A framework for variation discovery and genotyping using next-generation DNA sequencing data

Nature Genetics - Tập 43 Số 5 - Trang 491-498 - 2011
Mark A. DePristo1, Eric Banks1, Ryan Poplin1, Kiran Garimella1, Jared Maguire1, Chris Hartl1, Anthony Philippakis1, Guillermo del Angel1, Manuel A. Rivas1, Matt Hanna1, Aaron McKenna1, Tim Fennell1, Andrew Kernytsky1, Andrey Sivachenko1, Kristian Cibulskis1, Stacey Gabriel1, David Altshuler1, Mark J. Daly2
1Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
2Harvard Medical School Boston Massachusetts USA

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The 1000 Genomes Project Consortium. et al. A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010).

Yi, X. et al. Sequencing of 50 human exomes reveals adaptation to high altitude. Science 329, 75–78 (2010).

Ng, S.B. et al. Exome sequencing identifies the cause of a mendelian disorder. Nat. Genet. 42, 30–35 (2009).

Lee, W. et al. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 465, 473–477 (2010).

Pleasance, E.D. et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463, 191–196 (2009).

Beroukhim, R. et al. The landscape of somatic copy-number alteration across human cancers. Nature 463, 899–905 (2010).

Roach, J.C. et al. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328, 636–639 (2010).

Li, R. et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966–1967 (2009).

Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851–1858 (2008).

Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

Ning, Z., Cox, A.J. & Mullikin, J.C. SSAHA: a fast search method for large DNA databases. Genome Res. 11, 1725–1729 (2001).

Ewing, B. & Green, P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186–194 (1998).

Brockman, W. et al. Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res. 18, 763–770 (2008).

Li, M., Nordborg, M. & Li, L.M. Adjust quality scores from alignment and improve sequencing accuracy. Nucleic Acids Res. 32, 5183–5191 (2004).

Li, R. et al. SNP detection for massively parallel whole-genome resequencing. Genome Res. 19, 1124–1132 (2009).

Drmanac, R. et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327, 78–81 (2010).

Bentley, D.R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53–59 (2008).

Koboldt, D., Chen, K., Wylie, T. & Larson, D. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25, 2283–2285 (2009).

Wheeler, D.A. et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872–876 (2008).

Mokry, M. et al. Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries. Nucleic Acids Res. 38, e116 (2010).

Shen, Y. et al. A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res. 20, 273–280 (2010).

Hoberman, R. et al. A probabilistic approach for SNP discovery in high-throughput human resequencing data. Genome Res. 19, 1542–1552 (2009).

Malhis, N. & Jones, S. High quality SNP calling using Illumina data at shallow coverage. Bioinformatics 26, 1029 (2010).

Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

Handsaker, R.E., Korn, J.M., Nemesh, J. & McCarroll, S.A. Discovery and genotyping of genome structural polymorphism by sequencing on a population scale. Nat. Genet. 43, 269–276 (2011).

McKenna, A.H. et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).

Browning, B.L. & Yu, Z. Simultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genome-wide association studies. Am. J. Hum. Genet. 85, 847–861 (2009).

Langmead, B., Schatz, M.C., Lin, J., Pop, M. & Salzberg, S.L. Searching for SNPs with cloud computing. Genome Biol. 10, R134 (2009).

Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

Green, R.E. et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010).

Gnirke, A. et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27, 182–189 (2009).

Ng, S., Turner, E., Robertson, P. & Flygare, S. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461, 272–276 (2009).

Mckernan, K.J. et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res. 19, 1527–1541 (2009).

Ebersberger, I., Metzler, D., Schwarz, C. & Pääbo, S. Genomewide comparison of DNA sequences between humans and chimpanzees. Am. J. Hum. Genet. 70, 1490–1497 (2002).

Freudenberg-Hua, Y. et al. Single nucleotide variation analysis in 65 candidate genes for CNS disorders in a representative sample of the European population. Genome Res. 13, 2271–2276 (2003).

Durbin, R., Eddy, S., Krogh, A. & Mitchison, G. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. (Cambridge University Press, Cambridge, UK, 1998).

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

HUGO Consortium. et al. Mapping human genetic diversity in Asia. Science 326, 1541–1545 (2009).

Bishop, C. Pattern Recognition and Machine Learning (Springer, New York, New York, USA, 2006).