Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags

Qiang Gong, Yong Tao, Jian Rong Yang, Jun Cai, Yunfei Yuan, Jue Ruan, Jin Yang, Hailiang Liu, Wanghua Li, Xuemei Lu, Shi Mei Zhuang, San Ming Wang, Chung I. Wu

Research output: Contribution to journalArticle

Abstract

Background: Genomic deletions are known to be widespread in many species. Variant sequencing-based approaches for identifying deletions have been developed, but their powers to detect those deletions that affect medium-sized regions are limited when the sequencing coverage is low.Results: We present a cost-effective method for identifying medium-sized deletions in genomic regions with low genomic coverage. Two mate-paired libraries were separately constructed from human cancerous tissue to generate paired short reads (ditags) from restriction fragments digested with a 4-base restriction enzyme. A total of 3 Gb of paired reads (1.0× genome size) was collected, and 175 deletions were inferred by identifying the ditags with disorder alignments to the reference genome sequence. Sanger sequencing results confirmed an overall detection accuracy of 95%. Good reproducibility was verified by the deletions that were detected by both libraries.Conclusions: We provide an approach to accurately identify medium-sized deletions in large genomes with low sequence coverage. It can be applied in studies of comparative genomics and in the identification of germline and somatic variants.

Original languageEnglish (US)
Article number51
JournalBMC genomics
Volume14
Issue number1
DOIs
StatePublished - Jan 24 2013

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Libraries
Genome
Genome Size
Genomics
Costs and Cost Analysis
Enzymes

Keywords

  • Medium-sized deletion
  • Next generation sequencing
  • Restriction enzymes
  • Structural variation

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Gong, Q., Tao, Y., Yang, J. R., Cai, J., Yuan, Y., Ruan, J., ... Wu, C. I. (2013). Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags. BMC genomics, 14(1), [51]. https://doi.org/10.1186/1471-2164-14-51

Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags. / Gong, Qiang; Tao, Yong; Yang, Jian Rong; Cai, Jun; Yuan, Yunfei; Ruan, Jue; Yang, Jin; Liu, Hailiang; Li, Wanghua; Lu, Xuemei; Zhuang, Shi Mei; Wang, San Ming; Wu, Chung I.

In: BMC genomics, Vol. 14, No. 1, 51, 24.01.2013.

Research output: Contribution to journalArticle

Gong, Q, Tao, Y, Yang, JR, Cai, J, Yuan, Y, Ruan, J, Yang, J, Liu, H, Li, W, Lu, X, Zhuang, SM, Wang, SM & Wu, CI 2013, 'Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags', BMC genomics, vol. 14, no. 1, 51. https://doi.org/10.1186/1471-2164-14-51
Gong, Qiang ; Tao, Yong ; Yang, Jian Rong ; Cai, Jun ; Yuan, Yunfei ; Ruan, Jue ; Yang, Jin ; Liu, Hailiang ; Li, Wanghua ; Lu, Xuemei ; Zhuang, Shi Mei ; Wang, San Ming ; Wu, Chung I. / Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags. In: BMC genomics. 2013 ; Vol. 14, No. 1.
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AU - Ruan, Jue

AU - Yang, Jin

AU - Liu, Hailiang

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AU - Wang, San Ming

AU - Wu, Chung I.

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AB - Background: Genomic deletions are known to be widespread in many species. Variant sequencing-based approaches for identifying deletions have been developed, but their powers to detect those deletions that affect medium-sized regions are limited when the sequencing coverage is low.Results: We present a cost-effective method for identifying medium-sized deletions in genomic regions with low genomic coverage. Two mate-paired libraries were separately constructed from human cancerous tissue to generate paired short reads (ditags) from restriction fragments digested with a 4-base restriction enzyme. A total of 3 Gb of paired reads (1.0× genome size) was collected, and 175 deletions were inferred by identifying the ditags with disorder alignments to the reference genome sequence. Sanger sequencing results confirmed an overall detection accuracy of 95%. Good reproducibility was verified by the deletions that were detected by both libraries.Conclusions: We provide an approach to accurately identify medium-sized deletions in large genomes with low sequence coverage. It can be applied in studies of comparative genomics and in the identification of germline and somatic variants.

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