Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing

Nature Protocols

Volumn 4, Issue 6, 2009, Pages 960-978

  Hodges, Emily ^a   Rooks, Michelle ^a,b   Xuan, Zhenyu ^a   Bhattacharjee, Arindam ^c   Gordon, D Benjamin ^b   Brizuela, Leonardo ^c   McCombie, W Richard ^c   Hannon, Gregory J ^a,b  

^a Cold Spring Harbor Laboratory ^*  (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^c AGILENT TECHNOLOGIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ANALYZER; ARTICLE; DNA FRAGMENTATION; DNA HYBRIDIZATION; DNA LIBRARY; EXON; GENOME ANALYSIS; HAPLOTYPE MAP; MICROARRAY ANALYSIS; MOLECULAR PROBE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; BASE SEQUENCE; DNA PRIMERS; GENE LIBRARY; GENOMICS; HUMANS; MICE; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA;

EID: 66749159688     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2009.68     Document Type: Article

References (21)

1. Kaiser, J. DNA sequencing. A plan to capture human diversity in 1000 genomes. Science 319, 395 (2008).
2. Siva, N. 1000 Genomes Project. Nat. Biotechnol. 26, 256 (2008).
3. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061-1068 (2008).
4. Collins, F.S. & Barker, A.D. Mapping the cancer genome. Pinpointing the genes involved in cancer will help chart anew course across the complex landscape of human malignancies. Sci. Am. 296, 50-57 (2007).
5. Levy, S. et al. The diploid genome sequence of an individual human. PLoS Biol. 5, e254 (2007).
6. Wheeler, D.A. et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872-876 (2008).
7. Wang, J. et al. The diploid genome sequence of an Asian individual. Nature 456, 60-65 (2008).
8. Ley, T.J. et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456, 66-72 (2008).
9. Erlich, Y., Mitra, P.P., delaBastide, M., McCombie, W.R. & Hannon, G.J. Alta-Cyclic: A self-optimizing base caller for next-generation sequencing. Nat. Methods 5, 679-682 (2008).
10. Dohm, J.C., Lottaz, C., Borodina, T. & Himmelbauer, H. Substantial biases in ultrashort read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 36, e105 (2008).
11. Bentley, D.R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-59 (2008).
12. Albert, T.J. et al. Direct selection of human genomic loci by microarray hybridization. Nat. Methods 4, 903-905 (2007).
13. Hodges, E. et al. Genome-wide in situ exon capture for selective resequencing. Nat. Genet. 39, 1522-1527 (2007).
14. Okou, D.T. et al. Microarray-based genomic selection for high-throughput resequencing. Nat. Methods 4, 907-909 (2007).
15. Porreca, G.J. et al. Multiplex amplification of large sets of human exons. Nat. Methods 4, 931-936 (2007).
16. Bashiardes, S. et al. Direct genomic selection. Nat. Methods 2, 63-69 (2005).
17. Gnirke, A. et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. (2009).
18. Cleary, M.A. et al. Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis. Nat. Methods 1, 241-248 (2004).
19. Morgulis, A., Gertz, E.M., Schaffer, A.A. & Agarwala, R. WindowMasker: window-based masker for sequenced genomes. Bioinformatics 22 134-141 (2006).
20. Quail, M.A. et al. A large genome center's improvements to the Illumina sequencing system. Nat. Methods 5, 1005-1010 (2008).
21. Lander, E.S. & Waterman, M.S. Genomic mapping by fingerprinting randomclones: A mathematical analysis. Genomics 2, 231-239 (1988).