Targeted next-generation sequencing to diagnose disorders of HDL cholesterol
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...
Main Authors: | , , , , , , , , , , , , , , |
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Format: | Article |
Language: | English |
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Elsevier
2015-10-01
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Series: | Journal of Lipid Research |
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Online Access: | http://www.sciencedirect.com/science/article/pii/S0022227520309743 |
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doaj-d70d79cdd481407b9644a9666ec59f06 |
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record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Singh N. Sadananda Jia Nee Foo Meng Tiak Toh Lubomira Cermakova Laia Trigueros-Motos Teddy Chan Herty Liany Jennifer A. Collins Sima Gerami Roshni R. Singaraja Michael R. Hayden Gordon A. Francis Jiri Frohlich Chiea Chuen Khor Liam R. Brunham |
spellingShingle |
Singh N. Sadananda Jia Nee Foo Meng Tiak Toh Lubomira Cermakova Laia Trigueros-Motos Teddy Chan Herty Liany Jennifer A. Collins Sima Gerami Roshni R. Singaraja Michael R. Hayden Gordon A. Francis Jiri Frohlich Chiea Chuen Khor Liam R. Brunham Targeted next-generation sequencing to diagnose disorders of HDL cholesterol Journal of Lipid Research ATP binding cassette transporter A1 diagnostic tools genetics genomics high density lipoprotein atherosclerosis |
author_facet |
Singh N. Sadananda Jia Nee Foo Meng Tiak Toh Lubomira Cermakova Laia Trigueros-Motos Teddy Chan Herty Liany Jennifer A. Collins Sima Gerami Roshni R. Singaraja Michael R. Hayden Gordon A. Francis Jiri Frohlich Chiea Chuen Khor Liam R. Brunham |
author_sort |
Singh N. Sadananda |
title |
Targeted next-generation sequencing to diagnose disorders of HDL cholesterol |
title_short |
Targeted next-generation sequencing to diagnose disorders of HDL cholesterol |
title_full |
Targeted next-generation sequencing to diagnose disorders of HDL cholesterol |
title_fullStr |
Targeted next-generation sequencing to diagnose disorders of HDL cholesterol |
title_full_unstemmed |
Targeted next-generation sequencing to diagnose disorders of HDL cholesterol |
title_sort |
targeted next-generation sequencing to diagnose disorders of hdl cholesterol |
publisher |
Elsevier |
series |
Journal of Lipid Research |
issn |
0022-2275 |
publishDate |
2015-10-01 |
description |
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. |
topic |
ATP binding cassette transporter A1 diagnostic tools genetics genomics high density lipoprotein atherosclerosis |
url |
http://www.sciencedirect.com/science/article/pii/S0022227520309743 |
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doaj-d70d79cdd481407b9644a9666ec59f062021-04-29T04:34:32ZengElsevierJournal of Lipid Research0022-22752015-10-01561019932001Targeted next-generation sequencing to diagnose disorders of HDL cholesterolSingh N. Sadananda0Jia Nee Foo1Meng Tiak Toh2Lubomira Cermakova3Laia Trigueros-Motos4Teddy Chan5Herty Liany6Jennifer A. Collins7Sima Gerami8Roshni R. Singaraja9Michael R. Hayden10Gordon A. Francis11Jiri Frohlich12Chiea Chuen Khor13Liam R. Brunham14Translational Laboratory in Genetic Medicine,Agency for Science Technology and Research (A*STAR) and National University of Singapore, SingaporeHuman Genetics, Genome Institute of Singapore,Agency for Science Technology and Research (A*STAR), SingaporeTranslational Laboratory in Genetic Medicine,Agency for Science Technology and Research (A*STAR) and National University of Singapore, SingaporeHealthy Heart Program Prevention Clinic, St. Paul's Hospital, Vancouver, CanadaTranslational Laboratory in Genetic Medicine,Agency for Science Technology and Research (A*STAR) and National University of Singapore, SingaporeCentre for Heart Lung Innovation, University of British Columbia, Vancouver, CanadaHuman Genetics, Genome Institute of Singapore,Agency for Science Technology and Research (A*STAR), SingaporeCentre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, CanadaHealthy Heart Program Prevention Clinic, St. Paul's Hospital, Vancouver, CanadaTranslational Laboratory in Genetic Medicine,Agency for Science Technology and Research (A*STAR) and National University of Singapore, SingaporeTranslational Laboratory in Genetic Medicine,Agency for Science Technology and Research (A*STAR) 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, SingaporeHealthy 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, CanadaHealthy Heart Program Prevention Clinic, St. Paul's Hospital, Vancouver, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, CanadaHuman Genetics, Genome Institute of Singapore,Agency for Science Technology and Research (A*STAR), SingaporeTranslational Laboratory in Genetic Medicine,Agency for Science Technology and Research (A*STAR) 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; To whom correspondence should be addressed.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.http://www.sciencedirect.com/science/article/pii/S0022227520309743ATP binding cassette transporter A1diagnostic toolsgeneticsgenomicshigh density lipoproteinatherosclerosis |