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Tani R, Matsunaga K, Toda Y, Inoue T, Fu HY, Minamino T. Phenotypic homozygous familial hypercholesterolemia successfully treated with proprotein convertase subtilisin/kexin type 9 inhibitors. Clin Case Rep 2024; 12:e8537. [PMID: 38380379 PMCID: PMC10876917 DOI: 10.1002/ccr3.8537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/22/2024] Open
Abstract
Recent data reveal phenotypic HoFH patients may be responsive to PCSK9 inhibitors, challenging prior assumptions. Genetic testing advancements now more accurately forecast patient responses to these therapies, improving treatment strategies.
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Affiliation(s)
- Ryosuke Tani
- Department of Cardiorenal and Cerebrovascular Medicine, Faculty of MedicineKagawa UniversityKagawaJapan
| | - Keiji Matsunaga
- Department of Cardiorenal and Cerebrovascular Medicine, Faculty of MedicineKagawa UniversityKagawaJapan
| | - Yuta Toda
- Department of Cardiorenal and Cerebrovascular Medicine, Faculty of MedicineKagawa UniversityKagawaJapan
| | - Tomoko Inoue
- Department of Cardiorenal and Cerebrovascular Medicine, Faculty of MedicineKagawa UniversityKagawaJapan
| | - Hai Ying Fu
- Department of Cardiorenal and Cerebrovascular Medicine, Faculty of MedicineKagawa UniversityKagawaJapan
| | - Tetsuo Minamino
- Department of Cardiorenal and Cerebrovascular Medicine, Faculty of MedicineKagawa UniversityKagawaJapan
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2
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Ibrahim S, van Rooij J, Verkerk AJ, de Vries J, Zuurbier L, Defesche J, Peter J, Schonck WA, Sedaghati-Khayat B, Kees Hovingh G, Uitterlinden AG, Stroes ES, Reeskamp LF. Low-Cost High-Throughput Genotyping for Diagnosing Familial Hypercholesterolemia. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2023; 16:462-469. [PMID: 37675602 PMCID: PMC10581440 DOI: 10.1161/circgen.123.004103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 08/11/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND Familial hypercholesterolemia (FH) is a common but underdiagnosed genetic disorder characterized by high low-density lipoprotein cholesterol levels and premature cardiovascular disease. Current sequencing methods to diagnose FH are expensive and time-consuming. In this study, we evaluated the accuracy of a low-cost, high-throughput genotyping array for diagnosing FH. METHODS An Illumina Global Screening Array was customized to include probes for 636 variants, previously classified as FH-causing variants. First, its theoretical coverage was assessed in all FH variant carriers diagnosed through next-generation sequencing between 2016 and 2022 in the Netherlands (n=1772). Next, the performance of the array was validated in another sample of FH variant carriers previously identified in the Dutch FH cascade screening program (n=1268). RESULTS The theoretical coverage of the array for FH-causing variants was 91.3%. Validation of the array was assessed in a sample of 1268 carriers of whom 1015 carried a variant in LDLR, 250 in APOB, and 3 in PCSK9. The overall sensitivity was 94.7% and increased to 98.2% after excluding participants with variants not included in the array design. Copy number variation analysis yielded a 89.4% sensitivity. In 18 carriers, the array identified a total of 19 additional FH-causing variants. Subsequent DNA analysis confirmed 5 of the additionally identified variants, yielding a false-positive result in 16 subjects (1.3%). CONCLUSIONS The FH genotyping array is a promising tool for genetically diagnosing FH at low costs and has the potential to greatly increase accessibility to genetic testing for FH. Continuous customization of the array will further improve its performance.
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Affiliation(s)
- Shirin Ibrahim
- Department of Vascular Medicine (S.I., J.P., W.A.M.S., G.K.H., E.S.G.S., L.F.R.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands (J.v.R., A.J.M.H.V., J.d.V., B.S.-K., A.G.U.)
| | - Annemieke J.M.H. Verkerk
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands (J.v.R., A.J.M.H.V., J.d.V., B.S.-K., A.G.U.)
| | - Jard de Vries
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands (J.v.R., A.J.M.H.V., J.d.V., B.S.-K., A.G.U.)
| | - Linda Zuurbier
- Department of Human Genetics (L.Z., J.D.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Joep Defesche
- Department of Human Genetics (L.Z., J.D.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Jorge Peter
- Department of Vascular Medicine (S.I., J.P., W.A.M.S., G.K.H., E.S.G.S., L.F.R.), Amsterdam UMC, University of Amsterdam, the Netherlands
- Department of Experimental Vascular Medicine (J.P., G.K.H.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Willemijn A.M. Schonck
- Department of Vascular Medicine (S.I., J.P., W.A.M.S., G.K.H., E.S.G.S., L.F.R.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Bahar Sedaghati-Khayat
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands (J.v.R., A.J.M.H.V., J.d.V., B.S.-K., A.G.U.)
| | - G. Kees Hovingh
- Department of Vascular Medicine (S.I., J.P., W.A.M.S., G.K.H., E.S.G.S., L.F.R.), Amsterdam UMC, University of Amsterdam, the Netherlands
- Department of Experimental Vascular Medicine (J.P., G.K.H.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - André G. Uitterlinden
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands (J.v.R., A.J.M.H.V., J.d.V., B.S.-K., A.G.U.)
