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Giussani M, Orlando A, Tassistro E, Torresani E, Lieti G, Patti I, Colombrita C, Bulgarelli I, Antolini L, Parati G, Genovesi S. Is lipoprotein(a) measurement important for cardiovascular risk stratification in children and adolescents? Ital J Pediatr 2024; 50:161. [PMID: 39227973 PMCID: PMC11373248 DOI: 10.1186/s13052-024-01732-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 08/17/2024] [Indexed: 09/05/2024] Open
Abstract
BACKGROUND Elevated lipoprotein (Lp(a)) levels are associated with increased risk of atherosclerotic processes and cardiovascular events in adults. The amount of Lp(a) is mainly genetically determined. Therefore, it is important to identify individuals with elevated Lp(a) as early as possible, particularly if other cardiovascular risk factors are present. The purpose of the study was to investigate whether, in a population of children and adolescents already followed for the presence of one or more cardiovascular risk factors (elevated blood pressure (BP), and/or excess body weight, and/or dyslipidemia), the measurement of Lp(a) can be useful for better stratifying their risk profile. METHODS In a sample of 195 children and adolescents, height, body weight, waist circumference and systolic (SBP) and diastolic (DBP) BP were measured. Body Mass Index (BMI) and SBP and DBP z-scores were calculated. Plasma Lp(a), total cholesterol, high-density lipoprotein (HDL), triglycerides, glucose, insulin, uric acid and creatinine were assessed. Low-density lipoprotein (LDL) cholesterol was calculated with the Friedewald formula. High Lp(a) was defined as ≥ 75 nmol/L and high LDL cholesterol as ≥ 3.37 mmol/L. RESULTS Our sample of children and adolescents (54.4% males, mean age 11.5 years) had median LDL cholesterol and Lp(a) values equal to 2.54 (interquartile range, IQR: 2.07-3.06) mmol/L and 22 (IQR: 7.8-68.6) nmol/L respectively. 13.8% of children had LDL cholesterol ≥ 3.37 mmol/L and 22.6 Lp(a) values ≥ 75 nmol/L. Lp(a) values were higher in children of normal weight than in those with excess weight (p = 0.007), but the difference disappeared if normal weight children referred for dyslipidemia only were excluded from the analysis (p = 0.210). 69.4% of children had normal Lp(a) and LDL cholesterol values and only 6.2% showed both elevated Lp(a) and LDL cholesterol levels. However, 16.6% of the sample, despite having normal LDL cholesterol, had elevated Lp(a) values. Multivariable analyses showed a significant association of LDL cholesterol both with Lp(a) values, and with the presence of elevated Lp(a) levels. For each mmol/L increase in LDL cholesterol the risk of having an elevated Lp(a) value increased by 73%. There was an inverse correlation between BMI z-score and Lp(a). Neither BP z-scores, nor other biochemical parameters were associated with Lp(a). CONCLUSIONS In our population more than one out of five children had elevated Lp(a) values, and in about 17% of children elevated Lp(a) values were present in the absence of increased LDL cholesterol. Our results suggest that Lp(a) measurement can be useful to better define the cardiovascular risk profile in children and adolescents already followed for the presence of other cardiovascular risk factors such as elevated BP, excess body weight and high LDL cholesterol.
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Affiliation(s)
- Marco Giussani
- Istituto Auxologico Italiano, IRCCS, Via L. Ariosto 13, Milano, 20145, Italy.
| | - Antonina Orlando
- Istituto Auxologico Italiano, IRCCS, Via L. Ariosto 13, Milano, 20145, Italy
| | - Elena Tassistro
- Biostatistics and Clinical Epidemiology, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Erminio Torresani
- Istituto Auxologico Italiano, IRCCS, Via L. Ariosto 13, Milano, 20145, Italy
| | - Giulia Lieti
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Ilenia Patti
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Claudia Colombrita
- Istituto Auxologico Italiano, IRCCS, Via L. Ariosto 13, Milano, 20145, Italy
| | - Ilaria Bulgarelli
- Istituto Auxologico Italiano, IRCCS, Via L. Ariosto 13, Milano, 20145, Italy
| | - Laura Antolini
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- Bicocca Center of Bioinformatics, Biostatistics and Bioimaging (B4 Center), University of Milano-Bicocca, Monza, Italy
| | - Gianfranco Parati
- Istituto Auxologico Italiano, IRCCS, Via L. Ariosto 13, Milano, 20145, Italy
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Simonetta Genovesi
- Istituto Auxologico Italiano, IRCCS, Via L. Ariosto 13, Milano, 20145, Italy
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
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Di Maio S, Zöscher P, Weissensteiner H, Forer L, Schachtl-Riess JF, Amstler S, Streiter G, Pfurtscheller C, Paulweber B, Kronenberg F, Coassin S, Schönherr S. Resolving intra-repeat variation in medically relevant VNTRs from short-read sequencing data using the cardiovascular risk gene LPA as a model. Genome Biol 2024; 25:167. [PMID: 38926899 PMCID: PMC11201333 DOI: 10.1186/s13059-024-03316-5] [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: 06/28/2023] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Variable number tandem repeats (VNTRs) are highly polymorphic DNA regions harboring many potentially disease-causing variants. However, VNTRs often appear unresolved ("dark") in variation databases due to their repetitive nature. One particularly complex and medically relevant VNTR is the KIV-2 VNTR located in the cardiovascular disease gene LPA which encompasses up to 70% of the coding sequence. RESULTS Using the highly complex LPA gene as a model, we develop a computational approach to resolve intra-repeat variation in VNTRs from largely available short-read sequencing data. We apply the approach to six protein-coding VNTRs in 2504 samples from the 1000 Genomes Project and developed an optimized method for the LPA KIV-2 VNTR that discriminates the confounding KIV-2 subtypes upfront. This results in an F1-score improvement of up to 2.1-fold compared to previously published strategies. Finally, we analyze the LPA VNTR in > 199,000 UK Biobank samples, detecting > 700 KIV-2 mutations. This approach successfully reveals new strong Lp(a)-lowering effects for KIV-2 variants, with protective effect against coronary artery disease, and also validated previous findings based on tagging SNPs. CONCLUSIONS Our approach paves the way for reliable variant detection in VNTRs at scale and we show that it is transferable to other dark regions, which will help unlock medical information hidden in VNTRs.
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Affiliation(s)
- Silvia Di Maio
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Peter Zöscher
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Hansi Weissensteiner
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas Forer
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Stephan Amstler
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gertraud Streiter
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Cathrin Pfurtscheller
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Bernhard Paulweber
- Department of Internal Medicine I, Paracelsus Medical University/Salzburger Landeskliniken, Salzburg, Austria
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Stefan Coassin
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria.
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3
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Mahmoud M, Harting J, Corbitt H, Chen X, Jhangiani SN, Doddapaneni H, Meng Q, Han T, Lambert C, Zhang S, Baybayan P, Henno G, Shen H, Hu J, Han Y, Riegler C, Metcalf G, Henno G, Chinn IK, Eberle MA, Kingan S, Farinholt T, Carvalho CM, Gibbs RA, Kronenberg Z, Muzny D, Sedlazeck FJ. Closing the gap: Solving complex medically relevant genes at scale. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.14.24304179. [PMID: 38562723 PMCID: PMC10984040 DOI: 10.1101/2024.03.14.24304179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Comprehending the mechanism behind human diseases with an established heritable component represents the forefront of personalized medicine. Nevertheless, numerous medically important genes are inaccurately represented in short-read sequencing data analysis due to their complexity and repetitiveness or the so-called 'dark regions' of the human genome. The advent of PacBio as a long-read platform has provided new insights, yet HiFi whole-genome sequencing (WGS) cost remains frequently prohibitive. We introduce a targeted sequencing and analysis framework, Twist Alliance Dark Genes Panel (TADGP), designed to offer phased variants across 389 medically important yet complex autosomal genes. We highlight TADGP accuracy across eleven control samples and compare it to WGS. This demonstrates that TADGP achieves variant calling accuracy comparable to HiFi-WGS data, but at a fraction of the cost. Thus, enabling scalability and broad applicability for studying rare diseases or complementing previously sequenced samples to gain insights into these complex genes. TADGP revealed several candidate variants across all cases and provided insight into LPA diversity when tested on samples from rare disease and cardiovascular disease cohorts. In both cohorts, we identified novel variants affecting individual disease-associated genes (e.g., IKZF1, KCNE1). Nevertheless, the annotation of the variants across these 389 medically important genes remains challenging due to their underrepresentation in ClinVar and gnomAD. Consequently, we also offer an annotation resource to enhance the evaluation and prioritization of these variants. Overall, we can demonstrate that TADGP offers a cost-efficient and scalable approach to routinely assess the dark regions of the human genome with clinical relevance.
