, and 17 genes (9.7%) met all four. CONCLUSION: This study classified the severity of a large set of Mendelian genes by collaborative clinical expert application of a trait-based algorithm. Further, it operationalized difficult to interpret ACOG severity criteria via mapping of disease traits, thereby promoting consistency of ACOG criteria interpretation.

Technology-Driven Noninvasive Prenatal Screening Results Disclosure and Management.

Background: Noninvasive prenatal screening (NIPS) utilization has grown dramatically and is increasingly offered to the general population by nongenetic specialists. Web-based technologies and telegenetic services offer potential solutions for efficient results delivery and genetic counseling. Introduction: All major guidelines recommend patients with both negative and positive results be counseled. The main objective of this study was to quantify patient utilization, motivation for posttest counseling, and satisfaction of a technology platform designed for large-scale dissemination of NIPS results. Methods: The technology platform provided general education videos to patients, results delivery through a secure portal, and access to telegenetic counseling through phone. Automatic results delivery to patients was sent only to patients with screen-negative results. For patients with screen-positive results, either the ordering provider or a board-certified genetic counselor contacted the patient directly through phone to communicate the test results and provide counseling. Results: Over a 39-month period, 67,122 NIPS results were issued through the platform, and 4,673 patients elected genetic counseling consultations; 95.2% (n = 4,450) of consultations were for patients receiving negative results. More than 70% (n = 3,370) of consultations were on-demand rather than scheduled. A positive screen, advanced maternal age, family history, previous history of a pregnancy with a chromosomal abnormality, and other high-risk pregnancy were associated with the greatest odds of electing genetic counseling. By combining web education, automated notifications, and telegenetic counseling, we implemented a service that facilitates results disclosure for ordering providers. Discussion: This automated results delivery platform illustrates the use of technology in managing large-scale disclosure of NIPS results. Further studies should address effectiveness and satisfaction among patients and providers in greater detail. Conclusions: These data demonstrate the capability to deliver NIPS results, education, and counseling-congruent with professional society management guidelines-to a large population.

Clinical impact and cost-effectiveness of a 176-condition expanded carrier screen.

PURPOSE: Carrier screening identifies couples at high risk for conceiving offspring affected with serious heritable conditions. Minimal guidelines recommend offering testing for cystic fibrosis and spinal muscular atrophy, but expanded carrier screening (ECS) assesses hundreds of conditions simultaneously. Although medical societies consider ECS an acceptable practice, the health economics of ECS remain incompletely characterized. METHODS: Preconception screening was modeled using a decision tree comparing minimal screening and a 176-condition ECS panel. Carrier rates from >60,000 patients, primarily with private insurance, informed disease incidence estimates, while cost and life-years-lost data were aggregated from the literature and a cost-of-care database. Model robustness was evaluated using one-way and probabilistic sensitivity analyses. RESULTS: For every 100,000 pregnancies, 290 are predicted to be affected by ECS-panel conditions, which, on average, increase mortality by 26 undiscounted life-years and individually incur $1,100,000 in lifetime costs. Relative to minimal screening, preconception ECS reduces the affected birth rate and is estimated to be cost-effective (i.e.,<$50,000 incremental cost per life-year), findings robust to perturbation. CONCLUSION: Based on screened patients predominantly with private coverage, preconception ECS is predicted to reduce the burden of Mendelian disease in a cost-effective manner compared with minimal screening. The data and framework herein may facilitate similar assessments in other cohorts.

Clinical utility of expanded carrier screening: results-guided actionability and outcomes.

PURPOSE: Expanded carrier screening (ECS) informs couples of their risk of having offspring affected by certain genetic conditions. Limited data exists assessing the actions and reproductive outcomes of at-risk couples (ARCs). We describe the impact of ECS on planned and actual pregnancy management in the largest sample of ARCs studied to date. METHODS: Couples who elected ECS and were found to be at high risk of having a pregnancy affected by at least one of 176 genetic conditions were invited to complete a survey about their actions and pregnancy management. RESULTS: Three hundred ninety-one ARCs completed the survey. Among those screened before becoming pregnant, 77% planned or pursued actions to avoid having affected offspring. Among those screened during pregnancy, 37% elected prenatal diagnostic testing (PNDx) for that pregnancy. In subsequent pregnancies that occurred in both the preconception and prenatal screening groups, PNDx was pursued in 29%. The decision to decline PNDx was most frequently based on the fear of procedure-related miscarriage, as well as the belief that termination would not be pursued in the event of a positive diagnosis. CONCLUSION: ECS results impacted couples' reproductive decision-making and led to altered pregnancy management that effectively eliminates the risk of having affected offspring.

Sequencing as a first-line methodology for cystic fibrosis carrier screening.

PURPOSE: Medical society guidelines recommend offering genotyping-based cystic fibrosis (CF) carrier screening to pregnant women or women considering pregnancy. We assessed the performance of sequencing-based CF screening relative to genotyping, in terms of analytical validity, clinical validity, clinical impact, and clinical utility. METHODS: Analytical validity was assessed using orthogonal confirmation and reference samples. Clinical validity was evaluated using the CFTR2 database. Clinical impact was assessed using ~100,000 screened patients. Three screening strategies were compared: genotyping 23 guideline-recommended variants ("CF23"), sequencing all coding bases in CFTR ("NGS"), and sequencing with large copy-number variant (CNV) identification ("NGS + CNV"). Clinical utility was determined via self-reported actions of at-risk couples (ARCs). RESULTS: Analytical accuracy of NGS + CNV was 100% for SNVs, indels, and CNVs; interpretive clinical specificity relative to CFTR2 was 99.5%. NGS + CNV detected 58 ARCs, 18 of whom would have gone undetected with CF23 alone. Most ARCs (89% screened preconceptionally, 56% prenatally) altered pregnancy management, and no significant differences were observed between ARCs with or without at least one non-CF23 variant. CONCLUSION: Modern NGS and variant interpretation enable accurate sequencing-based CF screening. Limiting screening to 23 variants does not improve analytical validity, clinical validity, or clinical utility, but does fail to detect approximately 30% (18/58) of ARCs.

