Detecting Small Inversions Using SRinversion

  • Ruoyan ChenEmail author
  • Yu Lung Lau
  • Wanling Yang
Part of the Methods in Molecular Biology book series (MIMB, volume 1833)


Rapid development of next generation sequencing (NGS) technology has substantially improved our ability to detect genomic variations. However, unlike other variations, such as point mutations, insertions, and deletions, which can be identified in high sensitivities and specificities based on NGS reads, most of inversions, especially those shorter than 1 kb, remain difficult to detect. Here we introduce a new framework, SRinversion, which was developed specifically for detection of inversions shorter than 1 kb by splitting and realigning poorly mapped or unmapped reads of the NGS data.

Key words

Short inversion detection NGS Structural variations Split reads method 


  1. 1.
    Lakich D, Kazazian HH Jr, Antonarakis SE et al (1993) Inversions disrupting the factor VIII gene are a common cause of severe haemophilia A. Nat Genet 5(3):236–241CrossRefPubMedGoogle Scholar
  2. 2.
    Bondeson ML, Dahl N, Malmgren H et al (1995) Inversion of the IDS gene resulting from recombination with IDS-related sequences is a common cause of the Hunter syndrome. Hum Mol Genet 4(4):615–621CrossRefPubMedGoogle Scholar
  3. 3.
    Feuk L, Carson AR, Scherer SW (2006) Structural variation in the human genome. Nat Rev Genet 7(2):85–97CrossRefPubMedGoogle Scholar
  4. 4.
    Gimelli G, Pujana MA, Patricelli MG et al (2003) Genomic inversions of human chromosome 15q11-q13 in mothers of Angelman syndrome patients with class II (BP2/3) deletions. Hum Mol Genet 12(8):849–858CrossRefPubMedGoogle Scholar
  5. 5.
    Osborne LR, Li M, Pober B et al (2001) A 1.5 million-base pair inversion polymorphism in families with Williams–Beuren syndrome. Nat Genet 29(3):321–325CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Chen K, Wallis JW, McLellan MD et al (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6(9):677–681CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    He F, Li Y, Tang YH et al (2016) Identifying micro-inversions using high-throughput sequencing reads. BMC Genomics 17(Suppl 1):4CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Rausch T, Zichner T, Schlattl A et al (2012) DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28(18):i333–i339CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Trappe K, Emde AK, Ehrlich HC et al (2014) Gustaf: detecting and correctly classifying SVs in the NGS twilight zone. Bioinformatics 30(24):3484–3490CrossRefPubMedGoogle Scholar
  10. 10.
    Ye K, Schulz MH, Long Q et al (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25(21):2865–2871CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Stankiewicz P, Lupski JR (2010) Structural variation in the human genome and its role in disease. Annu Rev Med 61:437–455CrossRefPubMedGoogle Scholar
  12. 12.
    Chen R, Lau YL, Zhang Y et al (2016) SRinversion: a tool for detecting short inversions by splitting and re-aligning poorly mapped and unmapped sequencing reads. Bioinformatics 32(23):3559–3565PubMedGoogle Scholar
  13. 13.
    Cock PJA, Fields CJ, Goto N et al (2009) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 38(6):1767–1771CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Kent WJ, Sugnet CW, Furey TS et al (2002) The human genome browser at UCSC. Genome Res 12(6):996–1006CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 15:1754–1760CrossRefGoogle Scholar
  16. 16.
    Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25:2078–2079CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Daniel RZ, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829CrossRefGoogle Scholar
  18. 18.
    Boratyn GM, Camacho C, Cooper PS et al (2013) BLAST: a more efficient report with usability improvements. Nucleic Acids Res 41:W29–W33CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Paediatrics and Adolescent Medicine, LKS Faculty of MedicineThe University of Hong KongPokfulamHong Kong

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