title: Comparison of custom capture for targeted next-generation DNA sequencing.
abstract: Targeted, capture-based DNA sequencing is a cost-effective method to focus sequencing on a coding region or other customized region of the genome. There are multiple targeted sequencing methods available, but none has been systematically investigated and compared. We evaluated four commercially available custom-targeted DNA technologies for next-generation sequencing with respect to on-target sequencing, uniformity, and ability to detect single-nucleotide variations (SNVs) and copy number variations. The technologies that used sonication for DNA fragmentation displayed impressive uniformity of capture, whereas the others had shorter preparation times, but sacrificed uniformity. One of those technologies, which uses transposase for DNA fragmentation, has a drawback requiring sample pooling, and the last one, which uses restriction enzymes, has a limitation depending on restriction enzyme digest sites. Although all technologies displayed some level of concordance for calling SNVs, the technologies that require restriction enzymes or transposase missed several SNVs largely because of the lack of coverage. All technologies performed well for copy number variation calling when compared to single-nucleotide polymorphism arrays. These results enable laboratories to compare these methods to make informed decisions for their intended applications.
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.
authors.forename: Eric
authors.initials: E
authors.lastname: Samorodnitsky
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.
authors.forename: Jharna
authors.initials: J
authors.lastname: Datta
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.
authors.forename: Benjamin M
authors.initials: BM
authors.lastname: Jewell
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.
authors.forename: Raffi
authors.initials: R
authors.lastname: Hagopian
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.
authors.forename: Jharna
authors.initials: J
authors.lastname: Miya
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.
authors.forename: Michele R
authors.initials: MR
authors.lastname: Wing
authors.affiliation: Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio.
authors.forename: Senthilkumar
authors.initials: S
authors.lastname: Damodaran
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.
authors.forename: Juliana M
authors.initials: JM
authors.lastname: Lippus
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.
authors.forename: Julie W
authors.initials: JW
authors.lastname: Reeser
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.
authors.forename: Darshna
authors.initials: D
authors.lastname: Bhatt
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.
authors.forename: Cynthia D
authors.initials: CD
authors.lastname: Timmers
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio; Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio; Department of Pharmacology, The Ohio State University, Columbus, Ohio. Electronic address: sameek.roychowdhury@osumc.edu.
authors.forename: Sameek
authors.initials: S
authors.lastname: Roychowdhury
mesh_terms: D016022:Case-Control Studies; D045744:Cell Line, Tumor; D056915:DNA Copy Number Variations; D053938:DNA Fragmentation; D004262:DNA Restriction Enzymes / Q000737:chemistry; D015894:Genome, Human; D015698:Genomic Library; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000145:classification / Q000295:instrumentation / Q000379:methods*; D006801:Humans; D009369:Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000473:pathology; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods; D016366:Open Reading Frames; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity; D013010:Sonication; D019895:Transposases / Q000737:chemistry
chemical_list: D019895:Transposases; D004262:DNA Restriction Enzymes