Clinical exome sequencing of 1000 families with complex immune phenotypes: Toward comprehensive genomic evaluations.

BACKGROUND: Prospective genetic evaluation of patients at this referral research hospital presents clinical research challenges. OBJECTIVES: This study sought not only a single-gene explanation for participants' immune-related presentations, but viewed each participant holistically, with the potential to have multiple genetic contributions to their immune phenotype and other heritable comorbidities relevant to their presentation and health. METHODS: This study developed a program integrating exome sequencing, chromosomal microarray, phenotyping, results return with genetic counseling, and reanalysis in 1505 individuals from 1000 families with suspected or known inborn errors of immunity. RESULTS: Probands were 50.8% female, 71.5% were ≥18 years, and had diverse immune presentations. Overall, 327 of 1000 probands (32.7%) received 361 molecular diagnoses. These included 17 probands with diagnostic copy number variants, 32 probands with secondary findings, and 31 probands with multiple molecular diagnoses. Reanalysis added 22 molecular diagnoses, predominantly due to new disease-gene associations (9 of 22, 40.9%). One-quarter of the molecular diagnoses (92 of 361) did not involve immune-associated genes. Molecular diagnosis was correlated with younger age, male sex, and a higher number of organ systems involved. This program also facilitated the discovery of new gene-disease associations such as SASH3-related immunodeficiency. A review of treatment options and ClinGen actionability curations suggest that at least 251 of 361 of these molecular diagnoses (69.5%) could translate into ≥1 management option. CONCLUSIONS: This program contributes to our understanding of the diagnostic and clinical utility whole exome analysis on a large scale.

Are genetic counselors prepared to counsel active-duty service members? A survey of genetic counselors' self-efficacy, counseling techniques, and knowledge of military policy.

Given the expected rise in genomic sequencing projects within the US Military and the increased availability of genetic testing to the United States as a whole, current and prospective active-duty service members (SMs) may undergo genetic counseling services in the civilian sector for pre-test and post-test counseling. The overall goal of this study was to better understand genetic counselors' preparedness to address military-specific policies and psychosocial needs of patients from this underrepresented population. Members of the National Society of Genetic Counselors were asked to complete a four-part survey including demographic information, Likert scale questions to separately rate self-efficacy when working with civilians and SMs, case scenarios with multiple-choice options and open-ended responses to assess knowledge of military policy, and open-ended questions regarding psychosocial scenarios related to military service. Eighty-eight responses were analyzed using Microsoft Office Excel for the qualitive thematic analysis and SPSS/RStudio for the quantitative data. While over 75% (n = 69/88, SD = 0.48) of surveyed genetic counselors scored 4 of 4 on knowledge of military policy and reported similarly high levels of self-efficacy when working with SMs (mean = 26.77 out of 30, SD = 4.15) and the general population (mean = 27.99 out of 30, SD = 4.31), the qualitative data suggested an alternative perspective. Up to 57% (n = 50/88) of responses were scored as expressing low confidence concerning knowledge of military policy. One potential explanation for this uncertainty may be due to participants reporting that they never (69.32% (n = 61/88]) or are unsure if (12.50% (n = 11/88]) they received training related to providing counseling services to SMs. We suggest the establishment of educational initiatives for genetic counselors focusing on how to discuss genetic testing with SMs in relation to their health and safety, well-being, and potential employment implications.

Deep Screening for X Chromosome Parent-of-Origin Effects on Neurobehavioral and Neuroanatomical Phenotypes in 47,XXY Klinefelter Syndrome.

Background: X chromosome parent of origin (POX) has been proposed as a source of phenotypic variation within sex chromosome aneuploidies such as Klinefelter syndrome (XXY/KS) and between XX and XY individuals. However, previous studies have yielded conflicting results regarding the presence and nature of POX effects, which we sought to clarify in an expanded sample with deeper neurobehavioral phenotyping. Methods: A cohort of 58 individuals with XXY/KS underwent duo or trio genome sequencing with parents (n = 151), measurement of 66 neurobehavioral phenotypes by standardized research assessments, and measurement of over 1000 anatomical phenotypes by structural magnetic resonance imaging. We developed a novel algorithm, the uniparental disomy visualization for variant call format files, to determine proband POX and then systematically tested for POX associations with all neurobehavioral and neuroanatomical outcomes. Results: The uniparental disomy visualization for variant call format files algorithm showed maternal POX in 35 of 58 cases (60.3%). There were no statistically significant POX effects on any of the 66 subscale measures of cognition, psychopathology, or behavior. Neuroimaging analysis identified 2 regions in the right hemisphere with significantly higher surface area (mean effect size = 1.20) among individuals with paternal versus maternal POX (q = .021). Conclusions: Using deeper phenotyping in an expanded sample, we did not find evidence for substantial POX effects on neurobehavioral variability, except for localized unilateral modulations of surface area in the absence of co-occurring behavioral associations. These findings help to clarify previous inconsistencies in POX research and direct attention toward other sources of clinical variability in sex chromosome aneuploidies.

We investigated whether the parental origin of the extra X chromosome (POX) in Klinefelter syndrome (XXY/KS) affects cognitive, behavioral, and structural brain traits. Our study included 58 people with XXY/KS and used a new method to determine whether the extra X came from the mother (POXm) or father (POXp). Despite previous mixed results, our study found no significant differences in cognitive or behavioral traits based on POX. Imaging revealed some differences in surface area in 2 brain regions, but these findings were limited and require further research. Overall, our study suggests that POX has minimal impact on XXY/KS characteristics.

Chromosomal microarray analysis supplements exome sequencing to diagnose children with suspected inborn errors of immunity.

Purpose: Though copy number variants (CNVs) have been suggested to play a significant role in inborn errors of immunity (IEI), the precise nature of this role remains largely unexplored. We sought to determine the diagnostic contribution of CNVs using genome-wide chromosomal microarray analysis (CMA) in children with IEI. Methods: We performed exome sequencing (ES) and CMA for 332 unrelated pediatric probands referred for evaluation of IEI. The analysis included primary, secondary, and incidental findings. Results: Of the 332 probands, 134 (40.4%) received molecular diagnoses. Of these, 116/134 (86.6%) were diagnosed by ES alone. An additional 15/134 (11.2%) were diagnosed by CMA alone, including two likely de novo changes. Three (2.2%) participants had diagnostic molecular findings from both ES and CMA, including two compound heterozygotes and one participant with two distinct diagnoses. Half of the participants with CMA contribution to diagnosis had CNVs in at least one non-immune gene, highlighting the clinical complexity of these cases. Overall, CMA contributed to 18/134 diagnoses (13.4%), increasing the overall diagnostic yield by 15.5% beyond ES alone. Conclusion: Pairing ES and CMA can provide a comprehensive evaluation to clarify the complex factors that contribute to both immune and non-immune phenotypes. Such a combined approach to genetic testing helps untangle complex phenotypes, not only by clarifying the differential diagnosis, but in some cases by identifying multiple diagnoses contributing to the overall clinical presentation.