HiCancer: accurate and complete cancer genome phasing with Hi-C reads
| Autor: | Desheng Gong, Weihua Pan, Da Sun, Haohui Luo |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
0301 basic medicine
Linkage disequilibrium Science Single-nucleotide polymorphism Computational biology Biology Polymorphism Single Nucleotide Article 03 medical and health sciences 0302 clinical medicine Germline mutation Chromosome (genetic algorithm) Neoplasms Cancer genomics Computational models Humans Copy-number variation Sequence (medicine) Linkage (software) Multidisciplinary Genome Human Haplotype Computational biology and bioinformatics 030104 developmental biology Medicine K562 Cells Software 030217 neurology & neurosurgery Genome-Wide Association Study |
| Zdroj: | Scientific Reports, Vol 11, Iss 1, Pp 1-10 (2021) Scientific Reports |
| ISSN: | 2045-2322 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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