Barriers to Completion of Expanded Carrier Screening in an Inner City Population

PURPOSE

The American College of Medical Genetics and Genomics emphasizes a "consistent and equitable approach for offering carrier screening". At our academic center, publicly insured prenatal patients underwent universal Expanded Carrier Screening (ECS) to promote equitable care. The aim of the study was to evaluate rates, time, and barriers to complete ECS. This was defined as post-test counseling and partner testing after a patient was found heterozygous for a pathogenic variant.

METHODS

A descriptive retrospective cohort study from 2018-2021. Patients were offered ECS, consisting of 283 recessive and X-linked genes. Heterozygotes were contacted by genetic counselors (</=5 attempts), for education and partner testing. Rates of counseling, partner testing, diagnostic procedures, follow up times, and barriers to completion were assessed.

RESULTS

During this time, 643 women underwent ECS. 462/643 were heterozygotes and 326/462 had counseling. 222/462 partners obtained testing, with a median of 32 days from patient to partner result. 21 couples were heterozygous for the same pathogenic variant. One patient pursued diagnostic testing.

CONCLUSION

ECS offers useful information, however, this study highlights significant barriers to completion. There was suboptimal patient follow up and low partner screening, perhaps from insufficient time to educate and counsel. Future directions include implementing quality measures to ensure optimal completion.

A systematic review and evidence assessment of monogenic gene-disease relationships in human female infertility and differences in sex development

BACKGROUND

As in other domains of medicine, high-throughput sequencing methods have led to the identification of an ever-increasing number of gene variants in the fields of both male and female infertility. The increasing number of recently identified genes allows an accurate diagnosis for previously idiopathic cases of female infertility and more appropriate patient care. However, robust evidence of the gene-disease relationships (GDR) allowing the proper translation to clinical application is still missing in many cases.

OBJECTIVE AND RATIONALE

An evidence-based curation of currently identified genes involved in female infertility and differences in sex development (DSD) would significantly improve both diagnostic performance and genetic research. We therefore performed a systematic review to summarize current knowledge and assess the available GDR.

SEARCH METHODS

PRISMA guidelines were applied to curate all available information from PubMed and Web of Science on genetics of human female infertility and DSD leading to infertility, from 1 January 1988 to 1 November 2021. The reviewed pathologies include non-syndromic as well as syndromic female infertility, and endocrine and reproductive system disorders. The evidence that an identified phenotype is caused by pathogenic variants in a specific gene was assessed according to a standardized scoring system. A final score (no evidence, limited, moderate, strong, or definitive) was assigned to every GDR.

OUTCOMES

A total of 45 271 publications were identified and screened for inclusion of which 1078 were selected for gene and variant extraction. We have identified 395 genes and validated 466 GDRs covering all reported monogenic causes of female infertility and DSD. Furthermore, we present a genetic diagnostic flowchart including 105 genes with at least moderate evidence for female infertility and suggest recommendations for future research. The study did not take into account associated genetic risk factor(s) or oligogenic/polygenic causes of female infertility.

WIDER IMPLICATIONS

We have comprehensively reviewed the existing research on the genetics of female infertility and DSD, which will enable the development of diagnostic panels using validated genes. Whole genome analysis is shifting from predominantly research to clinical application, increasing its diagnostic potential. These new diagnostic possibilities will not only decrease the number of idiopathic cases but will also render genetic counselling more effective for infertile patients and their families.

The effects of an online decision aid to support the reproductive decision-making process of genetically at risk couples-A pilot study

