Mate Pair Sequencing: Next-Generation Sequencing for Structural Variant Detection

Beth A. Pitel, Eric Zimmerman Zuckerman, Linda B. Baughn

Research output: Chapter in Book/Report/Conference proceedingChapter


Structural variant detection by next-generation sequencing (NGS) methods have a higher molecular resolution than conventional cytogenetic techniques (Aypar et al., Eur J Haematol 102(1):87–96, 2019; Smadbeck et al., Blood Cancer J 9(12):103, 2019) and are particularly helpful in characterizing genomic rearrangements. Mate pair sequencing (MPseq) leverages a unique library preparation chemistry involving circularization of long DNA fragments, allowing for a unique application of paired-end sequencing of reads that are expected to map 2–5 kb apart in the genome. The unique orientation of the reads allows the user to estimate the location of breakpoints involved in a structural variant either within the sequenced reads or between the two reads. The precision of structural variant and copy number detection by this method allows for characterization of cryptic and complex rearrangements that may be otherwise undetectable by conventional cytogenetic methods (Singh et al., Leuk Lymphoma 60(5):1304–1307, 2019; Peterson et al., Blood Adv 3(8):1298–1302, 2019; Schultz et al., Leuk Lymphoma 61(4):975–978, 2020; Peterson et al., Mol Case Studies 5(2), 2019; Peterson et al., Mol Case Studies 5(3), 2019).

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages23
StatePublished - 2023

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Copy number
  • Cytogenetics
  • Fusion
  • Genomics
  • Inversion
  • Library preparation
  • MPseq
  • Mate pair
  • Molecular genetics
  • NGS
  • Paired end
  • Structural variants
  • Translocation

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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