| | - Erik S.G. Stroes
- Department of Vascular Medicine (S.I., J.P., W.A.M.S., G.K.H., E.S.G.S., L.F.R.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Laurens F. Reeskamp
- Department of Vascular Medicine (S.I., J.P., W.A.M.S., G.K.H., E.S.G.S., L.F.R.), Amsterdam UMC, University of Amsterdam, the Netherlands
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3
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Concolino P, De Paolis E, Moffa S, Onori ME, Soldovieri L, Ricciardi Tenore C, De Bonis M, Rabacchi C, Santonocito C, Rinelli M, Calandra S, Giaccari A, Urbani A, Minucci A. Identification and Molecular Characterization of a Novel Large-Scale Variant (Exons 4_18 Loss) in the LDLR Gene as a Cause of Familial Hypercholesterolaemia in an Italian Family. Genes (Basel) 2023; 14:1275. [PMID: 37372455 DOI: 10.3390/genes14061275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Next-generation sequencing (NGS) is nowadays commonly used for clinical purposes, and represents an efficient approach for the molecular diagnosis of familial hypercholesterolemia (FH). Although the dominant form of the disease is mostly due to the low-density lipoprotein receptor (LDLR) small-scale pathogenic variants, the copy number variations (CNVs) represent the underlying molecular defects in approximately 10% of FH cases. Here, we reported a novel large deletion in the LDLR gene involving exons 4-18, identified by the bioinformatic analysis of NGS data in an Italian family. A long PCR strategy was employed for the breakpoint region analysis where an insertion of six nucleotides (TTCACT) was found. Two Alu sequences, identified within intron 3 and exon 18, could underlie the identified rearrangement by a nonallelic homologous recombination (NAHR) mechanism. NGS proved to be an effective tool suitable for the identification of CNVs, together with small-scale alterations in the FH-related genes. For this purpose, the use and implementation of this cost-effective, efficient molecular approach meets the clinical need for personalized diagnosis in FH cases.
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Affiliation(s)
- Paola Concolino
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Genomics Core Facility, Gemelli Science and Technology Park (G-STeP), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Elisa De Paolis
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Genomics Core Facility, Gemelli Science and Technology Park (G-STeP), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Simona Moffa
- Center for Endocrine and Metabolic Diseases, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Maria Elisabetta Onori
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Genomics Core Facility, Gemelli Science and Technology Park (G-STeP), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Laura Soldovieri
- Center for Endocrine and Metabolic Diseases, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Claudio Ricciardi Tenore
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Genomics Core Facility, Gemelli Science and Technology Park (G-STeP), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Maria De Bonis
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Genomics Core Facility, Gemelli Science and Technology Park (G-STeP), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Claudio Rabacchi
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Concetta Santonocito
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Genomics Core Facility, Gemelli Science and Technology Park (G-STeP), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Roma, Italy
| | - Martina Rinelli
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Genomics Core Facility, Gemelli Science and Technology Park (G-STeP), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Sebastiano Calandra
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Andrea Giaccari
- Center for Endocrine and Metabolic Diseases, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Roma, Italy
| | - Andrea Urbani
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Roma, Italy
| | - Angelo Minucci
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Genomics Core Facility, Gemelli Science and Technology Park (G-STeP), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
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4
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Calling and Phasing of Single-Nucleotide and Structural Variants of the LDLR Gene Using Oxford Nanopore MinION. Int J Mol Sci 2023; 24:ijms24054471. [PMID: 36901902 PMCID: PMC10003201 DOI: 10.3390/ijms24054471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/27/2023] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
The LDLR locus has clinical significance for lipid metabolism, Mendelian familial hypercholesterolemia (FH), and common lipid metabolism-related diseases (coronary artery disease and Alzheimer's disease), but its intronic and structural variants are underinvestigated. The aim of this study was to design and validate a method for nearly complete sequencing of the LDLR gene using long-read Oxford Nanopore sequencing technology (ONT). Five PCR amplicons from LDLR of three patients with compound heterozygous FH were analyzed. We used standard workflows of EPI2ME Labs for variant calling. All rare missense and small deletion variants detected previously by massively parallel sequencing and Sanger sequencing were identified using ONT. One patient had a 6976 bp deletion (exons 15 and 16) that was detected by ONT with precisely located breakpoints between AluY and AluSx1. Trans-heterozygous associations between mutation c.530C>T and c.1054T>C, c.2141-966_2390-330del, and c.1327T>C, and between mutations c.1246C>T and c.940+3_940+6del of LDLR, were confirmed. We demonstrated the ability of ONT to phase variants, thereby enabling haplotype assignment for LDLR with personalized resolution. The ONT-based method was able to detect exonic variants with the additional benefit of intronic analysis in one run. This method can serve as an efficient and cost-effective tool for diagnosing FH and conducting research on extended LDLR haplotype reconstruction.
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Abstract
Atherosclerotic cardiovascular disease is the leading cause of death globally. Despite its important risk of premature atherosclerosis and cardiovascular disease, familial hypercholesterolemia (FH) is still largely underdiagnosed worldwide. It is one of the most frequently inherited diseases due to mutations, for autosomal dominant forms, in either of the LDLR, APOB, and PCSK9 genes or possibly a few mutations in the APOE gene and, for the rare autosomal forms, in the LDLRAP1 gene. The discovery of the genes implicated in the disease has largely helped to improve the diagnosis and treatment of FH from the LDLR by Brown and Goldstein, as well as the introduction of statins, to PCSK9 discovery in FH by Abifadel et al., and the very rapid availability of PCSK9 inhibitors. In the last two decades, major progress has been made in clinical and genetic diagnostic tools and the therapeutic arsenal against FH. Improving prevention, diagnosis, and treatment and making them more accessible to all patients will help reduce the lifelong burden of the disease.