Couples at risk of transmitting a genetic disease to their offspring may experience doubts about their reproductive options. This study examines the effects of an online decision aid (DA) on the (joint) reproductive decision-making process of couples (not pregnant at time of inclusion) at risk of transmitting a genetic disease to their offspring. The primary outcome is decisional conflict, and secondary outcomes are knowledge, realistic expectations, deliberation, joint informed decision-making, and decisional self-efficacy. These outcomes were measured with a pretest-posttest design: before use (T0), after use (T1), and 2 weeks after use (T2) of the decision aid (DA). Usability of the DA was assessed at T1. Paired sample t-tests were used to compute differences between baseline and subsequent measurements. The comparisons of T0-T1 and T0-T2 indicate a significant reduction in mean decisional conflict scores with stronger effects for participants with high baseline decisional conflict scores. Furthermore, use of the DA led to increased knowledge, improved realistic expectations, and increased levels of deliberation, with higher increase in participants with low baseline scores. Decision self-efficacy only improved for participants with lower baseline scores. Participants indicated that the information in the DA was comprehensible and clearly organized. These first results indicate that this online DA is an appropriate tool to support couples at risk of transmitting a genetic disease and a desire to have (a) child(ren) in their reproductive decision-making process.

Machine learning based prediction models in male reproductive health: Development of a proof-of-concept model for Klinefelter Syndrome in azoospermic patients

BACKGROUND

Due to the highly variable clinical phenotype, Klinefelter Syndrome is underdiagnosed.

OBJECTIVE

Assessment of supervised machine learning based prediction models for identification of Klinefelter Syndrome among azoospermic patients, and comparison to expert clinical evaluation.

MATERIALS AND METHODS

Retrospective patient data (karyotype, age, height, weight, testis volume, follicle-stimulating hormone, luteinizing hormone, testosterone, estradiol, prolactin, semen pH and semen volume) collected between January 2005 and June 2019 were retrieved from a patient data bank of a University Centre. Models were trained, validated and benchmarked based on different supervised machine learning algorithms. Models were then tested on an independent, prospectively acquired set of patient data (between July 2019 and July 2020). Benchmarking against physicians was performed in addition.

RESULTS

Based on average performance, support vector machines and CatBoost were particularly well-suited models, with 100% sensitivity and >93% specificity on the test dataset. Compared to a group of 18 expert clinicians, the machine learning models had significantly better median sensitivity (100% vs. 87.5%, p = 0.0455) and fared comparably with regards to specificity (90% vs. 89.9%, p = 0.4795), thereby possibly improving diagnosis rate. A Klinefelter Syndrome Score Calculator based on the prediction models is available on http://klinefelter-score-calculator.uni-muenster.de.

DISCUSSION

Differentiating Klinefelter Syndrome patients from azoospermic patients with normal karyotype (46,XY) is a problem that can be solved with supervised machine learning techniques, improving patient care.

CONCLUSIONS

Machine learning could improve the diagnostic rate of Klinefelter Syndrome among azoospermic patients, even more for less-experienced physicians.

Legal challenges in reproductive genetics

Recent advancements in reproductive genetics have resulted in the availability of an extraordinary amount of new and detailed information for patients and providers. Whereas this information can inform many who are facing difficult clinical decisions, it can also introduce complex and uncertain choices. Expanded carrier screening and preimplantation genetic diagnosis for aneuploidy are important examples of new genetic techniques that are now widely used in reproductive medicine. This paper will explore these techniques through a medical-legal prism to better understand the opportunities and obligations incumbent on both patients and providers in this new age of genetic diagnosis.

Expanded carrier screening in Flanders (Belgium): an online survey on the perspectives of nonpregnant reproductive-aged women

Aim: Despite a considerable interest in expanded carrier screening (ECS) in the general population, actual uptake of ECS remains low. More insights are needed to better understand the perspectives of reproductive-aged individuals. Materials & methods: Nonpregnant women of reproductive age recruited through public pharmacies throughout Flanders (Belgium) were invited to participate in an online survey. Results: Most participants (63.6%) indicated they would consider ECS for themselves in the future. About one in two participants showed a positive attitude toward ECS. Conclusion: This study reports valuable insights in the perspectives of nonpregnant reproductive-aged women in Flanders (Belgium) regarding ECS that can be used in the ongoing debate on the responsible implementation of ECS.

The status of preimplantation genetic testing in the UK and USA

STUDY QUESTION

Has the number of preimplantation genetic testing (PGT) cycles in the UK and USA changed between 2014 and 2016?

SUMMARY ANSWER

From 2014 to 2016, the number of PGT cycles in the UK has remained the same at just under 2% but in the USA has increased from 13% to 27%.

