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Dabravolski SA, Orekhov NA, Glanz VY, Sukhorukov VN, Pleshko EM, Orekhov AN. Role of ABCA1 in Atherosclerosis: Novel Mutations and Potential Plant-derived Therapies. Curr Med Chem 2025; 32:2069-2092. [PMID: 38529605 DOI: 10.2174/0109298673291917240315113845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/27/2024]
Abstract
ATP-binding cassette transporter A1 (ABCA1) is one of the key proteins regulating cholesterol homeostasis and playing a crucial role in atherosclerosis development. ABCA1 regulates the rate-limiting step of reverse cholesterol transport, facilitates the efflux of surplus intracellular cholesterol and phospholipids, and suppresses inflammation through several signalling pathways. At the same time, many mutations and Single Nucleotide Polymorphisms (SNPs) have been identified in the ABCA1 gene, which affects its biological function and is associated with several hereditary diseases (such as familial hypo-alpha-lipoproteinaemia and Tangier disease) and increased risk of cardiovascular diseases (CVDs). This review summarises recently identified mutations and SNPs in their connection to atherosclerosis and associated CVDs. Also, we discuss the recently described application of various plant-derived compounds to modulate ABCA1 expression in different in vitro and in vivo models. Herein, we present a comprehensive overview of the association of ABCA1 mutations and SNPs with CVDs and as a pharmacological target for different natural-derived compounds and highlight the potential application of these phytochemicals for treating atherosclerosis through modulation of ABCA1 expression.
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Affiliation(s)
- Siarhei A Dabravolski
- Department of Biotechnology Engineering, Braude Academic College of Engineering, Snunit 51, P.O. Box 78, Karmiel, 2161002, Israel
| | - Nikolay A Orekhov
- Institute of General Pathology and Pathophysiology, 8 Baltiyskaya Street, Moscow, 125315, Russia
| | - Victor Y Glanz
- Petrovsky Russian National Center of Surgery, 2 Abrikosovsky Lane, 119991, Moscow, Russia
| | - Vasily N Sukhorukov
- Petrovsky Russian National Center of Surgery, 2 Abrikosovsky Lane, 119991, Moscow, Russia
| | - Elizaveta M Pleshko
- Institute of General Pathology and Pathophysiology, 8 Baltiyskaya Street, Moscow, 125315, Russia
| | - Alexander N Orekhov
- Petrovsky Russian National Center of Surgery, 2 Abrikosovsky Lane, 119991, Moscow, Russia
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2
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Saidi LK, Md Rani ZZ, Sulaiman SA, Jamal R, Ismail A, Alim AA, Ayob SNSA, Dee CF, Hamzah AA, Abdul Murad NA. Development of DNA-Based Lateral Flow Assay for Detection of LDLR Gene Mutation for Familial Hypercholesterolemia. Malays J Med Sci 2024; 31:92-106. [PMID: 38984253 PMCID: PMC11229576 DOI: 10.21315/mjms2024.31.3.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/29/2023] [Indexed: 07/11/2024] Open
Abstract
Background The techniques for detecting single nucleotide polymorphisms (SNP) require lengthy and complex experimental procedures and expensive instruments that may only be available in some laboratories. Thus, a deoxyribonucleic acid (DNA)-based lateral flow assay (LFA) was developed as a point-of-care test (POCT) diagnostic tool for genotyping. In this study, single nucleotide variation (E101K) in the low-density lipoprotein receptor (LDLR) gene leading to familial hypercholesterolemia (FH) was chosen as a model. Methods Hypercholesterolemic individuals (n = 103) were selected from the Malaysian Cohort project (UKM Medical Molecular Biology Institute) while the control samples were selected from the Biobank (UKM Medical Molecular Biology Institute). The DNA samples were isolated from whole blood. Polymerase chain reaction (PCR) amplification process was performed using bifunctional labelled primers specifically designed to correspond to the variant that differentiates wild-type and mutant DNA for visual detection on LFA. The variant was confirmed using Sanger sequencing, and the sensitivity and specificity of the LFA detection method were validated using the Agena MassARRAY® technique. Results Out of 103 hypercholesterolemic individuals, 5 individuals (4.8%) tested positive for E101K, LDLR mutation and the rest, including healthy control individuals, tested negative. This result was concordant with Sanger sequencing and Agena MassARRAY®. These five individuals could be classified as Definite FH, as the DNA diagnosis was confirmed. The sensitivity and specificity of the variant detection by LFA is 100% compared to results using the genotyping method using Agena MassARRAY®. Conclusion The developed LFA can potentially be used in the POC setting for detecting the E101K variant in the LDLR gene. This LFA can also be used to screen family members with E101K variant in the LDLR gene and is applicable for other SNP's detection.
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Affiliation(s)
- Lina Khalida Saidi
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Zam Zureena Md Rani
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Siti Aishah Sulaiman
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Aziah Ismail
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Kelantan, Malaysia
| | - Anis Amirah Alim
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Sharipah Nadzirah Syed Ahmad Ayob
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Selangor, Malaysia
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Perlis, Malaysia
| | - Chang Fu Dee
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Azrul Azlan Hamzah
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Nor Azian Abdul Murad
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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Xu P, Al-Anesi MMA, Huang M, Wu S, Ge Y, Chai H, Li P, Hu Q. Copy number variation of metallothionein 1 (MT1) associates with MT1X isoform expression and the overall survival of hepatocellular carcinoma patients in Guangxi. GENE REPORTS 2024; 34:101889. [DOI: 10.1016/j.genrep.2024.101889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
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Shi H, Li T, Su M, Wang H, Li Q, Lang X, Ma Y. Identification of copy number variation in Tibetan sheep using whole genome resequencing reveals evidence of genomic selection. BMC Genomics 2023; 24:555. [PMID: 37726692 PMCID: PMC10510117 DOI: 10.1186/s12864-023-09672-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 09/12/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND Copy number variation (CNV) is an important source of structural variation in the mammalian genome. CNV assays present a new method to explore the genomic diversity of environmental adaptations in animals and plants and genes associated with complex traits. In this study, the genome-wide CNV distribution characteristics of 20 Tibetan sheep from two breeds (10 Oula sheep and 10 Panou sheep) were analysed using whole-genome resequencing to investigate the variation in the genomic structure of Tibetan sheep during breeding. RESULTS CNVs were detected using CNVnator, and the overlapping regions of CNVs between individual sheep were combined. Among them, a total of 60,429 CNV events were detected between the indigenous sheep breed (Oula) and the synthetic sheep breed (Panou). After merging the overlapping CNVs, 4927 CNV regions (CNVRs) were finally obtained. Of these, 4559 CNVRs were shared by two breeds, and there were 368 differential CNVRs. Deletion events have a higher percentage of occurrences than duplication events. Functional enrichment analysis showed that the shared CNVRs were significantly enriched in 163 GO terms and 62 KEGG pathways, which were mainly associated with organ development, neural regulation, immune regulation, digestion and metabolism. In addition, 140 QTLs overlapped with some of the CNVRs at more than 1 kb, such as average daily gain QTL, body weight QTL, and total lambs born QTL. Many of the CNV-overlapping genes such as PPP3CA, SSTR1 and FASN, overlap with the average daily weight gain and carcass weight QTL regions. Moreover, VST analysis showed that XIRP2, ABCB1, CA1, ASPA and EEF2 differed significantly between the synthetic breed and local sheep breed. The duplication of the ABCB1 gene may be closely related to adaptation to the plateau environment in Panou sheep, which deserves further study. Additionally, cluster analysis, based on all individuals, showed that the CNV clustering could be divided into two origins, indicating that some Tibetan sheep CNVs are likely to arise independently in different populations and contribute to population differences. CONCLUSIONS Collectively, we demonstrated the genome-wide distribution characteristics of CNVs in Panou sheep by whole genome resequencing. The results provides a valuable genetic variation resource and help to understand the genetic characteristics of Tibetan sheep. This study also provides useful information for the improvement and breeding of Tibetan sheep in the future.
