Methods for derivation of LOH and allelic copy numbers using SNP arrays

TY - CHAP

T1 - Methods for derivation of LOH and allelic copy numbers using SNP arrays

AU - Wiuf, Carsten

AU - Lamy, Philippe

AU - Andersen, Claus L.

PY - 2009/9/1

Y1 - 2009/9/1

N2 - This chapter discusses statistical methods to derive loss-of-heterozygosity (LOH) and allele specific copy numbers in cancer cells. SNP arrays enable simultaneous information about thousands of DNA markers and their allele specific copy numbers, but to extract the information advanced statistical tools are required. The chapter shows how Hidden Markov Models (HMM) can be applied to infer LOH from genotype data and how the allele intensities are informative about allelic copy number. The methods are illustrated by examples.

AB - This chapter discusses statistical methods to derive loss-of-heterozygosity (LOH) and allele specific copy numbers in cancer cells. SNP arrays enable simultaneous information about thousands of DNA markers and their allele specific copy numbers, but to extract the information advanced statistical tools are required. The chapter shows how Hidden Markov Models (HMM) can be applied to infer LOH from genotype data and how the allele intensities are informative about allelic copy number. The methods are illustrated by examples.

KW - Allelic copy number

KW - DNA marker

KW - Genotype

KW - Hidden markov model

KW - Loss-of-heterozygosity

UR - http://www.scopus.com/inward/record.url?scp=84920121084&partnerID=8YFLogxK

U2 - 10.1093/acprof:oso/9780199532872.003.0003

DO - 10.1093/acprof:oso/9780199532872.003.0003

M3 - Book chapter

AN - SCOPUS:84920121084

SN - 9780199532872

VL - 9780199532872

BT - Statistics and Informatics in Molecular Cancer Research

PB - Oxford University Press

ER -