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Affiliation(s)
- Medhat Mahmoud
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - John Harting
- Pacific Biosciences, Menlo Park, California, USA
| | | | - Xiao Chen
- Pacific Biosciences, Menlo Park, California, USA
| | | | - Harsha Doddapaneni
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - Qingchang Meng
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - Tina Han
- Twist Bioscience, South San Francisco, USA
| | | | - Siyuan Zhang
- Pacific Biosciences, Menlo Park, California, USA
| | | | - Geoff Henno
- Pacific Biosciences, Menlo Park, California, USA
| | - Hua Shen
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - Jianhong Hu
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - Yi Han
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | | | - Ginger Metcalf
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - Geoff Henno
- Pacific Biosciences, Menlo Park, California, USA
| | - Ivan K. Chinn
- Department of Pediatrics, Section of Immunology Allergy and Rheumatology, Center for Human Immunobiology, Texas Children’s Hospital and Baylor College of Medicine, Houston, Texas, USA
| | | | - Sarah Kingan
- Pacific Biosciences, Menlo Park, California, USA
| | | | | | - Richard A. Gibbs
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | | | - Donna Muzny
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - Fritz J. Sedlazeck
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Computer Science, Rice University, Houston, Texas, USA
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Pajuste FD, Remm M. GeneToCN: an alignment-free method for gene copy number estimation directly from next-generation sequencing reads. Sci Rep 2023; 13:17765. [PMID: 37853040 PMCID: PMC10584998 DOI: 10.1038/s41598-023-44636-z] [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: 05/04/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
Genomes exhibit large regions with segmental copy number variation, many of which include entire genes and are multiallelic. We have developed a computational method GeneToCN that counts the frequencies of gene-specific k-mers in FASTQ files and uses this information to infer copy number of the gene. We validated the copy number predictions for amylase genes (AMY1, AMY2A, AMY2B) using experimental data from digital droplet PCR (ddPCR) on 39 individuals and observed a strong correlation (R = 0.99) between GeneToCN predictions and experimentally determined copy numbers. An additional validation on FCGR3 genes showed a higher concordance for FCGR3A compared to two other methods, but reduced accuracy for FCGR3B. We further tested the method on three different genomic regions (SMN, NPY4R, and LPA Kringle IV-2 domain). Predicted copy number distributions of these genes in a set of 500 individuals from the Estonian Biobank were in good agreement with the previously published studies. In addition, we investigated the possibility to use GeneToCN on sequencing data generated by different technologies by comparing copy number predictions from Illumina, PacBio, and Oxford Nanopore data of the same sample. Despite the differences in variability of k-mer frequencies, all three sequencing technologies give similar predictions with GeneToCN.
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Affiliation(s)
- Fanny-Dhelia Pajuste
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Str., 51010, Tartu, Estonia.
| | - Maido Remm
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Str., 51010, Tartu, Estonia
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5
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Fogacci F, Di Micoli V, Avagimyan A, Giovannini M, Imbalzano E, Cicero AFG. Assessment of Apolipoprotein(a) Isoform Size Using Phenotypic and Genotypic Methods. Int J Mol Sci 2023; 24:13886. [PMID: 37762189 PMCID: PMC10531419 DOI: 10.3390/ijms241813886] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Apolipoprotein(a) (apo(a)) is the protein component that defines lipoprotein(a) (Lp(a)) particles and is encoded by the LPA gene. The apo(a) is extremely heterogeneous in size due to the copy number variations in the kringle-IV type 2 (KIV2) domains. In this review, we aim to discuss the role of genetics in establishing Lp(a) as a risk factor for coronary heart disease (CHD) by examining a series of molecular biology techniques aimed at identifying the best strategy for a possible application in clinical research and practice, according to the current gold standard.
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Affiliation(s)
- Federica Fogacci
- Hypertension and Cardiovascular Risk Research Center, Medical and Surgical Sciences Department, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy; (F.F.); (V.D.M.); (M.G.)
| | - Valentina Di Micoli
- Hypertension and Cardiovascular Risk Research Center, Medical and Surgical Sciences Department, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy; (F.F.); (V.D.M.); (M.G.)
| | - Ashot Avagimyan
- Pathological Anatomy Department, Yerevan State Medical University, Yerevan 0025, Armenia;
| | - Marina Giovannini
- Hypertension and Cardiovascular Risk Research Center, Medical and Surgical Sciences Department, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy; (F.F.); (V.D.M.); (M.G.)
| | - Egidio Imbalzano
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy;
| | - Arrigo F. G. Cicero
- Hypertension and Cardiovascular Risk Research Center, Medical and Surgical Sciences Department, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy; (F.F.); (V.D.M.); (M.G.)
- Cardiovascular Medicine Unit, Heart, Thoracic and Vascular Department, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40100 Bologna, Italy
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6
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Genovesi S, Giussani M, Lieti G, Orlando A, Patti I, Parati G. Evidence and Uncertainties on Lipoprotein(a) as a Marker of Cardiovascular Health Risk in Children and Adolescents. Biomedicines 2023; 11:1661. [PMID: 37371756 PMCID: PMC10295837 DOI: 10.3390/biomedicines11061661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Lipoprotein(a) (Lp(a)) is made up of apoprotein(a) (apo(a)) and an LDL-like particle. The LPA gene encodes apo(a) and thus determines the characteristics and amount of apo(a) and Lp(a). The proportion of Lp(a) in each individual is genetically determined and is only minimally modifiable by the environment or diet. Lp(a) has important pro-atherosclerotic and pro-inflammatory effects. It has been hypothesized that Lp(a) also has pro-coagulant and antifibrinolytic actions. For these reasons, high Lp(a) values are an important independent risk factor for cardiovascular disease and calcific aortic valve stenosis. Numerous studies have been performed in adults about the pathophysiology and epidemiology of Lp(a) and research is under way for the development of drugs capable of reducing Lp(a) plasma values. Much less information is available regarding Lp(a) in children and adolescents. The present article reviews the evidence on this topic. The review addresses the issues of Lp(a) changes during growth, the correlation between Lp(a) values in children and those in their parents, and between Lp(a) levels in children, and the presence of cardiovascular disease in the family. Gaining information on these points is particularly important for deciding whether Lp(a) assay may be useful for defining the cardiovascular risk in children, in order to plan a prevention program early.
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Affiliation(s)
- Simonetta Genovesi
- School of Medicine and Surgery, Milano-Bicocca University, 20126 Milan, Italy; (G.L.); (I.P.); (G.P.)
- Istituto Auxologico Italiano, Istituto Ricovero Cura Carattere Scientifico (IRCCS), 20135 Milan, Italy; (M.G.); (A.O.)
| | - Marco Giussani
- Istituto Auxologico Italiano, Istituto Ricovero Cura Carattere Scientifico (IRCCS), 20135 Milan, Italy; (M.G.); (A.O.)
| | - Giulia Lieti
- School of Medicine and Surgery, Milano-Bicocca University, 20126 Milan, Italy; (G.L.); (I.P.); (G.P.)
| | - Antonina Orlando
- Istituto Auxologico Italiano, Istituto Ricovero Cura Carattere Scientifico (IRCCS), 20135 Milan, Italy; (M.G.); (A.O.)
| | - Ilenia Patti
- School of Medicine and Surgery, Milano-Bicocca University, 20126 Milan, Italy; (G.L.); (I.P.); (G.P.)
| | - Gianfranco Parati
- School of Medicine and Surgery, Milano-Bicocca University, 20126 Milan, Italy; (G.L.); (I.P.); (G.P.)
- Istituto Auxologico Italiano, Istituto Ricovero Cura Carattere Scientifico (IRCCS), 20135 Milan, Italy; (M.G.); (A.O.)
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7
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Behera S, Belyeu JR, Chen X, Paulin LF, Nguyen NQH, Newman E, Mahmoud M, Menon VK, Qi Q, Joshi P, Marcovina S, Rossi M, Roller E, Han J, Onuchic V, Avery CL, Ballantyne CM, Rodriguez CJ, Kaplan RC, Muzny DM, Metcalf GA, Gibbs R, Yu B, Boerwinkle E, Eberle MA, Sedlazeck FJ. Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538128. [PMID: 37163057 PMCID: PMC10168217 DOI: 10.1101/2023.04.24.538128] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The abundance of Lp(a) protein holds significant implications for the risk of cardiovascular disease (CVD), which is directly impacted by the copy number (CN) of KIV-2, a 5.5 kbp sub-region. KIV-2 is highly polymorphic in the population and accurate analysis is challenging. In this study, we present the DRAGEN KIV-2 CN caller, which utilizes short reads. Data across 166 WGS show that the caller has high accuracy, compared to optical mapping and can further phase ~50% of the samples. We compared KIV-2 CN numbers to 24 previously postulated KIV-2 relevant SNVs, revealing that many are ineffective predictors of KIV-2 copy number. Population studies, including USA-based cohorts, showed distinct KIV-2 CN, distributions for European-, African-, and Hispanic-American populations and further underscored the limitations of SNV predictors. We demonstrate that the CN estimates correlate significantly with the available Lp(a) protein levels and that phasing is highly important.
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Affiliation(s)
- S Behera
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - X Chen
- Illumina Inc., San Diego, CA, USA
| | - L F Paulin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - N Q H Nguyen
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
| | - E Newman
- Illumina Inc., San Diego, CA, USA
| | - M Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - V K Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Q Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - P Joshi
- Medpace Reference Laboratories, Cincinnati, OH, USA
| | - S Marcovina
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - M Rossi
- Illumina Inc., San Diego, CA, USA
| | - E Roller
- Illumina Inc., San Diego, CA, USA
| | - J Han
- Illumina Inc., San Diego, CA, USA
| | | | - C L Avery
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - C M Ballantyne
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - C J Rodriguez
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - R C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Fred Hutchinson Cancer Center, Public Health Sciences Division, Seattle WA 98109
| | - D M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - G A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - R Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - B Yu
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
| | - E Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
| | | | - F J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, USA
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8
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Lipoprotein(a) in Atherosclerotic Diseases: From Pathophysiology to Diagnosis and Treatment. Molecules 2023; 28:molecules28030969. [PMID: 36770634 PMCID: PMC9918959 DOI: 10.3390/molecules28030969] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
Lipoprotein(a) (Lp(a)) is a low-density lipoprotein (LDL) cholesterol-like particle bound to apolipoprotein(a). Increased Lp(a) levels are an independent, heritable causal risk factor for atherosclerotic cardiovascular disease (ASCVD) as they are largely determined by variations in the Lp(a) gene (LPA) locus encoding apo(a). Lp(a) is the preferential lipoprotein carrier for oxidized phospholipids (OxPL), and its role adversely affects vascular inflammation, atherosclerotic lesions, endothelial function and thrombogenicity, which pathophysiologically leads to cardiovascular (CV) events. Despite this crucial role of Lp(a), its measurement lacks a globally unified method, and, between different laboratories, results need standardization. Standard antilipidemic therapies, such as statins, fibrates and ezetimibe, have a mediocre effect on Lp(a) levels, although it is not yet clear whether such treatments can affect CV events and prognosis. This narrative review aims to summarize knowledge regarding the mechanisms mediating the effect of Lp(a) on inflammation, atherosclerosis and thrombosis and discuss current diagnostic and therapeutic potentials.