WHAT IS KNOWN ALREADY

PGT was introduced as a treatment option for couples at risk of transmitting a known genetic or chromosomal abnormality to their child. This technology has also been applied as an embryo selection tool in the hope of increasing live birth rates per transfer. ART cycles are monitored in the UK by the Human Fertilisation and Embryology Authority (HFEA) and in the USA by the Society for Assisted Reproductive Technology (SART). Globally, data are monitored via the ESHRE PGT Consortium.

STUDY DESIGN, SIZE, DURATION

This cross-sectional study used the HFEA and SART databases to analyse PGT cycle data and make comparisons with IVF data to examine the success of and changes in patient treatment pathways. Both data sets were analysed from 2014 to 2016. The UK data included 3385 PGT cycles and the USA data included 94 935 PGT cycles.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Following an extensive review of both databases, filters were applied to analyse the data. An assessment of limitations of each database was also undertaken, taking into account data collection by the ESHRE PGT Consortium. In the UK and USA, the publicly available information from these datasets cannot be separated into different indications.

MAIN RESULTS AND THE ROLE OF CHANCE

The proportion of PGT cycles as a total of ART procedures has remained the same in the UK but increased annually in the USA from 13% to 27%. Between 2014 and 2016 inclusive, 3385 PGT cycles have been performed in the UK, resulting in 1074 PGT babies being born. In the USA 94 935 PGT cycles have been performed, resulting in 26 822 babies being born. This gave a success rate per egg collection for PGT of 32% for the UK and 28% for the USA. Analysis of the data by maternal age shows very different patient populations between the UK and USA. These differences may be related to the way PGT is funded in the UK and USA and the lack of HFEA support for PGT for aneuploidy.

LIMITATIONS, REASONS FOR CAUTION

Data reported by the HFEA and SART have different limitations. As undertaken by the ESHRE PGT Consortium, both data sets should separate PGT data by indication. Although the HFEA collects data from all IVF clinics in the UK, SART data only represent 83% of clinics in the USA.

WIDER IMPLICATIONS OF THE FINDINGS

Worldwide, a consistent reporting scheme is required in which success rates can convey the effectiveness of PGT approaches for all indications.

STUDY FUNDING/COMPETING INTEREST(S)

No specific funding was obtained and there are no competing interests to declare that are directly related to this project. Joyce Harper is the director of the Embryology and PGD Academy, which offers education in these fields.

Preconception genome medicine: current state and future perspectives to improve infertility diagnosis and reproductive and health outcomes based on individual genomic data

BACKGROUND

Our genetic code is now readable, writable and hackable. The recent escalation of genome-wide sequencing (GS) applications in population diagnostics will not only enable the assessment of risks of transmitting well-defined monogenic disorders at preconceptional stages (i.e. carrier screening), but also facilitate identification of multifactorial genetic predispositions to sub-lethal pathologies, including those affecting reproductive fitness. Through GS, the acquisition and curation of reproductive-related findings will warrant the expansion of genetic assessment to new areas of genomic prediction of reproductive phenotypes, pharmacogenomics and molecular embryology, further boosting our knowledge and therapeutic tools for treating infertility and improving women's health.

OBJECTIVE AND RATIONALE

In this article, we review current knowledge and potential development of preconception genome analysis aimed at detecting reproductive and individual health risks (recessive genetic disease and medically actionable secondary findings) as well as anticipating specific reproductive outcomes, particularly in the context of IVF. The extension of reproductive genetic risk assessment to the general population and IVF couples will lead to the identification of couples who carry recessive mutations, as well as sub-lethal conditions prior to conception. This approach will provide increased reproductive autonomy to couples, particularly in those cases where preimplantation genetic testing is an available option to avoid the transmission of undesirable conditions. In addition, GS on prospective infertility patients will enable genome-wide association studies specific for infertility phenotypes such as predisposition to premature ovarian failure, increased risk of aneuploidies, complete oocyte immaturity or blastocyst development failure, thus empowering the development of true reproductive precision medicine.

