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Massively parallel sequencing of the entire control region and targeted coding region SNPs of degraded mtDNA using a simplified library preparation method.

DC Field Value Language
dc.contributor.author신경진-
dc.contributor.author양우익-
dc.contributor.author이은영-
dc.contributor.author이환영-
dc.contributor.author정상은-
dc.contributor.author양인석-
dc.date.accessioned2017-02-27T07:46:45Z-
dc.date.available2017-02-27T07:46:45Z-
dc.date.issued2016-
dc.identifier.issn1872-4973-
dc.identifier.urihttps://ir.ymlib.yonsei.ac.kr/handle/22282913/146988-
dc.description.abstractThe application of next-generation sequencing (NGS) to forensic genetics is being explored by an increasing number of laboratories because of the potential of high-throughput sequencing for recovering genetic information from multiple markers and multiple individuals in a single run. A cumbersome and technically challenging library construction process is required for NGS. In this study, we propose a simplified library preparation method for mitochondrial DNA (mtDNA) analysis that involves two rounds of PCR amplification. In the first-round of multiplex PCR, six fragments covering the entire mtDNA control region and 22 fragments covering interspersed single nucleotide polymorphisms (SNPs) in the coding region that can be used to determine global haplogroups and East Asian haplogroups were amplified using template-specific primers with read sequences. In the following step, indices and platform-specific sequences for the MiSeq(®) system (Illumina) were added by PCR. The barcoded library produced using this simplified workflow was successfully sequenced on the MiSeq system using the MiSeq Reagent Nano Kit v2. A total of 0.4 GB of sequences, 80.6% with base quality of >Q30, were obtained from 12 degraded DNA samples and mapped to the revised Cambridge Reference Sequence (rCRS). A relatively even read count was obtained for all amplicons, with an average coverage of 5200 × and a less than three-fold read count difference between amplicons per sample. Control region sequences were successfully determined, and all samples were assigned to the relevant haplogroups. In addition, enhanced discrimination was observed by adding coding region SNPs to the control region in in silico analysis. Because the developed multiplex PCR system amplifies small-sized amplicons (<250 bp), NGS analysis using the library preparation method described here allows mtDNA analysis using highly degraded DNA samples.-
dc.description.statementOfResponsibilityrestriction-
dc.languageEnglish-
dc.publisherElsevier-
dc.relation.isPartOfFORENSIC SCIENCE INTERNATIONAL-GENETICS-
dc.rightsCC BY-NC-ND 2.0 KR-
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/2.0/kr/-
dc.subject.MESHAsian Continental Ancestry Group/genetics-
dc.subject.MESHBase Sequence-
dc.subject.MESHDNA Fingerprinting/methods-
dc.subject.MESHDNA Primers-
dc.subject.MESHDNA, Mitochondrial/analysis-
dc.subject.MESHDNA, Mitochondrial/genetics*-
dc.subject.MESHForensic Genetics/methods-
dc.subject.MESHGenomic Library*-
dc.subject.MESHHaplotypes-
dc.subject.MESHHigh-Throughput Nucleotide Sequencing/methods*-
dc.subject.MESHHumans-
dc.subject.MESHMultiplex Polymerase Chain Reaction/methods*-
dc.subject.MESHPolymorphism, Single Nucleotide-
dc.subject.MESHSequence Analysis, DNA-
dc.titleMassively parallel sequencing of the entire control region and targeted coding region SNPs of degraded mtDNA using a simplified library preparation method.-
dc.typeArticle-
dc.publisher.locationNetherlands-
dc.contributor.collegeCollege of Medicine-
dc.contributor.departmentDept. of Forensic Medicine-
dc.contributor.googleauthorEun Young Lee-
dc.contributor.googleauthorHwan Young Lee-
dc.contributor.googleauthorSe Yoon Oh-
dc.contributor.googleauthorSang-Eun Jung-
dc.contributor.googleauthorIn Seok Yang-
dc.contributor.googleauthorYang-Han Lee-
dc.contributor.googleauthorWoo Ick Yang-
dc.contributor.googleauthorKyoung-Jin Shin-
dc.identifier.doi10.1016/j.fsigen.2016.01.014-
dc.contributor.localIdA02085-
dc.contributor.localIdA02300-
dc.contributor.localIdA03041-
dc.contributor.localIdA03335-
dc.contributor.localIdA03614-
dc.relation.journalcodeJ00905-
dc.identifier.eissn1878-0326-
dc.identifier.pmid26844917-
dc.identifier.urlhttp://www.sciencedirect.com/science/article/pii/S187249731630014X-
dc.subject.keywordHaplogroup-
dc.subject.keywordLibrary preparation-
dc.subject.keywordMitochondrial DNA-
dc.subject.keywordNext-generation sequencing-
dc.contributor.alternativeNameShin, Kyoung Jin-
dc.contributor.alternativeNameYang, Woo Ick-
dc.contributor.alternativeNameLee, Eun Young-
dc.contributor.alternativeNameLee, Hwan Young-
dc.contributor.alternativeNameJung, Sang Eun-
dc.contributor.affiliatedAuthorShin, Kyoung Jin-
dc.contributor.affiliatedAuthorYang, Woo Ick-
dc.contributor.affiliatedAuthorLee, Eun Young-
dc.contributor.affiliatedAuthorLee, Hwan Young-
dc.contributor.affiliatedAuthorJung, Sang Eun-
dc.citation.volume22-
dc.citation.startPage37-
dc.citation.endPage43-
dc.identifier.bibliographicCitationFORENSIC SCIENCE INTERNATIONAL-GENETICS, Vol.22 : 37-43, 2016-
dc.date.modified2017-02-24-
dc.identifier.rimsid47021-
dc.type.rimsART-
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Biomedical Systems Informatics (의생명시스템정보학교실) > 1. Journal Papers
1. College of Medicine (의과대학) > Dept. of Forensic Medicine (법의학과) > 1. Journal Papers
1. College of Medicine (의과대학) > Dept. of Pathology (병리학교실) > 1. Journal Papers

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