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9
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Lipoprotein(a) beyond the kringle IV repeat polymorphism: The complexity of genetic variation in the LPA gene. Atherosclerosis 2022; 349:17-35. [PMID: 35606073 PMCID: PMC7613587 DOI: 10.1016/j.atherosclerosis.2022.04.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 02/23/2022] [Accepted: 04/01/2022] [Indexed: 12/24/2022]
Abstract
High lipoprotein(a) [Lp(a)] concentrations are one of the most important genetically determined risk factors for cardiovascular disease. Lp(a) concentrations are an enigmatic trait largely controlled by one single gene (LPA) that contains a complex interplay of several genetic elements with many surprising effects discussed in this review. A hypervariable coding copy number variation (the kringle IV type-2 repeat, KIV-2) generates >40 apolipoprotein(a) protein isoforms and determines the median Lp(a) concentrations. Carriers of small isoforms with up to 22 kringle IV domains have median Lp(a) concentrations up to 5 times higher than those with large isoforms (>22 kringle IV domains). The effect of the apo(a) isoforms are, however, modified by many functional single nucleotide polymorphisms (SNPs) distributed over the complete range of allele frequencies (<0.1% to >20%) with very pronounced effects on Lp(a) concentrations. A complex interaction is present between the apo (a) isoforms and LPA SNPs, with isoforms partially masking the effect of functional SNPs and, vice versa, SNPs lowering the Lp(a) concentrations of affected isoforms. This picture is further complicated by SNP-SNP interactions, a poorly understood role of other polymorphisms such as short tandem repeats and linkage structures that are poorly captured by common R2 values. A further layer of complexity derives from recent findings that several functional SNPs are located in the KIV-2 repeat and are thus not accessible to conventional sequencing and genotyping technologies. A critical impact of the ancestry on correlation structures and baseline Lp(a) values becomes increasingly evident. This review provides a comprehensive overview on the complex genetic architecture of the Lp(a) concentrations in plasma, a field that has made tremendous progress with the introduction of new technologies. Understanding the genetics of Lp(a) might be a key to many mysteries of Lp(a) and booster new ideas on the metabolism of Lp(a) and possible interventional targets.
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10
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Elevated lipoprotein(a) and genetic polymorphisms in the LPA gene may predict cardiovascular events. Sci Rep 2022; 12:3588. [PMID: 35246583 PMCID: PMC8897417 DOI: 10.1038/s41598-022-07596-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 02/21/2022] [Indexed: 11/18/2022] Open
Abstract
Elevated lipoprotein(a) [Lp(a)] is a risk factor for coronary heart disease (CHD), but there are few studies on the prediction of future cardiovascular events by Lp(a) and its LPA single nucleotide polymorphisms (SNPs). The aim of this study was to investigate whether elevated Lp(a) and its SNPs can predict cardiovascular events. We evaluated whether Lp(a) and LPA SNPs rs6415084 and rs12194138 were associated with the incidence rate and severity of CHD. All participants were followed up for 5 years. Elevated Lp(a) is an independent risk factor for the risk and severity of CHD (CHD group vs. control group: OR = 1.793, 95% CI: 1.053–2.882, p = 0.043; multiple-vessel disease group vs. single-vessel disease group: OR = 1.941, 95% CI: 1.113–3.242, p = 0.027; high GS group vs. low GS group: OR = 2.641, 95% CI: 1.102–7.436, p = 0.040). Both LPA SNPs were risk factors for CHD, and were positively associated with the severity of CHD (LPA SNPs rs6415084: CHD group vs. control group: OR = 1.577, 95% CI: 1.105–1.989, p = 0.004; multiple-vessel disease group vs. single-vessel disease group: OR = 1.613, 95% CI: 1.076–2.641, p = 0.030; high GS group vs. low GS group: OR = 1.580, 95% CI: 1.088–2.429, p = 0.024; LPA SNPs rs12194138: CHD group vs. control group: OR = 1.475, 95% CI: 1.040–3.002, p = 0.035; multiple-vessel disease group vs. single-vessel disease group: OR = 2.274, 95% CI: 1.060–5.148, p = 0.038; high GS group vs. low GS group: OR = 2.067, 95% CI: 1.101–4.647, p = 0.021). After 5 years of follow-up, elevated Lp(a) and LPA SNPs rs6415084 and rs12194138 can independently predict cardiovascular events. The increase of serum Lp(a) and LPA SNPs rs6415084 and rs12194138 are associated with increased prevalence and severity of CHD, and can independently predict cardiovascular events.
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11
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Mukamel RE, Handsaker RE, Sherman MA, Barton AR, Zheng Y, McCarroll SA, Loh PR. Protein-coding repeat polymorphisms strongly shape diverse human phenotypes. Science 2021; 373:1499-1505. [PMID: 34554798 PMCID: PMC8549062 DOI: 10.1126/science.abg8289] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Many human proteins contain domains that vary in size or copy number because of variable numbers of tandem repeats (VNTRs) in protein-coding exons. However, the relationships of VNTRs to most phenotypes are unknown because of difficulties in measuring such repetitive elements. We developed methods to estimate VNTR lengths from whole-exome sequencing data and impute VNTR alleles into single-nucleotide polymorphism haplotypes. Analyzing 118 protein-altering VNTRs in 415,280 UK Biobank participants for association with 786 phenotypes identified some of the strongest associations of common variants with human phenotypes, including height, hair morphology, and biomarkers of health. Accounting for large-effect VNTRs further enabled fine-mapping of associations to many more protein-coding mutations in the same genes. These results point to cryptic effects of highly polymorphic common structural variants that have eluded molecular analyses to date.
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Affiliation(s)
- Ronen E Mukamel
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Boston, MA, USA
| | - Robert E Handsaker
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Maxwell A Sherman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Boston, MA, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Boston, MA, USA
| | - Alison R Barton
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Boston, MA, USA
- Bioinformatics and Integrative Genomics Program, Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Yiming Zheng
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Boston, MA, USA
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Boston, MA, USA
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12
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Abstract
PURPOSE OF REVIEW Calcific aortic stenosis (CAVS) is the most common form of valvular heart disease in developed countries, increasing in prevalence with the aging population. Surgical or transcatheter aortic valve replacement is the only treatment available for CAVS. However, these interventions are typically reserved for severe symptomatic aortic stenosis (AS). The purpose of this review is to summarize the recent literature in uncovering the underlying pathophysiology of CAVS in the setting of lipoprotein (a) [Lp(a)] and emerging therapies targeting Lp(a) which may help halt disease progression in CAVS. RECENT FINDINGS Pathophysiologic, epidemiological, and genetic studies over the past two decades have provided strong evidence that Lp(a) is an important mediator of calcific aortic valvular disease (CAVD). Studies suggest that Lp(a) is a key carrier of pro-calcifying oxidized phospholipids (OxPL). The metabolism of OxPL results in a pro-inflammatory state and subsequent valvular thickening and mineralization through pro-osteogenic signaling. The identification of Lp(a) as a causal mediator of CAVD has allowed for opportunities for emerging therapeutic agents which may slow the progression of CAVD (Fig. 1JOURNAL/cocar/04.03/00001573-202109000-00007/figure1/v/2021-08-04T080204Z/r/image-jpeg). SUMMARY This review summarizes the current knowledge on the association of Lp(a) with CAVD and ongoing studies of potential Lp(a)-lowering therapies. Based on the rate-limiting and causal role of Lp(a) in progression of CAVS, these therapies may represent novel pharmacotherapies in AS and inform the developing role of Lp(a) in the clinical management of CAVD.
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13
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Trinder M, Uddin MM, Finneran P, Aragam KG, Natarajan P. Clinical Utility of Lipoprotein(a) and LPA Genetic Risk Score in Risk Prediction of Incident Atherosclerotic Cardiovascular Disease. JAMA Cardiol 2021; 6:287-295. [PMID: 33021622 PMCID: PMC7539232 DOI: 10.1001/jamacardio.2020.5398] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/15/2020] [Indexed: 12/24/2022]
Abstract
Importance Lipoprotein(a) is a highly heritable biomarker independently associated with atherosclerotic cardiovascular disease (ASCVD). It is unclear whether measured lipoprotein(a) or genetic factors associated with lipoprotein(a) can provide comparable or additional prognostic information for primary prevention. Objective To determine whether a genetic risk score (GRS) comprising 43 variants at the LPA gene, which encodes apolipoprotein(a), has clinical utility in assessing ASCVD risk compared with and in addition to lipoprotein(a) measurement. Design, Setting, and Participants The UK Biobank is a prospective observational study of approximately 500 000 volunteers aged 40 to 69 years who were recruited from 22 sites across the United Kingdom between 2006 and 2010. Using externally derived weights, an LPA GRS was calculated for 374 099 unrelated individuals with array-derived genotypes and lipoprotein(a) measures. Data were analyzed from April 2020 to March 2020. Exposures Measured lipoprotein(a) and LPA GRS. Main Outcomes and Measures We estimated the associations between measured lipoprotein(a) and LPA GRS with the incidence of ASCVD (peripheral arterial disease, coronary artery disease, myocardial infarction, ischemic stroke, and cardiovascular mortality) using Cox proportional hazards models. To determine the utility of using measured lipoprotein(a) and LPA GRS as risk enhancers for ASCVD, we assessed the potential improvement in ASCVD risk discrimination by QRISK3 and Pooled Cohort Equations among individuals with borderline to intermediate risk (n = 113 703 and 144 350, respectively). Results The mean age of the overall study population was 57.6 years, and 204 355 individuals were female (54.6%). During a median follow-up of 11.1 years (interquartile range, 1.4 years), 15 444 individuals developed an incident ASCVD event (5.1%). The LPA GRS explained approximately 60% of the variation in measured lipoprotein(a) for White/European individuals. Independently, both lipoprotein(a) and LPA GRS were associated with incident, composite ASCVD (hazard ratio per 120 nmol/L increase, 1.26; 95% CI, 1.23-1.28 vs hazard ratio, 1.29; 95% CI, 1.26-1.33; P < .001). The association between LPA GRS and ASCVD was substantially attenuated after adjusting for measured lipoprotein(a). Adding measured lipoprotein(a) or LPA GRS to QRISK3 provided modest improvements to the risk discrimination of incident ASCVD events (area under the receiver operating curve, 0.640; 95% CI, 0.633-0.647 vs 0.642; 95% CI, 0.635-0.649 for both; P = .005 and P = .01, respectively). Conclusions and Relevance When indicated, cardiovascular risk assessment with lipoprotein(a) at middle-age may include direct measurement or an LPA GRS.