SEARCH METHODS

Searches of the literature on PubMed Central included combinations of the following MeSH terms: human, genetics, genomics, variants, male, female, fertility, next generation sequencing, genome exome sequencing, expanded carrier screening, secondary findings, pharmacogenomics, controlled ovarian stimulation, preconception, genetics, genome-wide association studies, GWAS.

OUTCOMES

Through PubMed Central queries, we identified a total of 1409 articles. The full list of articles was assessed for date of publication, limiting the search to studies published within the last 15 years (2004 onwards due to escalating research output of next-generation sequencing studies from that date). The remaining articles' titles were assessed for pertinence to the topic, leaving a total of 644 articles. The use of preconception GS has the potential to identify inheritable genetic conditions concealed in the genome of around 4% of couples looking to conceive. Genomic information during reproductive age will also be useful to anticipate late-onset medically actionable conditions with strong genetic background in around 2-4% of all individuals. Genetic variants correlated with differential response to pharmaceutical treatment in IVF, and clear genotype-phenotype associations are found for aberrant sperm types, oocyte maturation, fertilization or pre- and post-implantation embryonic development. All currently known capabilities of GS at the preconception stage are reviewed along with persisting and forthcoming barriers for the implementation of precise reproductive medicine.

WIDER IMPLICATIONS

The expansion of sequencing analysis to additional monogenic and polygenic traits may enable the development of cost-effective preconception tests capable of identifying underlying genetic causes of infertility, which have been defined as 'unexplained' until now, thus leading to the development of a true personalized genomic medicine framework in reproductive health.

Oocyte maturation arrest produced by TUBB8 mutations: impact of genetic disorders in infertility treatment

Oocyte maturation defect is a challenging situation in the management of infertility, the etiology may be related to endocrine causes, protocols used in ovarian stimulation, oocyte intrinsic defects or procedures in embryology laboratory. We report three Mexican females in treatment for primary infertility with non-mature oocytes after ovary stimulation and oocyte capture in whom a genetic diagnosis of TUBB8-oocyte maturation defect was revealed by exome sequencing. Two couples achieved pregnancies though oocyte donation after establishing the genetic etiology. Our results expand the role of TUBB8-disorders in patients of non-Asian ethnicity. Oocyte maturation defects of monogenic origin are a growing group of disorders that endocrinologists and reproductive medicine specialists should be aware in order to provide referral to genetics for establish a correct and opportune diagnosis.

SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility

Unexplained infertility affects 2%-3% of reproductive-aged couples. One approach to identifying genes involved in infertility is to study subjects with this clinical phenotype and a de novo balanced chromosomal aberration (BCA). While BCAs may reduce fertility by production of unbalanced gametes, a chromosomal rearrangement may also disrupt or dysregulate genes important in fertility. One such subject, DGAP230, has severe oligozoospermia and 46,XY,t(20;22)(q13.3;q11.2). We identified exclusive overexpression of SYCP2 from the der(20) allele that is hypothesized to result from enhancer adoption. Modeling the dysregulation in budding yeast resulted in disrupted structural integrity of the synaptonemal complex, a common cause of defective spermatogenesis in mammals. Exome sequencing of infertile males revealed three heterozygous SYCP2 frameshift variants in additional subjects with cryptozoospermia and azoospermia. In sum, this investigation illustrates the power of precision cytogenetics for annotation of the infertile genome, suggests that these mechanisms should be considered as an alternative etiology to that of segregation of unbalanced gametes in infertile men harboring a BCA, and provides evidence of SYCP2-mediated male infertility in humans.

A systematic analysis of online marketing materials used by providers of expanded carrier screening

PURPOSE

Expanded carrier screening (ECS) for a large number of recessive disorders is available to prospective parents through commercial providers. This study aimed to analyze the content of marketing materials on ECS providers' websites.

METHODS

To identify providers of ECS tests, we undertook a comprehensive online search, reviewed recent academic literature on commercial carrier screening, and consulted with colleagues familiar with the current ECS landscape. The identified websites were archived in April 2017, and inductive content analysis was performed on website text, brochures and educational materials, and video transcripts.

