An empirical estimate of carrier frequencies for 400+ causal Mendelian variants: results from an ethnically diverse clinical sample of 23,453 individuals

Frequency of carriers for rare recessive Mendelian diseases in a Brazilian cohort of 320 patients

Several Mendelian disorders follow an autosomal recessive inheritance pattern. Epidemiological information on many inherited disorders may be useful to guide health policies for rare diseases, but it is often inadequate, particularly in developing countries. We aimed to calculate the carrier frequencies of rare autosomal recessive Mendelian diseases in a cohort of Brazilian patients using whole exome sequencing (WES). We reviewed the molecular findings of WES from 320 symptomatic patients who had carrier status for recessive diseases. Using the Hardy-Weinberg equation, we estimated recessive disease frequencies (q² ) considering the respective carrier frequencies (2pq) observed in our study. We calculated the sensitivity of carrier screening tests based on lists of genes from five different clinical laboratories that offer them in Brazil. A total of 425 occurrences of 351 rare variants were reported in 278 different genes from 230 patients (71.9%). Almost half (48.8%) were carriers of at least one heterozygous pathogenic/likely pathogenic variant for rare metabolic disorders, while 25.9% of epilepsy, 18.1% of intellectual disabilities, 15.6% of skeletal disorders, 10.9% immune disorders, and 9.1% of hearing loss. We estimated that an average of 67% of the variants would not have been detected by carrier screening panels. The combined frequencies of autosomal recessive diseases were estimated to be 26.39/10,000 (or ~0.26%). This study shows the potential research utility of WES to determine carrier status, which may be a possible strategy to evaluate the clinical and social burden of recessive diseases at the population level and guide the optimization of carrier screening panels.

Genetic landscape of recessive diseases in the Vietnamese population from large-scale clinical exome sequencing

Accurate profiling of population-specific recessive diseases is essential for the design of cost-effective carrier screening programs. However, minority populations and ethnic groups, including Vietnamese, are still underrepresented in existing genetic studies. Here, we reported the first comprehensive study of recessive diseases in the Vietnamese population. Clinical exome sequencing data of 4503 disease-associated genes obtained from a cohort of 985 Vietnamese individuals was analyzed to identify pathogenic variants, associated diseases and their carrier frequencies in the population. A total of 118 recessive diseases associated with 164 pathogenic or likely pathogenic variants were identified, among which 28 diseases had carrier frequencies of at least 1% (1 in 100 individuals). Three diseases were prevalent in the Vietnamese population with carrier frequencies of 2-12 times higher than in the world populations, including beta-thalassemia (1 in 23), citrin deficiency (1 in 31), and phenylketonuria (1 in 40). Seven novel pathogenic and two likely pathogenic variants associated with nine recessive diseases were discovered. The comprehensive profile of recessive diseases identified in this study enables the design of cost-effective carrier screening programs specific to the Vietnamese population.

Genetic epidemiology approach to estimating birth incidence and current disease prevalence for rhizomelic chondrodysplasia punctata

Background

Rhizomelic chondrodysplasia punctata (RCDP) is an inherited ultra-rare disease which results in severely impaired physical and mental development. Mutations in one of five genes involved in plasmalogen biosynthesis have been reported to drive disease pathology. Estimates of disease incidence have been extremely challenging due to the rarity of the disorder, preventing an understanding of the unmet medical need. To address this, we have prepared a disease incidence and prevalence model based on genetic epidemiology approaches to estimate the total number of RCDP patients affected, and their demographic characteristics.

Results

Extraction of allelic frequencies for known and predicted pathogenic variants in PEX7, GNPAT, AGPS, FAR1, PEX5 (limited to the PTS2 domain encoding region) genes, from large-scale human genetic diversity datasets (TopMed and gnomAD) revealed the mutational landscape contributing to the RCDP patient population in the US and Europe. We computed genetic prevalence to derive birth incidence for RCDP and modeled the impact to life expectancy to obtain high confidence estimates of disease prevalence. Our population genetics-based model indicates PEX7 variants are expected to contribute to the majority of RCDP cases in both the US and Europe; closely aligning with clinical reports. Furthermore, this model provides estimates for RCDP subtypes due to mutations in other genes, including exceedingly rare subtypes.

Conclusion

In total, the estimated number of RCDP patients in the US and the five largest European countries (UK, Germany, France, Italy and Spain) is between 516 and 847 patients, all under the age of 35 years old. This model provides a quantitative framework for better understanding the unmet medical need in RCDP, to help guide disease awareness and diagnosis efforts for this specific patient group.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13023-021-01889-z.

Interest in and uptake of genetic counseling for preconception carrier screening when offered to predominantly white reproductive-age persons seeking gynecologic care at a single U.S. academic medical center

The objective of this study was to assess the level of interest in preconception carrier screening among reproductive-aged persons presenting for gynecologic care and to identify demographic factors predictive of pursuing screening. Patients aged 18-40 who were presenting for gynecologic care at a single U.S. academic medical center were provided with information about current options for preconception carrier screening and were offered genetic counseling referral with the possibility to undergo screening. Outcomes of interest were desire for genetic counseling referral and attendance at genetic counseling visit. Statistical analyses were performed as appropriate using R version 3.6.1 with variables significant at 0.1 included in a multivariable logistic regression. Of 193 participants, 79 (41%) desired genetic counseling referral. Participants aged 25-34 (OR 3.39, 95% CI 1.47-8.10) and nulliparas (OR 2.69, 95% CI 1.23-6.03) were more likely to desire referral. Thirty-five participants (44.3% of those who desired referral) attended a visit with genetic counseling. Having an advanced degree (OR 3.27, 95% CI 1.06-10.4) was associated with visit attendance. Thirteen participants underwent screening, and five were found to be a carrier of at least one X-linked or autosomal recessive condition. Surprisingly, presenting for a gynecologic visit directly related to planning a pregnancy was not associated with increased interest in preconception carrier screening. Nulliparas and those aged 25-34 likely expressed greater interest in referral due to high potential for future childbearing in these groups. The increased level of visit attendance in participants with advanced degrees is likely confounded by the high level of health literacy and financial resources in this group.

[Our hidden genetic defects]

A systematic study analysing the exomes of several thousand individuals indicates that each of them carries at least one strongly deleterious mutation that is innocuous in a heterozygote but results in a severe phenotype in the homozygous state. Most of these mutations are very rare, while a few are present in 1 or 2% of the population. The frequency of at-risk couples is approximately 1.5%, but increases dramatically to 25% if the partners of the couple are first cousins. This work has important implications for carrier screening and population genetics in general.