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Affiliation(s)
- Huibin Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China
- College of Animal Science & Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, 450046, China
| | - Taotao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China
| | - Manchun Su
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China
| | - Huihui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China
| | - Qiao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China
| | - Xia Lang
- Institute of Animal & Pasture Science and Green Agriculture, Gansu Academy of Agricultural Science, Lanzhou, 730070, China
| | - Youji Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China.
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Perera SD, Wang J, McIntyre AD, Hegele RA. Variability of longitudinal triglyceride phenotype in patients heterozygous for pathogenic APOA5 variants. J Clin Lipidol 2023; 17:659-665. [PMID: 37586912 DOI: 10.1016/j.jacl.2023.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 07/15/2023] [Accepted: 08/03/2023] [Indexed: 08/18/2023]
Abstract
BACKGROUND Biallelic pathogenic variants in APOA5 are an infrequent cause of familial chylomicronemia syndrome characterized by severe, refractory hypertriglyceridemia (HTG), and fasting plasma triglyceride (TG) >10 mmol/L (>875 mg/dL). The TG phenotype of heterozygous individuals with one copy of a pathogenic APOA5 variant is less familiar. We evaluated the longitudinal TG phenotype of individuals with a single pathogenic APOA5 variant allele. METHODS Medically stable outpatients from Ontario, Canada were selected for study based on having: 1) a rare pathogenic APOA5 variant in a single allele; and 2) at least three serial fasting TG measurements obtained over >1.5 years of follow-up. RESULTS Seven patients were followed for a mean of 5.3 ± 3.7 years. Fasting TG levels varied widely both within and between patients. Three patients displayed at least one normal TG measurement (<2.0 mmol/L or <175 mg/dL). All patients displayed mild-to-moderate HTG (2 to 9.9 mmol/L or 175 to 875 mg/dL) at multiple time points. Five patients displayed at least one severe HTG measurement. 10%, 54%, and 36% of all TG measurements were in normal, mild-to-moderate, and severe HTG ranges, respectively. CONCLUSIONS Heterozygosity for pathogenic variants in APOA5 is associated with highly variable TG phenotypes both within and between patients. Heterozygosity confers susceptibility to elevated TG levels, with secondary factors likely modulating the phenotypic severity.
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Affiliation(s)
- Shehan D Perera
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Jian Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Adam D McIntyre
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Robert A Hegele
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.
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Huang T, Xiao Y, Zhang Y, Ge Y, Gao J. Combination of single-nucleus and bulk RNA-seq reveals the molecular mechanism of thalamus haemorrhage-induced central poststroke pain. Front Immunol 2023; 14:1174008. [PMID: 37153564 PMCID: PMC10157064 DOI: 10.3389/fimmu.2023.1174008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 04/10/2023] [Indexed: 05/09/2023] Open
Abstract
Central poststroke pain (CPSP) induced by thalamic haemorrhage (TH) can be continuous or intermittent and is accompanied by paresthesia, which seriously affects patient quality of life. Advanced insights into CPSP mechanisms and therapeutic strategies require a deeper understanding of the molecular processes of the thalamus. Here, using single-nucleus RNA sequencing (snRNA-seq), we sequenced the transcriptomes of 32332 brain cells, which revealed a total of four major cell types within the four thalamic samples from mice. Compared with the control group, the experimental group possessed the higher sensitivity to mechanical, thermal, and cold stimuli, and increased microglia numbers and decreased neuron numbers. We analysed a collection of differentially expressed genes and neuronal marker genes obtained from bulk RNA sequencing (bulk RNA-seq) data and found that Apoe, Abca1, and Hexb were key genes verified by immunofluorescence (IF). Immune infiltration analysis found that these key genes were closely related to macrophages, T cells, related chemokines, immune stimulators and receptors. Gene Ontology (GO) enrichment analysis also showed that the key genes were enriched in biological processes such as protein export from nucleus and protein sumoylation. In summary, using large-scale snRNA-seq, we have defined the transcriptional and cellular diversity in the brain after TH. Our identification of discrete cell types and differentially expressed genes within the thalamus can facilitate the development of new CPSP therapeutics.
