title: Unexpected effects of different genetic backgrounds on identification of genomic rearrangements via whole-genome next generation sequencing.
abstract: 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).
  
  
  
  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.
  
  
  
  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.
authors: Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, 12800 E, 19th Ave, Mail Stop 8333, Aurora, CO, 80045, USA.|Department of Biomedical Research, National Jewish Health, Denver, CO, 80206, USA.
authors: Zhangguo
authors: Z
authors: Chen
authors: Department of Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA.
authors: Katherine
authors: K
authors: Gowan
authors: Department of Biomedical Research, National Jewish Health, Denver, CO, 80206, USA.|Integrated Center for Genes, Environment and Health, National Jewish Health, Denver, CO, 80206, USA.
authors: Sonia M
authors: SM
authors: Leach
authors: Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, 12800 E, 19th Ave, Mail Stop 8333, Aurora, CO, 80045, USA.
authors: Sawanee S
authors: SS
authors: Viboolsittiseri
authors: Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, 12800 E, 19th Ave, Mail Stop 8333, Aurora, CO, 80045, USA.
authors: Ameet K
authors: AK
authors: Mishra
authors: Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, 12800 E, 19th Ave, Mail Stop 8333, Aurora, CO, 80045, USA.
authors: Tanya
authors: T
authors: Kadoishi
authors: Genomic and Microarray Core, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA.
authors: Katrina
authors: K
authors: Diener
authors: Genomic and Microarray Core, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA.
authors: Bifeng
authors: B
authors: Gao
authors: Department of Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA.
authors: Kenneth
authors: K
authors: Jones
authors: Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, 12800 E, 19th Ave, Mail Stop 8333, Aurora, CO, 80045, USA. jing.wang@ucdenver.edu.|Department of Biomedical Research, National Jewish Health, Denver, CO, 80206, USA. jing.wang@ucdenver.edu.
authors: Jing H
authors: JH
authors: Wang
mesh_terms: D000818:Animals; D001402:B-Lymphocytes / Q000276:immunology / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D015321:Gene Rearrangement; D000068617:Genetic Background; D016678:Genome; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D008223:Lymphoma / Q000235:genetics; D051379:Mice; D008822:Mice, Transgenic; D015203:Reproducibility of Results; D014178:Translocation, Genetic
keywords: B cell lymphoma; Different genetic background; Genomic instability; Whole genome next generation sequencing; de novo assembly