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Affiliation(s)
- Mark Trinder
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard, Cambridge, Massachusetts
| | - Md Mesbah Uddin
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard, Cambridge, Massachusetts
| | - Phoebe Finneran
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard, Cambridge, Massachusetts
- Massachusetts General Hospital, Cardiology Division, Harvard Medical School, Boston, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
| | - Krishna G. Aragam
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard, Cambridge, Massachusetts
- Massachusetts General Hospital, Cardiology Division, Harvard Medical School, Boston, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
- Massachusetts General Hospital, Department of Medicine, Harvard Medical School, Boston
| | - Pradeep Natarajan
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard, Cambridge, Massachusetts
- Massachusetts General Hospital, Cardiology Division, Harvard Medical School, Boston, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
- Massachusetts General Hospital, Department of Medicine, Harvard Medical School, Boston
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14
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Di Maio S, Grüneis R, Streiter G, Lamina C, Maglione M, Schoenherr S, Öfner D, Thorand B, Peters A, Eckardt KU, Köttgen A, Kronenberg F, Coassin S. Investigation of a nonsense mutation located in the complex KIV-2 copy number variation region of apolipoprotein(a) in 10,910 individuals. Genome Med 2020; 12:74. [PMID: 32825847 PMCID: PMC7442989 DOI: 10.1186/s13073-020-00771-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/05/2020] [Indexed: 01/23/2023] Open
Abstract
Background The concentrations of the highly atherogenic lipoprotein(a) [Lp(a)] are mainly genetically determined by the LPA gene locus. However, up to 70% of the coding sequence is located in the complex so-called kringle IV type 2 (KIV-2) copy number variation, a region hardly accessible by common genotyping and sequencing technologies. Despite its size, little is known about genetic variants in this complex region. The R21X variant is a functional variant located in this region, but it has never been analyzed in large cohorts. Methods We typed R21X in 10,910 individuals from three European populations using a newly developed high-throughput allele-specific qPCR assay. R21X allelic location was determined by separating the LPA alleles using pulsed-field gel electrophoresis (PFGE) and typing them separately. Using GWAS data, we identified a proxy SNP located outside of the KIV-2. Linkage disequilibrium was determined both statistically and by long-range haplotyping using PFGE. Worldwide frequencies were determined by reanalyzing the sequencing data of the 1000 Genomes Project with a dedicated pipeline. Results R21X carriers (frequency 0.016–0.021) showed significantly lower mean Lp(a) concentrations (− 11.7 mg/dL [− 15.5; − 7.82], p = 3.39e−32). The variant is located mostly on medium-sized LPA alleles. In the 1000 Genome data, R21X mostly occurs in Europeans and South Asians, is absent in Africans, and shows varying frequencies in South American populations (0 to 0.022). Of note, the best proxy SNP was another LPA null mutation (rs41272114, D′ = 0.958, R2 = 0.281). D′ was very high in all 1000G populations (0.986–0.996), although rs41272114 frequency varies considerably (0–0.182). Co-localization of both null mutations on the same allele was confirmed by PFGE-based long-range haplotyping. Conclusions We performed the largest epidemiological study on an LPA KIV-2 variant so far, showing that it is possible to assess LPA KIV-2 mutations on a large scale. Surprisingly, in all analyzed populations, R21X was located on the same haplotype as the splice mutation rs41272114, creating “double-null” LPA alleles. Despite being a nonsense variant, the R21X status does not provide additional information beyond the rs41272114 genotype. This has important implications for studies using LPA loss-of-function mutations as genetic instruments and emphasizes the complexity of LPA genetics.
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Affiliation(s)
- Silvia Di Maio
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Schöpfstrasse 41, A-6020, Innsbruck, Austria
| | - Rebecca Grüneis
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Schöpfstrasse 41, A-6020, Innsbruck, Austria
| | - Gertraud Streiter
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Schöpfstrasse 41, A-6020, Innsbruck, Austria
| | - Claudia Lamina
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Schöpfstrasse 41, A-6020, Innsbruck, Austria
| | - Manuel Maglione
- Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Schoenherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Schöpfstrasse 41, A-6020, Innsbruck, Austria
| | - Dietmar Öfner
- Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, Innsbruck, Austria
| | - Barbara Thorand
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Neuherberg, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.,Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Schöpfstrasse 41, A-6020, Innsbruck, Austria
| | - Stefan Coassin
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Schöpfstrasse 41, A-6020, Innsbruck, Austria.
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15
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Youssef A, Clark JR, Koschinsky ML, Boffa MB. Lipoprotein(a): Expanding our knowledge of aortic valve narrowing. Trends Cardiovasc Med 2020; 31:305-311. [PMID: 32525013 DOI: 10.1016/j.tcm.2020.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/01/2020] [Accepted: 06/03/2020] [Indexed: 01/05/2023]
Abstract
Elevated levels of lipoprotein(a) [Lp(a)] have been identified as an independent and causal risk factor for atherosclerotic cardiovascular disease (ASCVD) and, more recently, calcific aortic valve disease (CAVD). CAVD is a slow, progressive disorder presenting as severe trileaflet calcification known as aortic valve stenosis (AS) that impairs valve motion and restricts ventricular outflow. AS afflicts 2% of the aging population (≥ 65 years) and tends to be quite advanced by the time it presents clinical symptoms of exertional angina, syncope, or heart failure. Currently, the only effective clinical therapy for AS patients is surgical or transcatheter aortic valve replacement. Evidence is accumulating that Lp(a) can exacerbate pathophysiological processes in CAVD, specifically, endothelial dysfunction, formation of foam cells, and promotion of a pro-inflammatory state. In the valve milieu, the pro-inflammatory effects of Lp(a) are manifested in valve thickening and mineralization through pro-osteogenic signaling and changes in gene expression in valve interstitial cells that is primarily facilitated by the oxidized phospholipid content of Lp(a). In AS pathogenesis, an incomplete understanding of the role of Lp(a) at the molecular level and the absence of appropriate animal models are barriers for the development of specific and effective clinical interventions designed to mitigate the role of Lp(a) in AS. However, the advent of effective therapies that dramatically lower Lp(a) provides the possibility of the first medical treatment to halt AS progression.
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Affiliation(s)
| | | | - Marlys L Koschinsky
- Robarts Research Institute, Canada; Department of Physiology & Pharmacology, Canada.
| | - Michael B Boffa
- Department of Biochemistry, Schulich School of Medicine & Dentistry, The University of Western Ontario, Room 2260 Robarts Research Institute, 1151 Richmond Street North London, London N6A 5B7, ON, Canada
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16
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Morgan BM, Brown AN, Deo N, Harrop TWR, Taiaroa G, Mace PD, Wilbanks SM, Merriman TR, Williams MJA, McCormick SPA. Nonsynonymous SNPs in LPA homologous to plasminogen deficiency mutants represent novel null apo(a) alleles. J Lipid Res 2019; 61:432-444. [PMID: 31806727 DOI: 10.1194/jlr.m094540] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 11/18/2019] [Indexed: 12/20/2022] Open
Abstract
Plasma lipoprotein (a) [Lp(a)] levels are largely determined by variation in the LPA gene, which codes for apo(a). Genome-wide association studies (GWASs) have identified nonsynonymous variants in LPA that associate with low Lp(a) levels, although their effect on apo(a) function is unknown. We investigated two such variants, R990Q and R1771C, which were present in four null Lp(a) individuals, for structural and functional effects. Sequence alignments showed the R990 and R1771 residues to be highly conserved and homologous to each other and to residues associated with plasminogen deficiency. Structural modeling showed both residues to make several polar contacts with neighboring residues that would be ablated on substitution. Recombinant expression of the WT and R1771C apo(a) in liver and kidney cells showed an abundance of an immature form for both apo(a) proteins. A mature form of apo(a) was only seen with the WT protein. Imaging of the recombinant apo(a) proteins in conjunction with markers of the secretory pathway indicated a poor transit of R1771C into the Golgi. Furthermore, the R1771C mutant displayed a glycosylation pattern consistent with ER, but not Golgi, glycosylation. We conclude that R1771 and the equivalent R990 residue facilitate correct folding of the apo(a) kringle structure and mutations at these positions prevent the proper folding required for full maturation and secretion. To our knowledge, this is the first example of nonsynonymous variants in LPA being causative of a null Lp(a) phenotype.