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Affiliation(s)
- Marianne Abifadel
- UMR1148, Inserm, Hôpital Bichat-Claude Bernard, 46 rue Henri Huchard, F-75018 Paris, France.,Laboratory of Biochemistry and Molecular Therapeutics (LBTM), Faculty of Pharmacy, Pôle Technologie-Santé, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Catherine Boileau
- UMR1148, Inserm, Hôpital Bichat-Claude Bernard, 46 rue Henri Huchard, F-75018 Paris, France.,Département de Génétique, AP-HP, Hôpital Bichat-Claude Bernard, Paris, France
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6
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Berberich AJ, Hegele RA. The advantages and pitfalls of genetic analysis in the diagnosis and management of lipid disorders. Best Pract Res Clin Endocrinol Metab 2022; 37:101719. [PMID: 36641373 DOI: 10.1016/j.beem.2022.101719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The increasing affordability of and access to next-generation DNA sequencing has increased the feasibility of incorporating genetic analysis into the diagnostic pathway for dyslipidaemia. But should genetic diagnosis be used routinely? DNA testing for any medical condition has potential benefits and pitfalls. For dyslipidaemias, the overall balance of advantages versus drawbacks differs according to the main lipid disturbance. For instance, some patients with severely elevated low-density lipoprotein cholesterol levels have a monogenic disorder, namely heterozygous familial hypercholesterolaemia. In these patients, DNA diagnosis can be definitive, in turn yielding several benefits for patient care that tend to outweigh any potential disadvantages. In contrast, hypertriglyceridaemia is almost always a polygenic condition without a discrete monogenic basis, except for ultrarare monogenic familial chylomicronaemia syndrome. Genetic testing in patients with hypertriglyceridaemia is therefore predominantly non-definitive and evidence for benefit is presently lacking. Here we consider advantages and limitations of genetic testing in dyslipidaemias.
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Affiliation(s)
- Amanda J Berberich
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street, London N6A 5C1, ON, Canada.
| | - Robert A Hegele
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street, London N6A 5C1, ON, Canada; Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street, London N6A 5B7, ON, Canada.
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7
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Berberich AJ, Hegele RA. Genetic testing in dyslipidaemia: An approach based on clinical experience. Best Pract Res Clin Endocrinol Metab 2022; 37:101720. [PMID: 36682941 DOI: 10.1016/j.beem.2022.101720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We have used DNA sequencing in our lipid clinic for >20 years. Dyslipidaemia is typically ascertained biochemically. For moderate deviations in the lipid profile, the etiology is often a combination of a polygenic susceptibility component plus secondary non-genetic factors. For severe dyslipidaemia, a monogenic etiology is more likely, although a discrete single-gene cause is frequently not found. A severe phenotype can also result from strong polygenic predisposition that is aggravated by secondary factors. A young age of onset plus a family history of dyslipidaemia or atherosclerotic cardiovascular disease can suggest a monogenic etiology. With severe dyslipidaemia, clinical examination focuses on detecting manifestations of monogenic syndromic conditions. For all patients with dyslipidaemia, secondary causes must be ruled out. Here we describe an experience-based practical approach to genetic testing of patients with severe deviations of low-density lipoprotein, triglycerides, high-density lipoprotein and also combined hyperlipidaemia and dysbetalipoproteinemia.
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Affiliation(s)
- Amanda J Berberich
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON, N6A 5C1, Canada; Western University, Division of Endocrinology & Metabolism, St. Joseph's Hospital, 268 Grosvenor Street, London, Ontario, Canada.
| | - Robert A Hegele
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON, N6A 5C1, Canada; Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 4288A-1151 Richmond Street North, London, ON, N6A 5B7, Canada.
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8
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Genetic Testing for Familial Hypercholesterolemia: Health Technology Assessment. ONTARIO HEALTH TECHNOLOGY ASSESSMENT SERIES 2022; 22:1-155. [PMID: 36158868 PMCID: PMC9470216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
BACKGROUND Familial hypercholesterolemia (FH) is an inherited disorder characterized by abnormally elevated low-density lipoprotein (LDL) cholesterol serum levels from birth, which increases the risk of premature atherosclerotic cardiovascular disease. Genetic testing is a type of a medical test that looks for changes in genes or chromosome structure to discover genetic differences, anomalies, or mutations that may prove pathological. It is regarded as the gold standard for screening and diagnosing FH. We conducted a health technology assessment on genetic testing for people with FH and their relatives (i.e., cascade screening). The assessment included an evaluation of clinical utility (the ability of a test to improve health outcomes), the diagnostic yield (ability of a test to identify people with FH), cost-effectiveness, the budget impact of publicly funding genetic testing for FH, and patient preferences and values. METHODS We performed a systematic literature search of the clinical evidence. For evaluation of clinical utility, we assessed the risk of bias of each included study using the ROBINS-I tool and the quality of the body of evidence according to the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) Working Group criteria.We performed a systematic economic literature search and conducted a