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ABSTRACT: Exome data of a novel syndromic entity combining immunodeficiency, lymphoproliferation and HLH-like phenotypes

PROVIDER: PRJNA604669 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11012403_1.fastq.gz	Fastqsanger.gz
	SRR11012403_2.fastq.gz	Fastqsanger.gz
	SRR11012404_1.fastq.gz	Fastqsanger.gz
	SRR11012404_2.fastq.gz	Fastqsanger.gz
	SRR11012405_1.fastq.gz	Fastqsanger.gz

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RNAseq on PBMC of two patients with a novel syndromic entity combining immunodeficiency, lymphoproliferation and HLH-like phenotypes, and three age and sex-matched controls for each patient.

Project description:RNAseq on PBMC of two patients with a novel syndromic entity combining immunodeficiency, lymphoproliferation and HLH-like phenotypes, and three age and sex-matched controls for each patient.

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NCKAP1L defects lead to primary immunodeficincy and lymphoproliferation within a Hemophagocytic Lymphohistiocytosis-like syndrome

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Exome sequencing and genome-wide copy number variant mapping reveal novel associations with sensorineural hereditary hearing loss

Project description:Background The genetic diversity of loci and mutations underlying hereditary hearing loss is an active area of investigation. To identify loci associated with predominantly non-syndromic sensorineural hearing loss, we performed exome sequencing of families and of single probands, as well as copy number variation (CNV) mapping in a case-control cohort. Results Analysis of three distinct families revealed several candidate loci in two families and a single strong candidate gene, MYH7B, for hearing loss in one family. MYH7B encodes a Type II myosin, consistent with a role for cytoskeletal proteins in hearing. High-resolution genome-wide CNV analysis of 150 cases and 157 controls revealed deletions in genes known to be involved in hearing (e.g. GJB6, OTOA, and STRC, encoding connexin 30, otoancorin, and stereocilin, respectively), supporting CNV contributions to hearing loss phenotypes. Additionally, a novel region on chromosome 16 containing part of the PDXDC1 gene was found to be frequently deleted in hearing loss patients (OR = 3.91, 95% CI: 1.62-9.40, p = 1.45 x 10-7). Conclusions We conclude that many known as well as novel loci and distinct types of mutations not typically tested in clinical settings can contribute to the etiology of hearing loss. Our study also demonstrates the challenges of exome sequencing and genome-wide CNV mapping for direct clinical application, and illustrates the need for functional and clinical follow-up as well as curated open-access databases. Single replicates of 151 non-syndromic hereditary hearing loss cases and 157 controls with normal hearing were analyzed.

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Project description:To investigate the structure of the bodywall muscle differentiation network, we sought to both identify what these transcription factors regulate in bodywall muscle. Through loss of function analysis, we identified genome-wide regulatory targets of hlh-1 and unc-120 using RNA-seq. 1445 targets of hlh-1 and 3674 targets of unc-120 were identified, with 760 of these genes being targets of both. Crosstalk was identified between the networks of hlh-1 and hlh-8, which is involved in non-bodywall muscle development. In the process, we quantified bodywall muscle RNA. Our data suggest that shared target genes and overlapping regulation buffer the hlh-1 and unc-120 mutant phenotypes. RNA expression genome-wide in the early embryo

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Genome-wide RNA expression in muscle-enriched embryos across different mutations.

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