RESULTS

We identified 18 ECS providers, including 16 commercial genetic testing companies. Providers typically described ECS as an important family planning tool. The content differed in both the tone used to promote ECS and the accuracy and completeness of the test information provided. We found that most providers offered complimentary genetic counseling to their consumers, although this was often optional, limited to the posttest context, and, in some cases, appeared to be available only to test-positive individuals.

CONCLUSION

The quality of ECS providers' websites could be improved by offering more complete and accurate information about ECS and their tests. Providers should also ensure that all carrier couples receive posttest genetic counseling to inform their subsequent reproductive decision making.

Genetic analysis of Mayer-Rokitansky-Kuster-Hauser syndrome in a large cohort of families

OBJECTIVE

To study the genetic cause of Mayer-Rokitansky-Kuster-Hauser syndrome (MRKH). Although a few candidate genes and genomic domains for have been reported for MRKH, the genetic underpinnings remain largely unknown. Some of the top candidate genes are WNT4, HNF1B, and LHX1. The goals of this study were to: 1) determine the prevalence of WNT4, HNF1B, and LHX1 point mutations, as well as new copy number variants (CNVs) in people with MRKH; and 2) identify and characterize MRKH cohorts.

DESIGN

Laboratory- and community-based study.

SETTING

Academic medical centers.

PATIENT(S)

A total of 147 MRKH probands and available family members.

INTERVENTIONS(S)

DNA sequencing of WNT4, HNF1B, and LHX1 in 100 MRKH patients, chromosomal microarray analysis in 31 North American MRKH patients, and characterization and sample collection of 147 North American and Turkish MRKH probands and their families.

MAIN OUTCOME MEASURE(S)

DNA sequence variants and CNVs; pedigree structural analysis.

RESULT(S)

We report finding CNVs in 6/31 people (∼19%) with MRKH, but no point mutations or small indels in WNT4, HNF1B, or LHX1 in 100 MRKH patients. Our MRKH families included 43 quads, 26 trios, and 30 duos. Of our MRKH probands, 87/147 (59%) had MRKH type 1 and 60/147 (41%) had type 2 with additional anomalies.

CONCLUSION(S)

Although the prevalence of WNT4, HNF1B, and LHX1 point mutations is low in people with MRKH, the prevalence of CNVs was ∼19%. Further analysis of our large familial cohort of patients will facilitate gene discovery to better understand the complex etiology of MRKH.

Growing complexity of (expanded) carrier screening: Direct-to-consumer, physician-mediated, and clinic-based offers

Since the introduction of out-of-hospital health-related genetic tests more than a decade ago, the landscape of genetic testing services has grown in complexity. Although initially most genetic tests for health purposes were offered as direct-to-consumer services, that is, without the mediation of a medical professional, currently many commercial providers require that their tests be ordered by a licensed physician. At the same time, some commercially developed health-related genetic tests are gaining support from the professional medical community and are finding their way into clinical practice. Therefore, we differentiated between three types of genetic testing offers: direct-to-consumer, physician-mediated, and clinic-based genetic testing. Expanded carrier screening tests for recessive disorders are currently available through all the three models of genetic testing. Herein, we review the present landscape of expanded carrier screening offers by highlighting the distinct issues associated with each of the three types of genetic testing.

Failures of Imagination: Disability and the Ethics of Selective Reproduction

The article addresses the problem of disability in the context of reproductive decisions based on genetic information. It poses the question of whether selective procreation should be considered as a moral obligation of prospective parents. To answer this question, a number of different ethical approaches to the problem are presented and critically analysed: the utilitarian; Julian Savulescu's principle of procreative beneficence; the rights-based. The main thesis of the article is that these approaches fail to provide any appealing principles on which reproductive decisions should be based. They constitute failures of imagination which may result in counter-intuitive moral judgments about both life with disability and genetic selection. A full appreciation of the ethical significance of recognition in procreative decisions leads to a more nuanced and morally satisfying view than other leading alternatives presented in the article.