title: Targeted next-generation sequencing to diagnose disorders of HDL cholesterol.
abstract: A low level of HDL cholesterol (HDL-C) is a common clinical scenario and an important marker for increased cardiovascular risk. Many patients with very low or very high HDL-C have a rare mutation in one of several genes, but identification of the molecular abnormality in patients with extreme HDL-C is rarely performed in clinical practice. We investigated the accuracy and diagnostic yield of a targeted next-generation sequencing (NGS) assay for extreme levels of HDL-C. We developed a targeted NGS panel to capture the exons, intron/exon boundaries, and untranslated regions of 26 genes with highly penetrant effects on plasma lipid levels. We sequenced 141 patients with extreme HDL-C levels and prioritized variants in accordance with medical genetics guidelines. We identified 35 pathogenic and probably pathogenic variants in HDL genes, including 21 novel variants, and performed functional validation on a subset of these. Overall, a molecular diagnosis was established in 35.9% of patients with low HDL-C and 5.2% with high HDL-C, and all prioritized variants identified by NGS were confirmed by Sanger sequencing. Our results suggest that a molecular diagnosis can be identified in a substantial proportion of patients with low HDL-C using targeted NGS.
authors.affiliation: Translational Laboratory in Genetic Medicine, Agency for Science Technology and Research (ASTAR) and National University of Singapore, Singapore.
authors.forename: Singh N
authors.initials: SN
authors.lastname: Sadananda
authors.affiliation: Human Genetics, Genome Institute of Singapore, Agency for Science Technology and Research (ASTAR), Singapore.
authors.forename: Jia Nee
authors.initials: JN
authors.lastname: Foo
authors.affiliation: Translational Laboratory in Genetic Medicine, Agency for Science Technology and Research (ASTAR) and National University of Singapore, Singapore.
authors.forename: Meng Tiak
authors.initials: MT
authors.lastname: Toh
authors.affiliation: Healthy Heart Program Prevention Clinic, St. Paul's Hospital, Vancouver, Canada.
authors.forename: Lubomira
authors.initials: L
authors.lastname: Cermakova
authors.affiliation: Translational Laboratory in Genetic Medicine, Agency for Science Technology and Research (ASTAR) and National University of Singapore, Singapore.
authors.forename: Laia
authors.initials: L
authors.lastname: Trigueros-Motos
authors.affiliation: Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada.
authors.forename: Teddy
authors.initials: T
authors.lastname: Chan
authors.affiliation: Human Genetics, Genome Institute of Singapore, Agency for Science Technology and Research (ASTAR), Singapore.
authors.forename: Herty
authors.initials: H
authors.lastname: Liany
authors.affiliation: Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada.
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Collins
authors.affiliation: Healthy Heart Program Prevention Clinic, St. Paul's Hospital, Vancouver, Canada.
authors.forename: Sima
authors.initials: S
authors.lastname: Gerami
authors.affiliation: Translational Laboratory in Genetic Medicine, Agency for Science Technology and Research (ASTAR) and National University of Singapore, Singapore.
authors.forename: Roshni R
authors.initials: RR
authors.lastname: Singaraja
authors.affiliation: Translational Laboratory in Genetic Medicine, Agency for Science Technology and Research (ASTAR) and National University of Singapore, Singapore Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Hayden
authors.affiliation: Healthy Heart Program Prevention Clinic, St. Paul's Hospital, Vancouver, Canada Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada Departments of Medicine University of British Columbia, Vancouver, Canada.
authors.forename: Gordon A
authors.initials: GA
authors.lastname: Francis
authors.affiliation: Healthy Heart Program Prevention Clinic, St. Paul's Hospital, Vancouver, Canada Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.
authors.forename: Jiri
authors.initials: J
authors.lastname: Frohlich
authors.affiliation: Human Genetics, Genome Institute of Singapore, Agency for Science Technology and Research (ASTAR), Singapore.
authors.forename: Chiea Chuen
authors.initials: CC
authors.lastname: Khor
authors.affiliation: Translational Laboratory in Genetic Medicine, Agency for Science Technology and Research (ASTAR) and National University of Singapore, Singapore Healthy Heart Program Prevention Clinic, St. Paul's Hospital, Vancouver, Canada Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore Departments of Medicine University of British Columbia, Vancouver, Canada.
authors.forename: Liam R
authors.initials: LR
authors.lastname: Brunham
mesh_terms: D064286:ATP Binding Cassette Transporter 1 / Q000097:blood / Q000235:genetics*; D000483:Alleles; D002318:Cardiovascular Diseases / Q000097:blood / Q000175:diagnosis / Q000235:genetics*; D008076:Cholesterol, HDL / Q000097:blood* / Q000235:genetics*; D005091:Exons; D005260:Female; D056726:Genetic Association Studies; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D006937:Hypercholesterolemia / Q000097:blood* / Q000235:genetics*; D007438:Introns; D008297:Male; D008875:Middle Aged; D012307:Risk Factors
chemical_list: C577836:ABCA1 protein, human; D064286:ATP Binding Cassette Transporter 1; D008076:Cholesterol, HDL
keywords: ATP binding cassette transporter A1; atherosclerosis; diagnostic tools; genetics; genomics; high density lipoprotein; molecular diagnosis