國立虎尾科技大學 |

Loose Ends in Cancer Genome Structure.

紀錄類型:	書目-語言資料,手稿 : Monograph/item
正題名/作者:	Loose Ends in Cancer Genome Structure./
作者:	Choo, Zi-Ning.
面頁冊數:	1 online resource (162 pages)
附註:	Source: Dissertations Abstracts International, Volume: 85-01, Section: B.
Contained By:	Dissertations Abstracts International85-01B.
標題:	Cellular biology. -
電子資源:	click for full text (PQDT)
ISBN:	9798379903732

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

Loose Ends in Cancer Genome Structure. - 1 online resource (162 pages)

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

Thesis (Ph.D.)--Weill Medical College of Cornell University, 2024.

Includes bibliographical references

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.

Electronic reproduction.
Ann Arbor, Mich. :
ProQuest,
2024

Mode of access: World Wide Web

ISBN: 9798379903732Subjects--Topical Terms:

1148666
Cellular biology.
Subjects--Index Terms:

Cancer genome structureIndex Terms--Genre/Form:

554714
Electronic books.

Loose Ends in Cancer Genome Structure.
LDR:02789ntm a22003977 4500 001 1148698
005 20240930100120.5
006 m o d
007 cr bn ---uuuuu
008 250605s2024 xx obm 000 0 eng d
020 $a 9798379903732
035 $a (MiAaPQ)AAI30531438
035 $a AAI30531438
040 $a MiAaPQ $b eng $c MiAaPQ $d NTU
100 1 $a Choo, Zi-Ning. $3 1474730
245 1 0 $a Loose Ends in Cancer Genome Structure.
264 0 $c 2024
300 $a 1 online resource (162 pages)
336 $a text $b txt $2 rdacontent
337 $a computer $b c $2 rdamedia
338 $a online resource $b cr $2 rdacarrier
500 $a Source: Dissertations Abstracts International, Volume: 85-01, Section: B.
500 $a Advisor: Imielinski, Marcin.
502 $a Thesis (Ph.D.)--Weill Medical College of Cornell University, 2024.
504 $a Includes bibliographical references
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.
533 $a Electronic reproduction. $b Ann Arbor, Mich. : $c ProQuest, $d 2024
538 $a Mode of access: World Wide Web
650 4 $a Cellular biology. $3 1148666
650 4 $a Oncology. $3 593951
650 4 $a Genetics. $3 578972
653 $a Cancer genome structure
653 $a Short-read sequencing
653 $a Cancer genome evolution
653 $a Homology-directed repair
653 $a Homologous recombination
655 7 $a Electronic books. $2 local $3 554714
690 $a 0369
690 $a 0992
690 $a 0379
710 2 $a Weill Medical College of Cornell University. $b Physiology, Biophysics & Systems Biology. $3 1474731
710 2 $a ProQuest Information and Learning Co. $3 1178819
773 0 $t Dissertations Abstracts International $g 85-01B.
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=30531438 $z click for full text (PQDT)