Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
Biostatistics. 2010 Jan;11(1):164-75. doi: 10.1093/biostatistics/kxp045. Epub 2009 Oct 15.

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

Author information

  • 1Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. cdg@sanger.ac.uk

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.

PMID:
19837654
[PubMed - indexed for MEDLINE]
PMCID:
PMC2800165
Free PMC Article

Images from this publication.See all images (3)Free text

Fig. 1.
Fig. 2.
Fig. 3.
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Icon for HighWire Icon for PubMed Central
    Loading ...
    Write to the Help Desk