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Affiliation(s)
- Tianfeng Huang
- Northern Jiangsu People's Hospital Affiliated to Yangzhou University/Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu, China
- Yangzhou Key Laboratory of Anesthesiology, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, China
| | - Yinggang Xiao
- Northern Jiangsu People's Hospital Affiliated to Yangzhou University/Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu, China
- Yangzhou Key Laboratory of Anesthesiology, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, China
| | - Yang Zhang
- Northern Jiangsu People's Hospital Affiliated to Yangzhou University/Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu, China
- Yangzhou Key Laboratory of Anesthesiology, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, China
| | - Yali Ge
- Northern Jiangsu People's Hospital Affiliated to Yangzhou University/Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu, China
- Yangzhou Key Laboratory of Anesthesiology, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, China
| | - Ju Gao
- Northern Jiangsu People's Hospital Affiliated to Yangzhou University/Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu, China
- Yangzhou Key Laboratory of Anesthesiology, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, China
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7
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Perera SD, Wang J, McIntyre AD, Dron JS, Hegele RA. The longitudinal triglyceride phenotype in heterozygotes with LPL pathogenic variants. J Clin Lipidol 2023; 17:87-93. [PMID: 36476373 DOI: 10.1016/j.jacl.2022.11.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/07/2022] [Accepted: 11/14/2022] [Indexed: 11/23/2022]
Abstract
BACKGROUND Biallelic pathogenic variants in lipoprotein lipase (LPL) cause familial chylomicronemia syndrome with severe hypertriglyceridemia (HTG), defined as plasma triglycerides (TG) > 10 mmol/L (> 885 mg/dL). TG levels in individuals with one copy of a pathogenic LPL gene variant is less familiar; some assume that the phenotype is intermediate between homozygotes and controls. OBJECTIVE We undertook an evaluation of the longitudinal TG phenotype of individuals heterozygous for pathogenic LPL variants. METHODS Medically stable outpatients were evaluated based on having: (1) a single copy of a rare pathogenic LPL variant; and (2) serial fasting TG measurements obtained over > 1.5 years of follow-up. RESULTS Fifteen patients with a single pathogenic LPL variant were followed for a mean of 10.3 years (range 1.5 to 30.3 years). TG levels varied widely both within and between patients. One patient had normal TG levels < 2.0 mmol/L (< 175 mg/dL) continuously, while four patients had at least one normal TG level. Most patients fluctuated between mild-to-moderate and severe HTG: five patients had only mild-to-moderate HTG, with TG levels ranging from 2.0 to 9.9 mmol/L (175 to 885 mg/dL), while 6 patients had at least one instance of severe HTG. Of the 203 total TG measurements from these patients, 14.8%, 67.0% and 18.2% were in the normal, mild-to-moderate and severe HTG ranges, respectively. CONCLUSION The heterozygous LPL deficient phenotype is highly variable both within and between patients. Heterozygosity confers susceptibility to a wide range of TG phenotypes, with severity likely depending on secondary factors.
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Affiliation(s)
- Shehan D Perera
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 4288A-1151 Richmond Street North, London, Ontario N6A 5B7, Canada (Perera, Wang, McIntyre and Hegele); Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada (Perera and Hegele)
| | - Jian Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 4288A-1151 Richmond Street North, London, Ontario N6A 5B7, Canada (Perera, Wang, McIntyre and Hegele)
| | - Adam D McIntyre
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 4288A-1151 Richmond Street North, London, Ontario N6A 5B7, Canada (Perera, Wang, McIntyre and Hegele)
| | - Jacqueline S Dron
- Center for Genomic Medicine, Massachusetts General Hopsital, Boston, Massachusetts, USA (Dron)
| | - Robert A Hegele
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 4288A-1151 Richmond Street North, London, Ontario N6A 5B7, Canada (Perera, Wang, McIntyre and Hegele); Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada (Perera and Hegele); Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada (Hegele).
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Hu L, Zhang L, Li Q, Liu H, Xu T, Zhao N, Han X, Xu S, Zhao X, Zhang C. Genome-wide analysis of CNVs in three populations of Tibetan sheep using whole-genome resequencing. Front Genet 2022; 13:971464. [PMID: 36160022 PMCID: PMC9490000 DOI: 10.3389/fgene.2022.971464] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/23/2022] [Indexed: 01/29/2023] Open
Abstract
Copy number variation (CNV), an important source of genomic structural variation, can disturb genetic structure, dosage, regulation and expression, and is associated with phenotypic diversity and adaptation to local environments in mammals. In the present study, 24 resequencing datasets were used to characterize CNVs in three ecotypic populations of Tibetan sheep and assess CNVs related to domestication and adaptation in Qinghai-Tibetan Plateau. A total of 87,832 CNV events accounting for 0.3% of the sheep genome were detected. After merging the overlapping CNVs, 2777 CNV regions (CNVRs) were obtained, among which 1098 CNVRs were shared by the three populations. The average length of these CNVRs was more than 3 kb, and duplication events were more frequent than deletions. Functional analysis showed that the shared CNVRs were significantly enriched in 56 GO terms and 18 KEGG pathways that were mainly concerned with ABC transporters, olfactory transduction and oxygen transport. Moreover, 188 CNVRs overlapped with 97 quantitative trait loci (QTLs), such as growth and carcass QTLs, immunoglobulin QTLs, milk yield QTLs and fecal egg counts QTLs. PCDH15, APP and GRID2 overlapped with body weight QTLs. Furthermore, Vst analysis showed that RUNX1, LOC101104348, LOC105604082 and PAG11 were highly divergent between Highland-type Tibetan Sheep (HTS) and Valley-type Tibetan sheep (VTS), and RUNX1 and LOC101111988 were significantly differentiated between VTS and Oura-type Tibetan sheep (OTS). The duplication of RUNX1 may facilitate the hypoxia adaptation of OTS and HTS in Qinghai-Tibetan Plateau, which deserves further research in detail. In conclusion, for the first time, we represented the genome-wide distribution characteristics of CNVs in Tibetan sheep by resequencing, and provided a valuable genetic variation resource, which will facilitate the elucidation of the genetic basis underlying the distinct phenotypic traits and local adaptation of Tibetan sheep.
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Affiliation(s)
- Linyong Hu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Qi Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Hongjin Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Tianwei Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Na Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Xueping Han
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Technology Extension Service of Animal Husbandry of Qinghai, Xining, China
| | - Shixiao Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Xinquan Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Cunfang Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- *Correspondence: Cunfang Zhang,
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Gill PK, Dron JS, Dilliott AA, McIntyre AD, Cao H, Wang J, Movsesyan IG, Malloy MJ, Pullinger CR, Kane JP, Hegele RA. Ancestry-specific profiles of genetic determinants of severe hypertriglyceridemia. J Clin Lipidol 2021; 15:88-96. [PMID: 33303403 DOI: 10.1016/j.jacl.2020.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/31/2020] [Accepted: 11/17/2020] [Indexed: 12/01/2022]
Abstract
BACKGROUND Susceptibility to severe hypertriglyceridemia (HTG), defined as plasma triglyceride (TG) levels ≥10 mmol/L (880 mg/dL), is conferred by both heterozygous rare variants in five genes involved in TG metabolism and numerous common single-nucleotide polymorphisms (SNPs) associated with TG levels. OBJECTIVE To date, these genetic susceptibility factors have been comprehensively assessed primarily in severe HTG patients of European ancestry. Here, we expand our analysis to HTG patients of East Asian and Hispanic ancestry. METHODS The genomic DNA of 336, 63 and 199 severe HTG patients of European, East Asian and Hispanic ancestry, respectively, was evaluated using a targeted next-generation sequencing panel to screen for: 1) rare variants in LPL, APOA5, APOC2, GPIHBP1 and LMF1; 2) common, small-to-moderate effect SNPs, quantified using a polygenic score; and 3) common, large-effect polymorphisms, APOA5 p.G185C and p.S19W. RESULTS While the proportion of individuals with high polygenic scores was similar, frequency of rare variant carriers varied across ancestries. Compared with ancestry-matched controls, Hispanic patients were the most likely to have a rare variant (OR = 5.02; 95% CI 3.07-8.21; p < 0.001), while European patients were the least likely (OR = 2.56; 95% CI 1.58-4.13; p < 0.001). The APOA5 p.G185C polymorphism, exclusive to East Asians, was significantly enriched in patients compared with controls (OR = 10.1; 95% CI 5.6-18.3; p < 0.001), showing the highest enrichment among the measured genetic factors. CONCLUSION While TG-associated rare variants and common SNPs are both found in statistical excess in severe HTG patients of different ancestral backgrounds, the overall genetic profiles of each ancestry group were distinct.
