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

Abstract 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 suboptim...

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Autores principales:	Weihua Pan, Desheng Gong, Da Sun, Haohui Luo
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/460b0ebe7f5446b4a76b9c5335960bcc
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spelling	oai:doaj.org-article:460b0ebe7f5446b4a76b9c5335960bcc2021-12-02T13:24:26ZHiCancer: accurate and complete cancer genome phasing with Hi-C reads10.1038/s41598-021-86104-62045-2322https://doaj.org/article/460b0ebe7f5446b4a76b9c5335960bcc2021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-86104-6https://doaj.org/toc/2045-2322Abstract 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.Weihua PanDesheng GongDa SunHaohui LuoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Weihua Pan Desheng Gong Da Sun Haohui Luo HiCancer: accurate and complete cancer genome phasing with Hi-C reads
description	Abstract 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.
format	article
author	Weihua Pan Desheng Gong Da Sun Haohui Luo
author_facet	Weihua Pan Desheng Gong Da Sun Haohui Luo
author_sort	Weihua Pan
title	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_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_sort	hicancer: accurate and complete cancer genome phasing with hi-c reads
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/460b0ebe7f5446b4a76b9c5335960bcc
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_version_	1718393090493906944

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

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