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Loose Ends in Cancer Genome Structure /

Choo, Zi-Ning,

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Loose Ends in Cancer Genome Structure /

Record Type:	Electronic resources : Monograph/item
Title/Author:	Loose Ends in Cancer Genome Structure // Zi-Ning Choo.
Author:	Choo, Zi-Ning,
Description:	1 electronic resource (162 pages)
Notes:	Source: Dissertations Abstracts International, Volume: 85-01, Section: B.
Contained By:	Dissertations Abstracts International85-01B.
Subject:	Genetics. -
Online resource:	https://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=30531438
ISBN:	9798379903732

Loose Ends in Cancer Genome Structure /
Choo, Zi-Ning,

Loose Ends in Cancer Genome Structure /Zi-Ning Choo. - 1 electronic resource (162 pages)

Source: Dissertations Abstracts International, Volume: 85-01, Section: B.

Short-read sequencing (SRS) forms the basis of our understanding of cancer genome evolution, yet it is widely thought to be inadequate for detecting structural variants (SVs). To understand the nature of cancer SVs missed by SRS, we introduce the concept of "loose ends", sites of missing rearrangements revealed by balancing copy number (CN) across the genomic intervals and adjacencies of a genome graph. Analyzing loose ends across 1,330 pan-cancer genome graphs inferred by a state-of-the-art algorithm (JaBbA v1), we found that most large (>10 Kbp) clonal SVs are fully resolved by SRS in the 87% of the genome where CN can be reliably measured. Some loose ends corresponded to new chromosome ends that arose when previously interstitial sequences acquired neotelomeres, most frequently in tumors harboring the alternative lengthening of telomeres phenotype. While somatic loose ends frequently occurred near repeats, their location and orientation was rarely consistent with homology-directed repair. We confirmed our pan-cancer findings by profiling 38 melanoma and breast cancer tumor-normal pairs with high physical coverage SRS and long molecule sequencing. Extrapolating our results to the recent telomere-to-telomere human genome assembly suggests that the majority of large cancer SVs are fully mapped by SRS and are unlikely to be the result of aberrant homologous recombination.

English

ISBN: 9798379903732Subjects--Topical Terms:

530508
Genetics.
Subjects--Index Terms:

Cancer genome structure

Loose Ends in Cancer Genome Structure /
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520 $a Short-read sequencing (SRS) forms the basis of our understanding of cancer genome evolution, yet it is widely thought to be inadequate for detecting structural variants (SVs). To understand the nature of cancer SVs missed by SRS, we introduce the concept of "loose ends", sites of missing rearrangements revealed by balancing copy number (CN) across the genomic intervals and adjacencies of a genome graph. Analyzing loose ends across 1,330 pan-cancer genome graphs inferred by a state-of-the-art algorithm (JaBbA v1), we found that most large (>10 Kbp) clonal SVs are fully resolved by SRS in the 87% of the genome where CN can be reliably measured. Some loose ends corresponded to new chromosome ends that arose when previously interstitial sequences acquired neotelomeres, most frequently in tumors harboring the alternative lengthening of telomeres phenotype. While somatic loose ends frequently occurred near repeats, their location and orientation was rarely consistent with homology-directed repair. We confirmed our pan-cancer findings by profiling 38 melanoma and breast cancer tumor-normal pairs with high physical coverage SRS and long molecule sequencing. Extrapolating our results to the recent telomere-to-telomere human genome assembly suggests that the majority of large cancer SVs are fully mapped by SRS and are unlikely to be the result of aberrant homologous recombination.
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650 4 $a Oncology. $3 751006
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653 $a Cancer genome evolution
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653 $a Homologous recombination
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