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Affiliation(s)
- Praneet K Gill
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada; Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Jacqueline S Dron
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada; Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Allison A Dilliott
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada; Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Adam D McIntyre
- Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Henian Cao
- Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Jian Wang
- Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Irina G Movsesyan
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mary J Malloy
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Clive R Pullinger
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - John P Kane
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Robert A Hegele
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada; Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada.
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Gill PK, Dron JS, Berberich AJ, Wang J, McIntyre AD, Cao H, Hegele RA. Combined hyperlipidemia is genetically similar to isolated hypertriglyceridemia. J Clin Lipidol 2021; 15:79-87. [PMID: 33303402 DOI: 10.1016/j.jacl.2020.11.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/24/2020] [Accepted: 11/17/2020] [Indexed: 11/24/2022]
Abstract
BACKGROUND Combined hyperlipidemia (CHL) is a common disorder defined by concurrently elevated low-density lipoprotein cholesterol (LDL-C) and triglyceride (TG) levels. Despite decades of study, the genetic basis of CHL remains unclear. OBJECTIVE To characterize the genetic profiles of patients with CHL and compare them to those in patients with isolated hypercholesterolemia and isolated hypertriglyceridemia (HTG). METHODS DNA from 259, 379 and 124 patients with CHL, isolated hypercholesterolemia and isolated HTG, respectively, underwent targeted sequencing. We assessed: 1) rare variants disrupting canonical LDL-C or TG metabolism genes; and 2) two polygenic scores-for elevated LDL-C and TG-calculated using common trait-associated single-nucleotide polymorphisms (SNPs). Genetic profiles were compared against 1000 Genomes Project controls. RESULTS Both CHL and isolated HTG patients had significantly increased odds of a high polygenic score for TG: 2.50 (95% confidence interval [CI] 1.61-3.88; P < 0.001) and 3.72 (95% CI 2.24-6.19; P < 0.001), respectively. CHL patients had neither a significant accumulation of rare variants for LDL-C or TG, nor a high polygenic score for LDL-C. In contrast, patients with isolated hypercholesterolemia had a 3.03-fold increased odds (95% CI 2.22-4.13; P < 0.001) of carrying rare variants associated with familial hypercholesterolemia, while patients with isolated HTG had a 2.78-fold increased odds (95% CI 1.27-6.10; P = 0.0136) of carrying rare variants associated with severe HTG. CONCLUSION CHL is genetically similar to isolated HTG, a known polygenic trait. Both cohorts had a significant accumulation of common TG-raising variants. Elevated LDL-C levels in CHL are not associated with common or rare LDL-C-related genetic variants.
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Affiliation(s)
- Praneet K Gill
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada
| | - Jacqueline S Dron
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada; Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada
| | - Amanda J Berberich
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada; Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada; Department of Medicine, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada
| | - Jian Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada
| | - Adam D McIntyre
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada
| | - Henian Cao
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada
| | - Robert A Hegele
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada; Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada; Department of Medicine, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada.
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11
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Hegele RA, Dron JS. 2019 George Lyman Duff Memorial Lecture: Three Decades of Examining DNA in Patients With Dyslipidemia. Arterioscler Thromb Vasc Biol 2020; 40:1970-1981. [PMID: 32762461 DOI: 10.1161/atvbaha.120.313065] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Dyslipidemias include both rare single gene disorders and common conditions that have a complex underlying basis. In London, ON, there is fortuitous close physical proximity between the Lipid Genetics Clinic and the London Regional Genomics Centre. For >30 years, we have applied DNA sequencing of clinical samples to help answer scientific questions. More than 2000 patients referred with dyslipidemias have participated in an ongoing translational research program. In 2013, we transitioned to next-generation sequencing; our targeted panel is designed to concurrently assess both monogenic and polygenic contributions to dyslipidemias. Patient DNA is screened for rare variants underlying 25 mendelian dyslipidemias, including familial hypercholesterolemia, hepatic lipase deficiency, abetalipoproteinemia, and familial chylomicronemia syndrome. Furthermore, polygenic scores for LDL (low-density lipoprotein) and HDL (high-density lipoprotein) cholesterol, and triglycerides are calculated for each patient. We thus simultaneously document both rare and common genetic variants, allowing for a broad view of genetic predisposition for both individual patients and cohorts. For instance, among patients referred with severe hypertriglyceridemia, defined as ≥10 mmol/L (≥885 mg/dL), <1% have a mendelian disorder (ie, autosomal recessive familial chylomicronemia syndrome), ≈15% have heterozygous rare variants (a >3-fold increase over normolipidemic individuals), and ≈35% have an extreme polygenic score (a >3-fold increase over normolipidemic individuals). Other dyslipidemias show a different mix of genetic determinants. Genetic results are discussed with patients and can support clinical decision-making. Integrating DNA testing into clinical care allows for a bidirectional flow of information, which facilitates scientific discoveries and clinical translation.
