publication . Article . Other literature type . 2009

Solution Hybrid Selection with Ultra-long Oligonucleotides for Massively Parallel Targeted Sequencing

Gnirke, Andreas; Melnikov, Alexandre; Maguire, Jared; Rogov, Peter; LeProust, Emily M; Brockman, William; Fennell, Timothy; Giannoukos, Georgia; Fisher, Sheila; Russ, Carsten; ...
Open Access
  • Published: 01 Feb 2009
  • Publisher: Springer Nature
Abstract
Targeting genomic loci by massively parallel sequencing requires new methods to enrich templates to be sequenced. We developed a capture method that uses biotinylated RNA “baits” to “fish” targets out of a “pond” of DNA fragments. The RNA is transcribed from PCR-amplified oligodeoxynucleotides originally synthesized on a microarray, generating sufficient bait for multiple captures at concentrations high enough to drive the hybridization. We tested this method with 170-mer baits that target >15,000 coding exons (2.5 Mb) and four regions (1.7 Mb total) using Illumina sequencing as read-out. About 90% of uniquely aligning bases fell on or near bait sequence; up to ...
Subjects
free text keywords: Article
25 references, page 1 of 2

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Wheeler, DA. The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008; 452: 872-876 [PubMed]

Dahl, F, Gullberg, M, Stenberg, J, Landegren, U, Nilsson, M. Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments. Nucleic Acids Res. 2005; 33: e71 [OpenAIRE] [PubMed]

Albert, TJ. Direct selection of human genomic loci by microarray hybridization. Nat Methods. 2007; 4: 903-905 [PubMed]

Dahl, F. Multigene amplification and massively parallel sequencing for cancer mutation discovery. Proc Natl Acad Sci USA. 2007; 104: 9387-9392 [OpenAIRE] [PubMed]

Fredriksson, S. Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector. Nucleic Acids Res. 2007; 35: e47 [OpenAIRE] [PubMed]

Hodges, E. Genome-wide in situ exon capture for selective resequencing. Nat Genet. 2007; 39: 1522-1527 [OpenAIRE] [PubMed]

Okou, DT. Microarray-based genomic selection for high-throughput resequencing. Nat Methods. 2007; 4: 907-909 [OpenAIRE] [PubMed]

Porreca, GJ. Multiplex amplification of large sets of human exons. Nat Methods. 2007; 4: 931-936 [PubMed]

Krishnakumar, S. A comprehensive assay for targeted multiplex amplification of human DNA sequences. Proc Natl Acad Sci USA. 2008; 105: 9296-9301 [OpenAIRE] [PubMed]

25 references, page 1 of 2
Abstract
Targeting genomic loci by massively parallel sequencing requires new methods to enrich templates to be sequenced. We developed a capture method that uses biotinylated RNA “baits” to “fish” targets out of a “pond” of DNA fragments. The RNA is transcribed from PCR-amplified oligodeoxynucleotides originally synthesized on a microarray, generating sufficient bait for multiple captures at concentrations high enough to drive the hybridization. We tested this method with 170-mer baits that target >15,000 coding exons (2.5 Mb) and four regions (1.7 Mb total) using Illumina sequencing as read-out. About 90% of uniquely aligning bases fell on or near bait sequence; up to ...
Subjects
free text keywords: Article
25 references, page 1 of 2

Margulies, M. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005; 437: 376-380 [OpenAIRE] [PubMed]

Shendure, J. Accurate multiplex polony sequencing of an evolved bacterial genome. Science. 2005; 309: 1728-1732 [PubMed]

Bentley, DR. Accurate whole genome sequencing using reversible terminator chemistry. Nature. 2008; 456: 53-59 [OpenAIRE] [PubMed]

Smith, DR. Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res. 2008; 18: 1638-1642 [OpenAIRE] [PubMed]

Ley, TJ. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature. 2008; 456: 66-72 [OpenAIRE] [PubMed]

Wang, J. The diploid genome sequence of an Asian individual. Nature. 2008; 456: 60-66 [OpenAIRE] [PubMed]

Wheeler, DA. The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008; 452: 872-876 [PubMed]

Dahl, F, Gullberg, M, Stenberg, J, Landegren, U, Nilsson, M. Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments. Nucleic Acids Res. 2005; 33: e71 [OpenAIRE] [PubMed]

Albert, TJ. Direct selection of human genomic loci by microarray hybridization. Nat Methods. 2007; 4: 903-905 [PubMed]

Dahl, F. Multigene amplification and massively parallel sequencing for cancer mutation discovery. Proc Natl Acad Sci USA. 2007; 104: 9387-9392 [OpenAIRE] [PubMed]

Fredriksson, S. Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector. Nucleic Acids Res. 2007; 35: e47 [OpenAIRE] [PubMed]

Hodges, E. Genome-wide in situ exon capture for selective resequencing. Nat Genet. 2007; 39: 1522-1527 [OpenAIRE] [PubMed]

Okou, DT. Microarray-based genomic selection for high-throughput resequencing. Nat Methods. 2007; 4: 907-909 [OpenAIRE] [PubMed]

Porreca, GJ. Multiplex amplification of large sets of human exons. Nat Methods. 2007; 4: 931-936 [PubMed]

Krishnakumar, S. A comprehensive assay for targeted multiplex amplification of human DNA sequences. Proc Natl Acad Sci USA. 2008; 105: 9296-9301 [OpenAIRE] [PubMed]

25 references, page 1 of 2
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