SVAtools for junction detection of genome-wide chromosomal rearrangements by mate-pair sequencing (MPseq)

Sarah H. Johnson, James B. Smadbeck, Stephanie A. Smoley, Athanasios Gaitatzes, Stephen J. Murphy, Faye R. Harris, Travis M. Drucker, Roman M. Zenka, Beth A. Pitel, Ross A. Rowsey, Nicole L. Hoppman, Umut Aypar, William R. Sukov, Robert B. Jenkins, Andrew L. Feldman, Hutton M. Kearney, George Vasmatzis

Research output: Contribution to journalArticlepeer-review

45 Scopus citations


Mate-pair sequencing (MPseq), using long-insert, paired-end genomic libraries, is a powerful next-generation sequencing-based approach for the detection of genomic structural variants. SVAtools is a set of algorithms to detect both chromosomal rearrangements and large (>10 kb) copy number variants (CNVs) in genome-wide MPseq data. SVAtools can also predict gene disruptions and gene fusions, and characterize the genomic structure of complex rearrangements. To illustrate the power of SVAtools’ junction detection methods to provide comprehensive molecular karyotypes, MPseq data were compared against a set of samples previously characterized by traditional cytogenetic methods. Karyotype, FISH and chromosomal microarray (CMA), performed for 29 patients in a clinical laboratory setting, collectively revealed 285 breakpoints in 87 rearrangements. The junction detection methods of SVAtools detected 87% of these breakpoints compared to 48%, 42% and 57% for karyotype, FISH and CMA respectively. Breakpoint resolution was also reported to 1 kb or less and additional genomic rearrangement complexities not appreciable by standard cytogenetic techniques were revealed. For example, 63% of CNVs detected by CMA were shown by SVAtools’ junction detection to occur secondary to a rearrangement other than a simple deletion or tandem duplication. SVAtools with MPseq provides comprehensive and accurate whole-genome junction detection with improved breakpoint resolution, compared to karyotype, FISH, and CMA combined. This approach to molecular karyotyping offers considerable diagnostic potential for the simultaneous detection of both novel and recurrent genomic rearrangements in hereditary and neoplastic disorders.

Original languageEnglish (US)
Pages (from-to)1-18
Number of pages18
JournalCancer Genetics
StatePublished - Feb 2018


  • Mate-pair sequencing
  • balanced rearrangement
  • gene fusion
  • junction/breakpoint
  • structural variant
  • whole genome

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Cancer Research


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