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Article: Targeted next-generation sequencing on hirschsprung disease: A pilot study exploits DNA pooling

TitleTargeted next-generation sequencing on hirschsprung disease: A pilot study exploits DNA pooling
Authors
KeywordsCDS
Rare variant
Targeted resequencing
RainDance
HSCR
Issue Date2014
Citation
Annals of Human Genetics, 2014, v. 78, n. 5, p. 381-387 How to Cite?
AbstractTo adopt an efficient approach of identifying rare variants possibly related to Hirschsprung disease (HSCR), a pilot study was set up to evaluate the performance of a newly designed protocol for next generation targeted resquencing. In total, 20 Chinese HSCR patients and 20 Chinese sex-matched individuals with no HSCR were included, for which coding sequences (CDS) of 62 genes known to be in signaling pathways relevant to enteric nervous system development were selected for capture and sequencing. Blood DNAs from eight pools of five cases or controls were enriched by PCR-based RainDance technology (RDT) and then sequenced on a 454 FLX platform. As technical validation, five patients from case Pool-3 were also independently enriched by RDT, indexed with barcode and sequenced with sufficient coverage. Assessment for CDS single nucleotide variants showed DNA pooling performed well (specificity/sensitivity at 98.4%/83.7%) at the common variant level; but relatively worse (specificity/sensitivity at 65.5%/61.3%) at the rare variant level. Further Sanger sequencing only validated five out of 12 rare damaging variants likely involved in HSCR. Hence more improvement at variant detection and sequencing technology is needed to realize the potential of DNA pooling for large-scale resequencing projects. © 2014 John Wiley & Sons Ltd/University College London.
Persistent Identifierhttp://hdl.handle.net/10722/220762
ISSN
2015 Impact Factor: 1.889
2015 SCImago Journal Rankings: 1.191
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorGui, Hongsheng-
dc.contributor.authorBao, Jessie Yunjuan-
dc.contributor.authorTang, Clara Sze Man-
dc.contributor.authorSo, Man Ting-
dc.contributor.authorNgo, Diem Ngoc-
dc.contributor.authorTran, Anh Quynh-
dc.contributor.authorBui, Duc Hau-
dc.contributor.authorPham, Duy Hien-
dc.contributor.authorNguyen, Thanh Liem-
dc.contributor.authorTong, Amy-
dc.contributor.authorLok, Si-
dc.contributor.authorSham, Pak Chung-
dc.contributor.authorTam, Paul Kwong Hang-
dc.contributor.authorCherny, Stacey S.-
dc.contributor.authorGarcia-Barcelo, Maria Mercè-
dc.date.accessioned2015-10-16T06:50:28Z-
dc.date.available2015-10-16T06:50:28Z-
dc.date.issued2014-
dc.identifier.citationAnnals of Human Genetics, 2014, v. 78, n. 5, p. 381-387-
dc.identifier.issn0003-4800-
dc.identifier.urihttp://hdl.handle.net/10722/220762-
dc.description.abstractTo adopt an efficient approach of identifying rare variants possibly related to Hirschsprung disease (HSCR), a pilot study was set up to evaluate the performance of a newly designed protocol for next generation targeted resquencing. In total, 20 Chinese HSCR patients and 20 Chinese sex-matched individuals with no HSCR were included, for which coding sequences (CDS) of 62 genes known to be in signaling pathways relevant to enteric nervous system development were selected for capture and sequencing. Blood DNAs from eight pools of five cases or controls were enriched by PCR-based RainDance technology (RDT) and then sequenced on a 454 FLX platform. As technical validation, five patients from case Pool-3 were also independently enriched by RDT, indexed with barcode and sequenced with sufficient coverage. Assessment for CDS single nucleotide variants showed DNA pooling performed well (specificity/sensitivity at 98.4%/83.7%) at the common variant level; but relatively worse (specificity/sensitivity at 65.5%/61.3%) at the rare variant level. Further Sanger sequencing only validated five out of 12 rare damaging variants likely involved in HSCR. Hence more improvement at variant detection and sequencing technology is needed to realize the potential of DNA pooling for large-scale resequencing projects. © 2014 John Wiley & Sons Ltd/University College London.-
dc.languageeng-
dc.relation.ispartofAnnals of Human Genetics-
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.rightsThe definitive version is available at www.blackwell-synergy.com-
dc.subjectCDS-
dc.subjectRare variant-
dc.subjectTargeted resequencing-
dc.subjectRainDance-
dc.subjectHSCR-
dc.titleTargeted next-generation sequencing on hirschsprung disease: A pilot study exploits DNA pooling-
dc.typeArticle-
dc.description.naturepostprint-
dc.identifier.doi10.1111/ahg.12076-
dc.identifier.pmid24947032-
dc.identifier.scopuseid_2-s2.0-84905913538-
dc.identifier.hkuros240067-
dc.identifier.hkuros232570-
dc.identifier.hkuros232571-
dc.identifier.volume78-
dc.identifier.issue5-
dc.identifier.spage381-
dc.identifier.epage387-
dc.identifier.eissn1469-1809-
dc.identifier.isiWOS:000340424200007-

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