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EGAS00001000317-sc-20140326 - samples

ABSTRACT: The exome sequencing is performed using Agilent SureSelect 50Mb exome v3 and Hiseq 75bp paired reads with an mean sequencing coverage target of 50X.

PROVIDER: EGAD00001000799 | EGA |

REPOSITORIES: EGA

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Publications

Rare variants in NR2F2 cause congenital heart defects in humans.

Al Turki Saeed S Manickaraj Ashok K AK Mercer Catherine L CL Gerety Sebastian S SS Hitz Marc-Phillip MP Lindsay Sarah S D'Alessandro Lisa C A LC Swaminathan G Jawahar GJ Bentham Jamie J Arndt Anne-Karin AK Louw Jacoba J Low Jacoba J Breckpot Jeroen J Gewillig Marc M Gewillig Marc M Thienpont Bernard B Abdul-Khaliq Hashim H Harnack Christine C Hoff Kirstin K Kramer Hans-Heiner HH Schubert Stephan S Siebert Reiner R Toka Okan O Cosgrove Catherine C Watkins Hugh H Lucassen Anneke M AM O'Kelly Ita M IM Salmon Anthony P AP Bu'lock Frances A FA Granados-Riveron Javier J Setchfield Kerry K Thornborough Chris C Brook J David JD Mulder Barbara B Klaassen Sabine S Bhattacharya Shoumo S Devriendt Koen K Fitzpatrick David F DF Wilson David I DI Mital Seema S Hurles Matthew E ME

American journal of human genetics 20140401 4

Congenital heart defects (CHDs) are the most common birth defect worldwide and are a leading cause of neonatal mortality. Nonsyndromic atrioventricular septal defects (AVSDs) are an important subtype of CHDs for which the genetic architecture is poorly understood. We performed exome sequencing in 13 parent-offspring trios and 112 unrelated individuals with nonsyndromic AVSDs and identified five rare missense variants (two of which arose de novo) in the highly conserved gene NR2F2, a very signifi ...[more]

PMID: 24702954

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Project description:The study included 15 patients (7 males, 8 females) with JMML. Peripheral blood and/or bone marrow aspirates were collected on EDTA at diagnosis. Non-hematopoietic tissues (fibroblasts) was derived from skin biopsy for each patient. Exome sequencing was performed in several distinct series between 2012 and 2017, which explains the differences in capture kit versions and reference genome version.Targeted enrichment and massive parallel sequencing were performed on paired genomic DNA from leukocytes and fibroblasts. Exome capture was carried out using the SureSelect Human All Exon V4+UTRs or V5 or V5+UTRs or SureSelect Clinical Research (Agilent Technologies, Santa Clara, CA, USA) according to manufacturer’s instruction and protocols by IntegraGen (Evry, France). Paired-end 75 bases sequencing was performed on a HiSeq2000 or HiSeq4000 instrument (Illumina, San Diego, CA, USA). Image analysis and base calling were performed using the Real Time Analysis (RTA) pipeline v. 1.14 (Illumina) with default parameters. The alignment of paired-end reads to the reference human genome (UCSC GRCh37/hg19 or UCSC GRCh38), variant calling and generation of Quality variants scores were carried out using the CASAVA v.1.8 pipeline (Illumina).

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