The landscape of autosomal-recessive pathogenic variants in European populations reveals phenotype-specific effects

The number and distribution of recessive alleles in the population for various diseases are not known at genome-wide-scale. Based on 6,447 exome sequences of healthy, genetically unrelated Europeans of two distinct ancestries, we estimate that every individual is a carrier of at least 2 pathogenic variants in currently known autosomal-recessive (AR) genes and that 0.8%-1% of European couples are at risk of having a child affected with a severe AR genetic disorder. This risk is 16.5-fold higher for first cousins but is significantly more increased for skeletal disorders and intellectual disabilities due to their distinct genetic architecture.

Clinical Implementation of Expanded Carrier Screening in Pregnant Women at Early Gestational Weeks: A Chinese Cohort Study

Demands for expanded carrier screening (ECS) are growing and ECS is becoming an important part of obstetrics practice and reproductive planning. The aim of this study is to evaluate the feasibility of a small-size ECS panel in clinical implementation and investigate Chinese couples’ attitudes towards ECS. An ECS panel containing 11 recessive conditions was offered to Chinese pregnant women below 16 gestational weeks. Sequential testing of their partners was recommended for women with a positive carrier status. The reproductive decision and pregnancy outcome were surveyed for at-risk couples. A total of 1321 women performed ECS successfully and the overall carrier rate was 19.23%. The estimated at-risk couple rate was 0.83%. Sequential testing was performed in less than half of male partners. Eight at-risk couples were identified and four of them performed prenatal diagnosis. Our study demonstrated that a small-size ECS panel could yield comparable clinical value to a larger-size panel when the carrier rate of the individual condition is equal or greater than 1%. In addition, more than half of male partners whose wives were carriers declined any types of sequential testing possibly due to a lack of awareness and knowledge of genetic disorders. Genetic education is warranted for the better implementation of ECS.

Effect of a high fructose diet on metabolic parameters in carriers for hereditary fructose intolerance

BACKGROUND & AIMS

Hyperuricemia is an independent risk factor for the metabolic syndrome and cardiovascular disease. We hypothesized that asymptomatic carriers for hereditary fructose intolerance (OMIM 22960) would have increased uric acid and altered component of the metabolic syndrome when exposed to fructose overfeeding.

METHODS

Six heterozygotes for HFI (hHFI) and 6 controls (Ctrl) were studied in a randomized, controlled, crossover trial. Participants ingested two identical test meals containing 0.7 g kg^-1 glucose and 0.7 g kg^-1 fructose according to a cross-over design, once after a 7-day on a low fructose diet (LoFruD, <10 g/d) and on another occasion after 7 days on a high fructose diet (HiFruD, 1.4 g kg^-1 day^-1 fructose + 0.1 g kg^-1 day^-1 glucose). Uric acid, glucose, and insulin concentrations were monitored in fasting conditions and over 2 h postprandial, and insulin resistance indexes were calculated.

RESULTS

HiFruD increased fasting uric acid (p < 0.05) and reduced fasting insulin sensitivity estimated by the homeostasis model assessment (HOMA) for insulin resistance (p < 0.05), in both groups. Postprandial glucose concentrations were not different between hHFI and Ctrl. However HiFruD increased postprandial plasma uric acid, insulin and hepatic insulin resistance index (HIRI) in hHFI only (all p < 0.05).

CONCLUSIONS

Seven days of HiFruD increased fasting uric acid and slightly reduced fasting HOMA index in both groups. In contrast, HiFruD increased postprandial uric acid, insulin concentration and HIRI in hHFI only, suggesting that heterozygosity for pathogenic Aldolase B variants may confer an increased susceptibility to the effects of dietary fructose on uric acid and hepatic insulin sensitivity. This trial was registered at the U.S. Clinical Trials Registry as NCT03545581.

ECHS1 disease in two unrelated families of Samoan descent: Common variant - rare disorder

Mutations in the short-chain enoyl-CoA hydratase (SCEH) gene, ECHS1, cause a rare autosomal recessive disorder of valine catabolism. Patients usually present with developmental delay, regression, dystonia, feeding difficulties, and abnormal MRI with bilateral basal ganglia involvement. We present clinical, biochemical, molecular, and functional data for four affected patients from two unrelated families of Samoan descent with identical novel compound heterozygous mutations. Family 1 has three affected boys while Family 2 has an affected daughter, all with clinical and MRI findings of Leigh syndrome and intermittent episodes of acidosis and ketosis. WES identified a single heterozygous variant in ECHS1 at position c.832G > A (p.Ala278Thr). However, western blot revealed significantly reduced ECHS1 protein for all affected family members. Decreased SCEH activity in fibroblasts and a mild increase in marker metabolites in urine further supported ECHS1 as the underlying gene defect. Additional investigations at the DNA (aCGH, WGS) and RNA (qPCR, RT-PCR, RNA-Seq, RNA-Array) level identified a silent, common variant at position c.489G > A (p.Pro163=) as the second mutation. This substitution, present at high frequency in the Samoan population, is associated with decreased levels of normally spliced mRNA. To our understanding, this is the first report of a novel, hypomorphic allele c.489G > A (p.Pro163=), associated with SCEH deficiency.

Concurrent Newborn Hearing and Genetic Screening in a Multi-Ethnic Population in South China

Hearing loss is a common sensory deficit in humans with intricate genomic landscape and mutational signature. Approximately 1-3 out of 1,000 newborns have hearing loss and up to 60% of these cases have a genetic etiology. In this study, we conducted the concurrent newborn hearing and genetic screening in 20 mutations (18 pathogenic variants in GJB2, SLC26A4, and MT-RNR1 and 2 uncertain clinical significance variants in GJB3) for 9,506 normal newborns (4,977 [52.4%] males) from 22 ethnic population in South China. A total of 1,079 (11.4%) newborns failed to pass the initial hearing screening; 160 (1.7%) infants failed to pass the re-screening, and 135 (1.4%) infants presented the diagnostic hearing loss. For the genetic screening, 220 (2.3%) newborns who presented at least one of the screened mutations were more likely to fail the hearing screening and have diagnostic hearing loss than mutation-negative newborns. In comparison to the differences of distribution of mutations, we did not identify any significant difference in the prevalence of screened mutations between Han group (n = 5,265) and Zhuang group (n = 3,464), despite the lack of number of minority ethnic groups. Studies including larger number of minority ethnic populations are needed in the future.

NGS-based expanded carrier screening for genetic disorders in North Indian population reveals unexpected results - a pilot study

Background

To determine the carrier frequency and pathogenic variants of common genetic disorders in the north Indian population by using next generation sequencing (NGS).

