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microDuMIP: target-enrichment technique for microarray-based duplex molecular inversion probes

 Jung-Ki Yoon  ;  Jinwoo Ahn  ;  Han Sang Kim  ;  Soo Min Han  ;  Hoon Jang  ;  Min Goo Lee  ;  Ji Hyun Lee  ;  Duhee Bang 
 NUCLEIC ACIDS RESEARCH, Vol.43(5) : 28, 2015 
Journal Title
Issue Date
DNA, Single-Stranded/genetics* ; Exome/genetics ; Molecular Probe Techniques* ; Oligonucleotide Array Sequence Analysis/methods* ; Oligonucleotide Probes/genetics* ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Reproducibility of Results ; Sequence Analysis, DNA/methods
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.
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2. College of Dentistry (치과대학) > Dept. of Oral Biology (구강생물학교실) > 1. Journal Papers
1. College of Medicine (의과대학) > Dept. of Pharmacology (약리학교실) > 1. Journal Papers
Yonsei Authors
Kim, Han Sang(김한상) ORCID logo https://orcid.org/0000-0002-6504-9927
Lee, Min Goo(이민구) ORCID logo https://orcid.org/0000-0001-7436-012X
Lee, Ji Hyun(이지현)
Han, Soo Min(한수민)
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