Dataset

Somatic mutations in 106 small intestine adenocarcinoma

Dataset ID Technology Samples
EGAD00001003802 N/A 106

Dataset Description

106 FFPE tumor samples from small bowel were sequenced with Illumina HiSeq 4000. Exome capture was performed with NimbleGen SeqCap EZ Exome Library v3 Kit. Reads were aligned with BWA–MEM v.0.7.12 to GRCh37 reference genome. Variant calls were produced with GATK HaplotypeCaller. Variant calls were filtered against all data from gnomAD database using allele frequency threshold 0.0001 in order to remove germline variation.

Who controls access to this dataset

For each dataset that requires controlled access, there is a corresponding Data Access Committee (DAC) who determine access permissions. Access to actual data files is not managed by the EGA. If you need to request access to this data set, please contact:

Data access committee for the pseudomyxoma peritonei exome sequencing vcf-files
Contact person: Janne Ravantti
Email: dac-tumorgenomics [at] helsinki [dot] fi
More details: EGAC00001000649

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