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

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