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PMID: 19837654 Published · ppublish English Journal Article

PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data.

Biostatistics (Oxford, England) ·Vol. 11 ·No. 1 ·2010-01-00 ·Pages 164-75

Greenman CD, Bignell G, Butler A, Edkins S, Hinton J, Beare D, Swamy S, Santarius T, Chen L, Widaa S, Futreal PA, Stratton MR

Abstract

High-throughput oligonucleotide microarrays are commonly employed to investigate genetic disease, including cancer. The algorithms employed to extract genotypes and copy number variation function optimally for diploid genomes usually associated with inherited disease. However, cancer genomes are aneuploid in nature leading to systematic errors when using these techniques. We introduce a preprocessing transformation and hidden Markov model algorithm bespoke to cancer. This produces genotype classification, specification of regions of loss of heterozygosity, and absolute allelic copy number segmentation. Accurate prediction is demonstrated with a combination of independent experimental techniques. These methods are exemplified with affymetrix genome-wide SNP6.0 data from 755 cancer cell lines, enabling inference upon a number of features of biological interest. These data and the coded algorithm are freely available for download.

MeSH Terms
Algorithms Alleles Aneuploidy Bayes Theorem Bias Cell Line, Tumor DNA Copy Number Variations/genetics Genes, Tumor Suppressor Genetic Testing Genotype Humans Internet Loss of Heterozygosity/genetics Markov Chains Models, Statistical Neoplasms/diagnosis,genetics Oligonucleotide Array Sequence Analysis/methods Polymorphism, Single Nucleotide/genetics Polyploidy Reproducibility of Results Sensitivity and Specificity Software
Authors & Affiliations
12 authors, click to expand affiliations / ORCID
Greenman Chris D
Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. cdg@sanger.ac.uk
Bignell Graham
Butler Adam
Edkins Sarah
Hinton Jon
Beare Dave
Swamy Sajani
Santarius Thomas
Chen Lina
Widaa Sara
Futreal P Andy
Stratton Michael R
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Article Info
Journal
Biostatistics (Oxford, England)
Abbr.
Biostatistics
ISSN
1468-4357
DOI
10.1093/biostatistics/kxp045
Email
cdg@sanger.ac.uk
Published
2010-01-00
Epub
2009-00-15
Pages
164-75
Language
English
Region
England
NLM ID
100897327
PMCID
PMC2800165
Subset
IM
External Links
PubMed source DOI: 10.1093/biostatistics/kxp045 PMC Full Text View journal details
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