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Affiliation(s)
- Robert A Hegele
- From the Department of Medicine (R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Biochemistry (R.A.H., J.S.D.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Robarts Research Institute (R.A.H., J.S.D.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Jacqueline S Dron
- Department of Biochemistry (R.A.H., J.S.D.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Robarts Research Institute (R.A.H., J.S.D.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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12
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Guan D, Martínez A, Castelló A, Landi V, Luigi-Sierra MG, Fernández-Álvarez J, Cabrera B, Delgado JV, Such X, Jordana J, Amills M. A genome-wide analysis of copy number variation in Murciano-Granadina goats. Genet Sel Evol 2020; 52:44. [PMID: 32770942 PMCID: PMC7414533 DOI: 10.1186/s12711-020-00564-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In this work, our aim was to generate a map of the copy number variations (CNV) segregating in a population of Murciano-Granadina goats, the most important dairy breed in Spain, and to ascertain the main biological functions of the genes that map to copy number variable regions. RESULTS Using a dataset that comprised 1036 Murciano-Granadina goats genotyped with the Goat SNP50 BeadChip, we were able to detect 4617 and 7750 autosomal CNV with the PennCNV and QuantiSNP software, respectively. By applying the EnsembleCNV algorithm, these CNV were assembled into 1461 CNV regions (CNVR), of which 486 (33.3% of the total CNVR count) were consistently called by PennCNV and QuantiSNP and used in subsequent analyses. In this set of 486 CNVR, we identified 78 gain, 353 loss and 55 gain/loss events. The total length of all the CNVR (95.69 Mb) represented 3.9% of the goat autosomal genome (2466.19 Mb), whereas their size ranged from 2.0 kb to 11.1 Mb, with an average size of 196.89 kb. Functional annotation of the genes that overlapped with the CNVR revealed an enrichment of pathways related with olfactory transduction (fold-enrichment = 2.33, q-value = 1.61 × 10-10), ABC transporters (fold-enrichment = 5.27, q-value = 4.27 × 10-04) and bile secretion (fold-enrichment = 3.90, q-value = 5.70 × 10-03). CONCLUSIONS A previous study reported that the average number of CNVR per goat breed was ~ 20 (978 CNVR/50 breeds), which is much smaller than the number we found here (486 CNVR). We attribute this difference to the fact that the previous study included multiple caprine breeds that were represented by small to moderate numbers of individuals. Given the low frequencies of CNV (in our study, the average frequency of CNV is 1.44%), such a design would probably underestimate the levels of the diversity of CNV at the within-breed level. We also observed that functions related with sensory perception, metabolism and embryo development are overrepresented in the set of genes that overlapped with CNV, and that these loci often belong to large multigene families with tens, hundreds or thousands of paralogous members, a feature that could favor the occurrence of duplications or deletions by non-allelic homologous recombination.
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Affiliation(s)
- Dailu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Amparo Martínez
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Anna Castelló
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Vincenzo Landi
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain.,Department of Veterinary Medicine, University of Bari "Aldo Moro", SP. 62 per Casamassima km. 3, 70010, Valenzano, BA, Italy
| | - María Gracia Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Javier Fernández-Álvarez
- Asociación Nacional de Criadores de Caprino de Raza Murciano-Granadina (CAPRIGRAN), 18340, Granada, Spain
| | - Betlem Cabrera
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | | | - Xavier Such
- Group of Research in Ruminants (G2R), Department of Animal and Food Science, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Jordi Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. .,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
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13
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Dron JS, Dilliott AA, Lawson A, McIntyre AD, Davis BD, Wang J, Cao H, Movsesyan I, Malloy MJ, Pullinger CR, Kane JP, Hegele RA. Loss-of-Function
CREB3L3
Variants in Patients With Severe Hypertriglyceridemia. Arterioscler Thromb Vasc Biol 2020; 40:1935-1941. [DOI: 10.1161/atvbaha.120.314168] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Objective:
Genetic determinants of severe hypertriglyceridemia include both common variants with small effects (assessed using polygenic risk scores) plus heterozygous and homozygous rare variants in canonical genes directly affecting triglyceride metabolism. Here, we broadened our scope to detect associations with rare loss-of-function variants in genes affecting noncanonical pathways, including those known to affect triglyceride metabolism indirectly.
Approach and Results:
From targeted next-generation sequencing of 69 metabolism-related genes in 265 patients of European descent with severe hypertriglyceridemia (≥10 mmol/L or ≥885 mg/dL) and 477 normolipidemic controls, we focused on the association of rare heterozygous loss-of-function variants in individual genes. We observed that compared with controls, severe hypertriglyceridemia patients were 20.2× (95% CI, 1.11–366.1;
P
=0.03) more likely than controls to carry a rare loss-of-function variant in
CREB3L3
, which encodes a transcription factor that regulates several target genes with roles in triglyceride metabolism.
Conclusions:
Our findings indicate that rare variants in a noncanonical gene for triglyceride metabolism, namely
CREB3L3
, contribute significantly to severe hypertriglyceridemia. Secondary genes and pathways should be considered when evaluating the genetic architecture of this complex trait.
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Affiliation(s)
- Jacqueline S. Dron
- From the Robarts Research Institute (J.S.D., A.A.D., A.L., A.D.M., J.W., H.C., R.A.H.), Western University, London, ON, Canada
- Department of Biochemistry (J.S.D., A.A.D., A.L., R.A.H.), Western University, London, ON, Canada
| | - Allison A. Dilliott
- From the Robarts Research Institute (J.S.D., A.A.D., A.L., A.D.M., J.W., H.C., R.A.H.), Western University, London, ON, Canada
- Department of Biochemistry (J.S.D., A.A.D., A.L., R.A.H.), Western University, London, ON, Canada
| | - Arden Lawson
- From the Robarts Research Institute (J.S.D., A.A.D., A.L., A.D.M., J.W., H.C., R.A.H.), Western University, London, ON, Canada
- Department of Biochemistry (J.S.D., A.A.D., A.L., R.A.H.), Western University, London, ON, Canada
| | - Adam D. McIntyre
- From the Robarts Research Institute (J.S.D., A.A.D., A.L., A.D.M., J.W., H.C., R.A.H.), Western University, London, ON, Canada
| | - Brent D. Davis
- Schulich School of Medicine and Dentistry, and Department of Computer Science (B.D.D.), Western University, London, ON, Canada
| | - Jian Wang
- From the Robarts Research Institute (J.S.D., A.A.D., A.L., A.D.M., J.W., H.C., R.A.H.), Western University, London, ON, Canada
| | - Henian Cao
- From the Robarts Research Institute (J.S.D., A.A.D., A.L., A.D.M., J.W., H.C., R.A.H.), Western University, London, ON, Canada
| | - Irina Movsesyan
- Cardiovascular Research Institute, University of California, San Francisco (I.M., M.J.M., C.R.P., J.P.K.)
| | - Mary J. Malloy
- Cardiovascular Research Institute, University of California, San Francisco (I.M., M.J.M., C.R.P., J.P.K.)
| | - Clive R. Pullinger
- Cardiovascular Research Institute, University of California, San Francisco (I.M., M.J.M., C.R.P., J.P.K.)
| | - John P. Kane
- Cardiovascular Research Institute, University of California, San Francisco (I.M., M.J.M., C.R.P., J.P.K.)