cost-effectiveness and cost-utility analysis with a lifetime horizon from a public payer perspective. We assessed the cost-effectiveness of using genetic testing both for confirming a FH clinical diagnosis and for cascade screening in relatives of genetically confirmed cases. We evaluated the cost effectiveness of cascade screening strategies with genetic testing, sequential testing, and lipid testing approaches. We also analyzed the budget impact of publicly funding genetic testing in Ontario. RESULTS We included 11 studies in the clinical evidence review. Overall, our review found that genetic testing to diagnose FH improves several health outcomes (GRADE: Moderate) compared with clinical evaluation without a genetic test. We also found that genetic cascade screening leads to a high diagnostic yield of FH.According to our primary economic evaluation, genetic testing is a dominant strategy (more effective and less costly) compared with no genetic testing for individuals with a FH clinical diagnosis. It reduced the number of FH diagnoses, led to fewer cardiovascular events, and improved QALYs. For first-degree relatives of genetically confirmed cases, all cascade screening strategies (genetic testing, sequential testing, and lipid testing) were cost-effective when compared with no cascade screening in a pairwise fashion. The ICERs of cascade screening with genetic, sequential, and lipid testing compared with no cascade screening were $58,390, $50,220, and $45,754 per QALY gained, respectively. When comparing all screening strategies together, cascade screening with lipid testing was the most cost-effective strategy. At commonly used willingness-to-pay values of $50,000 and $100,000 per QALY gained, the probability of lipid cascade screening being cost-effective was 53.5% and 71.5%, respectively.The annual budget impact of publicly funding genetic testing for individuals with a clinical FH diagnosis in Ontario ranged from a cost saving of $2 million in year 1 to $64 million in year 5, for a total of $141 million saved over the next 5 years, assuming the cost of genetic testing remains at $490 per person. If only testing-related costs were considered, the budget impact was estimated to be an additional cost of $7 million in year 1, increasing to $20 million in year 5, for a total cost of $64 million over the next 5 years. For relatives of genetically confirmed cases, publicly funding genetic cascade screening would lead to an additional cost of $5 million in year 1, increasing to $27 million in year 5, for a total cost of $73 million over the next 5 years. If only testing-related costs were considered, the budget impact was estimated to be an additional of $66 million. CONCLUSIONS Genetic testing for FH has a higher clinical utility than clinical evaluation without a genetic test. It also results in a high diagnostic yield of FH through cascade screening. For individuals with a clinical diagnosis of FH, genetic testing would be a cost-saving and more effective diagnostic strategy. For relatives of index cases confirmed through genetic testing, genetic and lipid cascade screening are both cost-effective compared with no screening, but genetic cascade screening is less cost-effective than lipid cascade screening. We estimated that publicly funding genetic testing for individuals with a clinical diagnosis of FH in Ontario would save $141 million, and publicly funding genetic testing in a cascade screening program for relatives would cost an additional $73 million over the next five years.Most people with a positive genetic test perceived the screening, diagnosis, and treatment for FH more positively. The discovery of the condition can lead people to adhere to relevant treatments in an effort to control their cholesterol levels. People we spoke with felt that greater awareness and education would allow for more efficient uptake of cascade screening.
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9
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Dilliott AA, Zhang KK, Wang J, Abrahao A, Binns MA, Black SE, Borrie M, Dowlatshahi D, Finger E, Fischer CE, Frank A, Freedman M, Grimes D, Hassan A, Jog M, Kumar S, Lang AE, Mandzia J, Masellis M, Pasternak SH, Pollock BG, Rajji TK, Rogaeva E, Sahlas DJ, Saposnik G, Sato C, Seitz D, Shoesmith C, Steeves TDL, Swartz RH, Tan B, Tang-Wai DF, Tartaglia MC, Turnbull J, Zinman L, Hegele RA. Targeted copy number variant identification across the neurodegenerative disease spectrum. Mol Genet Genomic Med 2022; 10:e1986. [PMID: 35666053 PMCID: PMC9356547 DOI: 10.1002/mgg3.1986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 03/19/2022] [Accepted: 05/03/2022] [Indexed: 11/11/2022] Open
Abstract
Background Although genetic factors are known to contribute to neurodegenerative disease susceptibility, there remains a large amount of heritability unaccounted for across the diagnoses. Copy number variants (CNVs) contribute to these phenotypes, but their presence and influence on disease state remains relatively understudied. Methods Here, we applied a depth of coverage approach to detect CNVs in 80 genes previously associated with neurodegenerative disease within participants of the Ontario Neurodegenerative Disease Research Initiative (n = 519). Results In total, we identified and validated four CNVs in the cohort, including: (1) a heterozygous deletion of exon 5 in OPTN in an Alzheimer's disease participant; (2) a duplication of exons 1–5 in PARK7 in an amyotrophic lateral sclerosis participant; (3) a duplication of >3 Mb, which encompassed ABCC6, in a cerebrovascular disease (CVD) participant; and (4) a duplication of exons 7–11 in SAMHD1 in a mild cognitive impairment participant. We also identified 43 additional CNVs that may be candidates for future replication studies. Conclusion The identification of the CNVs suggests a portion of the apparent missing heritability of the phenotypes may be due to these structural variants, and their assessment is imperative for a thorough understanding of the genetic spectrum of neurodegeneration.
