Genetic landscape of a large cohort of Primary Ovarian Insufficiency : New genes and pathways and implications for personalized medicine

Background Primary Ovarian Insufficiency (POI), a public health problem, affects 1-3.7% of women under 40 yield-ing infertility and a shorter lifespan. Most causes are unknown. Recently, genetic causes were identified, mostly in single families. We studied an unprecedented large cohort of POI to unravel its molecular pathophysiology.Methods 375 patients with 70 families were studied using targeted (88 genes) or whole exome sequencing with pathogenic/likely-pathogenic variant selection. Mitomycin-induced chromosome breakages were studied in patients' lymphocytes if necessary. Findings A high-yield of 29.3% supports a clinical genetic diagnosis of POI. In addition, we found strong evidence of pathogenicity for nine genes not previously related to a Mendelian phenotype or POI: ELAVL2, NLRP11, CENPE, SPATA33, CCDC150, CCDC185, including DNA repair genes: C17orf53(HROB), HELQ, SWI5 yielding high chromo-somal fragility. We confirmed the causal role of BRCA2, FANCM, BNC1, ERCC6, MSH4, BMPR1A, BMPR1B, BMPR2, ESR2, CAV1, SPIDR, RCBTB1 and ATG7 previously reported in isolated patients/families. In 8.5% of cases, POI is the only symptom of a multi-organ genetic disease. New pathways were identified: NF-kB, post-translational regulation, and mitophagy (mitochondrial autophagy), providing future therapeutic targets. Three new genes have been shown to affect the age of natural menopause supporting a genetic link.Interpretation We have developed high-performance genetic diagnostic of POI, dissecting the molecular pathogene-sis of POI and enabling personalized medicine to i) prevent/cure comorbidities for tumour/cancer susceptibility genes that could affect life-expectancy (37.4% of cases), or for genetically-revealed syndromic POI (8.5% of cases), ii) predict residual ovarian reserve (60.5% of cases). Genetic diagnosis could help to identify patients who may benefit from the promising in vitro activation-IVA technique in the near future, greatly improving its success in treating infertility.Funding Universite? Paris Saclay, Agence Nationale de Biome?decine.Copyright (c) 2022 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)Peer reviewe

Altered Chromosomal Positioning, Compaction, and Gene Expression with a Lamin A/C Gene Mutation

Lamins A and C, encoded by the LMNA gene, are filamentous proteins that form the core scaffold of the nuclear lamina. Dominant LMNA gene mutations cause multiple human diseases including cardiac and skeletal myopathies. The nuclear lamina is thought to regulate gene expression by its direct interaction with chromatin. LMNA gene mutations may mediate disease by disrupting normal gene expression.To investigate the hypothesis that mutant lamin A/C changes the lamina's ability to interact with chromatin, we studied gene misexpression resulting from the cardiomyopathic LMNA E161K mutation and correlated this with changes in chromosome positioning. We identified clusters of misexpressed genes and examined the nuclear positioning of two such genomic clusters, each harboring genes relevant to striated muscle disease including LMO7 and MBNL2. Both gene clusters were found to be more centrally positioned in LMNA-mutant nuclei. Additionally, these loci were less compacted. In LMNA mutant heart and fibroblasts, we found that chromosome 13 had a disproportionately high fraction of misexpressed genes. Using three-dimensional fluorescence in situ hybridization we found that the entire territory of chromosome 13 was displaced towards the center of the nucleus in LMNA mutant fibroblasts. Additional cardiomyopathic LMNA gene mutations were also shown to have abnormal positioning of chromosome 13, although in the opposite direction.These data support a model in which LMNA mutations perturb the intranuclear positioning and compaction of chromosomal domains and provide a mechanism by which gene expression may be altered

Twist exome capture allows for lower average sequence coverage in clinical exome sequencing

Background Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. Results We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. Conclusion We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

Oceanic surface water isotopic compositions calibrated data from POLARSTERN cruise PS95.1 (ANT-XXXI/1.1)

Isotopic measurements of seawater sampled on-board Polarstern research vesse

Oceanic surface water isotopic compositions calibrated data from POLARSTERN cruise PS98 (ANT-XXXI/4)

Isotopic measurements of seawater sampled on-board Polarstern research vesse

Oceanic surface water isotopic compositions calibrated data from POLARSTERN cruise PS95.2 (ANT-XXXI/1.2)

Isotopic measurements of seawater sampled on-board Polarstern research vesse

American Association for the Surgery of Trauma Prevention Committee review: Family Justice Centers—a not-so-novel, but unknown gem

The American College of Surgeons Committee on Trauma requires that trauma centers demonstrate adequate financial support for an injury prevention program as part of the verification process. With the ongoing challenges that arise with important social determinants of health, trauma centers have the important task of navigating a patient through the complex process of obtaining services and tools for success. This summary from the American Association for the Surgery of Trauma Prevention Committee focuses on a model that has been present for several years, but has not been brought to full awareness in the trauma world. It highlights the importance of the Family Justice Center concept that brings a multitude of organizations under one roof, thus eliminating the hurdles encompassed by trauma patients, seeking life-changing resources necessary to mitigate the impact of both community violence exposure and intimate partner/domestic violence. It discusses the potential benefits of a partnership between trauma centers and Family Justice Centers and similar models. Finally, it also raises awareness of important programmatic evaluation research required in the arena of injury prevention targeting a population whose outcomes are difficult to measure

Gender distribution and leadership trends in trauma surgery societies.

IntroductionWomen are under-represented in the surgical disciplines and gender bias is believed to play a factor. We aimed to understand the gender distribution of membership, leadership opportunities, and scientific contributions to annual trauma professional meetings as a case study of gender issues in trauma surgery.MethodsRetrospective collection of membership, leadership, presentation and publication data from 2016 to 2018 Trauma/Acute Care Surgery/Surgical Critical Care (TACSCC) Annual Meetings. Gender was assigned based on self-identification in demographic information, established relationships, or public sources.ResultsWomen remain under-represented with only 28.1% of those ascertaining American Board of Surgery certification in critical care self-identifying as female. The proportion of female members in Eastern Association for the Surgery of Trauma (EAST) was comparable (29.4%), slightly lower for Western Trauma Association (WTA) (19.0%), and lowest for American Association for the Surgery of Trauma (AAST) (12.8%, p<0.05). In contrast, AAST had the highest proportion of female participants in executive leadership (AAST 32.5%, WTA 19.0%, EAST 18.8%) and WTA the highest for committee chairs (WTA 33.3%, AAST 27.8%, EAST 20.5%). AAST had the most significant increase in executive leadership during the last 3 years (AAST 28.6% to 41.6%). Invited lectureships, masters, panelists and senior author scientific contributions demonstrated the largest gap of academic representation of female TACSCC surgeons.ConclusionFewer women than men pursue careers in the trauma field. Continuing to provide mentorship, leadership, and scientific recognition will increase gender diversity in TACSCC. We must continue to promote, sponsor, recognize, invite, and elect 'her'.Level of evidenceIII, Epidemiology