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Affiliation(s)
- Benjamin M Morgan
- Department of Biochemistry, School of Biomedical Sciences University of Otago, Dunedin, New Zealand
| | - Aimee N Brown
- Department of Biochemistry, School of Biomedical Sciences University of Otago, Dunedin, New Zealand
| | - Nikita Deo
- Department of Biochemistry, School of Biomedical Sciences University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Tom W R Harrop
- Department of Biochemistry, School of Biomedical Sciences University of Otago, Dunedin, New Zealand
| | - George Taiaroa
- Department of Biochemistry, School of Biomedical Sciences University of Otago, Dunedin, New Zealand
| | - Peter D Mace
- Department of Biochemistry, School of Biomedical Sciences University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Sigurd M Wilbanks
- Department of Biochemistry, School of Biomedical Sciences University of Otago, Dunedin, New Zealand
| | - Tony R Merriman
- Department of Biochemistry, School of Biomedical Sciences University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Michael J A Williams
- Department of Medicine, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Sally P A McCormick
- Department of Biochemistry, School of Biomedical Sciences University of Otago, Dunedin, New Zealand .,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
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17
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Ward NC, Kostner KM, Sullivan DR, Nestel P, Watts GF. Molecular, Population, and Clinical Aspects of Lipoprotein(a): A Bridge Too Far? J Clin Med 2019; 8:E2073. [PMID: 31783529 PMCID: PMC6947201 DOI: 10.3390/jcm8122073] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/15/2019] [Accepted: 11/15/2019] [Indexed: 12/16/2022] Open
Abstract
There is now significant evidence to support an independent causal role for lipoprotein(a) (Lp(a)) as a risk factor for atherosclerotic cardiovascular disease. Plasma Lp(a) concentrations are predominantly determined by genetic factors. However, research into Lp(a) has been hampered by incomplete understanding of its metabolism and proatherogeneic properties and by a lack of suitable animal models. Furthermore, a lack of standardized assays to measure Lp(a) and no universal consensus on optimal plasma levels remain significant obstacles. In addition, there are currently no approved specific therapies that target and lower elevated plasma Lp(a), although there are recent but limited clinical outcome data suggesting benefits of such reduction. Despite this, international guidelines now recognize elevated Lp(a) as a risk enhancing factor for risk reclassification. This review summarises the current literature on Lp(a), including its discovery and recognition as an atherosclerotic cardiovascular disease risk factor, attempts to standardise analytical measurement, interpopulation studies, and emerging therapies for lowering elevated Lp(a) levels.
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Affiliation(s)
- Natalie C. Ward
- School of Public Health, Curtin University, Perth 6102, Australia;
- School of Medicine, University of Western Australia, Perth 6009, Australia
| | - Karam M. Kostner
- Department of Cardiology, Mater Hospital, Brisbane 4104, Australia;
- School of Medicine University of Queensland, Brisbane 4072, Australia
| | - David R. Sullivan
- Medical School, The University of Sydney, Sydney 2006, Australia;
- Charles Perkins Centre, The University of Sydney, Sydney 2006, Australia
- Department of Biochemistry, Royal Prince Alfred Hospital, Sydney 2050, Australia
| | - Paul Nestel
- Baker Heart & Diabetes Institute, Melbourne 3004, Australia;
- Department of Cardiology, The Alfred Hospital, Melbourne 3004, Australia
| | - Gerald F. Watts
- School of Medicine, University of Western Australia, Perth 6009, Australia
- Lipid Disorders Clinic, Department of Cardiology, Royal Perth Hospital, Perth 6000, Australia
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18
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Deng L, Lou H, Zhang X, Thiruvahindrapuram B, Lu D, Marshall CR, Liu C, Xie B, Xu W, Wong LP, Yew CW, Farhang A, Ong RTH, Hoque MZ, Thuhairah AR, Jong B, Phipps ME, Scherer SW, Teo YY, Kumar SV, Hoh BP, Xu S. Analysis of five deep-sequenced trio-genomes of the Peninsular Malaysia Orang Asli and North Borneo populations. BMC Genomics 2019; 20:842. [PMID: 31718558 PMCID: PMC6852992 DOI: 10.1186/s12864-019-6226-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/25/2019] [Indexed: 12/18/2022] Open
Abstract
Background Recent advances in genomic technologies have facilitated genome-wide investigation of human genetic variations. However, most efforts have focused on the major populations, yet trio genomes of indigenous populations from Southeast Asia have been under-investigated. Results We analyzed the whole-genome deep sequencing data (~ 30×) of five native trios from Peninsular Malaysia and North Borneo, and characterized the genomic variants, including single nucleotide variants (SNVs), small insertions and deletions (indels) and copy number variants (CNVs). We discovered approximately 6.9 million SNVs, 1.2 million indels, and 9000 CNVs in the 15 samples, of which 2.7% SNVs, 2.3% indels and 22% CNVs were novel, implying the insufficient coverage of population diversity in existing databases. We identified a higher proportion of novel variants in the Orang Asli (OA) samples, i.e., the indigenous people from Peninsular Malaysia, than that of the North Bornean (NB) samples, likely due to more complex demographic history and long-time isolation of the OA groups. We used the pedigree information to identify de novo variants and estimated the autosomal mutation rates to be 0.81 × 10− 8 – 1.33 × 10− 8, 1.0 × 10− 9 – 2.9 × 10− 9, and ~ 0.001 per site per generation for SNVs, indels, and CNVs, respectively. The trio-genomes also allowed for haplotype phasing with high accuracy, which serves as references to the future genomic studies of OA and NB populations. In addition, high-frequency inherited CNVs specific to OA or NB were identified. One example is a 50-kb duplication in DEFA1B detected only in the Negrito trios, implying plausible effects on host defense against the exposure of diverse microbial in tropical rainforest environment of these hunter-gatherers. The CNVs shared between OA and NB groups were much fewer than those specific to each group. Nevertheless, we identified a 142-kb duplication in AMY1A in all the 15 samples, and this gene is associated with the high-starch diet. Moreover, novel insertions shared with archaic hominids were identified in our samples. Conclusion Our study presents a full catalogue of the genome variants of the native Malaysian populations, which is a complement of the genome diversity in Southeast Asians. It implies specific population history of the native inhabitants, and demonstrated the necessity of more genome sequencing efforts on the multi-ethnic native groups of Malaysia and Southeast Asia.
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Affiliation(s)
- Lian Deng
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Haiyi Lou
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoxi Zhang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | | | - Dongsheng Lu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Christian R Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Chang Liu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Bo Xie
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wanxing Xu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Lai-Ping Wong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117597, Singapore
| | - Chee-Wei Yew
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Aghakhanian Farhang
- Jefrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway, 46150, Subang Jaya, Selangor, Malaysia.,Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, 46150 Sunway, Subang Jaya, Selangor, Malaysia
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117597, Singapore
| | - Mohammad Zahirul Hoque
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Abdul Rahman Thuhairah
- Clinical Pathology Diagnostic Centre Research Laboratory, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, 47000 Sg Buloh, Subang Jaya, Selangor, Malaysia
| | - Bhak Jong
- Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea.,Geromics, Ulsan, 44919, Republic of Korea.,Biomedical Engineering Department, The Genomics Institute, UNIST, Ulsan, Republic of Korea
| | - Maude E Phipps
- Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, 46150 Sunway, Subang Jaya, Selangor, Malaysia
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117597, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, 117456, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
| | - Subbiah Vijay Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia.
| | - Boon-Peng Hoh
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,Faculty of Medicine and Health Sciences, UCSI University, Jalan Menara Gading, Taman Connaught, Cheras, 56000, Kuala Lumpur, Malaysia.
| | - Shuhua Xu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China. .,Collaborative Innovation Center of Genetics and Development, Shanghai, 200438, China. .,Human Phenome Institute, Fudan University, Shanghai, 201203, China.
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19
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Rouhani B, Ghaderian SMH, Salehi Z. Investigation of LPA sequence variants rs6415084, rs3798220 with conventional coronary artery disease in Iranian CAD patients. Hum Antibodies 2019; 27:99-104. [PMID: 30594920 DOI: 10.3233/hab-180353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Conventional coronary artery disease (CAD) is the leading cause of morbidity and mortality in the general population. In recent years, multiple CAD promising risk factors have been reported and used for risk stratification. Lipoprotein(a) [LPA] concentration in plasma was shown associated with CAD risk and LPA genetic variants in different ethnic groups remains less clear. METHODS We obtained data from 100 affected patients with established CAD and 100 healthy controls. We tested Body mass index (BMI), total cholesterol level (TC), systolic blood pressure (SBP), diastolic blood pressure (DBP), low-density lipoprotein (LDL), high-density lipoprotein (HDL), triglycerides (TG), fasting blood sugar (FBS) and two LPA (rs10455872 and rs3798220 SNPs) between cases and healthy controls. TaqMan SNP genotyping assays were performed to detect variants. RESULTS Obtained data for BMI, TC, SBP, DBP, and LDL have significantly difference between two groups. Individually, the single SNPs were not associated with CAD in different analysis models. Also there was no significant difference in the incidence of CAD among cases carrying different genotypes of the two variants in LPA with p> 0.05. DISCUSSION In this study patients with CAD, lipoprotein(a) concentrations and genetic variants showed no associations and we conclude that these variables are not useful risk factors to predict progression to disease is Iranian population. However, the prevalence and association of LPA SNPs with size of LPA and isoforms are highly variable and genetic background-specific. CONCLUSION Our data did not indicate a relationship between genomic LPA variants (rs10455872 and rs3798220) and subsequent cardiovascular events in Iranian CAD patients. We did not confirm the association of the theses SNPs with CAD in our samples of Iranian patients. For the studied variants, our finding is consistent with reports which showed the lack of this genetic association in other populations.