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Affiliation(s)
- Allison A Dilliott
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada
| | - Kristina K Zhang
- Department of Microbiology & Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Jian Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Agessandro Abrahao
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Malcolm A Binns
- Rotman Research Institute, Baycrest Health Sciences, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Sandra E Black
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada.,LCCampbell Cognitive Neurology Research Unit, Hurvitz Brain Sciences Research Program Sunnybrook Health Sciences Research Program, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Michael Borrie
- St. Joseph's Health Care Centre, London, Ontario, Canada.,Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Dar Dowlatshahi
- Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Elizabeth Finger
- Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Lawson Health Research Institute, London, Ontario, Canada
| | - Corinne E Fischer
- Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Andrew Frank
- Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Bruyère Research Institute, Ottawa, Ontario, Canada
| | - Morris Freedman
- Rotman Research Institute, Baycrest Health Sciences, Toronto, Ontario, Canada.,Division of Neurology, Department of Medicine, Baycrest Health Sciences, Mt. Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - David Grimes
- Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Ayman Hassan
- Thunder Bay Regional Research Institute, Northern Ontario School of Medicine, Thunder Bay, Ontario, Canada
| | - Mandar Jog
- Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,London Health Sciences Centre, London, Ontario, Canada
| | - Sanjeev Kumar
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.,Department of Psychiatry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Anthony E Lang
- Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, Toronto, Ontario, Canada.,Department of Medicine, Division of Neurology, University of Toronto, Toronto, Ontario, Canada
| | - Jennifer Mandzia
- Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Mario Masellis
- Department of Medicine, Division of Neurology, University of Toronto, Toronto, Ontario, Canada.,Cognitive & Movement Disorders Clinic, L.C. Campbell Cognitive Neurology Research Unit, Hurvitz Brain ScienceProgram, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Stephen H Pasternak
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Cognitive Neurology and Alzheimer's Disease Research Centre, Parkwood Institute, St. Joseph's Health Care, London, Ontario, Canada
| | - Bruce G Pollock
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.,Department of Psychiatry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Tarek K Rajji
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.,Department of Psychiatry and Toronto Dementia Research Alliance, University of Toronto, Toronto, Ontario, Canada
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
| | | | - Gustavo Saposnik
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Clinical Outcomes and Decision Neuroscience Unit, St. Michael's Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Christine Sato
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
| | - Dallas Seitz
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | - Thomas D L Steeves
- Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Division of Neurology, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Richard H Swartz
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada.,LCCampbell Cognitive Neurology Research Unit, Hurvitz Brain Sciences Research Program Sunnybrook Health Sciences Research Program, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada.,Department of Medicine, Division of Neurology, University of Toronto, Toronto, Ontario, Canada
| | - Brian Tan
- Rotman Research Institute, Baycrest Health Sciences, Toronto, Ontario, Canada
| | - David F Tang-Wai
- Department of Medicine, Division of Neurology, University of Toronto, Toronto, Ontario, Canada.,Krembil Research Institute, Toronto Western Hospital, Toronto, Ontario, Canada.,University Health Network Memory Clinic, Toronto Western Hospital, Toronto, Ontario, Canada
| | - Maria C Tartaglia
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
| | - John Turnbull
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Lorne Zinman
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | | | - Robert A Hegele
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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10
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Clarke SL, Tcheandjieu C, Hilliard AT, Lee KM, Lynch J, Chang KM, Miller D, Knowles JW, O’Donnell C, Tsao P, Rader DJ, Wilson PW, Sun YV, Gaziano M, Assimes TL. Coronary Artery Disease Risk of Familial Hypercholesterolemia Genetic Variants Independent of Clinically Observed Longitudinal Cholesterol Exposure. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2022; 15:e003501. [PMID: 35143253 PMCID: PMC10593360 DOI: 10.1161/circgen.121.003501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 01/17/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND Familial hypercholesterolemia (FH) genetic variants confer risk for coronary artery disease independent of LDL-C (low-density lipoprotein cholesterol) when considering a single measurement. In real clinical settings, longitudinal LDL-C data are often available through the electronic health record. It is unknown whether genetic testing for FH variants provides additional risk-stratifying information once longitudinal LDL-C is considered. METHODS We used the extensive electronic health record data available through the Million Veteran Program to conduct a nested case-control study. The primary outcome was coronary artery disease, derived from electronic health record codes for acute myocardial infarction and coronary revascularization. Incidence density sampling was used to match case/control exposure windows, defined by the date of the first LDL-C measurement to the date of the first coronary artery disease code of the index case. Adjustments for the first, maximum, or mean LDL-C were analyzed. FH variants in LDLR, APOB, and PCSK9 (Proprotein convertase subtilisin/kexin type 9) were assessed by custom genotype array. RESULTS In a cohort of 23 091 predominantly prevalent cases at enrollment and 230 910 matched controls, FH variant carriers had an increased risk for coronary artery disease (odds ratio [OR], 1.53 [95% CI, 1.24-1.89]). Adjusting for mean LDL-C led to the greatest attenuation of the risk estimate, but significant risk remained (odds ratio, 1.33 [95% CI, 1.08-1.64]). The degree of attenuation was not affected by the number and the spread of LDL-C measures available. CONCLUSIONS The risk associated with carrying an FH variant cannot be fully captured by the LDL-C data available in the electronic health record, even when considering multiple LDL-C measurements spanning more than a decade.
