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Resolving the haplotype complexity of colorectal cancer genomes with droplet barcode sequencing
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- Siga, Humam (author)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi
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- Höjer, Pontus (author)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Pourbozorgi, Parham (author)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- (creator_code:org_t)
- English.
- Other publication (other academic/artistic)
Abstract
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- Cancer genomes are prone to elevated rates of genomic alterations. Massive parallel sequencing technologies can answer some questions related to these aberrations; however, they remain limited when it comes to resolving the haplotype information. In this study, we applied the linked-read droplet barcode sequencing (DBS) technology to resolve the haplotype complexity of colorectal cancer genomes, using paired tumor/normal samples. The results show short somatic variants associated with almost all TCGA-identified oncogenic pathways. Several cancer-related genes had multiple variants in either one or both haplotypes. In the tumor suppressor gene APC, two nonsense variants ~2kb apart on separate haplotypes were identified in one patient. Additionally, a number haplotype-resolved somatic structural variants (SV) and copy number alterations (CNA) were detected and correlated with the small variants. The study demonstrates that DBS technology can characterize complex genetic variations in a haplotype context, revealing an extra layer of cancer genome complexity.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Cancer och onkologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Cancer and Oncology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
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