Dataset features

Specifications


Application: SNP array data analysis
Number of samples: 32
Release date: Feb 14 2018
Last update date: Feb 14 2018
Access: Public
Diseases: Brain Neoplasms, Colorectal Neoplasms, Tumor Lysis Syndrome, Neoplasms, Second Primary
Dataset link Copy Number Profiles of Paired Primary and Metastatic Colorectal Cancer to Investigate Clonal Tumour Changes

Experimental Protocol


Paired primary CRC and metastatic liver tumour DNA, and normal patient DNA was assayed with the Omni 2.5-8, V1.0 and V1.1 IlluminaBeadChips as per manufacturer’s instructions (Illumina). SNP arrays were scanned on an iScan (Illumina), data was processed using the Genotyping module (v.1.9.4) in GenomeStudio v.2011.1 (Illumina) to calculate B-allele frequencies (BAF) and logR ratios. GAP[36] software was used to segment the SNP array data and determine the level of copy number which was classified into one of 5 categories: homozygous deletion (copy number: 0), loss (copy number:1), copy neutral LOH (copy number:2), gain (copy number: 3-5) and amplification (copy number: 6-8).

Repositories


GEO

GSE100787

BioProject

PRJNA393043

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Contact


Katia Nones

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