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Affiliation(s)
- Shoa L. Clarke
- VA Palo Alto Health Care system, Palo Alto, CA
- Dept of Medicine, Division of Cardiovascular Medicine, Stanford Univ School of Medicine, Stanford, CA
| | - Catherine Tcheandjieu
- VA Palo Alto Health Care system, Palo Alto, CA
- Dept of Medicine, Division of Cardiovascular Medicine, Stanford Univ School of Medicine, Stanford, CA
| | - Austin T. Hilliard
- VA Palo Alto Health Care system, Palo Alto, CA
- Dept of Medicine, Division of Cardiovascular Medicine, Stanford Univ School of Medicine, Stanford, CA
| | - Kyung Min Lee
- VA Informatics & Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT
| | - Julie Lynch
- VA Informatics & Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT
- College of Nursing & Health Sciences, Univ of Massachusetts, Boston, MA
| | - Kyong-Mi Chang
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA
- Dept of Medicine, Univ of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Donald Miller
- Edith Nourse Rogers Memorial VA Hospital, Bedford, MA
- Center for Population Health, Univ of Massachusetts, Lowell, MA
| | - Joshua W. Knowles
- Dept of Medicine, Division of Cardiovascular Medicine, Stanford Univ School of Medicine, Stanford, CA
- Diabetes Research Center, Stanford Univ School of Medicine, Stanford, CA
- Cardiovascular Institute, Stanford Univ School of Medicine, Stanford, CA
| | - Christopher O’Donnell
- VA Boston Healthcare System, Boston, MA
- Dept of Medicine, Harvard Medical School, Boston, MA
| | - Phil Tsao
- VA Palo Alto Health Care system, Palo Alto, CA
- Dept of Medicine, Division of Cardiovascular Medicine, Stanford Univ School of Medicine, Stanford, CA
- Cardiovascular Institute, Stanford Univ School of Medicine, Stanford, CA
| | - Daniel J. Rader
- Dept of Medicine, Univ of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Peter W. Wilson
- Atlanta VA Medical Center, Decatur, GA
- Dept of Medicine, Emory Univ School of Medicine, Atlanta, GA
- Dept of Epidemiology, Emory Univ Rollins School of Public Health, Atlanta, GA
| | - Yan V. Sun
- Atlanta VA Medical Center, Decatur, GA
- Dept of Epidemiology, Emory Univ Rollins School of Public Health, Atlanta, GA
| | | | - Themistocles L. Assimes
- VA Palo Alto Health Care system, Palo Alto, CA
- Dept of Medicine, Division of Cardiovascular Medicine, Stanford Univ School of Medicine, Stanford, CA
- Cardiovascular Institute, Stanford Univ School of Medicine, Stanford, CA
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11
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Rosman N, Nawawi HM, Al-Khateeb A, Chua YA, Chua AL. Development of an Optimized Tetra-Amplification Refractory Mutation System PCR for Detection of 12 Pathogenic Familial Hypercholesterolemia Variants in the Asian Population. J Mol Diagn 2022; 24:120-130. [PMID: 35074074 DOI: 10.1016/j.jmoldx.2021.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 10/03/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022] Open
Abstract
Early detection of genetic diseases such as familial hypercholesterolemia (FH), and the confirmation of related pathogenic variants, are crucial in reducing the risk for premature coronary artery disease. Currently, next-generation sequencing is used for detecting FH-related candidate genes but is expensive and time-consuming. There is a lack of kits suitable for the detection of the common FH-related variants in the Asia-Pacific region. Thus, this study addressed that need with the development of an optimized tetra-amplification mutation system (T-ARMS) PCR-based assay for the detection of 12 pathogenic variants of FH in the Asian population. The two important parameters for T-ARMS PCR assay performance-annealing temperature and the ratio of outer/inner primer concentrations-were optimized in this study. The optimal annealing temperature of all 12 T-ARMS PCR reactions was 64.6°C. The ideal ratios of outer/inner primer concentrations with each pathogenic variant were: A1, 1:2; A2, 1:4; L1, 1:10; L2, 1:1; L3, 1:2; L4, 1:8; L5, 1:1; L6, 1:2; L7, 1:8; L8, 1:8; L9, 1:2; and L10, 1:8. The lowest limit of detection using DNA extracted from patients was 0.1 ng. The present article highlights the beneficial findings on T-ARMS PCR as part of the development of a PCR-based detection kit for use in detecting FH in economically developing countries in Asia with a greater prevalence of FH.
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Affiliation(s)
- Norhidayah Rosman
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia; Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Hapizah M Nawawi
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia; Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Alyaa Al-Khateeb
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia; Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Yung-An Chua
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Ang-Lim Chua
- Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia.
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12
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Saotome M, Maekawa Y. Multiple Ligation-dependent Probe Amplification Along with Whole Exome Sequencing Should be Required for the Diagnosis of Structural Heterozygous Familial Hypercholesteremia. Intern Med 2022; 61:2829-2830. [PMID: 36184533 PMCID: PMC9593164 DOI: 10.2169/internalmedicine.9412-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Masao Saotome
- Division of Cardiology, Internal Medicine III Hamamatsu University School of Medicine, Japan
| | - Yuichiro Maekawa
- Division of Cardiology, Internal Medicine III Hamamatsu University School of Medicine, Japan
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13
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Okada H, Tada H, Nomura A, Nohara A, Okeie K, Nozue T, Michishita I, Takamura M, Takemura H, Kawashiri MA. Whole Exome Sequencing Insufficient for a Definitive Diagnosis of a Patient with Compound Heterozygous Familial Hypercholesterolemia. Intern Med 2022; 61:2883-2889. [PMID: 36184534 PMCID: PMC9593155 DOI: 10.2169/internalmedicine.8989-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Homozygous familial hypercholesterolemia (HoFH) is a rare genetic disorder, and a genetic analysis is important to make a definitive diagnosis. A comprehensive genetic analysis using next generation sequencing (NGS) and whole exome sequencing (WES) is feasible. However, the application of NGS in the assessment of genomic structural variations is generally limited, and a substantial number of control samples are needed for such assessments. Thus, NGS alone is unlikely to detect genomic structural variations in a "singleton." We present the case of a patient with compound HeFH (heterozygous FH), whose causative mutations in the LDLR gene could not be identified by WES, necessitating the application of the multiplex ligation-dependent probe amplification (MLPA) technique.
