Dataset Information

A Study of the Genomic Variations Associated with Autistic Spectrum Disorders in a Russian Cohort of Patients Using Whole-Exome Sequencing.

ABSTRACT: This study provides new data on the whole-exome sequencing of a cohort of children with autistic spectrum disorders (ASD) from an underexplored Russian population. Using both a cross-sectional approach involving a control cohort of the same ancestry and an annotation-based approach involving relevant public databases, we explored exonic single nucleotide variants and copy-number variation potentially involved in the manifestation of ASD. The study results reveal new potential ASD candidate-variants found in the studied Russian cohort and show a high prevalence of common ASD-associated genomic variants, especially those in the genes known to be associated with the manifestation of intellectual disabilities. Our screening of an ASD cohort from a previously understudied population allowed us to flag at least a few novel genes (IGLJ2, FAM21A, OR11H12, HIP1, PRAMEF10, and ZNF717) regarding their potential involvement in ASD.

SUBMITTER: Gibitova EA

PROVIDER: S-EPMC9141003 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature

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A Study of the Genomic Variations Associated with Autistic Spectrum Disorders in a Russian Cohort of Patients Using Whole-Exome Sequencing.

Gibitova Ekaterina A EA Dobrynin Pavel V PV Pomerantseva Ekaterina A EA Musatova Elizaveta V EV Kostareva Anna A Evsyukov Igor I Rychkov Sergey Y SY Zhukova Olga V OV Naumova Oxana Y OY Grigorenko Elena L EL

Genes 20220520 5

This study provides new data on the whole-exome sequencing of a cohort of children with autistic spectrum disorders (ASD) from an underexplored Russian population. Using both a cross-sectional approach involving a control cohort of the same ancestry and an annotation-based approach involving relevant public databases, we explored exonic single nucleotide variants and copy-number variation potentially involved in the manifestation of ASD. The study results reveal new potential ASD candidate-varia ...[more]

PMID: 35627305

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Project description:The global trend toward the reduction of human spermatogenic function observed in many countries, including Russia, raised the problem of extensive screening and monitoring of male fertility and elucidation of its genetic and ethnic mechanisms. Recently, whole-exome sequencing (WES) was developed as a powerful tool for genetic analysis of complex traits. We present here the first Russian WES study for identification of new genes associated with semen quality. The experimental 3 × 2 design of the WES study was based on the analysis of 157 samples including three ethnic groups-Slavs (59), Buryats (n = 49), and Yakuts (n = 49), and two different semen quality groups-pathozoospermia (n = 95) and normospermia (n = 62). Additionally, our WES study group was negative for complete AZF microdeletions of the Y-chromosome. The normospermia group included men with normal sperm parameters in accordance with the WHO-recommended reference limit. The pathozoospermia group included men with impaired semen quality, namely, with any combined parameters of sperm concentration <15 × 106/ml, and/or progressive motility <32%, and/or normal morphology <4%. The WES was performed for all 157 samples. Subsequent calling and filtering of variants were carried out according to the GATK Best Practices recommendations. On the genotyping stage, the samples were combined into four cohorts: three sets corresponded to three ethnic groups, and the fourth set contained all the 157 whole-exome samples. Association of the obtained polymorphisms with semen quality parameters was investigated using the χ2 test. To prioritize the obtained variants associated with pathozoospermia, their effects were determined using Ensembl Variant Effect Predictor. Moreover, polymorphisms located in genes expressed in the testis were revealed based on the genomic annotation. As a result, the nine potential SNP markers rs6971091, rs557806, rs610308, rs556052, rs1289658, rs278981, rs1129172, rs12268007, and rs17228441 were selected for subsequent verification on our previously collected population sample (about 1,500 males). The selected variants located in seven genes FAM71F1, PPP1R15A, TRIM45, PRAME, RBM47, WDFY4, and FSIP2 that are expressed in the testis and play an important role in cell proliferation, meiosis, and apoptosis.

Dataset Information

A Study of the Genomic Variations Associated with Autistic Spectrum Disorders in a Russian Cohort of Patients Using Whole-Exome Sequencing.

Publications

A Study of the Genomic Variations Associated with Autistic Spectrum Disorders in a Russian Cohort of Patients Using Whole-Exome Sequencing.

Similar Datasets

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