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Affiliation(s)
- Borzu Rouhani
- Department of Genetic, Faculty of Science, Tonekabon Branch, Islamic Azad University, Tonekabon, Iran
| | | | - Zivar Salehi
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
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20
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Coassin S, Schönherr S, Weissensteiner H, Erhart G, Forer L, Losso JL, Lamina C, Haun M, Utermann G, Paulweber B, Specht G, Kronenberg F. A comprehensive map of single-base polymorphisms in the hypervariable LPA kringle IV type 2 copy number variation region. J Lipid Res 2018; 60:186-199. [PMID: 30413653 PMCID: PMC6314250 DOI: 10.1194/jlr.m090381] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Indexed: 12/21/2022] Open
Abstract
Lipoprotein (a) [Lp(a)] concentrations are among the strongest genetic risk factors for cardiovascular disease and present pronounced interethnic and interindividual differences. Approximately 90% of Lp(a) variance is controlled by the LPA gene, which contains a 5.6-kb-large copy number variation [kringle IV type 2 (KIV-2) repeat] that generates >40 protein isoforms. Variants within the KIV-2 region are not called in common sequencing projects, leaving up to 70% of the LPA coding region currently unaddressed. To completely assess the variability in LPA, we developed a sequencing strategy for this region and report here the first map of genetic variation in the KIV-2 region, a comprehensively evaluated ultradeep sequencing protocol, and an easy-to-use variant analysis pipeline. We sequenced 123 Central-European individuals and reanalyzed public data of 2,504 individuals from 26 populations. We found 14 different loss-of-function and splice-site mutations, as well as >100, partially even common, missense variants. Some coding variants were frequent in one population but absent in others. This provides novel candidates to explain the large ethnic and individual differences in Lp(a) concentrations. Importantly, our approach and pipeline are also applicable to other similar copy number variable regions, allowing access to regions that are not captured by common genome sequencing.
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Affiliation(s)
- Stefan Coassin
- Division of Genetic Epidemiology Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Schönherr
- Division of Genetic Epidemiology Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Hansi Weissensteiner
- Division of Genetic Epidemiology Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gertraud Erhart
- Division of Genetic Epidemiology Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas Forer
- Division of Genetic Epidemiology Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Jamie Lee Losso
- Division of Genetic Epidemiology Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Claudia Lamina
- Division of Genetic Epidemiology Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Margot Haun
- Division of Genetic Epidemiology Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gerd Utermann
- Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Bernhard Paulweber
- First Department of Internal Medicine, Paracelsus Private Medical University, Salzburg, Austria
| | - Günther Specht
- Department of Database and Information Systems, Institute of Computer Science, University of Innsbruck, Innsbruck, Austria
| | - Florian Kronenberg
- Division of Genetic Epidemiology Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
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21
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Zekavat SM, Ruotsalainen S, Handsaker RE, Alver M, Bloom J, Poterba T, Seed C, Ernst J, Chaffin M, Engreitz J, Peloso GM, Manichaikul A, Yang C, Ryan KA, Fu M, Johnson WC, Tsai M, Budoff M, Vasan RS, Cupples LA, Rotter JI, Rich SS, Post W, Mitchell BD, Correa A, Metspalu A, Wilson JG, Salomaa V, Kellis M, Daly MJ, Neale BM, McCarroll S, Surakka I, Esko T, Ganna A, Ripatti S, Kathiresan S, Natarajan P. Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries. Nat Commun 2018; 9:2606. [PMID: 29973585 PMCID: PMC6031652 DOI: 10.1038/s41467-018-04668-w] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/15/2018] [Indexed: 02/06/2023] Open
Abstract
Lipoprotein(a), Lp(a), is a modified low-density lipoprotein particle that contains apolipoprotein(a), encoded by LPA, and is a highly heritable, causal risk factor for cardiovascular diseases that varies in concentrations across ancestries. Here, we use deep-coverage whole genome sequencing in 8392 individuals of European and African ancestry to discover and interpret both single-nucleotide variants and copy number (CN) variation associated with Lp(a). We observe that genetic determinants between Europeans and Africans have several unique determinants. The common variant rs12740374 associated with Lp(a) cholesterol is an eQTL for SORT1 and independent of LDL cholesterol. Observed associations of aggregates of rare non-coding variants are largely explained by LPA structural variation, namely the LPA kringle IV 2 (KIV2)-CN. Finally, we find that LPA risk genotypes confer greater relative risk for incident atherosclerotic cardiovascular diseases compared to directly measured Lp(a), and are significantly associated with measures of subclinical atherosclerosis in African Americans.
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Affiliation(s)
- Seyedeh M Zekavat
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Yale School of Medicine, New Haven, CT, 06510, USA
- Department of Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06510, USA
| | - Sanni Ruotsalainen
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
| | - Robert E Handsaker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Maris Alver
- Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Genome Center, Tallinn, Estonia
| | - Jonathan Bloom
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Boston, MA, 02142, USA
| | - Timothy Poterba
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Boston, MA, 02142, USA
| | - Cotton Seed
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Boston, MA, 02142, USA
| | - Jason Ernst
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Mark Chaffin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jesse Engreitz
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22904, USA
| | - Chaojie Yang
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22904, USA
| | - Kathleen A Ryan
- Program in Personalized and Genomic Medicine, Division of Endocrinology, Diabetes & Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Mao Fu
- Program in Personalized and Genomic Medicine, Division of Endocrinology, Diabetes & Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - W Craig Johnson
- Department of Biostatistics, School of Public Health and Community Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Michael Tsai
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Matthew Budoff
- Division of Cardiology, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Los Angeles, CA, 90509, USA
| | - Ramachandran S Vasan
- NHLBI Framingham Heart Study, Framingham, MA, 20892, USA
- Sections of Preventive medicine and Epidemiology, and cardiovascular medicine, Departments of Medicine and Epidemiology, Boston university Schools of Medicine and Public health, Boston, MA, 02118, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
- NHLBI Framingham Heart Study, Framingham, MA, 20892, USA
| | - Jerome I Rotter
- Departments of Pediatrics and Medicine, The Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA, 90509, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22904, USA
| | - Wendy Post
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | | | - James G Wilson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Manolis Kellis
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, MA, 02139, USA
| | - Mark J Daly
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Boston, MA, 02142, USA
| | - Benjamin M Neale
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Boston, MA, 02142, USA
| | - Steven McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Ida Surakka
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
| | - Tonu Esko
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Estonian Genome Center, Tallinn, Estonia
| | - Andrea Ganna
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Boston, MA, 02142, USA
| | - Samuli Ripatti
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sekar Kathiresan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA.
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA.
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22
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Coassin S, Erhart G, Weissensteiner H, Eca Guimarães de Araújo M, Lamina C, Schönherr S, Forer L, Haun M, Losso JL, Köttgen A, Schmidt K, Utermann G, Peters A, Gieger C, Strauch K, Finkenstedt A, Bale R, Zoller H, Paulweber B, Eckardt KU, Hüttenhofer A, Huber LA, Kronenberg F. A novel but frequent variant in LPA KIV-2 is associated with a pronounced Lp(a) and cardiovascular risk reduction. Eur Heart J 2018; 38:1823-1831. [PMID: 28444229 PMCID: PMC5837733 DOI: 10.1093/eurheartj/ehx174] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/21/2017] [Indexed: 01/21/2023] Open
Abstract
Aims Lp(a) concentrations represent a major cardiovascular risk factor and are almost entirely controlled by one single locus (LPA). However, many genetic factors in LPA governing the enormous variance of Lp(a) levels are still unknown. Since up to 70% of the LPA coding sequence are located in a difficult to access hypervariable copy number variation named KIV-2, we hypothesized that it may contain novel functional variants with pronounced effects on Lp(a) concentrations. We performed a large scale mutation analysis in the KIV-2 using an extreme phenotype approach. Methods and Results We compiled an discovery set of 123 samples showing discordance between LPA isoform phenotype and Lp(a) concentrations and controls. Using ultra-deep sequencing, we identified a splice site variant (G4925A) in preferential association with the smaller LPA isoforms. Follow-up in a European general population (n = 2892) revealed an exceptionally high carrier frequency of 22.1% in the general population. The variant explains 20.6% of the Lp(a) variance in carriers of low molecular weight (LMW) apo(a) isoforms (P = 5.75e-38) and reduces Lp(a) concentrations by 31.3 mg/dL. Accordingly the odds ratio for cardiovascular disease was reduced from 1.39 [95% confidence interval (CI): 1.17–1.66, P = 1.89e-04] for wildtype LMW individuals to 1.19 [95%CI: 0.92; 1.56, P = 0.19] in LMW individuals who were additionally positive for G4925A. Functional studies point towards a reduction of splicing efficiency by this novel variant. Conclusion A highly frequent but until now undetected variant in the LPA KIV-2 region is strongly associated with reduced Lp(a) concentrations and reduced cardiovascular risk in LMW individuals.