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Affiliation(s)
- Hirofumi Okada
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Japan
| | - Hayato Tada
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Japan
| | - Akihiro Nomura
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Japan
| | - Atsushi Nohara
- Department of Genetics, Ishikawa Prefectural Central Hospital, Japan
| | - Kazuyasu Okeie
- Department of Cardiology, Koseiren Takaoka Hospital, Japan
| | - Tsuyoshi Nozue
- Division of Cardiology, Department of Internal Medicine, Yokohama Sakae Kyosai Hospital, Japan
| | - Ichiro Michishita
- Division of Cardiology, Department of Internal Medicine, Yokohama Sakae Kyosai Hospital, Japan
| | - Masayuki Takamura
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Japan
| | | | - Masa-Aki Kawashiri
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Japan
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14
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Vikulova DN, Trinder M, Mancini GBJ, Pimstone SN, Brunham LR. Familial Hypercholesterolemia, Familial Combined Hyperlipidemia, and Elevated Lipoprotein(a) in Patients With Premature Coronary Artery Disease. Can J Cardiol 2021; 37:1733-1742. [PMID: 34455025 DOI: 10.1016/j.cjca.2021.08.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Familial hypercholesterolemia (FH), familial combined hyperlipidemia (FCHL), and elevated lipoprotein (a) (Lp[a]) increase risk of premature coronary artery disease (CAD). The objective of this study was to assess the prevalence of FH, FCHL, elevated Lp(a) and their impact on management in patients with premature CAD. METHODS We prospectively recruited men ≤ 50 years and women ≤ 55 with obstructive CAD. FH was defined as Dutch Lipid Clinic Network scores ≥ 6. FCHL was defined as apolipoprotein B > 1.2 g/L, triglyceride and total cholesterol > 90th population percentile, and family history of premature cardiovascular disease. Lp(a) ≥ 50 mg/dL was considered to be elevated. RESULTS Among 263 participants, 9.1% met criteria for FH, 12.5% for FCHL, and 19.4% had elevated Lp(a). Among patients with FH, 37.5% had FH-causing DNA variants. Patients with FH, but not other dyslipidemias, were more likely than nondyslipidemic patients to have received lipid-lowering therapy before presenting with CAD (33.3% vs 12.3%, P = 0.04) and combined lipid-lowering therapy after the presentation (41.7% vs 7.7%, P < 0.001). One year after presentation, 58.3%, 54.5%, and 58.8% of patients with FH, FCHL, and elevated Lp(a) had low-density lipoprotein cholesterol (LDL-C) < 1.8 mmol/L, respectively, compared with 68.0 % in reference group. Patients with FCHL were more likely to have non-high-density lipoprotein (HDL) and apolipoprotein B above recommended lipid goals (70.0% and 87.9%, respectively). CONCLUSIONS FH, FCHL, and elevated Lp(a) are common in patients with premature CAD and have differing impact on treatment and achievement of lipid targets. Assessment for these conditions in patients with premature CAD provides valuable information for individualized management.
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Affiliation(s)
- Diana N Vikulova
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark Trinder
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - G B John Mancini
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Division of Cardiology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Simon N Pimstone
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Liam R Brunham
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
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15
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Kim H, Lee CJ, Kim SH, Kim JY, Choi SH, Kang HJ, Park KS, Cho BR, Kim BJ, Sung KC, Jeong IK, Jeong JO, Bae JW, Park JM, Lee Y, Jeong I, Han H, Lee JH, Lee SH. Phenotypic and Genetic Analyses of Korean Patients with Familial Hypercholesterolemia: Results from the KFH Registry 2020. J Atheroscler Thromb 2021; 29:1176-1187. [PMID: 34456200 PMCID: PMC9371750 DOI: 10.5551/jat.63062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Aims: Familial hypercholesterolemia (FH) is currently a worldwide health issue. Understanding the characteristics of patients is important for proper diagnosis and treatment. This study aimed to analyze the phenotypic and genetic features, including threshold cholesterol levels, of Korean patients with FH.
Methods: A total of 296 patients enrolled in the Korean FH registry were included, according to the following criteria: low-density lipoprotein-cholesterol (LDL-C) >190 mg/dL with tendon xanthoma or family history compatible with FH, or LDL-C >225 mg/dL. DNA sequences of three FH-associated genes were obtained using whole-exome or target exome sequencing. Threshold cholesterol levels for differentiating patients with FH/pathogenic variant (PV) carriers and predictors of PVs were identified.
Results: Of the 296 patients, 104 had PVs and showed more obvious clinical findings, including higher cholesterol levels. PV rates ranged from 30% to 64% when patients were categorized by possible or definite type according to the Simon Broome criteria. Frequent PV types included missense variants and copy number variations (CNVs), while the most frequent location of PVs was p.P685L inLDLR. The threshold LDL-C levels for patient differentiation and PV prediction were 177 and 225 mg/dL, respectively. Younger age, tendon xanthoma, and higher LDL-C levels were identified as independent predictors of PVs, while traditional cardiovascular risk factors were predictors of coronary artery disease.
Conclusions: Korean patients with FH had variable PV rates depending on diagnostic criteria and distinctive PV locations. The reported threshold LDL-C levels pave the way for efficient patient care in this population.