| | - Robert A. Hegele
- From the Robarts Research Institute (J.S.D., A.A.D., A.L., A.D.M., J.W., H.C., R.A.H.), Western University, London, ON, Canada
- Department of Biochemistry (J.S.D., A.A.D., A.L., R.A.H.), Western University, London, ON, Canada
- Department of Medicine (R.A.H.), Western University, London, ON, Canada
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14
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Berberich AJ, Wang J, Cao H, McIntyre AD, Spaic T, Miller DB, Stock S, Huot C, Stein R, Knoll J, Yang P, Robinson JF, Hegele RA. Simplifying Detection of Copy-Number Variations in Maturity-Onset Diabetes of the Young. Can J Diabetes 2020; 45:71-77. [PMID: 33011132 DOI: 10.1016/j.jcjd.2020.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 11/30/2022]
Abstract
OBJECTIVES Copy-number variations (CNVs) are large-scale deletions or duplications of DNA that have required specialized detection methods, such as microarray-based genomic hybridization or multiplex ligation probe amplification. However, recent advances in bioinformatics have made it possible to detect CNVs from next-generation DNA sequencing (NGS) data. Maturity-onset diabetes of the young (MODY) 5 is a subtype of autosomal-dominant diabetes that is often caused by heterozygous deletions involving the HNF1B gene on chromosome 17q12. We evaluated the utility of bioinformatic processing of raw NGS data to detect chromosome 17q12 deletions in MODY5 patients. METHODS NGS data from 57 patients clinically suspected to have MODY but who were negative for pathogenic mutations using a targeted panel were re-examined using a CNV calling tool (CNV Caller, VarSeq version 1.4.3). Potential CNVs for MODY5 were then confirmed using whole-exome sequencing, cytogenetic analysis and breakpoint analysis when possible. RESULTS Whole-gene deletions in HNF1B, ranging from 1.46 to 1.85 million basepairs in size, were detected in 3 individuals with features of MODY5. These were confirmed by independent methods to be part of a more extensive 17q12 deletion syndrome. Two additional patients carrying a 17q12 deletion were subsequently diagnosed using this method. CONCLUSIONS Large-scale deletions are the most common cause of MODY5 and can be detected directly from NGS data, without the need for additional methods.
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Affiliation(s)
- Amanda J Berberich
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.
| | - Jian Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Henian Cao
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Adam D McIntyre
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Tamara Spaic
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - David B Miller
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Suzanne Stock
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Celine Huot
- Department of Pediatrics, CHU Sainte-Justine, University of Montreal, Montréal, Quebec, Canada
| | - Robert Stein
- Department of Pediatrics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Joan Knoll
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Ping Yang
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - John F Robinson
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Robert A Hegele
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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15
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Dron JS, Wang J, McIntyre AD, Iacocca MA, Robinson JF, Ban MR, Cao H, Hegele RA. Six years' experience with LipidSeq: clinical and research learnings from a hybrid, targeted sequencing panel for dyslipidemias. BMC Med Genomics 2020; 13:23. [PMID: 32041611 PMCID: PMC7011550 DOI: 10.1186/s12920-020-0669-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 01/23/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND In 2013, our laboratory designed a targeted sequencing panel, "LipidSeq", to study the genetic determinants of dyslipidemia and metabolic disorders. Over the last 6 years, we have analyzed 3262 patient samples obtained from our own Lipid Genetics Clinic and international colleagues. Here, we highlight our findings and discuss research benefits and clinical implications of our panel. METHODS LipidSeq targets 69 genes and 185 single-nucleotide polymorphisms (SNPs) either causally related or associated with dyslipidemia and metabolic disorders. This design allows us to simultaneously evaluate monogenic-caused by rare single-nucleotide variants (SNVs) or copy-number variants (CNVs)-and polygenic forms of dyslipidemia. Polygenic determinants were assessed using three polygenic scores, one each for low-density lipoprotein cholesterol, triglyceride, and high-density lipoprotein cholesterol. RESULTS Among 3262 patient samples evaluated, the majority had hypertriglyceridemia (40.1%) and familial hypercholesterolemia (28.3%). Across all samples, we identified 24,931 unique SNVs, including 2205 rare variants predicted disruptive to protein function, and 77 unique CNVs. Considering our own 1466 clinic patients, LipidSeq results have helped in diagnosis and improving treatment options. CONCLUSIONS Our LipidSeq design based on ontology of lipid disorders has enabled robust detection of variants underlying monogenic and polygenic dyslipidemias. In more than 50 publications related to LipidSeq, we have described novel variants, the polygenic nature of many dyslipidemias-some previously thought to be primarily monogenic-and have uncovered novel mechanisms of disease. We further demonstrate several tangible clinical benefits of its use.
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Affiliation(s)
- Jacqueline S. Dron
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street, London, ON N6A 5B7 Canada
| | - Jian Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
| | - Adam D. McIntyre
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
| | - Michael A. Iacocca
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street, London, ON N6A 5B7 Canada
- Department of Biomedical Data Science, Stanford School of Medicine, Stanford University, 450 Serra Mall, Stanford, CA 94305 USA
| | - John F. Robinson
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
| | - Matthew R. Ban
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
| | - Henian Cao
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
| | - Robert A. Hegele
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street, London, ON N6A 5B7 Canada
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
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16
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Dron JS, Wang J, McIntyre AD, Cao H, Hegele RA. The polygenic nature of mild-to-moderate hypertriglyceridemia. J Clin Lipidol 2020; 14:28-34.e2. [PMID: 32033914 DOI: 10.1016/j.jacl.2020.01.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/01/2020] [Accepted: 01/06/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Patients with mild-to-moderate hypertriglyceridemia (HTG) are thought to share specific genetic susceptibility factors that are also present in patients with severe HTG, but no data have been reported on this issue. OBJECTIVE The objective of this study was to characterize genetic profiles of patients with mild-to-moderate HTG and compare them to patients with severe HTG. METHODS DNA from patients with mild-to-moderate HTG was sequenced using our targeted sequencing panel, "LipidSeq". For each patient, we assessed 1) rare variants disrupting five TG metabolism genes and 2) the accumulation of 16 common single-nucleotide polymorphisms (SNPs) using a polygenic risk score. The genetic profiles for these patients were then compared with normolipidemic controls from the 1000 Genomes Project and with patients with severe HTG. RESULTS Across 134 patients with mild-to-moderate HTG, 9.0% carried heterozygous rare variants and 26.9% had an excess accumulation of common SNPs. Patients with mild-to-moderate HTG were 2.38 times (95% CI [1.13-4.99]; P = .021) more likely to carry a rare variant and 3.26 times (95% CI [2.02-5.26]; P < .0001) more likely to have an extreme polygenic risk score compared with the 1000 Genomes Project. In addition, patients with severe HTG were 1.86 times (95% CI [0.98-3.51]; P = .032) more likely to carry a rare variant and 1.63 times (95% CI [1.07-2.48]; P = .013) more likely to have an extreme polygenic risk score than patients with mild-to-moderate HTG. CONCLUSIONS We report an increased prevalence of genetic determinants in patients with an increased severity of the HTG phenotype when considering either rare variants disrupting TG metabolism genes or an excess accumulation of common SNPs. As well, the findings confirm that the most prevalent genetic contributor to HTG, regardless of severity, is polygenic SNP accumulation.
