Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants (Human660W-Quad)

ABSTRACT: Systematic evaluation of eleven array platforms commonly used for CNV detection to address parameters of quality and CNV calling. 36 Samples

ORGANISM(S): Homo sapiens

SUBMITTER: Dalila Pinto

PROVIDER: E-GEOD-28103 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants.

Pinto Dalila D Darvishi Katayoon K Shi Xinghua X Rajan Diana D Rigler Diane D Fitzgerald Tom T Lionel Anath C AC Thiruvahindrapuram Bhooma B Macdonald Jeffrey R JR Mills Ryan R Prasad Aparna A Noonan Kristin K Gribble Susan S Prigmore Elena E Donahoe Patricia K PK Smith Richard S RS Park Ji Hyeon JH Hurles Matthew E ME Carter Nigel P NP Lee Charles C Scherer Stephen W SW Feuk Lars L

Nature biotechnology 20110508 6

We have systematically compared copy number variant (CNV) detection on eleven microarrays to evaluate data quality and CNV calling, reproducibility, concordance across array platforms and laboratory sites, breakpoint accuracy and analysis tool variability. Different analytic tools applied to the same raw data typically yield CNV calls with <50% concordance. Moreover, reproducibility in replicate experiments is <70% for most platforms. Nevertheless, these findings should not preclude detection of ...[more]

PMID: 21552272

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Project description:In colorectal cancer (CRC), chromosomal instability (CIN) is typically studied using comparative-genomic hybridization (CGH) arrays. We studied paired (tumor and surrounding healthy) fresh-frozen tissue from 86 CRC patients using Illumina’s Infinium-based SNP array. This method allowed us to study CIN in CRC, with simultaneous analysis of copy number (CN) and B-allele frequency (BAF), which is a representation of allelic composition. This data helped us to detect mono-allelic and bi-allelic amplifications/deletion, copy neutral loss of heterozygosity, and levels of mosaicism for mixed cell populations, some of which can not be assessed with other methods that do not measure BAF. We identified associations between CN abnormalities and different CRC phenotypes (MSI, histological diagnosis, location, tumor grade, stage, MSI and presence of lymph node metastasis). We showed commonalities between regions of CN change observed in CRC and the regions reported in previous studies of other solid cancers (e.g., amplifications of 20q, 13q, 8q, 5p and deletions of 18q, 17p and 8p). From the Therapeutic Target Database we found relevant drugs, targeted to the genes located in these regions with CN changes, approved or in trials for other cancers and common diseases. These drugs may be considered for future therapeutic trials in CRC, based on personalized cytogenetic diagnosis. We also found many regions harboring genes which are not currently targeted by any relevant drugs that may be considered for future drug discovery studies. Our study shows the application of high-density SNP arrays for cytogenetic study in CRC and its importance for personalized treatment. DNA was extracted from colon tissue samples provided by 86 CRC patients. Each patient provided paired CRC tumor tissue and adjacent normal colon mucosa samples, which were fresh-frozen after resection. Samples were genotyped using Illumina's Infinium-based 610 Quad and CytoSNP 12 microarray chips. The genotype data from paired tumor and normal samples was used to detect tumor-specific chromosomal instabilities in copy number, including copy-neutral LOH, which cannot be assessed by many other cytogenetic methods. Supplementary file "GSE34678_raw_GPL8887.txt" includes the raw data for Samples using GPL8887 (GSM853162-GSM853239); supplementary file "GSE34678_raw_GPL13829.txt" includes the raw data for Samples using GPL13829 (GSM853240-GSM853363).

Dataset Information

A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants (Human660W-Quad)

Publications

Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants.

Similar Datasets

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