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Affiliation(s)
- Stefan Coassin
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Schoepfstrasse 41, 6020 Innsbruck, Austria
| | - Gertraud Erhart
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Schoepfstrasse 41, 6020 Innsbruck, Austria
| | - Hansi Weissensteiner
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Schoepfstrasse 41, 6020 Innsbruck, Austria
| | | | - Claudia Lamina
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Schoepfstrasse 41, 6020 Innsbruck, Austria
| | - Sebastian Schönherr
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Schoepfstrasse 41, 6020 Innsbruck, Austria
| | - Lukas Forer
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Schoepfstrasse 41, 6020 Innsbruck, Austria
| | - Margot Haun
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Schoepfstrasse 41, 6020 Innsbruck, Austria
| | - Jamie Lee Losso
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Schoepfstrasse 41, 6020 Innsbruck, Austria
| | - Anna Köttgen
- Division of Genetic Epidemiology, Division of Genetic Epidemiology - Faculty of Medicine and Medical Center - University of Freiburg, Hugstetter Strasse 49, 79106 Freiburg, Germany
| | - Konrad Schmidt
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Schoepfstrasse 41, 6020 Innsbruck, Austria
| | - Gerd Utermann
- Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Peter-Mayr-Strasse 1, 6020 Innsbruck, Austria
| | - Annette Peters
- German Center for Diabetes Research, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany.,Munich Heart Alliance, German Center for Cardiovascular Disease Research, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Christian Gieger
- Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany.,Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Marchioninistrasse 15, 81377 Munich, Germany
| | - Armin Finkenstedt
- Internal Medicine I, Medical University Innsbruck, Anichstrasse 35, 6020 Innsbruck, Austria
| | - Reto Bale
- Section of Interventional Oncology - Microinvasive Therapy (SIP), Department of Radiology, Medical University Innsbruck, Anichstrasse 35, 6020 Innsbruck, Austria
| | - Heinz Zoller
- Internal Medicine I, Medical University Innsbruck, Anichstrasse 35, 6020 Innsbruck, Austria
| | - Bernhard Paulweber
- First Department of Internal Medicine, Paracelsus Private Medical University, Müllner Hauptstrasse 48, 5020 Salzburg, Austria
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, University of Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany
| | - Alexander Hüttenhofer
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Lukas A Huber
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Schoepfstrasse 41, 6020 Innsbruck, Austria
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23
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Xu Y, Shi W, Song R, Long W, Guo H, Yuan S, Zhang T. Divergent patterns of genic copy number variation in KCNIP1 gene reveal risk locus of type 2 diabetes in Chinese population. Endocr J 2018; 65:537-545. [PMID: 29491224 DOI: 10.1507/endocrj.ej17-0496] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Copy number variation (CNV) has emerged as another important genetic marker in addition to SNP for understanding etiology of complex disease. Kv channel interacting protein 1 (KCNIP1) is a Ca2+-dependent transcriptional modulator that contributes to the regulation of insulin secretion. Previous genome-wide CNV assay identified the KCNIP1 gene encompassing a CNV region, however, its further effect and risk rate on type 2 diabetes (T2D) have rarely been addressed, especially in Chinese population. The current study aims to detect and excavate genetic distribution profile of KCNIP1 CNV in Chinese T2D and control populations, and further to investigate the associations with clinical characteristics. Divergent patterns of the KCNIP1 CNV were identified (p < 0.01), in which the copy number gain was predominant in T2D, while the copy number normal accounted for the most in control group. Consistently, the individuals with copy number gain showed significant risk on T2D (OR = 4.550, p < 0.01). The KCNIP1 copy numbers presented significantly positive correlations with fasting plasma glucose and glycated hemoglobin in T2D. For OGTT test, the T2D patients with copy number gain had remarkably elevated glucose contents (60, 120, 180-min, p < 0.05 or p < 0.01) and diminished insulin levels (60, 120-min, p < 0.05) than those with copy number loss and normal, which suggested that the KCNIP1 CNV was correlated with the glucose and insulin action. This is the first CNV association study of the KCNIP1 gene in Chinese population, and these data indicated that KCNIP1 might function as a T2D-susceptibility gene whose dysregulation alters insulin production.
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Affiliation(s)
- Yao Xu
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Weilin Shi
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Ruhui Song
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Wenlin Long
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Hui Guo
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Shiliang Yuan
- Tianyou Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei 430064, China
| | - Tongcun Zhang
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
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24
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Sun L, Zong M, Chen C, Xie L, Wu F, Yu M, Fan L. Low LPA gene kringle IV-2 repeat copy number association with elevated lipoprotein (a) concentration as an independent risk factor of coronary atherosclerotic heart disease in the Chinese Han population. Lipids Health Dis 2018; 17:111. [PMID: 29747697 PMCID: PMC5946444 DOI: 10.1186/s12944-018-0753-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 04/23/2018] [Indexed: 11/10/2022] Open
Abstract
Background Lipoprotein (a) [Lp(a)], which is genetically determined by the LPA gene kringle IV type 2 (KIV-2) repeat copy number, has previously been reported in different populations. However, it is uncertain if the same occurs in the Chinese Han population. This study explored the correlation of Lp(a) mass or particle concentration with KIV-2 repeat copy number and application for coronary atherosclerotic heart disease (CAHD) risk assessment. Methods A cross-sectional study including 884 subjects was conducted. The Lp(a) level and routine risk factors of CAHD were compared. The KIV-2 copy number distribution, relationship with Lp(a), and assessment for CAHD risk were explored. Results The mean of Lp(a) mass or particle concentration in the CAHD group was higher than that in the non-CAHD group, while the KIV-2 copy number in the CAHD group was lower. Lp(a) had auxiliary values in gauging the type of plaque and was significantly higher in the soft-plaque group than that in the other two groups (200 mg/L [21.5 nmol/L], 166 mg/L [18.6 nmol/L], 149 mg/L [17.1 nmol/L], respectively, P < 0.05). Kappa test indicated divergence for the same individual using two Lp(a) concentrations (kappa value was 0.536 [< 0.75]). Elevated Lp(a) was an independent CAHD risk factor, whatever mass or particle concentration, and large KIV-2 copy number was a protective factor. Conclusion Lp(a) level and small KIV-2 copy number are risk factors for CAHD in the Chinese Han population; furthermore, elevated Lp(a) may gauge the type of coronary plaque.
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Affiliation(s)
- Lishan Sun
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai, 200120, People's Republic of China
| | - Ming Zong
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai, 200120, People's Republic of China
| | - Cuncun Chen
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai, 200120, People's Republic of China
| | - Lihong Xie
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai, 200120, People's Republic of China
| | - Fei Wu
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai, 200120, People's Republic of China
| | - Ming Yu
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai, 200120, People's Republic of China
| | - Lieying Fan
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai, 200120, People's Republic of China.
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25
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Ellis KL, Boffa MB, Sahebkar A, Koschinsky ML, Watts GF. The renaissance of lipoprotein(a): Brave new world for preventive cardiology? Prog Lipid Res 2017; 68:57-82. [DOI: 10.1016/j.plipres.2017.09.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/01/2017] [Accepted: 09/05/2017] [Indexed: 12/24/2022]
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26
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Noureen A, Ronke C, Khalifa M, Halbwax M, Fischer A, André C, Atencia R, Garriga R, Mugisha L, Ceglarek U, Thiery J, Utermann G, Schmidt K. Significant differentiation in the apolipoprotein(a)/lipoprotein(a) trait between chimpanzees from Western and Central Africa. Am J Primatol 2017; 79. [PMID: 28671714 DOI: 10.1002/ajp.22683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 06/07/2017] [Accepted: 06/11/2017] [Indexed: 12/20/2022]
Abstract
Elevated Lipoprotein(a) (Lp(a)) plasma concentrations are a risk factor for cardiovascular disease in humans, largely controlled by the LPA gene encoding apolipoprotein(a) (apo(a)). Lp(a) is composed of low-density lipoprotein (LDL) and apo(a) and restricted to Catarrhini. A variable number of kringle IV (KIV) domains in LPA lead to a size polymorphism of apo(a) that is inversely correlated with Lp(a) concentrations. Smaller apo(a) isoforms and higher Lp(a) levels in central chimpanzees (Pan troglodytes troglodytes [PTT]) compared to humans from Europe had been reported. We studied apo(a) isoforms and Lp(a) concentrations in 75 western (Pan troglodytes verus [PTV]) and 112 central chimpanzees, and 12 bonobos (Pan paniscus [PPA]), all wild born and living in sanctuaries in Sierra Leone, Republic of the Congo, and DR Congo, respectively, and 116 humans from Gabon. Lp(a) levels were severalfold higher in western than in central chimpanzees (181.0 ± 6.7 mg/dl vs. 56.5 ± 4.3 mg/dl), whereas bonobos showed intermediate levels (134.8 ± 33.4 mg/dl). Apo(a) isoform sizes differed significantly between subspecies (means 20.9 ± 2.2, 22.9 ± 4.4, and 23.8 ± 3.8 KIV repeats in PTV, PTT, and PPA, respectively). However, far higher isoform-associated Lp(a) concentrations for all isoform sizes in western chimpanzees offered the main explanation for the higher overall Lp(a) levels in this subspecies. Human Lp(a) concentrations (mean 47.9 ± 2.8 mg/dl) were similar to those in central chimpanzees despite larger isoforms (mean 27.1 ± 4.9 KIV). Lp(a) and LDL, apoB-100, and total cholesterol levels only correlated in PTV. This remarkable differentiation between chimpanzees from different African habitats and the trait's similarity in humans and chimpanzees from Central Africa poses the question of a possible impact of an environmental factor that has shaped the genetic architecture of LPA. Overall, studies on the cholesterol-containing particles of Lp(a) and LDL in chimpanzees should consider differentiation between subspecies.