Methods

After pre-test counselling, 200 unrelated individuals (including 88 couples) were screened for pathogenic variants in 88 genes by NGS technology. The variants were classified as per American College of Medical Genetics criteria. Pathogenic and likely pathogenic variants were subjected to thorough literature-based curation in addition to the regular filters. Variants of unknown significance were not reported. Individuals were counselled explaining the implications of the results, and cascade screening was advised when necessary.

Results

Of the 200 participants, 52 (26%) were found to be carrier of one or more disorders. Twelve individuals were identified to be carriers for congenital deafness, giving a carrier frequency of one in 17 for one of the four genes tested (SLC26A4, GJB2, TMPRSS3 and TMC1 in decreasing order). Nine individuals were observed to be carriers for cystic fibrosis, with a frequency of one in 22. Three individuals were detected to be carriers for Pompe disease (frequency one in 67). None of the 88 couples screened were found to be carriers for the same disorder. The pathogenic variants observed in many disorders (such as deafness, cystic fibrosis, Pompe disease, Canavan disease, primary hyperoxaluria, junctional epidermolysis bullosa, galactosemia, medium chain acyl CoA deficiency etc.) were different from those commonly observed in the West.

Conclusion

A higher carrier frequency for genetic deafness, cystic fibrosis and Pompe disease was unexpected, and contrary to the generally held view about their prevalence in Asian Indians. In spite of the small sample size, this study would suggest that population-based carrier screening panels for India would differ from those in the West, and need to be selected with due care. Testing should comprise the study of all the coding exons with its boundaries in the genes through NGS, as all the variants are not well characterized. Only study of entire coding regions in the genes will detect carriers with adequate efficiency, in order to reduce the burden of genetic disorders in India and other resource poor countries.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12881-020-01153-4.

FREQMAX provides an alternative approach for determining high-resolution allele frequency thresholds in carrier screening

As whole-genome data become available for increasing numbers of individuals across diverse populations, the list of genomic variants of unknown significance (VOUS) continues to grow. One powerful tool in VOUS interpretation is determining whether an allele is too common to be considered pathogenic. As genetic and epidemiological parameters vary across disease models, so too does the pathogenic allele frequency threshold for each disease gene. One threshold-setting approach is the maximum credible allele frequency (MCAF) method. However, estimating some of the input values MCAF requires, especially those involving heterogeneity, can present nontrivial statistical challenges. Here, we introduce FREQMAX, our alternative approach for determining allele frequency thresholds in carrier screening. FREQMAX makes efficient use of the data available for well-studied traits and exhibits flexibility for traits where information may be less complete. For cystic fibrosis, more alleles are excluded as benign by FREQMAX than by MCAF. For less-comprehensively characterized traits like ciliary dyskinesia and Smith-Lemli-Opitz syndrome, FREQMAX is able to set the allele frequency threshold without requiring a priori estimates of maximum genetic and allelic contributions. Furthermore, though we describe FREQMAX in the context of carrier screening, its classical population genetics framework also provides context for adaptation to other trait models.

Which types of conditions should be included in reproductive genetic carrier screening? Views of parents of children with a genetic condition

Reproductive genetic carrier screening identifies couples with an increased chance of having children with autosomal and X-linked recessive conditions. Initially only offered for single conditions to people with a high priori risk, carrier screening is becoming increasingly offered to individuals/couples in the general population for a wider range of genetic conditions. Despite advances in genomic testing technology and greater availability of carrier screening panels, there is no consensus around which types of conditions to include in carrier screening panels. This study sought to identify which types of conditions parents of children with a genetic condition believe should be included in carrier screening. Participants (n = 150) were recruited through Royal Children's Hospital (RCH) Melbourne outpatient clinics, the Genetic Support Network of Victoria (GSNV) and a databank of children with hearing loss (VicCHILD). This study found that the majority of participants support offering carrier screening for: neuromuscular conditions (n = 128/134, 95.5%), early fatal neurodegenerative conditions (n = 130/141, 92.2%), chronic multi-system disorders (n = 124/135, 91.9%), conditions which cause intellectual disability (n = 128/139, 92.1%) and treatable metabolic conditions (n = 120/138, 87.0%). Views towards the inclusion of non-syndromic hearing loss (n = 88/135, 65.2%) and preventable adult-onset conditions (n = 75/135, 55.6%) were more mixed. Most participants indicated that they would use reproductive options to avoid having a child with the more clinically severe conditions, but most would not do so for clinically milder conditions. A recurring association was observed between participants' views towards carrier screening and their lived experience of having a child with a genetic condition.

Reproductive male partner testing when the female is identified to be a genetic disease carrier

OBJECTIVE

To quantify carrier testing uptake rates for male partners of women found to be a carrier(s) for autosomal recessive conditions and to understand reasons for declining testing (uptake rate).

METHODS

A retrospective chart review of 513 female patients seen at Rutgers-Robert Wood Johnson Medical School found to be carriers through expanded carrier screening (ECS) panels. The aims of this study were to determine how often their male partner chose testing, reasons for declining and the type of methodology chosen for their screening.

RESULTS

Male partner uptake rate was 77%. We identified that the most significant barrier to male partner testing is female patients not following up on their own carrier screening results, thus missing the opportunity for partner testing. When male partners were provided options for testing, the most reported reason for declining is the belief it would have no impact on pregnancy management (20%). A carrier couple rate of 8.3% was identified of partners tested.

CONCLUSION

Despite a relatively high male testing uptake rate, a quarter of carrier females did not proceed with testing their partner. To ascertain fetal risk, results for both parents is necessary. Pretest counseling should stress need for potential male partner follow-up testing.

Novel Compound Heterozygous Mutations in CRTAP Cause Rare Autosomal Recessive Osteogenesis Imperfecta

Whole-exome sequencing (WES) has advantages over the traditional molecular test by screening 20,000 genes simultaneously and has become an invaluable tool for genetic diagnosis in clinical practice. Here, we reported a family with a child and a fetus presenting undiagnosed skeletal dysplasia phenotypes, while the parents were asymptomatic. WES was applied to the parents and affected fetus to identify the genetic cause of the phenotypes. We identified novel compound heterozygous mutations consisting of a single-nucleotide variant (SNV) and a large deletion in the CRTAP gene (NM_006371.4:c.1153-3C > G/hg19 chr3:g.32398837_34210906del). Genetic alterations of CRTAP are known to cause osteogenesis imperfecta (OI) in an autosomal recessive manner. Further examination of the proband’s elder sibling who was diagnosed as OI after birth found that she shares the inherited compound heterozygous mutations of CRTAP; thus, the findings support the disease-causing role of CRTAP mutations. Through the in vitro molecular test and in silico analysis, the deleterious effects of the splicing-altering SNV in CRTAP (c.1153-3C > G) on gene product were confirmed. Collectively, our WES-based pathogenic variant discovery pipeline identifies the SNVs and copy number variation to delineate the genetic cause on the proband affected with OI. The data not only extend the knowledge of mutation spectrum in patients with skeletal dysplasia but also demonstrate that WES holds great promise for genetic screening of rare diseases in clinical settings.

