A rigorous approach for selection of optimal variant sets for carrier screening with demonstration of clinical utility

Clinical utility of expanded carrier screening in the preconception and prenatal population: A Chinese cohort study

OBJECTIVES

To evaluate the clinical utility of expanded carrier screening (ECS) in Chinese preconception and prenatal populations, focusing on carrier frequency and the impact on at-risk couples (ARCs).

METHODS

Data from 6,298 Chinese individuals from 4,420 families who underwent a 149-gene ECS panel at a single center were analyzed. The prevalence of positive carriers and ARCs was determined, with follow-up on reproductive decisions and pregnancy outcomes for ARCs.

RESULTS

Of the individuals screened, 2,673 (42.4 %) were carriers of at least one pathogenic or likely pathogenic variant, and 98 (2.22 %) ARCs were identified. GJB2-related deafness and Duchenne muscular dystrophy were the most common autosomal recessive (AR) and X-linked disorders. Screening the top 11 (gene carrier rate [GCR] ≥ 1/100), 22 (GCR ≥ 1/200), and 41 (GCR ≥ 1/331) AR genes could identify 53.5 %, 67.9 %, and 81.3 % of variants, respectively. The corresponding ratios for identified ARCs were 90.4 %, 94.0 %, and 100 %. Follow-up data from 80 ARCs indicated that 75.0 % (60/80) took significant action based on the ECS results. Additionally, four families (3.5 %, 4/115) were identified at risk for a second disease unrelated to their initial family monogenic history.

CONCLUSIONS

This study, representing the largest cohort of a moderate-sized ECS panel test in the Chinese population, demonstrates the clinical utility of ECS in both healthy individuals and those with a family history of monogenic disorders. The data obtained provide valuable insights for developing a Chinese-specific ECS panel. Tailored approaches are critical for wider adoption and successful routine application of ECS.

Pilot study of expanded carrier screening for 11 recessive diseases in China: results from 10,476 ethnically diverse couples

Expanded carrier screening (ECS) has been demonstrated to increase the detection rate of carriers compared with traditional tests. The aim of this study was to assess the potential value of ECS for clinical application in Southern China, a region with high prevalence of thalassemia and with diverse ethnic groups, and to provide a reference for future implementations in areas with similar population characteristics. A total of 10,476 prenatal/preconception couples from 34 self-reported ethnic groups were simultaneously tested and analyzed anonymously for 11 Mendelian disorders using targeted next-generation sequencing. Overall, 27.49% of individuals without self-reported family history of disorders were found to be carriers of at least 1 of the 11 conditions, and the carrier frequency varied greatly between ethnic groups, ranging from 4.15% to 81.35%. Furthermore, 255 couples (2.43%) were identified as carrier couples at an elevated risk having an affected baby, sixty-five of which would not have been identified through the existing screening strategy, which only detects thalassemia. The modeled risk of fetuses being affected by any of the selected disorders was 531 per 100,000 (95% CI, 497-567 per 100,000). Our data demonstrate the feasibility of ECS, and provide evidence that ECS is a promising alternative to traditional one-condition screening strategies. The lessons learned from this experience should be applicable for other countries or regions with diverse ethnic groups.

Pros and cons of implementing a carrier genetic test in an infertility practice

PURPOSE OF REVIEW

Carrier screening is promptly evolving thanks to the rapid development of new technologies and mutation knowledge. Expanded carrier screening is already being used in assisted reproduction. Medical, ethical, psychological and legal aspects appear from the general public, patients, healthcare providers and scientific societies. Pros and cons of implementing this technique are highlighted.

RECENT FINDINGS

Recent publications show the development of wider gene screening panels with lowering cost. Human genome is continually being updated as are the number of mutations and their corresponding phenotype known. Classical criteria established to consider a genetic screening protocol are nowadays overtaken, and scientific societies are developing guidelines and criteria adapted to expanded genetic testing. There is no universal agreement on the mutations that should be included in the panel. Patients' perceptions on carrier genetic testing seem to be positive. Counselling patients is of paramount importance stressing implications when testing positive on their clinical decision making. Gamete donor genetic testing implies a modified approach and blinded matching must be offered.

SUMMARY

There are important positive aspects implementing a carrier genetic test in assisted reproductive technique, but controversial issues appear. Reproductive providers must be appropriately aware and follow the new guidelines.

Current controversies in traditional and expanded carrier screening

PURPOSE OF REVIEW

Expanded carrier screening, which detects carriers for a large number of autosomal recessive and X-linked diseases, is increasing in clinical utilization. A recent joint statement from multiple professional societies, in addition to a growing literature base, offers perspective on rationale, decision points, and reasonable methods of implementation.

