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

Abstract: 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.