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Affiliation(s)
- Jacqueline S Dron
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Jian Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Adam D McIntyre
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Henian Cao
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Robert A Hegele
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.
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17
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Dron JS, Wang J, McIntyre AD, Cao H, Robinson JF, Duell PB, Manjoo P, Feng J, Movsesyan I, Malloy MJ, Pullinger CR, Kane JP, Hegele RA. Partial LPL deletions: rare copy-number variants contributing towards severe hypertriglyceridemia. J Lipid Res 2019; 60:1953-1958. [PMID: 31519763 DOI: 10.1194/jlr.p119000335] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/09/2019] [Indexed: 01/31/2023] Open
Abstract
Severe hypertriglyceridemia (HTG) is a relatively common form of dyslipidemia with a complex pathophysiology and serious health complications. HTG can develop in the presence of rare genetic factors disrupting genes involved in the triglyceride (TG) metabolic pathway, including large-scale copy-number variants (CNVs). Improvements in next-generation sequencing technologies and bioinformatic analyses have better allowed assessment of CNVs as possible causes of or contributors to severe HTG. We screened targeted sequencing data of 632 patients with severe HTG and identified partial deletions of the LPL gene, encoding the central enzyme involved in the metabolism of TG-rich lipoproteins, in four individuals (0.63%). We confirmed the genomic breakpoints in each patient with Sanger sequencing. Three patients carried an identical heterozygous deletion spanning the 5' untranslated region (UTR) to LPL exon 2, and one patient carried a heterozygous deletion spanning the 5'UTR to LPL exon 1. All four heterozygous CNV carriers were determined to have multifactorial severe HTG. The predicted null nature of our identified LPL deletions may contribute to relatively higher TG levels and a more severe clinical phenotype than other forms of genetic variation associated with the disease, particularly in the polygenic state. The identification of novel CNVs in patients with severe HTG suggests that methods for CNV detection should be included in the diagnostic workup and molecular genetic evaluation of patients with high TG levels.
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Affiliation(s)
- Jacqueline S Dron
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada.,Departments of Biochemistry Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
| | - Jian Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
| | - Adam D McIntyre
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
| | - Henian Cao
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
| | - John F Robinson
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
| | - P Barton Duell
- Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR 97239
| | - Priya Manjoo
- Department of Medicine, Gordon and Leslie Diamond Centre, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - James Feng
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158
| | - Irina Movsesyan
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158
| | - Mary J Malloy
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158
| | - Clive R Pullinger
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158
| | - John P Kane
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158
| | - Robert A Hegele
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada .,Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada.,Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
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18
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Berberich AJ, Huot C, Cao H, McIntyre AD, Robinson JF, Wang J, Hegele RA. Copy Number Variation in GCK in Patients With Maturity-Onset Diabetes of the Young. J Clin Endocrinol Metab 2019; 104:3428-3436. [PMID: 30912798 PMCID: PMC6594302 DOI: 10.1210/jc.2018-02574] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/20/2019] [Indexed: 12/20/2022]
Abstract
PURPOSE Next generation sequencing (NGS) methods to diagnose maturity-onset diabetes of the young (MODY), a monogenic autosomal dominant cause of diabetes, do not typically detect large-scale copy number variations (CNVs). New techniques may allow assessment for CNVs using output data from targeted NGS, without requiring additional sequencing. Using this technique, two kindreds of patients presenting with features of MODY were found to bear the same heterozygous large-scale deletion in GCK. METHODS Patients suspected of having MODY but with negative targeted NGS pathogenic variant calling were reanalyzed using the CNV caller tool (VarSeq v1.4.3). Two patients were identified as having a possible heterozygous whole exon deletion affecting exon 1 of GCK. For confirmation and determination of the exact breakpoints, whole exome sequencing followed by Sanger sequencing were used. Familial samples from both affected and nonaffected first-degree relatives were then analyzed for each proband. RESULTS A heterozygous whole-exon deletion spanning 4763 bp affecting the entire exon 1 of GCK was detected in two apparently unrelated patients with clinical features of MODY. This deletion showed segregation concordance across generations in affected and nonaffected family members. CONCLUSIONS Our findings confirm the utility of applying the CNV caller tool to screen for CNVs in GCK from NGS data. In so doing, we identified a deletion of exon 1 of GCK as likely causal for MODY. Our data indicate that incorporating CNV analysis routinely when assessing for MODY via targeted NGS may increase diagnostic yield and reduce false negative genetic testing rates.
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Affiliation(s)
- Amanda J Berberich
- Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Céline Huot
- Department of Pediatrics, CHU Sainte-Justine, University of Montreal, Montreal, Quebec, Canada
| | - Henian Cao
- Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Adam D McIntyre
- Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - John F Robinson
- Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Jian Wang
- Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Robert A Hegele
- Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
- Correspondence and Reprint Requests: Robert A. Hegele, MD, FRCPC, FACP, Robarts Research Institute, 4288A-1151 Richmond Street North, London, Ontario N6A 5B7, Canada. E-mail:
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19
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Abstract
PURPOSE OF REVIEW DNA copy number variations (CNVs) are large-scale mutations that include deletions and duplications larger than 50 bp in size. In the era when single-nucleotide variations were the major focus of genetic technology and research, CNVs were largely overlooked. However, CNVs clearly underlie a substantial proportion of clinical disorders. Here, we update recent progress in identifying CNVs in dyslipidemias. RECENT FINDINGS Until last year, only the LDLR and LPA genes were appreciated as loci within which clinically relevant CNVs contributed to familial hypercholesterolemia and variation in Lp(a) levels, respectively. Since 2017, next-generation sequencing panels have identified pathogenic CNVs in at least five more genes underlying dyslipidemias, including a PCSK9 whole-gene duplication in familial hypercholesterolemia; LPL, GPIHBP1, and APOC2 deletions in hypertriglyceridemia; and ABCA1 deletions in hypoalphalipoproteinemia. SUMMARY CNVs are an important class of mutation that contribute to the molecular genetic heterogeneity underlying dyslipidemias. Clinical applications of next-generation sequencing technologies need to consider CNVs concurrently with familiar small-scale genetic variation, given the likely implications for improved diagnosis and treatment.