Beyond the "Jewish panel": the importance of offering expanded carrier screening to the Ashkenazi Jewish population

Objective

To assess whether or not the current American College of Obstetricians and Gynecologists (ACOG) recommendations regarding carrier screening are sufficiently robust in detecting mutations in the Ashkenazi Jewish (AJ) population.

Design

Cross-sectional study.

Setting

Outreach program at university community center.

Patient(s)

Self-identified Jewish students, 18–24 years of age, interested in genetic carrier testing.

Intervention(s)

Expanded carrier screening (ECS) with the use of a commercially available targeted genotyping panel including >700 mutations in 180 genes.

Main Outcome Measure(s)

Gene mutations found in this population were grouped into three categories based on ACOG’s 2017 committee opinion regarding carrier screening: category 1: the four commonly recommended genetic conditions known to be a risk for this population; category 2: 14 genetic disorders that should be considered for more comprehensive screening, including those of category 1; and category 3: the ECS panel, which includes category 2.

Result(s)

A total of 81 students underwent screening and 36 (44.4%) were ascertained to be carriers of at least one mutation. A total of 45 mutations were identified, as 8 students were carriers for more than one condition. If testing were limited to category 1, 84% of the mutations would not have been identified, and if limited to category 2, 55% of mutations would have gone undetected.

Conclusion(s)

Individuals of Ashkenazi Jewish descent are at significant risk for carrying a variety of single-gene mutations and therefore they should be offered panethnic ECS to increase the likelihood of detecting preventable disorders.

Clinical experience with carrier screening in a general population: support for a comprehensive pan-ethnic approach

PURPOSE

To present results from a large cohort of individuals receiving expanded carrier screening (CS) in the United States.

METHODS

Single-gene disorder carrier status for 381,014 individuals was determined using next-generation sequencing (NGS) based CS for up to 274 genes. Detection rates were compared with literature-reported values derived from disease prevalence and carrier frequencies. Combined theoretical affected pregnancy rates for the 274 screened disorders were calculated.

RESULTS

For Ashkenazi Jewish (AJ) diseases, 81.6% (4434/5435) of carriers identified did not report AJ ancestry. For cystic fibrosis, 44.0% (6260/14,229) of carriers identified had a variant not on the standard genotyping panel. Individuals at risk of being a silent spinal muscular atrophy carrier, not detectable by standard screening, comprised 1/39 (8763/344,407) individuals. For fragile X syndrome, compared with standard premutation screening, AGG interruption analysis modified risk in 83.2% (1128/1356) premutation carriers. Assuming random pairing across the study population, approximately 1/175 pregnancies would be affected by a disorder in the 274-gene screening panel.

CONCLUSION

Compared with standard screening, NGS-based CS provides additional information that may impact reproductive choices. Pan-ethnic CS leads to substantially increased identification of at-risk couples. These data support offering NGS-based CS to all reproductive-aged women.

Preimplantation Genetic Testing for Polygenic Disease Relative Risk Reduction: Evaluation of Genomic Index Performance in 11,883 Adult Sibling Pairs

Preimplantation genetic testing for polygenic disease risk (PGT-P) represents a new tool to aid in embryo selection. Previous studies demonstrated the ability to obtain necessary genotypes in the embryo with accuracy equivalent to in adults. When applied to select adult siblings with known type I diabetes status, a reduction in disease incidence of 45-72% compared to random selection was achieved. This study extends analysis to 11,883 sibling pairs to evaluate clinical utility of embryo selection with PGT-P. Results demonstrate simultaneous relative risk reduction of all diseases tested in parallel, which included diabetes, cancer, and heart disease, and indicate applicability beyond patients with a known family history of disease.

Patient perspectives and experiences with in vitro fertilization and genetic testing options

Objective:

Decision-making and patient experiences with embryo selection during in vitro fertilization often include genetic testing options. The purpose of this study was to gain insight about the experiences and perspectives of women using in vitro fertilization and genetic technologies.

Methods:

Interviews (n = 37) were conducted among female patients who had undergone in vitro fertilization, underwent expanded carrier screening, and were offered pre-implantation genetic testing for aneuploidy between July 2016 and July 2017. The interviews were transcribed and a content analysis was conducted on the transcripts.

Results:

Categories that emerged from the data analysis included unexpected outcomes, uncertainty, unanticipated emotional consequences, too much emphasis on the woman’s contributions and questions about embryo viability. Patient experiences with genetic technologies during in vitro fertilization played a significant role within these results.

Conclusion:

The emotional and psychological impacts of infertility during in vitro fertilization were the primary concerns discussed by participants. Future research is needed to identify ways to help manage unexpected outcomes and continuous uncertainty, including the increasing use of genetic technologies, to not add to the psychological burden of infertility. There is a need to explore more support options or counseling services for patients struggling with infertility during in vitro fertilization treatment.

Before the beginning: the genetic risk of a couple aiming to conceive

Disorders of genetic etiology exist in 2%-3% of live-born infants. Identifying couples with increased susceptibility for offspring with anomalies or genetic disorders is increasingly effective as a result of molecular advances. Preimplantation genetic testing (PGT) with the use of trophectoderm biopsy, 24-chromosome testing, and molecular testing have allowed wider applicability for avoiding a clinical pregnancy termination. Cell-free DNA in maternal blood is another targeted option, although invasive prenatal genetic diagnosis provides the greatest amount of genetic information. DNA-based methods to detect subtle chromosomal abnormalities are much more sensitive than traditional karyotypes and do not require cultured cells. Aneuploidy and structural chromosomal abnormalities can be readily detected with the use of small amounts of DNA, if necessary amplified, as in PGT. Novel approaches exist for detecting perturbations in single-gene disorders. Not only has the molecular basis for many monogenic disorders been elucidated, but modest costs for DNA sequencing has made testing feasible. As the number of testable genetic disorders has increased, principles underlying screening have advanced. Genetic screening for disorders of high incidence in certain ethnic groups was initiated decades ago; however, limitations exist, and reduction in live-born incidence is not infrequently small. Expanded carrier screening is now offered in panethnic fashion, extending surveillance to couples of mixed ethnicities and involving many more genetic conditions. Targeted gene panels (e.g., adult-onset cancer genes) further increase the number of genetic disorders amenable to screening, often leading to PGT.

