title: microDuMIP: target-enrichment technique for microarray-based duplex molecular inversion probes.
abstract: Molecular inversion probe (MIP)-based capture is a scalable and effective target-enrichment technology that can use synthetic single-stranded oligonucleotides as probes. Unlike the straightforward use of synthetic oligonucleotides for low-throughput target capture, high-throughput MIP capture has required laborious protocols to generate thousands of single-stranded probes from DNA microarray because of multiple enzymatic steps, gel purifications and extensive PCR amplifications. Here, we developed a simple and efficient microarray-based MIP preparation protocol using only one enzyme with double-stranded probes and improved target capture yields by designing probes with overlapping targets and unique barcodes. To test our strategy, we produced 11 510 microarray-based duplex MIPs (microDuMIPs) and captured 3554 exons of 228 genes in a HapMap genomic DNA sample (NA12878). Under our protocol, capture performance and precision of calling were compatible to conventional MIP capture methods, yet overlapping targets and unique barcodes allowed us to precisely genotype with as little as 50 ng of input genomic DNA without library preparation. microDuMIP method is simpler and cheaper, allowing broader applications and accurate target sequencing with a scalable number of targets.
authors.affiliation: College of Medicine, Seoul National University, Seoul 110-799, Korea dr.jkyoon@gmail.com.
authors.forename: Jung-Ki
authors.initials: JK
authors.lastname: Yoon
authors.affiliation: Department of Chemistry, Yonsei University, Seoul 120-752, Korea.
authors.forename: Jinwoo
authors.initials: J
authors.lastname: Ahn
authors.affiliation: Department of Pharmacology, Pharmacogenomic Research Center for Membrane Transporters, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 120-752, Korea Yonsei Cancer Center, Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 120-752, Korea.
authors.forename: Han Sang
authors.initials: HS
authors.lastname: Kim
authors.affiliation: Department of Pharmacology, Pharmacogenomic Research Center for Membrane Transporters, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 120-752, Korea.
authors.forename: Soo Min
authors.initials: SM
authors.lastname: Han
authors.affiliation: Department of Chemistry, Yonsei University, Seoul 120-752, Korea.
authors.forename: Hoon
authors.initials: H
authors.lastname: Jang
authors.affiliation: Department of Pharmacology, Pharmacogenomic Research Center for Membrane Transporters, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 120-752, Korea.
authors.forename: Min Goo
authors.initials: MG
authors.lastname: Lee
authors.affiliation: Department of Oral Biology, Yonsei University College of Dentistry, Seoul 120-752, Korea jihyni@yuhs.ac.
authors.forename: Ji Hyun
authors.initials: JH
authors.lastname: Lee
authors.affiliation: Department of Chemistry, Yonsei University, Seoul 120-752, Korea duheebang@yonsei.ac.kr.
authors.forename: Duhee
authors.initials: D
authors.lastname: Bang
mesh_terms: D004277:DNA, Single-Stranded / Q000235:genetics*; D059472:Exome / Q000235:genetics; D015336:Molecular Probe Techniques; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes / Q000235:genetics*; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D004277:DNA, Single-Stranded; D015345:Oligonucleotide Probes