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

By Andreas Gnirke, A. Melnikov, J. Maguire, P. Rogov, E. Leproust, W. Brockman, Tim Fennell, G. Giannoukos, Sheila Fisher, C. Russ and 4 more. Nature Biotechnology, 2009

1,475 citations recorded by the source corpus.

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 50% lay on exons proper. The uniformity was such that ∼60% of target bases in the exonic 'catch', and ∼80% in the regional catch, had at least half the mean coverage. One lane of Illumina sequence was sufficient to call high-confidence genotypes for 89% of the targeted exon space.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/cc354c02e5c6d3b995dc6b460de6cb1aab79a455

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Citations in the corpus

Identifying conserved genomic elements and designing universal bait sets to enrich them (2017, methodology): “One popular reduced representation approach is the targeted enrichment (Gnirke et al. 2009) of conserved or ultraconserved genomic elements (sensu Faircloth et al. 2012).”
Exploiting the mutanome for tumor vaccination. (2012, methodology): “Exome capture for DNA resequencing was carried out in triplicate with the Agilent mouse whole-exome SureSelect assay (9).”
High‐throughput DNA sequencing – concepts and limitations (2010, background): “a genomic locus, from sequence capture experiments [67–69]) in multiple individuals/ samples instead of sequencing one sample in excessive depth.”
Evolution and impact of subclonal mutations in chronic lymphocytic leukemia (2013, positive): “Libraries for WES were constructed and sequenced on either an Illumina HiSeq 2000 or GA-IIX using 76 bp paired-end reads (Berger et al., 2011; Chapman et al., 2011).”
Economic Importance, Breeding Objectives and Achievements (2011, background): “2008), targeted resequencing (Gnirke et al. 2009), discovery of transcription factor binding sites, transcript and non-coding RNA expression profi ling, and other functional genomic studies (Eveland et al.”
Carrier Testing for Severe Childhood Recessive Diseases by Next-Generation Sequencing (2011, methodology): “SureSelect enrichment of 6-, 8-, or 12-plex pooled libraries was per Agilent protocols (15), with 100 ng of custom bait library, blocking oligonucleotides specific for paired-end sequencing libraries and 60-hour hybridization.”
Comparison of Next-Generation Sequencing Systems (2012, methodology): “[29] developed a captured method that uses an RNA “baits” to capture target DNA fragments from the “pond” and then uses the Illumina platform to read out the sequence.”
Lessons from the cancer genome. (2013, neutral): “In parallel, methods were developed that employ hybridization to oligonucleotide ‘‘baits’’ in aqueous solution to capture specific portions of the genome— most importantly, the 2%of genomic DNA that contains known exons (the ‘‘exome’’) (Gnirke et al., 2009; Hodges et al., 2007).”
Integrated Genomic Analyses of Ovarian Carcinoma (2011, background): “Sood(31,32), Pathways: Chris Sander(9), Ethan Cerami(9), Nikolaus Schultz(9), Giovanni Ciriello(9), Barry S.”