Biallelic mutations in SORD cause a common and potentially treatable hereditary neuropathy with implications for diabetes

Here we report biallelic mutations in the sorbitol dehydrogenase gene (SORD) as the most frequent recessive form of hereditary neuropathy. We identified 45 individuals from 38 families across multiple ancestries carrying the nonsense c.757delG (p.Ala253GlnfsTer27) variant in SORD, in either a homozygous or compound heterozygous state. SORD is an enzyme that converts sorbitol into fructose in the two-step polyol pathway previously implicated in diabetic neuropathy. In patient-derived fibroblasts, we found a complete loss of SORD protein and increased intracellular sorbitol. Furthermore, the serum fasting sorbitol levels in patients were dramatically increased. In Drosophila, loss of SORD orthologs caused synaptic degeneration and progressive motor impairment. Reducing the polyol influx by treatment with aldose reductase inhibitors normalized intracellular sorbitol levels in patient-derived fibroblasts and in Drosophila, and also dramatically ameliorated motor and eye phenotypes. Together, these findings establish a novel and potentially treatable cause of neuropathy and may contribute to a better understanding of the pathophysiology of diabetes.

Interest in expanded carrier screening among individuals and couples in the general population: systematic review of the literature

BACKGROUND

Through carrier screening, prospective parents can acquire information about whether they have an increased risk of conceiving a child affected with an autosomal recessive or X-linked condition. Within the last decade, advances in genomic technologies have facilitated a shift from condition-directed carrier screening to expanded carrier screening (ECS). Following the introduction of ECS, several studies have been performed to gauge the interest in this new technology among individuals and couples in the general population.

OBJECTIVE AND RATIONALE

The aim of this systematic review was to synthesize evidence from empirical studies that assess the interest in ECS among individuals and couples in the general population. As the availability and accessibility of ECS grow, more couples who are a priori not at risk based on their personal or family history will be presented with the choice to accept or decline such an offer. Their attitudes and beliefs, as well as the perceived usefulness of this screening modality, will likely determine whether ECS is to become a widespread reproductive genetic test.

SEARCH METHODS

Four databases (Pubmed, Web of Science, CINAHL, Cochrane Library) were systematically searched to identify English language studies performed between January 2009 and January 2019 using the following search terms: carrier screening, carrier testing, attitudes, intention, interest, views, opinions, perspectives and uptake. Studies were eligible for inclusion if they reported on intentions to undergo a (hypothetical) ECS test, uptake of an actual ECS offer or both. Two researchers performed a multistep selection process independently for validation purposes.

OUTCOMES

Twelve empirical studies performed between 2015 and 2019 were included for analysis. The studies originated from the USA (n = 6), the Netherlands (n = 3), Belgium (n = 1), Sweden (n = 1) and Australia (n = 1). The sample size of the studies varied from 80 to 1669. In the included studies, 32%–76% of respondents were interested in a (hypothetical) ECS test, while uptake rates for actual ECS offers ranged from 8% to 50%. The highest overall uptake was observed when ECS was offered to pregnant women (50%). By contrast, studies focusing on the preconception population reported lower overall uptake rates (8–34%) with the exception of one study where women were counseled preconception in preparation for IVF (68.7%).

WIDER IMPLICATIONS

Our findings suggest that there may be discrepancies between prospective parents’ reported intentions to undergo ECS and their actual uptake, particularly during the preconception period. As ECS is a new and relatively unknown test for most future parents, the awareness and comprehension within the general population could be rather limited. Adequate pre- and post-test counseling services should be made available to couples offered ECS to ensure informed reproductive decision-making, together with guidelines for primary health care professionals. Due to restricted nature of the samples and methods of the underlying primary studies, some of the reported results might not be transferable to a broader population. More research is needed to see if the observed trends also apply to a broader and more diverse population.

The Israeli national population program of genetic carrier screening for reproductive purposes. How should it be continued?

The Israeli population genetic screening program for reproductive purposes, is a population-specific screening that includes all known, severe diseases and relatively frequent in a specific population (carrier frequency at or above 1:60 and/or disease frequency at or above 1 in 15,000 live births). The carrier screening program is free of charge and offers testing according to disease frequency in the different groups within the population.

The extraordinary technical changes that occurred in the last decade as well as the changes in the type of marriages within the Israeli population necessitate a revision in the basis of the program.

The screening should include instead of only the relatively frequent variants, all the variants that were reported among patients causing a severe disease for which the natural history is well known without regard of their frequency. The population-specific screening that determine which variants are included according to the origin of the couple should be abandoned for a general screening including either all the Jewish population or all the Israeli Arab population.

Expanded universal carrier screening and its implementation within a publicly funded healthcare service

Carrier screening, a well-established clinical initiative, has been slow to take advantage of the new possibilities offered by high-throughput next generation sequencing technologies. There is evidence of significant benefit in expanding carrier screening to include multiple autosomal recessive conditions and offering a ‘universal’ carrier screen that could be used for a pan-ethnic population. However, the challenges of implementing such a programme and the difficulties of demonstrating efficacy worthy of public health investment are significant barriers. In order for such a programme to be successful, it would need to be applicable and acceptable to the population, which may be ethnically and culturally diverse. There are significant practical and ethical implications associated with determining which variants, genes and conditions to include whilst maintaining adequate sensitivity and accuracy. Although preconception screening would maximise the potential benefits from universal carrier screening, the resource implications of different modes of delivery need to be carefully evaluated and balanced against maximising reproductive autonomy and ensuring equity of access. Currently, although a number of existing initiatives are increasing access to carrier screening, there is insufficient evidence to inform the development of a publicly funded, expanded, universal carrier screening programme that would justify investment over other healthcare interventions.

Utility and First Clinical Application of Screening Embryos for Polygenic Disease Risk Reduction

For over 2 decades preimplantation genetic testing (PGT) has been in clinical use to reduce the risk of miscarriage and genetic disease in patients with advanced maternal age and risk of transmitting disease. Recently developed methods of genome-wide genotyping and machine learning algorithms now offer the ability to genotype embryos for polygenic disease risk with accuracy equivalent to adults. In addition, contemporary studies on adults indicate the ability to predict polygenic disorders with risk equivalent to monogenic disorders. Existing biobanks provide opportunities to model the clinical utility of polygenic disease risk reduction among sibling adults. Here, we provide a mathematical model for the use of embryo screening to reduce the risk of type 1 diabetes. Results indicate a 45-72% reduced risk with blinded genetic selection of one sibling. The first clinical case of polygenic risk scoring in human preimplantation embryos from patients with a family history of complex disease is reported. In addition to these data, several common and accepted practices place PGT for polygenic disease risk in the applicable context of contemporary reproductive medicine. In addition, prediction of risk for PCOS, endometriosis, and aneuploidy are of particular interest and relevance to patients with infertility and represent an important focus of future research on polygenic risk scoring in embryos.