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Affiliation(s)
- Michael A Iacocca
- Robarts Research Institute, and Department of Biochemistry, Schulich School of Medicine and Dentistry
| | - Jacqueline S Dron
- Robarts Research Institute, and Department of Biochemistry, Schulich School of Medicine and Dentistry
| | - Robert A Hegele
- Robarts Research Institute, and Department of Biochemistry, Schulich School of Medicine and Dentistry
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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20
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Song J, Jiang X, Cao Y, Juan J, Wu T, Hu Y. Interaction between an ATP-Binding Cassette A1 (ABCA1) Variant and Egg Consumption for the Risk of Ischemic Stroke and Carotid Atherosclerosis: a Family-Based Study in the Chinese Population. J Atheroscler Thromb 2019; 26:835-845. [PMID: 30828007 PMCID: PMC6753237 DOI: 10.5551/jat.46615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aims: ATP-binding cassette A1 (ABCA1) plays an important role in reducing the risk of stroke. Egg is the major source of dietary cholesterol and is known to be associated with the risk of stroke and atherosclerosis. We aimed to assess the effects of interaction between an ABCA1 variant (rs2066715) and egg consumption on the risk of ischemic stroke (IS), carotid plaque, and carotid-intima media thickness (CIMT) in the Chinese population. Methods: In total, 5869 subjects (including 1213 IS cases) across 1128 families were enrolled and divided into two groups based on the median egg consumption (4 eggs per week). In the analyses for the presence of carotid plaque and CIMT, 3171 out of 4656 IS-free controls without self-reported history of coronary heart disease and lipid-lowering medications were included. Multilevel logistic regression models were used to model the genetic association of rs2066715 with the risk of IS, and mixed-effect linear regression for the genetic association of rs2066715 with carotid plaque, and CIMT. The gene-by-egg cross-product term was included in the regression model for interaction analysis. Results: We found that rs2066715 was associated with the increased risk of carotid plaque among those who consumed < 4 eggs per week after adjustment (odds ratio [95% confidence interval]: 1.61 [1.08, 2.39], P = 0.019). A significant effect of interaction between rs2066715 and egg consumption on the risk of carotid plaque was identified (P = 0.011). Conclusion: rs2066715 was found to interact with egg consumption in modifying the risk of carotid plaque in the Chinese population.
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Affiliation(s)
- Jing Song
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University
| | - Xia Jiang
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health.,Unit of Cardiovascular Epidemiology, Institute of Environmental Health, Karolinska Institute
| | - Yaying Cao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University
| | - Juan Juan
- Department of Obstetrics and Gynecology, Peking University First Hospital
| | - Tao Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University
| | - Yonghua Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University
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21
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Berberich AJ, Hegele RA. The role of genetic testing in dyslipidaemia. Pathology 2019; 51:184-192. [DOI: 10.1016/j.pathol.2018.10.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 01/28/2023]
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22
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Severe hypertriglyceridemia is primarily polygenic. J Clin Lipidol 2019; 13:80-88. [DOI: 10.1016/j.jacl.2018.10.006] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 10/13/2018] [Accepted: 10/16/2018] [Indexed: 12/22/2022]
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23
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Geller AS, Polisecki EY, Diffenderfer MR, Asztalos BF, Karathanasis SK, Hegele RA, Schaefer EJ. Genetic and secondary causes of severe HDL deficiency and cardiovascular disease. J Lipid Res 2018; 59:2421-2435. [PMID: 30333156 DOI: 10.1194/jlr.m088203] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/13/2018] [Indexed: 02/07/2023] Open
Abstract
We assessed secondary and genetic causes of severe HDL deficiency in 258,252 subjects, of whom 370 men (0.33%) and 144 women (0.099%) had HDL cholesterol levels <20 mg/dl. We excluded 206 subjects (40.1%) with significant elevations of triglycerides, C-reactive protein, glycosylated hemoglobin, myeloperoxidase, or liver enzymes and men receiving testosterone. We sequenced 23 lipid-related genes in 201 (65.3%) of 308 eligible subjects. Mutations (23 novel) and selected variants were found at the following gene loci: 1) ABCA1 (26.9%): 2 homozygotes, 7 compound or double heterozygotes, 30 heterozygotes, and 2 homozygotes and 13 heterozygotes with variants rs9282541/p.R230C or rs111292742/c.-279C>G; 2) LCAT (12.4%): 1 homozygote, 3 compound heterozygotes, 13 heterozygotes, and 8 heterozygotes with variant rs4986970/p.S232T; 3) APOA1 (5.0%): 1 homozygote and 9 heterozygotes; and 4) LPL (4.5%): 1 heterozygote and 8 heterozygotes with variant rs268/p.N318S. In addition, 4.5% had other mutations, and 46.8% had no mutations. Atherosclerotic cardiovascular disease (ASCVD) prevalence rates in the ABCA1, LCAT, APOA1, LPL, and mutation-negative groups were 37.0%, 4.0%, 40.0%, 11.1%, and 6.4%, respectively. Severe HDL deficiency is uncommon, with 40.1% having secondary causes and 48.8% of the subjects sequenced having ABCA1, LCAT, APOA1, or LPL mutations or variants, with the highest ASCVD prevalence rates being observed in the ABCA1 and APOA1 groups.
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Affiliation(s)
- Andrew S Geller
- Boston Heart Diagnostics, Framingham, MA 01702.,Cardiovascular Nutrition Laboratory, Human Nutrition Research Center on Aging at Tufts University and Tufts University School of Medicine, Boston, MA 02111
| | | | | | - Bela F Asztalos
- Cardiovascular Nutrition Laboratory, Human Nutrition Research Center on Aging at Tufts University and Tufts University School of Medicine, Boston, MA 02111
| | | | - Robert A Hegele
- Cardiovascular Nutrition Laboratory, Human Nutrition Research Center on Aging at Tufts University and Tufts University School of Medicine, Boston, MA 02111
| | - Ernst J Schaefer
- Boston Heart Diagnostics, Framingham, MA 01702 .,Cardiovascular Nutrition Laboratory, Human Nutrition Research Center on Aging at Tufts University and Tufts University School of Medicine, Boston, MA 02111
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24
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Iacocca MA, Wang J, Sarkar S, Dron JS, Lagace T, McIntyre AD, Lau P, Robinson JF, Yang P, Knoll JH, Cao H, McPherson R, Hegele RA. Whole-Gene Duplication of PCSK9 as a Novel Genetic Mechanism for Severe Familial Hypercholesterolemia. Can J Cardiol 2018; 34:1316-1324. [DOI: 10.1016/j.cjca.2018.07.479] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 07/30/2018] [Accepted: 07/31/2018] [Indexed: 01/23/2023] Open
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