Validation of a digital identification tool for individuals at risk for hereditary cancer syndromes.

BACKGROUND: The number of individuals meeting criteria for genetic counseling and testing for hereditary cancer syndromes (HCS) is far less than the number that actually receive it. To facilitate identification of patients at risk for HCS, Counsyl developed a digital identification tool (digital ID tool) to match personal and family cancer history to National Comprehensive Cancer Network (NCCN) BRCA-related Hereditary Breast and Ovarian Cancer (HBOC), Lynch syndrome, and polyposis testing criteria in one-to-one, automated fashion. The purpose of this study was to validate the ability of the digital ID tool to accurately identify histories that do and do not meet NCCN testing criteria. METHODS: Third-party recorded three-generation pedigrees were retrospectively reviewed by a certified genetic counselor (CGC) to determine if independent events included in pedigree histories met NCCN guidelines, and were then sorted into groups: high risk events (meets criteria) and low risk events (does not meet criteria). Events were entered into the digital ID tool to determine the extent of its concordance with events sorted by CGC review. Statistical tests of accuracy were calculated at a 95% confidence interval (CI). RESULTS: One hundred ninety-seven pedigrees were reviewed consecutively representing 765 independent events for analysis across groups. 382/382 (100%) high risk events identified by the digital ID tool and 381/383 (99.47%) low risk events identified by the digital ID tool were concordant with CGC sorting. The digital ID tool had a sensitivity of 100% (99.04-100% CI) and specificity of 99.48% (98.13-99.94% CI). The overall accuracy of the digital ID tool was estimated to be 99.74% (99.06-99.97% CI), reflecting the rate at which the digital ID tool reached the same conclusion as that of CGC review of pedigree events for the recommendation of genetic testing for individuals at risk for HCS. CONCLUSIONS: The digital ID tool accurately matches NCCN criteria in one-to-one fashion to identify at-risk individuals for HCS and may be useful in clinical practice, specifically for BRCA-related HBOC and Lynch Syndrome.

What works in genomics education: outcomes of an evidenced-based instructional model for community-based physicians.

PURPOSE: Education of practicing health professionals is likely to be one factor that will speed appropriate integration of genomics into routine clinical practice. Yet many health professionals, including physicians, find it difficult to keep up with the rapid pace of clinical genomic advances and are often uncomfortable using genomic information in practice. METHODS: Having identified the genomics educational needs of physicians in a Silicon Valley-area community hospital, we developed, implemented, and evaluated an educational course entitled Medicine's Future: Genomics for Practicing Doctors. The course structure and approach were based on best practices in adult learning, including interactivity, case-based learning, skill-focused objectives, and sequential monthly modules. RESULTS: Approximately 20-30 physicians attended each module. They demonstrated significant gains in genomics knowledge and confidence in practice skills that were sustained throughout and following the course. Six months following the course, the majority of participants reported that they had changed their practice to incorporate skills learned during the course. CONCLUSION: We believe the adult-learning principles underlying the development and delivery of Medicine's Future were responsible for participants' outcomes. These principles form a model for the development and delivery of other genomics educational programs for health professionals.Genet Med 18 7, 737-745.

Fragile X syndrome carrier screening accompanied by genetic consultation has clinical utility in populations beyond those recommended by guidelines.

BACKGROUND: Fragile X syndrome (FXS) is the most common inherited form of intellectual disability. Many providers offer preconception or prenatal FXS carrier screening. However, guidelines recommend screening only for those with a family history or undergoing fertility evaluation. Wider screening has been resisted because of concerns about patient understanding of FXS-associated inheritance patterns and phenotypes. Additionally, the clinical utility has been questioned. METHODS: We addressed these concerns by analyzing reproductive decision-making and pregnancy management informed by post-test genetic consultation among 122 FMR1 premutation carriers identified by expanded carrier screening. RESULTS: Sixty-three percent of those screened met guidelines screening criteria; the remaining 37% did not. Ninety-eight percent had undergone post-test genetic consultation. Of respondents screened preconceptionally, 74% reported planning or pursuing actions to reduce the risk of an affected pregnancy; the extent to which couples planned/pursued these actions was not significantly different between those meeting either screening criterion (76%) versus those meeting neither criterion (55%). Of respondents screened prenatally, 41% pursued prenatal diagnostic testing; the extent to which couples pursued prenatal diagnosis was not significantly different between those who met either screening criterion (37%) versus those who met neither criterion (31%). CONCLUSION: These results support the expansion of FXS screening criteria in guidelines.

Challenges and Opportunities for Genomics Education: Insights from an Institute of Medicine Roundtable Activity.

Despite the growing availability of genomic tools for clinical care, many health care providers experience gaps in genomics knowledge and skills that serve as impediments to widespread and appropriate integration of genomics into routine care. A workshop recently held by the Institute of Medicine (IOM) Roundtable on Translating Genomics-Based Research for Health explored 1) the barriers that result in a perception among health care providers that the need for genomics education is not urgent and 2) the drivers that may spur a change in that attitude. This commentary promotes continuing and graduate education-informed by an awareness of barriers, drivers, and best practices-as the most effective approaches for preparing the workforce for genomic medicine and ultimately improving patient care, and argues that the time for education is now.