DNA-Seq 101

Here is a list of papers on DNA sequencing, mainly exome and whole genome sequencing. It is a growing list, please do suggest any missing interesting papers on exome/whole genome sequencing.

Review Papers

  1. De novo mutations in human genetic disease, Joris A. Veltman & Han G. Brunner, Nature Reviews Genetics 13, 565-575 (August 2012) | doi:10.1038/nrg3241
  2. Exome sequencing as a tool for Mendelian disease gene discovery, Michael J. Bamshad, Sarah B. Ng, Abigail W. Bigham, Holly K. Tabor, Mary J. Emond, Deborah A. Nickerson & Jay Shendure, Nature Reviews Genetics 12, 745-755 (November 2011) | doi:10.1038/nrg3031
  3. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data, Gregory M. Cooper & Jay Shendure, Nature Reviews Genetics 12, 628-640 (September 2011) | doi:10.1038/nrg3046
  4. Genome structural variation discovery and genotyping, Can Alkan, Bradley P. Coe & Evan E. Eichler, Nature Reviews Genetics 12, 363-376 (May 2011) | doi:10.1038/nrg2958
  5. Uncovering the roles of rare variants in common disease through whole-genome sequencing, Elizabeth T. Cirulli & David B. Goldstein, Nature Reviews Genetics 11, 415–425 (1 June 2010) | doi:10.1038/nrg2779
  6. Performance comparison of whole-genome sequencing platforms, Hugo Y K Lam, Michael J Clark, Rui Chen, Rong Chen, Georges Natsoulis, Maeve O’Huallachain, Frederick E Dewey, Lukas Habegger, Euan A Ashley, Mark B Gerstein, Atul J Butte, Hanlee P Ji & Michael Snyder, Nature Biotechnology 30, 78–82 (2012) doi:10.1038/nbt.2065
  7. Performance comparison of exome DNA sequencing technologies,Michael J Clark, Rui Chen, Hugo Y K Lam, Konrad J Karczewski, Rong Chen, Ghia Euskirchen, Atul J Butte & Michael Snyder, Nature Biotechnology 29, 908–914 (2011) doi:10.1038/nbt.1975

Methods

  1. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA., Genome Res. 2010 Sep;20(9):1297-303. doi: 10.1101/gr.107524.110
  2. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing., Abyzov A, Urban AE, Snyder M, Gerstein M., Genome Res. 2011 Jun;21(6):974-84. doi: 10.1101/gr.114876.110
  3. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing,  Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK., Genome Res. 2012 Mar;22(3):568-76. doi: 10.1101/gr.129684.111.
  4. Copy number variation detection and genotyping from exome sequence data Niklas Krumm, Peter H. Sudmant, Arthur Ko, Brian J. O’Roak, Maika Malig, Bradley P. Coe, NHLBI Exome Sequencing Project, Aaron R. Quinlan, Deborah A. Nickerson and Evan E. Eichler, Genome Res. 2012 Aug;22(8):1525-32. doi: 10.1101/gr.138115.112.