{"doi":"10.1038/nprot.2009.68","title":"Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing","abstract":"Complementary techniques that deepen information content and minimize reagent costs are required to realize the full potential of massively parallel sequencing. Here, we describe a resequencing approach that directs focus to genomic regions of high interest by combining hybridization-based purification of multi-megabase regions with sequencing on the Illumina Genome Analyzer (GA). The capture matrix is created by a microarray on which probes can be programmed as desired to target any non-repeat portion of the genome, while the method requires only a basic familiarity with microarray hybridization. We present a detailed protocol suitable for 1-2 microg of input genomic DNA and highlight key design tips in which high specificity (>65% of reads stem from enriched exons) and high sensitivity (98% targeted base pair coverage) can be achieved. We have successfully applied this to the enrichment of coding regions, in both human and mouse, ranging from 0.5 to 4 Mb in length. From genomic DNA library production to base-called sequences, this procedure takes approximately 9-10 d inclusive of array captures and one Illumina flow cell run.","journal":"Nature Protocols","year":2009,"id":3034,"datarank":11.662272900239879,"base_score":5.209486152841421,"endowment":5.209486152841421,"self_citation_contribution":0.7814229229262133,"citation_network_contribution":10.880849977313666,"self_endowment_contribution":0.7814229229262133,"citer_contribution":10.880849977313666,"corpus_percentile":null,"corpus_rank":null,"citation_count":182,"citer_count":173,"citers_with_citation_signal":155,"citers_with_endowment":155,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.0406,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2009-05-28","algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":45117,"name":"Joseph A. Prinz","orcid":null,"position":1,"is_corresponding":false},{"id":33865,"name":"Zhenyu Xuan","orcid":"0000-0001-9344-8493","position":2,"is_corresponding":false},{"id":33866,"name":"Arindam Bhattacharjee","orcid":"0000-0001-9470-6386","position":3,"is_corresponding":false},{"id":23583,"name":"D. Benjamin Gordon","orcid":null,"position":4,"is_corresponding":false},{"id":33867,"name":"Leonardo Brizuela","orcid":null,"position":5,"is_corresponding":false},{"id":33868,"name":"W. Richard McCombie","orcid":"0000-0003-1899-0682","position":6,"is_corresponding":false},{"id":11809,"name":"Gregory J. Hannon","orcid":"0000-0003-4021-3898","position":7,"is_corresponding":false},{"id":17369,"name":"Emily Hodges","orcid":"0000-0001-6513-610X","position":0,"is_corresponding":true}],"reference_count":21,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}