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

Nature Genetics

Volumn 43, Issue 5, 2011, Pages 491-501

  Depristo, Mark A ^a   Banks, Eric ^a   Poplin, Ryan ^a   Garimella, Kiran V ^a   Maguire, Jared R ^a   Hartl, Christopher ^a   Philippakis, Anthony A ^a,b,c   Del Angel, Guillermo ^a   Rivas, Manuel A ^a   Hanna, Matt ^a   McKenna, Aaron ^a   Fennell, Tim J ^a   Kernytsky, Andrew M ^a   Sivachenko, Andrey Y ^a   Cibulskis, Kristian ^a   Gabriel, Stacey B ^a   Altshuler, David ^a,c   Daly, Mark J ^a,c  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA SEQUENCE; GENE MAPPING; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; NONHUMAN; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

DATA INTERPRETATION, STATISTICAL; DATABASES, NUCLEIC ACID; EXONS; GENETIC VARIATION; GENETICS, POPULATION; GENOME, HUMAN; GENOTYPE; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 79955483667     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.806     Document Type: Article

References (39)

1. The 1000 Genomes Project Consortium. et al. A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073 (2010).
2. Yi, X. et al. Sequencing of 50 human exomes reveals adaptation to high altitude. Science 329, 75-78 (2010).
3. Ng, S.B. et al. Exome sequencing identifes the cause of a mendelian disorder. Nat Genet. 42, 30-35 (2009).
4. Lee, W. et al. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 465, 473-477 (2010).
5. Pleasance, E.D. et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463, 191-196 (2009).
6. Beroukhim, R. et al. The landscape of somatic copy-number alteration across human cancers. Nature 463, 899-905 (2010).
7. Roach, J.C. et al. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328, 636-639 (2010).
8. Li, R. et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966-1967 (2009).
9. Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851-1858 (2008).
10. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
11. Ning, Z., Cox, A.J. & Mullikin, J.C. SSAHA: a fast search method for large DNA databases. Genome Res. 11, 1725-1729 (2001). (Pubitemid 33040499)
12. Ewing, B. & Green, P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186-194 (1998). (Pubitemid 28177230)
13. Brockman, W. et al. Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res. 18, 763-770 (2008). (Pubitemid 351645066)
14. Li, M., Nordborg, M. & Li, L.M. Adjust quality scores from alignment and improve sequencing accuracy. Nucleic Acids Res. 32, 5183-5191 (2004). (Pubitemid 39445505)
15. Li, R. et al. SNP detection for massively parallel whole-genome resequencing. Genome Res. 19, 1124-1132 (2009).
16. Drmanac, R. et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327, 78-81 (2010).
17. Bentley, D.R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-59 (2008).
18. 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).
19. Wheeler, D.A. et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872-876 (2008). (Pubitemid 351550870)
20. 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).
21. Shen, Y. et al. A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res. 20, 273-280 (2010).
22. Hoberman, R. et al. A probabilistic approach for SNP discovery in high-throughput human resequencing data. Genome Res. 19, 1542-1552 (2009).
23. Malhis, N. & Jones, S. High quality SNP calling using Illumina data at shallow coverage. Bioinformatics 26, 1029 (2010).
24. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
25. 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).
26. 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).
27. 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).
28. Langmead, B., Schatz, M.C., Lin, J., Pop, M. & Salzberg, S.L. Searching for SNPs with cloud computing. Genome Biol. 10, R134 (2009).
29. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-effcient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
30. Green, R.E. et al. A draft sequence of the Neandertal genome. Science 328, 710-722 (2010).
31. Gnirke, A. et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol. 27, 182-189 (2009).
32. Ng, S., Turner, E., Robertson, P. & Flygare, S. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461, 272-276 (2009).
33. 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).
34. 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). (Pubitemid 34533896)
35. 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). (Pubitemid 37265993)
36. Durbin, R., Eddy, S., Krogh, A. & Mitchison, G. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. (Cambridge University Press, Cambridge, UK, 1998).
37. 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).
38. HUGO Consortium. et al. Mapping human genetic diversity in Asia. Science 326, 1541-1545 (2009).
39. Bishop, C Pattern Recognition and Machine Learning (Springer, New York, New York, USA, 2006).