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HiCancer: accurate and complete cancer genome phasing with Hi-C reads

Due to the high complexity of cancer genome, it is too difficult to generate complete cancer genome map which contains the sequence of every DNA molecule until now. Nevertheless, phasing each chromosome in cancer genome into two haplotypes according to germline mutations provides a suboptimal soluti...

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Autores principales: Pan, Weihua, Gong, Desheng, Sun, Da, Luo, Haohui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7987978/
https://www.ncbi.nlm.nih.gov/pubmed/33758310
http://dx.doi.org/10.1038/s41598-021-86104-6
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author Pan, Weihua
Gong, Desheng
Sun, Da
Luo, Haohui
author_facet Pan, Weihua
Gong, Desheng
Sun, Da
Luo, Haohui
author_sort Pan, Weihua
collection PubMed
description Due to the high complexity of cancer genome, it is too difficult to generate complete cancer genome map which contains the sequence of every DNA molecule until now. Nevertheless, phasing each chromosome in cancer genome into two haplotypes according to germline mutations provides a suboptimal solution to understand cancer genome. However, phasing cancer genome is also a challenging problem, due to the limit in experimental and computational technologies. Hi-C data is widely used in phasing in recent years due to its long-range linkage information and provides an opportunity for solving the problem of phasing cancer genome. The existing Hi-C based phasing methods can not be applied to cancer genome directly, because the somatic mutations in cancer genome such as somatic SNPs, copy number variations and structural variations greatly reduce the correctness and completeness. Here, we propose a new Hi-C based pipeline for phasing cancer genome called HiCancer. HiCancer solves different kinds of somatic mutations and variations, and take advantage of allelic copy number imbalance and linkage disequilibrium to improve the correctness and completeness of phasing. According to our experiments in K562 and KBM-7 cell lines, HiCancer is able to generate very high-quality chromosome-level haplotypes for cancer genome with only Hi-C data.
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spelling pubmed-79879782021-03-25 HiCancer: accurate and complete cancer genome phasing with Hi-C reads Pan, Weihua Gong, Desheng Sun, Da Luo, Haohui Sci Rep Article Due to the high complexity of cancer genome, it is too difficult to generate complete cancer genome map which contains the sequence of every DNA molecule until now. Nevertheless, phasing each chromosome in cancer genome into two haplotypes according to germline mutations provides a suboptimal solution to understand cancer genome. However, phasing cancer genome is also a challenging problem, due to the limit in experimental and computational technologies. Hi-C data is widely used in phasing in recent years due to its long-range linkage information and provides an opportunity for solving the problem of phasing cancer genome. The existing Hi-C based phasing methods can not be applied to cancer genome directly, because the somatic mutations in cancer genome such as somatic SNPs, copy number variations and structural variations greatly reduce the correctness and completeness. Here, we propose a new Hi-C based pipeline for phasing cancer genome called HiCancer. HiCancer solves different kinds of somatic mutations and variations, and take advantage of allelic copy number imbalance and linkage disequilibrium to improve the correctness and completeness of phasing. According to our experiments in K562 and KBM-7 cell lines, HiCancer is able to generate very high-quality chromosome-level haplotypes for cancer genome with only Hi-C data. Nature Publishing Group UK 2021-03-23 /pmc/articles/PMC7987978/ /pubmed/33758310 http://dx.doi.org/10.1038/s41598-021-86104-6 Text en © The Author(s) 2021 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Pan, Weihua
Gong, Desheng
Sun, Da
Luo, Haohui
HiCancer: accurate and complete cancer genome phasing with Hi-C reads
title HiCancer: accurate and complete cancer genome phasing with Hi-C reads
title_full HiCancer: accurate and complete cancer genome phasing with Hi-C reads
title_fullStr HiCancer: accurate and complete cancer genome phasing with Hi-C reads
title_full_unstemmed HiCancer: accurate and complete cancer genome phasing with Hi-C reads
title_short HiCancer: accurate and complete cancer genome phasing with Hi-C reads
title_sort hicancer: accurate and complete cancer genome phasing with hi-c reads
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7987978/
https://www.ncbi.nlm.nih.gov/pubmed/33758310
http://dx.doi.org/10.1038/s41598-021-86104-6
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