Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity.
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.
Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Akademiska sjukhuset, SE-751 85 Uppsala, Sweden.
Markus
M
Rasmussen
Magnus
M
Sundström
Hanna
H
Göransson Kultima
Johan
J
Botling
Patrick
P
Micke
Helgi
H
Birgisson
Bengt
B
Glimelius
Anders
A
Isaksson
D059786:Abnormal Karyotype; D000465:Algorithms; D000483:Alleles; D000782:Aneuploidy; D045744:Cell Line, Tumor; D003110:Colonic Neoplasms / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D018628:Gene Dosage; D052138:Genes, Neoplasm; D018740:Genetic Heterogeneity; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity; D012984:Software