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利用全基因组单核苷酸多态性阵列基于分割法检测癌细胞中的等位基因不平衡和杂合性缺失

Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays.

作者信息

Staaf Johan, Lindgren David, Vallon-Christersson Johan, Isaksson Anders, Göransson Hanna, Juliusson Gunnar, Rosenquist Richard, Höglund Mattias, Borg Ake, Ringnér Markus

机构信息

Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden.

出版信息

Genome Biol. 2008;9(9):R136. doi: 10.1186/gb-2008-9-9-r136. Epub 2008 Sep 16.

DOI:10.1186/gb-2008-9-9-r136
PMID:18796136
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2592714/
Abstract

We present a strategy for detection of loss-of-heterozygosity and allelic imbalance in cancer cells from whole genome single nucleotide polymorphism genotyping data. Using a dilution series of a tumor cell line mixed with its paired normal cell line and data generated on Affymetrix and Illumina platforms, including paired tumor-normal samples and tumors characterized by fluorescent in situ hybridization, we demonstrate a high sensitivity and specificity of the strategy for detecting both minute and gross allelic imbalances in heterogeneous tumor samples.

摘要

我们提出了一种从全基因组单核苷酸多态性基因分型数据中检测癌细胞杂合性缺失和等位基因不平衡的策略。通过将肿瘤细胞系与其配对的正常细胞系混合的稀释系列，以及在Affymetrix和Illumina平台上生成的数据，包括配对的肿瘤-正常样本和通过荧光原位杂交表征的肿瘤，我们证明了该策略在检测异质性肿瘤样本中微小和明显等位基因不平衡方面具有高灵敏度和特异性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2603/2592714/27e07eeaf8c3/gb-2008-9-9-r136-11.jpg
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