Conditional random pattern algorithm for LOH inference and segmentation

Ling Yun Wu, Xiaobo Zhou, Fuhai Li, Xiaorong Yang, Chung Che Chang, Stephen T.C. Wong

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

Motivation: Loss of heterozygosity (LOH) is one of the most important mechanisms in the tumor evolution. LOH can be detected from the genotypes of the tumor samples with or without paired normal samples. In paired sample cases, LOH detection for informative single nucleotide polymorphisms (SNPs) is straightforward if there is no genotyping error. But genotyping errors are always unavoidable, and there are about 70% non-informative SNPs whose LOH status can only be inferred from the neighboring informative SNPs. Results: This article presents a novel LOH inference and segmentation algorithm based on the conditional random pattern (CRP) model. The new model explicitly considers the distance between two neighboring SNPs, as well as the genotyping error rate and the heterozygous rate. This new method is tested on the simulated and real data of the Affymetrix Human Mapping 500K SNP arrays. The experimental results show that the CRP method outperforms the conventional methods based on the hidden Markov model (HMM).

Original languageEnglish
Pages (from-to)61-67
Number of pages7
JournalBioinformatics
Volume25
Issue number1
DOIs
StatePublished - Jan 2009

Fingerprint Dive into the research topics of 'Conditional random pattern algorithm for LOH inference and segmentation'. Together they form a unique fingerprint.

Cite this