Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity

被引：74
|
作者：
Rasmussen, Markus [1 ]
Sundstrom, Magnus [2 ]
Kultima, Hanna Goransson [1 ]
Botling, Johan [2 ]
Micke, Patrick [2 ]
Birgisson, Helgi [3 ]
Glimelius, Bengt [4 ,5 ]
Isaksson, Anders [1 ]
机构：
[1] Uppsala Univ, Dept Med Sci, Sci Life Lab, Akad Sjukhuset, SE-75185 Uppsala, Sweden
[2] Uppsala Univ, Rudbeck Lab, Dept Immunol Genet & Pathol, SE-75185 Uppsala, Sweden
[3] Uppsala Univ, Akad Sjukhuset, Dept Surg Sci, SE-75185 Uppsala, Sweden
[4] Uppsala Univ, Akad Sjukhuset, Dept Radiol Oncol & Radiat Sci, SE-75185 Uppsala, Sweden
[5] Karolinska Inst, Dept Pathol & Oncol, SE-17177 Stockholm, Sweden
来源：
GENOME BIOLOGY | 2011年 / 12卷 / 10期
关键词：
LUNG-CANCER; GENOTYPING DATA; SNP ARRAYS; ABERRATIONS; RESOLUTION; MICROARRAYS; PLOIDY;
D O I：
10.1186/gb-2011-12-10-r108
中图分类号：
Q81 [生物工程学（生物技术）]; Q93 [微生物学];
学科分类号：
071005 ; 0836 ; 090102 ; 100705 ;
摘要：
We describe a bioinformatic tool, Tumor Aberration Prediction Suite (TAPS), for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays. It includes detailed visualization of genomic segment characteristics and iterative pattern recognition for copy number identification, and does not require patient-matched normal samples. TAPS can be used to identify chromosomal aberrations with high sensitivity even when the proportion of tumor cells is as low as 30%. Analysis of cancer samples indicates that TAPS is well suited to investigate samples with aneuploidy and tumor heterogeneity, which is commonly found in many types of solid tumors.
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页数：10
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