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Allele-specific cop...
Allele-specific copy number analysis of tumors
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Van Loo, P (författare)
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Nordgard, SH (författare)
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Lingjaerde, OC (författare)
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Russnes, HG (författare)
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Rye, IH (författare)
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Sun, W (författare)
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Weigman, VJ (författare)
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Marynen, P (författare)
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- Zetterberg, A (författare)
- Karolinska Institutet
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Naume, B (författare)
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Perou, CM (författare)
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Borresen-Dale, AL (författare)
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Kristensen, VN (författare)
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(creator_code:org_t)
- 2010-09-13
- 2010
- Engelska.
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 1091-6490. ; 107:39, s. 16910-16915
- Relaterad länk:
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http://www.pnas.org/...
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http://kipublication...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- We present an allele-specific copy number analysis of the in vivo breast cancer genome. We describe a unique bioinformatics approach, ASCAT (allele-specific copy number analysis of tumors), to accurately dissect the allele-specific copy number of solid tumors, simultaneously estimating and adjusting for both tumor ploidy and nonaberrant cell admixture. This allows calculation of “ASCAT profiles” (genome-wide allele-specific copy-number profiles) from which gains, losses, copy number-neutral events, and loss of heterozygosity (LOH) can accurately be determined. In an early-stage breast carcinoma series, we observe aneuploidy (>2.7n) in 45% of the cases and an average nonaberrant cell admixture of 49%. By aggregation of ASCAT profiles across our series, we obtain genomic frequency distributions of gains and losses, as well as genome-wide views of LOH and copy number-neutral events in breast cancer. In addition, the ASCAT profiles reveal differences in aberrant tumor cell fraction, ploidy, gains, losses, LOH, and copy number-neutral events between the five previously identified molecular breast cancer subtypes. Basal-like breast carcinomas have a significantly higher frequency of LOH compared with other subtypes, and their ASCAT profiles show large-scale loss of genomic material during tumor development, followed by a whole-genome duplication, resulting in near-triploid genomes. Finally, from the ASCAT profiles, we construct a genome-wide map of allelic skewness in breast cancer, indicating loci where one allele is preferentially lost, whereas the other allele is preferentially gained. We hypothesize that these alternative alleles have a different influence on breast carcinoma development.
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- art (ämneskategori)
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Van Loo, P
-
Nordgard, SH
-
Lingjaerde, OC
-
Russnes, HG
-
Rye, IH
-
Sun, W
-
visa fler...
-
Weigman, VJ
-
Marynen, P
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Zetterberg, A
-
Naume, B
-
Perou, CM
-
Borresen-Dale, A ...
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Kristensen, VN
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visa färre...
- Artiklar i publikationen
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Proceedings of t ...
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Proceedings of t ...
- Av lärosätet
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Karolinska Institutet