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Model-integrated estimation of normal tissue contamination for cancer SNP copy number data
KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Mathematical Statistics.
2011 (English)In: Cancer Informatics, ISSN 1176-9351, Vol. 10, 159-173 p.Article in journal (Refereed) Published
Abstract [en]

SNP allelic copy number data provides intensity measurements for the two different alleles separately. We present a method that estimates the number of copies of each allele at each SNP position, using a continuous-index hidden Markov model. The method is especially suited for cancer data, since it includes the fraction of normal tissue contamination, often present when studying data from cancer tumors, into the model. The continuous-index structure takes into account the distances between the SNPs, and is thereby appropriate also when SNPs are unequally spaced. In a simulation study we show that the method performs favorably compared to previous methods even with as much as 70% normal contamination. We also provide results from applications to clinical data produced using the Affymetrix genome-wide SNP 6.0 platform.

Place, publisher, year, edition, pages
2011. Vol. 10, 159-173 p.
Keyword [en]
Allelic copy number, Cancer, Hidden markov model, Normal cell contamination
National Category
Medical and Health Sciences
URN: urn:nbn:se:kth:diva-61153DOI: 10.4137/CIN.S6873ScopusID: 2-s2.0-80053618718OAI: diva2:478643
QC 20120117Available from: 2012-01-16 Created: 2012-01-16 Last updated: 2012-01-17Bibliographically approved

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Rydén, Tobias
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Mathematical Statistics
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