Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients

被引：21

作者：

Valle-Inclan, Jose Espejo ^{[1
,2
,3
]}

Stangl, Christina ^{[1
,2
,3
,4
]}

de Jong, Anouk C. ^{[5
]}

van Dessel, Lisanne F. ^{[5
]}

van Roosmalen, Markus J. ^{[2
,6
]}

Helmijr, Jean C. A. ^{[5
]}

Renkens, Ivo ^{[1
,2
]}

Janssen, Roel ^{[1
,2
,3
]}

de Blank, Sam ^{[1
,2
]}

de Witte, Chris J. ^{[1
,2
,3
]}

Martens, John W. M. ^{[5
]}

Jansen, Maurice P. H. M. ^{[5
]}

Lolkema, Martijn P. ^{[5
]}

Kloosterman, Wigard P. ^{[1
,2
,7
,8
]}

机构：

[1] Univ Med Ctr Utrecht, Ctr Mol Med, Dept Genet, Utrecht, Netherlands

[2] Univ Utrecht, Utrecht, Netherlands

[3] Oncode Inst, Utrecht, Netherlands

[4] Netherlands Canc Inst, Div Mol Oncol, Amsterdam, Netherlands

[5] Erasmus MC Canc Inst, Dept Med Oncol, Rotterdam, Netherlands

[6] Princess Maxima Ctr Pediat Oncol, Utrecht, Netherlands

[7] Cyclomics, Utrecht, Netherlands

[8] Frame Canc Therapeut, Amsterdam, Netherlands

来源：

GENOME MEDICINE | 2021年 / 13卷 / 01期

关键词：

Genomics; Liquid biopsies; Nanopore; Cancer; Structural variation; CELL-FREE DNA; COMPREHENSIVE EVALUATION; HUMAN GENOME; REARRANGEMENTS; DISCOVERY; PLATFORM;

D O I：

10.1186/s13073-021-00899-7

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Here, we describe a novel approach for rapid discovery of a set of tumor-specific genomic structural variants (SVs), based on a combination of low coverage cancer genome sequencing using Oxford Nanopore with an SV calling and filtering pipeline. We applied the method to tumor samples of high-grade ovarian and prostate cancer patients and validated on average ten somatic SVs per patient with breakpoint-spanning PCR mini-amplicons. These SVs could be quantified in ctDNA samples of patients with metastatic prostate cancer using a digital PCR assay. The results suggest that SV dynamics correlate with and may improve existing treatment-response biomarkers such as PSA.

引用

页数：14

共 54 条

[1] A global reference for human genetic variation
Altshuler, David M.
Durbin, Richard M.
Abecasis, Goncalo R.
Bentley, David R.
Chakravarti, Aravinda
Clark, Andrew G.
Donnelly, Peter
Eichler, Evan E.
Flicek, Paul
Gabriel, Stacey B.
Gibbs, Richard A.
Green, Eric D.
Hurles, Matthew E.
Knoppers, Bartha M.
Korbel, Jan O.
Lander, Eric S.
Lee, Charles
Lehrach, Hans
Mardis, Elaine R.
Marth, Gabor T.
McVean, Gil A.
Nickerson, Deborah A.
Wang, Jun
Wilson, Richard K.
Boerwinkle, Eric
Doddapaneni, Harsha
Han, Yi
Korchina, Viktoriya
Kovar, Christie
Lee, Sandra
Muzny, Donna
Reid, Jeffrey G.
Zhu, Yiming
Chang, Yuqi
Feng, Qiang
Fang, Xiaodong
Guo, Xiaosen
Jian, Min
Jiang, Hui
Jin, Xin
Lan, Tianming
Li, Guoqing
Li, Jingxiang
Li, Yingrui
Liu, Shengmao
Liu, Xiao
Lu, Yao
Ma, Xuedi
Tang, Meifang
Wang, Bo
[J]. NATURE, 2015, 526 (7571) : 68 - +
[2] Recent segmental duplications in the human genome
Bailey, JA
Gu, ZP
Clark, RA
Reinert, K
Samonte, RV
Schwartz, S
Adams, MD
Myers, EW
Li, PW
Eichler, EE
[J]. SCIENCE, 2002, 297 (5583) : 1003 - 1007
[3] Tandem repeats finder: a program to analyze DNA sequences
Benson, G
[J]. NUCLEIC ACIDS RESEARCH, 1999, 27 (02) : 573 - 580
[4] Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software
Cameron, Daniel L.
Di Stefano, Leon
Papenfuss, Anthony T.
[J]. NATURE COMMUNICATIONS, 2019, 10 (1)
[5] GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly
Cameron, Daniel L.
Schroder, Jan
Penington, Jocelyn Sietsma
Do, Hongdo
Molania, Ramyar
Dobrovic, Alexander
Speed, Terence P.
Papenfuss, Anthony T.
[J]. GENOME RESEARCH, 2017, 27 (12) : 2050 - 2060
[6] Cameron DL., 2020, BIORXIV, V22, P1, DOI [10.1101/2020.07.09.196527, DOI 10.1101/2020.07.09.196527]
[7] Cameron DL., 2019, Biorxiv, P781013
[8] Multi-platform discovery of haplotype-resolved structural variation in human genomes
Chaisson, Mark J. P.
Sanders, Ashley D.
Zhao, Xuefang
Malhotra, Ankit
Porubsky, David
Rausch, Tobias
Gardner, Eugene J.
Rodriguez, Oscar L.
Guo, Li
Collins, Ryan L.
Fan, Xian
Wen, Jia
Handsaker, Robert E.
Fairley, Susan
Kronenberg, Zev N.
Kong, Xiangmeng
Hormozdiari, Fereydoun
Lee, Dillon
Wenger, Aaron M.
Hastie, Alex R.
Antaki, Danny
Anantharaman, Thomas
Audano, Peter A.
Brand, Harrison
Cantsilieris, Stuart
Cao, Han
Cerveira, Eliza
Chen, Chong
Chen, Xintong
Chin, Chen-Shan
Chong, Zechen
Chuang, Nelson T.
Lambert, Christine C.
Church, Deanna M.
Clarke, Laura
Farrell, Andrew
Flores, Joey
Galeev, Timur
Gorkin, David U.
Gujral, Madhusudan
Guryev, Victor
Heaton, William Haynes
Korlach, Jonas
Kumar, Sushant
Kwon, Jee Young
Lam, Ernest T.
Lee, Jong Eun
Lee, Joyce
Lee, Wan-Ping
Lee, Sau Peng
[J]. NATURE COMMUNICATIONS, 2019, 10 (1)
[9] Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications
Chen, Xiaoyu
Schulz-Trieglaff, Ole
Shaw, Richard
Barnes, Bret
Schlesinger, Felix
Kallberg, Morten
Cox, Anthony J.
Kruglyakl, Semyon
Saunders, Christopher T.
[J]. BIOINFORMATICS, 2016, 32 (08) : 1220 - 1222
[10] Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome
De Coster, Wouter
De Rijk, Peter
De Roeck, Arne
De Pooter, Tim
D'Hert, Svenn
Strazisar, Mojca
Sleegers, Kristel
Van Broeckhoven, Christine
[J]. GENOME RESEARCH, 2019, 29 (07) : 1178 - 1187

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