RECENT FINDINGS

Current literature addresses three areas: pre- and posttest education, including optimal use of formal genetic counseling, and differing characteristics of laboratory tests. Surveys of obstetricians and genetics providers also offer insight into optimal practice methods.

SUMMARY

We review the carrier screening process in chronological sequence - pretest, test selection, and posttest results disclosure - and points to be considered, recommending possible practice protocols based on available literature and our combined laboratory and clinical practice experience.

Designing expanded carrier screening panels: results of a qualitative study with European geneticists

Aim: To explore the views of clinical and molecular geneticists on the inclusion of disorders and specific pathogenic mutations into expanded carrier screening (ECS) tests for reproductive purposes. Materials & methods: In-depth semistructured interviews were conducted with 16 European geneticists between April and September 2014. Results: All participants supported carrier screening for severe, childhood-onset autosomal recessive disorders with known natural history. Some participants were also in favor of screening for late-onset and X-linked disorders. Regarding selection of specific pathogenic mutations, our participants argued that ECS should include highly penetrant pathogenic mutations with known genotype–phenotype associations. Conclusion: This study highlights main challenges surrounding the development of ECS panels and offers suggestions for future research in this rapidly advancing field.

Carrier Screening is a Deficient Strategy for Determining Sperm Donor Eligibility and Reducing Risk of Disease in Recipient Children

Aims: DNA-based carrier screening is a standard component of donor eligibility protocols practiced by U.S. sperm banks. Applicants who test positive for carrying a recessive disease mutation are typically disqualified. The aim of our study was to examine the utility of a range of screening panels adopted by the industry and the effectiveness of the screening paradigm in reducing a future child's risk of inheriting disease. Methods: A cohort of 27 donor applicants, who tested negative on an initial cystic fibrosis carrier test, was further screened with three expanded commercial carrier testing panels. These results were then compared to a systematic analysis of the applicants' DNA using next-generation sequencing (NGS) data. Results: The carrier panels detected serious pediatric disease mutations in one, four, or six donor applicants. Because each panel screens distinct regions of the genome, no single donor was uniformly identified as carrier positive by all three panels. In contrast, systematic NGS analysis identified all donors as carriers of one or more mutations associated with severe monogenic pediatric disease. These included 30 variants classified as “pathogenic” based on clinical observation and 66 with a high likelihood of causing gene dysfunction. Conclusion: Despite tremendous advances in variant identification, understanding, and analysis, the vast majority of disease-causing mutation combinations remain undetected by commercial carrier screening panels, which cover a narrow, and often distinct, subset of genes and mutations. The biological reality is that all donors and recipients carry serious recessive disease mutations. This challenges the utility of any screening protocol that anchors donor eligibility to carrier status. A more effective approach to reducing recessive disease risk would consider joint comprehensive analysis of both donor and recipient disease mutations. This type of high-resolution recessive disease risk analysis is now available and affordable, but industry practice must be modified to incorporate its use.

Expanded carrier screening: A review of early implementation and literature

Carrier screening is the practice of testing individuals to identify those at increased risks of having children affected by genetic diseases. Professional guidelines on carrier screening have been available for more than 15 years, and have historically targeted specific diseases that occur at increased frequencies in defined ethnic populations. Enabled by rapidly evolving technology, expanded carrier screening aims to identify carriers for a broader array of diseases and may be applied universally (equally across all ethnic groups). This new approach deviates from the well-established criteria for screening models. In this review, we summarize the rationale for expanded carrier screening using available literature regarding clinical and technical data, as well as provider perspectives. We also discuss important avenues for further research in this burgeoning field.

Carrier screening by next-generation sequencing: health benefits and cost effectiveness

BACKGROUND

Compared with conventional genotyping, which typically tests for a limited number of mutations, next-generation DNA sequencing (NGS) provides increased accuracy for carrier screening. The objective of this study was to evaluate the cost effectiveness of carrier screening using NGS versus genotyping for 14 of the recessive disorders for which medical society guidelines recommend screening.

METHODS

Data from published literature, population surveys, and expert opinion were used to develop a decision tree model capturing decisions and outcomes related to carrier screening and reproductive health.

RESULTS

Modeling a population of 1,000,000 couples that was representative of the United States population and that contained 83,421 carriers of pathogenic mutations, carrier screening using NGS averted 21 additional affected births as compared with genotyping, and reduced costs by approximately $13 million. As compared with no screening, NGS carrier screening averted 223 additional affected births. The results are sensitive to assumptions regarding mutation detection rates and carrier frequencies in multiethnic populations.

CONCLUSION

This study demonstrated that NGS-based carrier screening offers the greater benefit in clinical outcomes and lower total healthcare cost as compared with genotyping.