Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

4381c9a9-1f66-44a2-9303-f23975b69cc3 - samples

ABSTRACT: This dataset contains paired whole exome sequence data of 5 patients (control/tumor pairs) and paired whole genome sequencing data of 1 patient (control/tumor pair) with Lynch Syndrome from the INFORM registry. Paired sequencing was done mostly on Illumina HiSeq 4000, few on HiSeq2500 and NovaSeq 6000. The library preparation was either with Agilent SureSelect Human_All_Exon V5 (hg19) or with Agilent SureSelectXT HS Human_All_Exon V7 (hg19). The WGS samples were prepared with Agilent SureSelect WGS.

PROVIDER: EGAD00001011098 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

b37f1437-f716-479a-8a23-8264673590d4 - samples

Project description:WES sequencing of 23 samples from PCNSL tumor and blood control samples. Sequencing was performed on a NovaSeq 6000 and NextSeq 500 using Agilent SureSelectXT HS Human All Exon V7 and V8. Sequencing was always paired.

| EGAD00001010847 | EGA

1a6b9c37-7fd9-4430-88ef-0538ee488e93 - samples

Project description:Whole-exome sequencing (WES) in a well-characterized sample of 14 matched EP tumour/healthy surrounding tissue samples. The sequencing was done with paired EXOME sequencing on Illumina HiSeq 4000 using Agilent SureSelect XT HS + Human All Exon V7.

| EGAD00001006395 | EGA

Exomes of human leukemic JMML (Juvenile MyeloMonocytic Leukemia) cells and paired fibroblasts (germilne controls) when available

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).

2018-03-14 | E-MTAB-6461 | biostudies-arrayexpress

Next generation sequencing for patients with hypomyelinating leukodystrophies

Project description:Targeted enrichment-based next-generation sequencing or whole exome sequencing were taken for patients with hypomyelinating leukodystrophies to reveal genetic aetiologies. All genomic DNA used in the experiments was extracted from the peripheral leukocytes. A complete kit was synthetized using the Agilent SureSelect Target Enrichment technique, capturing the coding regions from 104 candidate genes, including their exons and exon-intron boundaries (11,473 probes, 383.065 kbp in total). The following NGS which included equipment and reagents was performed on an Illumina NEXTSEQ500 platform manufactured by Illumina (San Diego, California, USA) using paired-end sequencing of 110 bp. The clean paired-end reads were aligned to the human reference genome build hg19, which was previously annotated using ANNOVAR, in addition to insertion-deletion (indel) and single-nucleotide polymorphism (SNP) calling.

2018-02-01 | E-MTAB-6054 | biostudies-arrayexpress

Next generation sequencing for patients with hypomyelinating leukodystrophies

2018-02-02 | E-MTAB-6404 | biostudies-arrayexpress

Exome sequencing in classic Hairy cell leukaemia reveals widespread variation in acquired somatic mutations between individual tumours apart from the signature BRAF V(600)E lesion

Project description:Whole exome sequencing of 5 HCLc tumor-germline pairs. Genomic DNA from HCLc tumor cells and T-cells for germline was used. Whole exome enrichment was performed with either Agilent SureSelect (50Mb, samples S3G/T, S5G/T, S9G/T) or Roche Nimblegen (44.1Mb, samples S4G/T and S6G/T). The resulting exome libraries were sequenced on the Illumina HiSeq platform with paired-end 100bp reads to an average depth of 120-134x. Bam files were generated using NovoalignMPI (v3.0) to align the raw fastq files to the reference genome sequence (hg19) and picard tools (v1.34) to flag duplicate reads (optical or pcr), unmapped reads, reads mapping to more than one location, and reads failing vendor QC.

2016-02-01 | E-MTAB-4313 | biostudies-arrayexpress

a88b4e36-3cc1-4051-a035-6238e910bb02 - samples

Project description:This dataset consists of paired-end DNA sequencing (whole exome and targeted-capture) of tumours for the BEACCON study. There are 240 unique samples consisting of 92 matched tumour-germline pairs and 56 unmatched tumours totalling 148 patients. There are 33 paired and 6 unpaired tumours sequenced using the Agilent SureSelect All Human Exon v6 libraries, 1 paired and 8 unpaired tumours sequenced using Agilent SureSelect All Human Exon v7 libraries and 48 paired and 3 unpaired tumours sequenced using Twist Bioscience Comprehensive Human Exome v1 libraries totalling 176 whole exome samples. There are 3 paired and 58 unpaired tumours sequenced using a custom Agilent SureSelectXT library totalling 64 targeted capture samples.

| EGAD00001009299 | EGA

Whole exome sequencing of DNA purified from colorectal tumors induced by 1% DSS and adjacent colon controls in MLH1-KO mice

Project description:In the process of searching for tumor-specific mutations to predict neoantigens for cancer immunotherapy in a Lynch Syndrome mouse model, tumorigenesis was induced with 1% DSS in drinking water. DNA was isolated from tumors and colon tissue separately from 4 MLH1-KO mice using the DNeasy Qiagen kit according to the manufacturer's protocol. Purity of the DNA was confirmed to be very high with the NanoDrop before sending samples to Illumina for next generation sequencing with the Agilent SureSelect XT Mouse All Exon kit. Finally, an analysis was performed in which common tumor-specific mutations were processed through in silico antigen prediction software in NetMHC.

2021-10-02 | E-MTAB-10962 | biostudies-arrayexpress

Bisulfite sequencing coupled to target enrichment in MCF-7

Project description:Sequencing of bisulfite-converted MCF-7 genomic DNA captured on SureSelect Methyl-Seq (Agilent).

2017-10-19 | GSE69505 | GEO

ena-DATASET-MUG-01-09-2020-11:04:33:638-689 - samples

Project description:All baseline samples and when available EOT were processed for high-resolution mutation analysis. We designed a SureSelectXT-HS custom panel (Agilent) covering 68 genes with a total size of 260kb using the Agilent SureDesign platform.

| EGAD00001006386 | EGA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data