It takes two: uptake of carrier screening among male reproductive partners

OBJECTIVE

To describe uptake of carrier screening by male reproductive partners of prenatal and preconception patients.

METHODS

A retrospective database review of all prenatal and preconception patients seen for genetic counseling in Maternal Fetal Medicine clinics was performed. Descriptive statistics and chi-square analysis were used on the data set.

RESULTS

Within the study period, 6087 patients were seen for genetic counseling, of whom 661 were identified as a carrier of an autosomal recessive disorder by their referring provider or genetic counselor. Despite guidelines recommending partner testing for risk clarification when a woman is known to be a carrier of an autosomal recessive condition, only 41.5% male partners elected carrier screening to clarify the couple's reproductive risk, with a majority of males (75%) having screening consecutively. Of all assessed variables, the only significant predictors of male carrier screening uptake were female parity and earlier gestational age (p < .0001, and p = .001, respectively).

CONCLUSION

With less than half of male partners pursuing carrier screening when indicated, its utility becomes severely diminished. More research is needed to explore reasons why males elect or decline carrier screening.

Development of a Multiplex Real-Time PCR Assay for the Newborn Screening of SCID, SMA, and XLA

Numerous studies have shown evidence supporting the benefits of universal newborn screening for primary immunodeficiencies (PID) and for Spinal Muscular Atrophy (SMA). We have developed a four-plex, real-time PCR assay to screen for Severe Combined Immune Deficiencies (SCID), X-linked agammaglobulinemia (XLA), and SMA in DNA extracted from a single 3.2 mm punch of a dried blood spot (DBS). A simple, high-throughput, semi-automated DNA extraction method was developed for a Janus liquid handler that can process 384 DBS punches in four 96-well plates in just over one hour with sample tracking capability. The PCR assay identifies the absence of exon 7 in the SMN1 gene, while simultaneously evaluating the copy number of T-cell receptor excision circles (TREC) and Kappa-deleting recombination excision circles (KREC) molecules. Additionally, the amplification of a reference gene, RPP30, was included in the assay as a quality/quantity indicator of DNA isolated from the DBS. The assay performance was demonstrated on over 3000 DNA samples isolated from punches of putative normal newborn DBS. The reliability and analytical accuracy were further evaluated using DBS controls, and contrived and confirmed positive samples. The results from this study demonstrate the potential of future molecular DBS assays, and highlight how a multiplex assay could benefit newborn screening programs.

Targeted capture enrichment followed by NGS: development and validation of a single comprehensive NIPT for chromosomal aneuploidies, microdeletion syndromes and monogenic diseases

BACKGROUND

Non-invasive prenatal testing (NIPT) has been widely adopted for the detection of fetal aneuploidies and microdeletion syndromes, nevertheless, limited clinical utilization has been reported for the non-invasive prenatal screening of monogenic diseases. In this study, we present the development and validation of a single comprehensive NIPT for prenatal screening of chromosomal aneuploidies, microdeletions and 50 autosomal recessive disorders associated with severe or moderate clinical phenotype.

RESULTS

We employed a targeted capture enrichment technology powered by custom TArget Capture Sequences (TACS) and multi-engine bioinformatics analysis pipeline to develop and validate a novel NIPT test. This test was validated using 2033 cell-fee DNA (cfDNA) samples from maternal plasma of pregnant women referred for NIPT and paternal genomic DNA. Additionally, 200 amniotic fluid and CVS samples were used for validation purposes. All NIPT samples were correctly classified exhibiting 100% sensitivity (CI 89.7-100%) and 100% specificity (CI 99.8-100%) for chromosomal aneuploidies and microdeletions. Furthermore, 613 targeted causative mutations, of which 87 were unique, corresponding to 21 monogenic diseases, were identified. For the validation of the assay for prenatal diagnosis purposes, all aneuploidies, microdeletions and point mutations were correctly detected in all 200 amniotic fluid and CVS samples.

CONCLUSIONS

We present a NIPT for aneuploidies, microdeletions, and monogenic disorders. To our knowledge this is the first time that such a comprehensive NIPT is available for clinical implementation.

How does carrier status for recessive disorders influence reproductive decisions? A systematic review of the literature

Introduction: Carrier screening for recessive disorders is undertaken by prospective parents to inform their reproductive decisions. With the growing availability of affordable and comprehensive expanded carrier screening (ECS), it is expected that carrier screening will become a standard practice in the future. However, the impact of positive carrier screening results on the reproductive decisions of at-risk couples (ARCs) remains underexplored.Areas covered: We performed a systematic literature review to identify peer-reviewed publications describing the reproductive decisions of ARCs. Our search identified 19 relevant publications spanning the period 1994-2018. By synthesizing available evidence, we found that most ARCs chose to prevent the birth of an affected child and the decision to utilize preventive reproductive options was strongly influenced by the clinical nature of a disorder. However, there was also some heterogeneity in reproductive decisions within the same recessive disorders, suggesting that choices of ARCs can be influenced by factors other than the clinical nature of a disorder.Expert opinion: ECS is becoming increasingly common, which will result in the routine identification of many ARCs. Reproductive decision-making by ARCs is a complex and emotionally challenging process, highlighting the critical role of genetic counseling in the care for these potentially vulnerable patients.

Expanded carrier screening: counseling and considerations

The primary goal of carrier screening is to identify asymptomatic individuals who carry variants associated with genetic diseases, to inform about the risk of having a child with a genetic disease. Carrier screening can be accomplished through different approaches including ethnicity-based screening, pan-ethnic screening, and expanded carrier screening (ECS), and the decision to pursue carrier screening is voluntary. ECS takes a broad approach by screening for a large number of genetic diseases irrespective of ethnic background, and ideally is performed prior to conception. ECS has many benefits, including that it does not depend on accuracy of reported ancestry, as well as its greater yield of information that can be used for reproductive decision-making. However, there are also many important limitations of ECS to consider, ranging from the yield of unexpected information, uncertainty about the phenotype of a particular disease for which an individual is a carrier, and greater downstream costs associated with further testing and genetic counseling. Detailed genetic counseling both prior to and after ECS is essential in order for patients to understand the breadth of this approach, potential and actual results, and limitations.

Whole-exome sequencing provides insights into monogenic disease prevalence in Northwest Russia

BACKGROUND

Allele frequency data from large exome and genome aggregation projects such as the Genome Aggregation Database (gnomAD) are of ultimate importance to the interpretation of medical resequencing data. However, allele frequencies might significantly differ in poorly studied populations that are underrepresented in large-scale projects, such as the Russian population.

