A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data

Article English OPEN
Sepúlveda, Nuno; Campino, Susana G; Assefa, Samuel A; Sutherland, Colin J; Pain, Arnab; Clark, Taane G;
(2013)
  • Publisher: Springer Nature
  • Journal: BMC Genomics,volume 14,pages128-128 (issn: 1471-2164, eissn: 1471-2164)
  • Related identifiers: doi: 10.1186/1471-2164-14-128, pmc: PMC3679970
  • Subject: Methodology Article | Biotechnology | Genetics

BACKGROUND: The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the sequence data involves mapping reads onto a refe... View more
  • References (38)
    38 references, page 1 of 4

    1. Zhang F, Gu W, Hurles ME, Lupski JR: Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet 2009, 10:451-481.

    2. Stankiewicz P, Lupski JR: Structural variation in the human genome and its role in disease. Annu Rev Med 2010, 61:437-455.

    3. Medvedev P, Stanciu M, Brudno M: Computational methods for discovering structural variation with next-generation sequencing. Nat Methods 2009, 6(11 Suppl):S13-S20.

    4. Yoon S, Xuan Z, Makarov V, Ye K, Sebat J: Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res 2009, 19:1586-1592.

    5. Boeva V, Zinovyev A, Bleakley K, Vert JP, Janoueix-Lerosey I, Delattre O, Barillot E: Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics 2011, 27:268-269.

    6. Klambauer G, Schwarzbauer K, Mayr A, Clevert DA, Mitterecker A, Bodenhofer U, Hochreiter S: cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate. Nucleic Acids Res 2012, 40(9):e69.

    7. Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ: A large genome center's improvements to the Illumina sequencing system. Nat Methods 2008, 5(12):1005-1010.

    8. Dohm JC, Lottaz C, Borodina T, Himmelbauer H: Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 2008, 36(16):e105.

    9. Cheung MS, Down TA, Latorre I, Ahringer J: Systematic bias in high-throughput sequencing data and its correction by BEADS. Nucleic Acids Res 2011, 39(15):e103.

    10. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL etal: Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456:53-59.

  • Related Research Results (1)
  • Metrics
    No metrics available
Share - Bookmark