Unexpected effects of different genetic backgrounds on identification of genomic rearrangements via whole-genome next generation sequencing

被引：2

作者：

Chen, Zhangguo ^{[1
,2
]}

Gowan, Katherine ^{[3
]}

Leach, Sonia M. ^{[4
]}

Viboolsittiseri, Sawanee S. ^{[1
]}

Mishra, Ameet K. ^{[1
]}

Kadoishi, Tanya ^{[1
]}

Diener, Katrina ^{[5
]}

Gao, Bifeng ^{[5
]}

Jones, Kenneth ^{[3
]}

Wang, Jing H. ^{[1
,2
]}

机构：

[1] Univ Colorado, Dept Immunol & Microbiol, Anschutz Med Campus,12800 E,19th Ave, Aurora, CO 80045 USA

[2] Natl Jewish Hlth, Dept Biomed Res, Denver, CO 80206 USA

[3] Univ Colorado, Dept Biochem & Mol Genet, Anschutz Med Campus, Aurora, CO 80045 USA

[4] Natl Jewish Hlth, Integrated Ctr Genes Environm & Hlth, Denver, CO 80206 USA

[5] Univ Colorado, Genom & Microarray Core, Anschutz Med Campus, Aurora, CO 80045 USA

来源：

BMC GENOMICS | 2016年 / 17卷

关键词：

Whole genome next generation sequencing; Genomic instability; B cell lymphoma; Different genetic background; de novo assembly; CLASS SWITCH RECOMBINATION; INITIATED DNA LESIONS; DOUBLE-STRAND BREAKS; B-CELLS; CANCER GENOMES; STRUCTURAL VARIATION; POPULATION-SCALE; LIGASE; REPAIR; TRANSLOCATIONS;

D O I：

10.1186/s12864-016-3153-9

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Background: Whole genome next generation sequencing (NGS) is increasingly employed to detect genomic rearrangements in cancer genomes, especially in lymphoid malignancies. We recently established a unique mouse model by specifically deleting a key non-homologous end-joining DNA repair gene, Xrcc4, and a cell cycle checkpoint gene, Trp53, in germinal center B cells. This mouse model spontaneously develops mature B cell lymphomas (termed G1XP lymphomas). Results: Here, we attempt to employ whole genome NGS to identify novel structural rearrangements, in particular inter-chromosomal translocations (CTXs), in these G1XP lymphomas. We sequenced six lymphoma samples, aligned our NGS data with mouse reference genome (in C57BL/6J (B6) background) and identified CTXs using CREST algorithm. Surprisingly, we detected widespread CTXs in both lymphomas and wildtype control samples, majority of which were false positive and attributable to different genetic backgrounds. In addition, we validated our NGS pipeline by sequencing multiple control samples from distinct tissues of different genetic backgrounds of mouse (B6 vs non-B6). Lastly, our studies showed that widespread false positive CTXs can be generated by simply aligning sequences from different genetic backgrounds of mouse. Conclusions: We conclude that mapping and alignment with reference genome might not be a preferred method for analyzing whole-genome NGS data obtained from a genetic background different from reference genome. Given the complex genetic background of different mouse strains or the heterogeneity of cancer genomes in human patients, in order to minimize such systematic artifacts and uncover novel CTXs, a preferred method might be de novo assembly of personalized normal control genome and cancer cell genome, instead of mapping and aligning NGS data to mouse or human reference genome. Thus, our studies have critical impact on the manner of data analysis for cancer genomics.

引用

页数：11