METHODS

In this work, we leveraged our access to a large dataset of 694 exome samples to analyze genetic variation in the Northwest Russia. We compared the spectrum of genetic variants to the dbSNP build 151, and made estimates of ClinVar-based autosomal recessive (AR) disease allele prevalence as compared to gnomAD r. 2.1.

RESULTS

An estimated 9.3% of discovered variants were not present in dbSNP. We report statistically significant overrepresentation of pathogenic variants for several Mendelian disorders, including phenylketonuria (PAH, rs5030858), Wilson's disease (ATP7B, rs76151636), factor VII deficiency (F7, rs36209567), kyphoscoliosis type of Ehlers-Danlos syndrome (FKBP14, rs542489955), and several other recessive pathologies. We also make primary estimates of monogenic disease incidence in the population, with retinal dystrophy, cystic fibrosis, and phenylketonuria being the most frequent AR pathologies.

CONCLUSION

Our observations demonstrate the utility of population-specific allele frequency data to the diagnosis of monogenic disorders using high-throughput technologies.

Should Clinicians Leave "Expanded" Carrier Screening Decisions to Patients?

Many patients choose to undergo some type of carrier screening when pregnant or planning to become pregnant. "Expanded" carrier screening products test all patients for the same conditions, regardless of family history, race, or ethnicity. Proponents of expanded screening argue that testing everyone for everything can identify more couples at risk of having an affected fetus. However, most conditions on expanded carrier screening panels do not adhere to criteria recommended by professional organizations and can leave patients with a positive test result but little helpful information about actual clinical risk for their future baby. Confusion persists about whether clinicians should leave carrier screening decisions to patients.

Congenital disorders of glycosylation and the challenge of rare diseases

The congenital disorders of glycosylation are a diverse group of disorders, which present both common and unique challenges in the diagnosis of rare disorders. These disorders affect a variety of structures and processes in their synthesis. Studies by Himmelreich and by Ng and their coworkers are discussed as they exemplify the extremes of such challenges. These include ascertainment bias associated with the recognition of only extreme phenotypes, variant classification limited by the rarity of the observed variant, limitations in glycan methodology, and expression patterns that can change with time and tissue type. The continuing importance of functional studies to help sort out these challenges is highlighted.

Tay-Sachs disease

Introduction: Lysosomal storage disease is caused by the deficiency of a single hydrolase (lysosomal enzymes). GM2 gangliosidoses are autosomal recessive disorders caused by deficiency of β-hexosaminidase and Tay-Sachs disease (TSD) is one of its three forms.Objective: To perform a review of the state of the art on TSD describing its definition, epidemiology, etiology, physiopathology, clinical manifestations and news in diagnosis and treatment.Materials and methods: A literature search was carried out in PubMed using the MeSH terms “Tay-Sachs Disease”.Results: 1 233 results were retrieved in total, of which 53 articles were selected. TSD is caused by the deficiency of the lysosomal enzyme β-hexosaminidase A (HexA), and is characterized by neurodevelopmental regression, hypotonia, hyperacusis and cherry-red spots in the macula. Research on molecular pathogenesis and the development of possible treatments has been limited, consequently there is no treatment established to date.Conclusion: TSD is an autosomal recessive neurodegenerative disorder. Death usually occurs before the age of five. More research and studies on this type of gangliosidosis are needed in order to find an adequate treatment.

Implementation of genomics in medical practice to deliver precision medicine for an Asian population

Whilst the underlying principles of precision medicine are comparable across the globe, genomic references, health practices, costs and discrimination policies differ in Asian settings compared to the reported initiatives involving European-derived populations. We have addressed these variables by developing an evolving reference base of genomic and phenotypic data and a framework to return medically significant variants to consenting research participants applicable for the Asian context. Targeting 10,000 participants, over 2000 Singaporeans, with no known pre-existing health conditions, have consented to an extensive clinical health screen, family health history collection, genome sequencing and ongoing follow-up. Genomic variants in a subset of genes associated with Mendelian disorders and drug responses are analysed using an in-house bioinformatics pipeline. A multidisciplinary team reviews the classification of variants and a research report is generated. Medically significant variants are returned to consenting participants through a bespoke return-of-result genomics clinic. Variant validation and subsequent clinical referral are advised as appropriate. The design and implementation of this flexible learning framework enables a cohort of detailed phenotyping and genotyping of healthy Singaporeans to be established and the frequency of disease-causing variants in this population to be determined. Our findings will contribute to international precision medicine initiatives, bridging gaps with ethnic-specific data and insights from this understudied population.

A Focus Group Study on African American Living Donors’ Treatment Preferences, Sociocultural Factors, and Health Beliefs About Apolipoprotein L1 Genetic Testing

Introduction:

Because apolipoprotein L1 ( APOL1) risk variants may contribute to live donors’ kidney failure postdonation, professional guidelines suggest informing potential donors with African ancestry about the availability of APOL1 genotyping. This study assessed African American (AA) donors’ perceptions of APOL1 genetic testing and how APOL1 may affect ethnic identity.

Methods/Approach:

Four focus groups were conducted with AA donors about their decision-making for and perceptions of APOL1 genetic testing and donation to inform a new culturally targeted educational brochure on APOL1 genetic testing. Qualitative data were analyzed by thematic analysis.

Findings:

Seventeen donors participated (47% participation rate). Four major themes emerged. (1) In hypothetical scenarios, most participants would have undergone APOL1 testing during donor evaluation to make a more informed decision, but many would have still donated. (2) Participants desired information about how having 2 APOL1 risk variants affects the donor’s and the recipient’s health. (3) Participants referred to diversity of genetic ancestry and cultural constructions of racial/ethnic identity to question the population at risk for APOL1 risk variants and recommended that all potential donors undergo genetic testing and receive education about APOL1. (4) Participants worried that out-of-pocket costs would deter APOL1 testing and that APOL1 could become a preexisting condition and discriminate against AAs.

Discussion:

Our findings suggest that AA donors desire APOL1 testing to foster informed consent. Transplant clinicians should be aware of these responses to APOL1 testing and be sensitive to historical issues of distrust and discrimination.

Recent developments in genetic/genomic medicine

Advances in genetic technology are having a major impact in the clinic, and mean that many perceptions of the role and scope of genetic testing are having to change. Genomic testing brings with it a greater opportunity for diagnosis, or predictions of future diagnoses, but also an increased chance of uncertain or unexpected findings, many of which may have impacts for multiple members of a person's family. In the past, genetic testing was rarely able to provide rapid results, but the increasing speed and availability of genomic testing is changing this, meaning that genomic information is increasingly influencing decisions around patient care in the acute inpatient setting. The landscape of treatment options for genetic conditions is shifting, which has evolving implications for clinical discussions around previously untreatable disorders. Furthermore, the point of access to testing is changing with increasing provision direct to the consumer outside the formal healthcare setting. This review outlines the ways in which genetic medicine is developing in light of technological advances.