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Affiliation(s)
- Asma Noureen
- Division of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria.,Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Claudius Ronke
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Mahmoud Khalifa
- Division of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria.,Molecular Biology Laboratory, Department of Zoology, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Michel Halbwax
- International Center of Medical Research of Franceville (CIRMF), Franceville, Gabon
| | - Anne Fischer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Claudine André
- Lola Ya Bonobo Sanctuary, "Petites Chutes de la Lukaya", Kinshasa, Democratic Republic of Congo
| | - Rebeca Atencia
- Réserve Naturelle Sanctuaire à Chimpanzés de Tchimpounga, Jane Goodall Institute, Pointe-Noire, Republic of Congo
| | - Rosa Garriga
- Tacugama Chimpanzee Sanctuary, Freetown, Sierra Leone
| | - Lawrence Mugisha
- Conservation & Ecosystem Health Alliance (CEHA), Kampala, Uganda.,College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Uta Ceglarek
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Joachim Thiery
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Gerd Utermann
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Konrad Schmidt
- Division of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria.,Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria.,Department for Tropical Medicine, Eberhard-Karls-University, Tuebingen, Germany.,Centre de Recherches Médicales de Lambaréné, Albert Schweitzer Hospital, Lambaréné, Gabon
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27
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Mack S, Coassin S, Rueedi R, Yousri NA, Seppälä I, Gieger C, Schönherr S, Forer L, Erhart G, Marques-Vidal P, Ried JS, Waeber G, Bergmann S, Dähnhardt D, Stöckl A, Raitakari OT, Kähönen M, Peters A, Meitinger T, Strauch K, Kedenko L, Paulweber B, Lehtimäki T, Hunt SC, Vollenweider P, Lamina C, Kronenberg F. A genome-wide association meta-analysis on lipoprotein (a) concentrations adjusted for apolipoprotein (a) isoforms. J Lipid Res 2017; 58:1834-1844. [PMID: 28512139 PMCID: PMC5580897 DOI: 10.1194/jlr.m076232] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/04/2017] [Indexed: 12/13/2022] Open
Abstract
High lipoprotein (a) [Lp(a)] concentrations are an independent risk factor for cardiovascular outcomes. Concentrations are strongly influenced by apo(a) kringle IV repeat isoforms. We aimed to identify genetic loci associated with Lp(a) concentrations using data from five genome-wide association studies (n = 13,781). We identified 48 independent SNPs in the LPA and 1 SNP in the APOE gene region to be significantly associated with Lp(a) concentrations. We also adjusted for apo(a) isoforms to identify loci affecting Lp(a) levels independently from them, which resulted in 31 SNPs (30 in the LPA, 1 in the APOE gene region). Seven SNPs showed a genome-wide significant association with coronary artery disease (CAD) risk. A rare SNP (rs186696265; MAF ∼1%) showed the highest effect on Lp(a) and was also associated with increased risk of CAD (odds ratio = 1.73, P = 3.35 × 10−30). Median Lp(a) values increased from 2.1 to 91.1 mg/dl with increasing number of Lp(a)-increasing alleles. We found the APOE2-determining allele of rs7412 to be significantly associated with Lp(a) concentrations (P = 3.47 × 10−10). Each APOE2 allele decreased Lp(a) by 3.34 mg/dl corresponding to ∼15% of the population’s mean values. Performing a gene-based test of association, including suspected Lp(a) receptors and regulators, resulted in one significant association of the TLR2 gene with Lp(a) (P = 3.4 × 10−4). In summary, we identified a large number of independent SNPs in the LPA gene region, as well as the APOE2 allele, to be significantly associated with Lp(a) concentrations.
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Affiliation(s)
- Salome Mack
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Stefan Coassin
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Rico Rueedi
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Noha A Yousri
- Department of Physiology and Biophysics, Weill Cornell Medical College-Qatar, Doha, Qatar.,Department of Computer and Systems Engineering, Alexandria University, 21526 Alexandria, Egypt
| | - Ilkka Seppälä
- Department of Clinical Chemistry, Fimlab Laboratories and University of Tampere School of Medicine, 33520 Tampere, Finland
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Sebastian Schönherr
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Lukas Forer
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Gertraud Erhart
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Pedro Marques-Vidal
- Department of Medicine, Internal Medicine, Lausanne University Hospital, 1015 Lausanne, Switzerland
| | - Janina S Ried
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Gerard Waeber
- Department of Medicine, Internal Medicine, Lausanne University Hospital, 1015 Lausanne, Switzerland
| | - Sven Bergmann
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Doreen Dähnhardt
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Andrea Stöckl
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Olli T Raitakari
- Department of Clinical Physiology, Turku University Hospital, 20520 Turku, Finland.,Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520 Turku, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and University of Tampere, 33521 Tampere, Finland
| | - Annette Peters
- Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany.,German Centre for Cardiovascular Research (DZHK), 80802 Munich, Germany.,German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Technische Universität München, 81675 München, Germany.,Institute of Human Genetics, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany.,Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany.,Institute of Medical Informatics, Biometry, and Epidemiology, Ludwig-Maximilians-Universität, 81377 Munich, Germany
| | | | - Ludmilla Kedenko
- First Department of Internal Medicine, Paracelsus Private Medical University, 5020 Salzburg, Austria
| | - Bernhard Paulweber
- First Department of Internal Medicine, Paracelsus Private Medical University, 5020 Salzburg, Austria
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and University of Tampere School of Medicine, 33520 Tampere, Finland
| | - Steven C Hunt
- Cardiovascular Genetics Division, University of Utah School of Medicine, Salt Lake City, UT 84108.,Department of Genetic Medicine, Weill Cornell Medicine, Doha, Qatar
| | - Peter Vollenweider
- Department of Medicine, Internal Medicine, Lausanne University Hospital, 1015 Lausanne, Switzerland
| | - Claudia Lamina
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
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28
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Schmidt K, Noureen A, Kronenberg F, Utermann G. Structure, function, and genetics of lipoprotein (a). J Lipid Res 2016; 57:1339-59. [PMID: 27074913 DOI: 10.1194/jlr.r067314] [Citation(s) in RCA: 319] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Indexed: 12/29/2022] Open
Abstract
Lipoprotein (a) [Lp(a)] has attracted the interest of researchers and physicians due to its intriguing properties, including an intragenic multiallelic copy number variation in the LPA gene and the strong association with coronary heart disease (CHD). This review summarizes present knowledge of the structure, function, and genetics of Lp(a) with emphasis on the molecular and population genetics of the Lp(a)/LPA trait, as well as aspects of genetic epidemiology. It highlights the role of genetics in establishing Lp(a) as a risk factor for CHD, but also discusses uncertainties, controversies, and lack of knowledge on several aspects of the genetic Lp(a) trait, not least its function.
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Affiliation(s)
- Konrad Schmidt
- Divisions of Human Genetics Medical University of Innsbruck, Innsbruck, Austria Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Asma Noureen
- Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Florian Kronenberg
- Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gerd Utermann
- Divisions of Human Genetics Medical University of Innsbruck, Innsbruck, Austria
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29
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Khalifa M, Noureen A, Ertelthalner K, Bandegi AR, Delport R, Firdaus WJJ, Geethanjali FS, Luthra K, Makemaharn O, Pang RWC, Salem AH, Sasaki J, Schiefenhoevel W, Lingenhel A, Kronenberg F, Utermann G, Schmidt K. Lack of association of rs3798220 with small apolipoprotein(a) isoforms and high lipoprotein(a) levels in East and Southeast Asians. Atherosclerosis 2015; 242:521-8. [PMID: 26302166 DOI: 10.1016/j.atherosclerosis.2015.07.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/06/2015] [Accepted: 07/07/2015] [Indexed: 12/20/2022]
Abstract
OBJECTIVE The variant allele of rs3798220 in the apolipoprotein(a) gene (LPA) is used to assess the risk for coronary artery disease (CAD) in Europeans, where it is associated with short alleles of the Kringle IV-2 (KIV-2) copy number variation (CNV) and high lipoprotein(a) (Lp(a)) concentrations. No association of rs3798220 with CAD was detected in a GWAS of East Asians. Our study investigated the association of rs3798220 with Lp(a) concentrations and KIV-2 CNV size in non-European populations to explain the missing association of the variant with CAD in Asians. METHODS We screened three populations from Africa and seven from Asia by TaqMan Assay for rs3798220 and determined KIV-2 CNV sizes of LPA alleles by pulsed-field gel electrophoresis (PFGE). Additionally, CAD cases from India were analysed. To investigate the phylogenetic origin of rs3798220, 40 LPA alleles from Chinese individuals were separated by PFGE and haplotyped for further SNPs. RESULTS The variant was not found in Africans. Allele frequencies in East and Southeast Asians ranged from 2.9% to 11.6%, and were very low (0.15%) in CAD cases and controls from India. The variant was neither associated with short KIV-2 CNV alleles nor elevated Lp(a) concentrations in Asians. CONCLUSION Our study shows that rs3798220 is no marker for short KIV-2 CNV alleles and high Lp(a) in East and Southeast Asians, although the haplotype background is shared with Europeans. It appears unlikely that this SNP confers atherogenic potential on its own. Furthermore, this SNP does not explain Lp(a) attributed risk for CAD in Asian Indians.
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Affiliation(s)
- Mahmoud Khalifa
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria; Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Asma Noureen
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria; Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Kathrin Ertelthalner
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ahmad Reza Bandegi
- Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Rhena Delport
- Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria; Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Wance J J Firdaus
- Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Finney S Geethanjali
- Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria; Department of Clinical Biochemistry, Christian Medical College Vellore, Tamil Nadu, India
| | - Kalpana Luthra
- Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria; Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Orawan Makemaharn
- Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria; Department of Obstetrics and Gynaecology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Richard W C Pang
- Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria; Division of Clinical Biochemistry, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Abdel-Halim Salem
- Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Jun Sasaki
- Graduate School of Pharmaceutical Medicine, International University of Health and Welfare, Fukuoka, Japan
| | | | - Arno Lingenhel
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria; Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gerd Utermann
- Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Konrad Schmidt
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria; Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria; Centre de Recherches Médicales de Lambaréné, Albert Schweitzer Hospital, Lambaréné, Gabon; Department for Tropical Medicine, Eberhard-Karls-University Tuebingen, Tuebingen, Germany.
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