title: A mass spectrometry-based multiplex SNP genotyping by utilizing allele-specific ligation and strand displacement amplification.
abstract: We herein describe a new mass spectrometry-based method for multiplex SNP genotyping by utilizing allele-specific ligation and strand displacement amplification (SDA) reaction. In this method, allele-specific ligation is first performed to discriminate base sequence variations at the SNP site within the PCR-amplified target DNA. The primary ligation probe is extended by a universal primer annealing site while the secondary ligation probe has base sequences as an overhang with a nicking enzyme recognition site and complementary mass marker sequence. The ligation probe pairs are ligated by DNA ligase only at specific allele in the target DNA and the resulting ligated product serves as a template to promote the SDA reaction using a universal primer. This process isothermally amplifies short DNA fragments, called mass markers, to be analyzed by mass spectrometry. By varying the sizes of the mass markers, we successfully demonstrated the multiplex SNP genotyping capability of this method by reliably identifying several BRCA mutations in a multiplex manner with mass spectrometry.
authors.affiliation: Department of Chemical and Biomolecular Engineering (BK21+ Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
authors.forename: Jung Hun
authors.initials: JH
authors.lastname: Park
authors.affiliation: Department of Chemical and Biomolecular Engineering (BK21+ Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
authors.forename: Hyowon
authors.initials: H
authors.lastname: Jang
authors.affiliation: Department of Chemical and Biomolecular Engineering (BK21+ Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea; School of Biomedical Engineering, Inje University, Inje-ro 197, Gimhae, Gyeongnam 50834, Republic of Korea.
authors.forename: Yun Kyung
authors.initials: YK
authors.lastname: Jung
authors.affiliation: Department of Chemical and Biomolecular Engineering (BK21+ Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea; Department of Business Opportunity Analysis, Technology Innovation Analysis Center, Korea Institute of Science and Technology Information (KISTI), Seoul 130-741, Republic of Korea.
authors.forename: Ye Lim
authors.initials: YL
authors.lastname: Jung
authors.affiliation: Labgenomics Co., Ltd. Korea Bio Park, 694-1 Sampyeong-dong, Bundang-gu, Seongnam-si, Gyeongi-do 463-400, Republic of Korea.
authors.forename: Inkyung
authors.initials: I
authors.lastname: Shin
authors.affiliation: Labgenomics Co., Ltd. Korea Bio Park, 694-1 Sampyeong-dong, Bundang-gu, Seongnam-si, Gyeongi-do 463-400, Republic of Korea.
authors.forename: Dae-Yeon
authors.initials: DY
authors.lastname: Cho
authors.affiliation: Department of Chemical and Biomolecular Engineering (BK21+ Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea. Electronic address: hgpark@kaist.ac.kr.
authors.forename: Hyun Gyu
authors.initials: HG
authors.lastname: Park
mesh_terms: D000483:Alleles; D015374:Biosensing Techniques / Q000379:methods; D001943:Breast Neoplasms / Q000235:genetics*; D005260:Female; D019398:Genes, BRCA1; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D021141:Nucleic Acid Amplification Techniques / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*
keywords: Allele-specific ligation; BRCA gene; Label-free biosensor; Mass spectrometry; SNP genotyping; Strand displacement amplification