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.

Interpretation of Genomic Sequencing Results in Healthy and Ill Newborns: Results from the BabySeq Project

Genomic sequencing provides many opportunities in newborn clinical care, but the challenges of interpreting and reporting newborn genomic sequencing (nGS) results need to be addressed for its broader and effective application. The BabySeq Project is a pilot randomized clinical trial that explores the medical, behavioral, and economic impacts of nGS in well newborns and those admitted to a neonatal intensive care unit (NICU). Here we present childhood-onset and actionable adult-onset disease risk, carrier status, and pharmacogenomics findings from nGS of 159 newborns in the BabySeq Project. nGS revealed a risk of childhood-onset disease in 15/159 (9.4%) newborns; none of the disease risks were anticipated based on the infants' known clinical or family histories. nGS also revealed actionable adult-onset disease risk in 3/85 (3.5%) newborns whose parents consented to receive this information. Carrier status for recessive diseases and pharmacogenomics variants were reported in 88% and 5% of newborns, respectively. Additional indication-based analyses were performed in 29/32 (91%) NICU newborns and 6/127 (5%) healthy newborns who later had presentations that prompted a diagnostic analysis. No variants that sufficiently explained the reason for the indications were identified; however, suspicious but uncertain results were reported in five newborns. Testing parental samples contributed to the interpretation and reporting of results in 13/159 (8%) newborns. Our results suggest that nGS can effectively detect risk and carrier status for a wide range of disorders that are not detectable by current newborn screening assays or predicted based on the infant's known clinical or family history, and the interpretation of results can substantially benefit from parental testing.

Approaches to carrier testing and results disclosure in translational genomics research: The clinical sequencing exploratory research consortium experience

BACKGROUND

Clinical genome and exome sequencing (CGES) is primarily used to address specific clinical concerns by detecting risk of future disease, clarifying diagnosis, or directing treatment. Additionally, CGES makes possible the disclosure of autosomal recessive and X-linked carrier results as additional secondary findings, and research about the impact of carrier results disclosure in this context is needed.

METHODS

Representatives from 11 projects in the clinical sequencing exploratory research (CSER) consortium collected data from their projects using a structured survey. The survey focused on project characteristics, which variants were offered and/or disclosed to participants as carrier results, methods for carrier results disclosure, and project-specific outcomes. We recorded quantitative responses and report descriptive statistics with the aim of describing the variability in approaches to disclosing carrier results in translational genomics research projects.

RESULTS

The proportion of participants with carrier results was related to the number of genes included, ranging from 3% (three genes) to 92% (4,600 genes). Between one and seven results were disclosed to those participants who received any positive result. Most projects offered participants choices about whether to receive some or all of the carrier results. There were a range of approaches to communicate results, and many projects used separate approaches for disclosing positive and negative results.

CONCLUSION

Future translational genomics research projects will need to make decisions regarding whether and how to disclose carrier results. The CSER consortium experience identifies approaches that balance potential participant interest while limiting impact on project resources.

Comparing ethnicity-based and expanded carrier screening methods at a single fertility center reveals significant differences in carrier rates and carrier couple rates

PURPOSE

To evaluate the efficiency of expanded carrier screening (ECS) compared with ethnicity-based screening in identifying carriers.

METHODS

A total of 4232 infertility patients underwent ECS from a single genetic testing laboratory at our center between June 2013 and July 2015. Self-reported ethnicity was recorded. Carrier rates based on ECS were calculated. In addition, carrier status was determined for two other screening panels: ethnicity-based guidelines or the ECS panel recommended by the American College of Obstetricians and Gynecologists (ACOG) using ECS results. Carrier rate and carrier couple rates were compared in the overall study population and in each self-reported ethnicity.

RESULTS

The ECS panel used to screen the patient population identified 1243 carriers (29.4%). For the same population, ethnicity-based screening and the ACOG panel would have identified 359 (8.5%) and 659 carriers (15.6%), respectively, representing statistically significant differences. Differences in identifying carriers across self-reported ethnicities varied. In 15 couples (1.2%), both partners carried pathogenic variants for the same genes, 47% of whom would have been missed had screening been ethnicity-based.

CONCLUSION

We propose that all reproductive-aged women should be offered ECS. Carrier couple rates would likely increase further with expansion of the panel, playing a pivotal role in preventing genetic disease in fertility clinics.

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.

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.

Industry perspectives on prenatal genetic testing

Until recent years, prenatal genetic tests have been almost exclusively developed and implemented by academic physicians and laboratories. In the last several years, industry has led the development of novel prenatal genetic tests, funded clinical trials and implemented these tests into clinical practice. That these efforts have been driven by industry has raised questions about diagnostics development regulations, consistency in reporting of results, and management of potential conflicts of interest. In this article, these topics are addressed from an industry perspective. While commercial laboratories may have the resources to develop and offer novel genetic tests, collaboration with healthcare providers is crucial for appropriate, effective, and efficient utilization of such tests.

Measuring the impact of genetic knowledge on intentions and attitudes of the community towards expanded preconception carrier screening

BACKGROUND

Preconception carrier screening (PCS) provides the potential to empower couples to make reproductive choices before having an affected child. An important question is what factors influence the decision to use or not use PCS.

METHODS

We analysed the relationship between knowledge, attitudes and intentions to participate in PCS using logistic regression in 832 participants in Western Australia.

RESULTS

Two-thirds of participants said they would take the test, with 92% of these supporting screening for diseases reducing the lifespan of children and infants. Those who had good genetic knowledge were seven times more likely to intend to use PCS (p≤0.001), while those with high genetic knowledge were four times more likely to (p=0.002) and raised concerns such as insurance and confidentiality.Decreasing genetic knowledge correlated positively with religiosity and apprehension (p≤0.001), which correlated negatively with intention to use PCS (p≤0.001). Increasing genetic knowledge correlated positively with factors representing positive attitudes (p≤0.001), which correlated positively with intention to use PCS (p≤0.001). Many participants with good genetic knowledge nevertheless answered questions that tested understanding incorrectly.80% of participants stated they would prefer to access the test through their general practitioners and 30% would pay up to $A200.

CONCLUSIONS

Knowledge is instrumental in influencing participation. Having good genetic knowledge may not be enough to understand core concepts of PCS and may impact informed decision-making. This study recommends that continuous education of health professionals and thus the community, in PCS is crucial to reduce misconceptions.