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Affiliation(s)
- Hyoeun Kim
- Department of Health Promotion, Yonsei University Health System
| | - Chan Joo Lee
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine
| | - Sang-Hyun Kim
- Division of Cardiology, Department of Internal Medicine, Boramae Medical Center, Seoul National University College of Medicine
| | - Jang Young Kim
- Division of Cardiology, Department of Internal Medicine, Yonsei University Wonju College of Medicine
| | - Sung Hee Choi
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine
| | - Hyun-Jae Kang
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine
| | - Kyong Soo Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine
| | - Byung Ryul Cho
- Cardiology Division, Department of Internal Medicine, Kangwon National University, School of Medicine
| | - Byung Jin Kim
- Division of Cardiology, Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine
| | - Ki Chul Sung
- Division of Cardiology, Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine
| | - In-Kyung Jeong
- Department of Endocrinology and Metabolism, Kyung Hee University Hospital at Gangdong, Kyung Hee University School of Medicine
| | - Jin-Ok Jeong
- Department of Internal Medicine, Cardiovascular Center, Chungnam National University Hospital, Chungnam National University School of Medicine
| | - Jang-Whan Bae
- Department of Internal Medicine, Chungbuk National University College of Medicine
| | - Jung Mi Park
- Department of Biostatistics and Computing, Yonsei University Graduate School
| | | | | | | | - Ji Hyun Lee
- Department of Clinical Pharmacology and Therapeutics, Kyung Hee University School of Medicine
| | - Sang-Hak Lee
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine
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16
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Sturm AC, Truty R, Callis TE, Aguilar S, Esplin ED, Garcia S, Haverfield EV, Morales A, Nussbaum RL, Rojahn S, Vatta M, Rader DJ. Limited-Variant Screening vs Comprehensive Genetic Testing for Familial Hypercholesterolemia Diagnosis. JAMA Cardiol 2021; 6:902-909. [PMID: 34037665 PMCID: PMC8156154 DOI: 10.1001/jamacardio.2021.1301] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Question How many clinically significant variants for familial hypercholesterolemia would be missed by limited-variant screening conducted on microarrays? Findings In this cross-sectional review of comprehensive genetic test results for individuals with indications for familial hypercholesterolemia, a limited-variant screen was found to have a significantly lower detection rate (8.4%) than the comprehensive diagnostic test (27%). Meaning The results of this study suggest that clinically significant findings for familial hypercholesterolemia would be missed for two-thirds of affected individuals if limited-variant screening was used. Importance Familial hypercholesterolemia (FH) is the most common inherited cardiovascular disease and carries significant morbidity and mortality risks. Genetic testing can identify affected individuals, but some array-based assays screen only a small subset of known pathogenic variants. Objective To identify the number of clinically significant variants associated with FH that would be missed by an array-based, limited-variant screen when compared with next-generation sequencing (NGS)–based comprehensive testing. Design, Setting, and Participants This cross-sectional study compared comprehensive genetic test results for clinically significant variants associated with FH with results for a subset of 24 variants screened by a limited-variant array. Data were deidentified next-generation sequencing results from indication-based or proactive gene panels. Individuals receiving next-generation sequencing–based genetic testing, either for an FH indication between November 2015 and June 2020 or as proactive health screening between February 2016 and June 2020 were included. Ancestry was reported by clinicians who could select from preset options or enter free text on the test requisition form. Main Outcomes and Measures Number of pathogenic or likely pathogenic (P/LP) variants identified. Results This study included 4563 individuals who were referred for FH diagnostic testing and 6482 individuals who received next-generation sequencing of FH-associated genes as part of a proactive genetic test. Among individuals in the indication cohort, the median (interquartile range) age at testing was 49 (32-61) years, 55.4% (2528 of 4563) were female, and 63.6% (2902 of 4563) were self-reported White/Caucasian. In the indication cohort, the positive detection rate would have been 8.4% (382 of 4563) for a limited-variant screen compared with the 27.0% (1230 of 4563) observed with the next-generation sequencing–based comprehensive test. As a result, 68.9% (848 of 1230) of individuals with a P/LP finding in an FH-associated gene would have been missed by the limited screen. The potential for missed findings in the indication cohort varied by ancestry; among individuals with a P/LP finding, 93.7% (59 of 63) of self-reported Black/African American individuals and 84.7% (122 of 144) of Hispanic individuals would have been missed by the limited-variant screen, compared with 33.3% (4 of 12) of Ashkenazi Jewish individuals. In the proactive cohort, the prevalence of clinically significant FH variants was approximately 1:191 per the comprehensive test, and 61.8% (21 of 34) of individuals with an FH-associated P/LP finding would have been missed by a limited-variant screen. Conclusions and Relevance Limited-variant screens may falsely reassure the majority of individuals at risk for FH that they do not carry a disease-causing variant, especially individuals of self-reported Black/African American and Hispanic ancestry.
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Affiliation(s)
- Amy C Sturm
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | | | | | | | | | | | | | | | | | | | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia.,Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
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17
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Improvement of Definite Diagnosis of Familial Hypercholesterolemia Using an Expanding Genetic Analysis. JACC: ASIA 2021; 1:82-89. [PMID: 36338372 PMCID: PMC9627923 DOI: 10.1016/j.jacasi.2021.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/24/2021] [Accepted: 04/06/2021] [Indexed: 11/24/2022]
Abstract
Background The deeper understanding of the complex hereditary basis of familial hypercholesterolemia (FH) has raised the rationale of genetic testing, which has been underutilized in clinical practice. Objectives The present study aimed to explore the variant spectrum of FH in an expanding manner and compare its diagnostic performance. Methods A total of 169 Chinese individuals (124 index cases and 45 relatives) with clinical definite/probable FH were consecutively enrolled. Next-generation sequencing was performed for genetic analysis of 9 genes associated with hypercholesterolemia (major genes: LDLR, APOB, and PCSK9; minor genes: LDLRAP1, LIPA, STAP1, APOE, ABCG5, and ABCG8) including the evaluations of small-scale variants and large-scale copy number variants (CNVs). Results Among the 169 clinical FH patients included, 98 (58.0%) were men. A total of 85 (68.5%) index cases carried FH-associated variants. The proportion of FH caused by small-scale variants in LDLR, APOB, and PCSK9 genes was 62.1% and then increased by 6.5% when other genes and CNVs were further included. Furthermore, the variants in LDLR, APOB, and PCSK9 genes occupied 75% of all FH-associated variants. Of note, there were 8 non-LDLR CNVs detected in the present study. Conclusions LDLR, APOB, and PCSK9 genes should be tested in the initial genetic screening, although variants in minor genes also could explain phenotypic FH, suggesting that an expanding genetic testing may be considered to further explain phenotypic FH.
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18
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Gill PK, Dron JS, Dilliott AA, McIntyre AD, Cao H, Wang J, Movsesyan IG, Malloy MJ, Pullinger CR, Kane JP, Hegele RA. Ancestry-specific profiles of genetic determinants of severe hypertriglyceridemia. J Clin Lipidol 2020; 15:88-96. [PMID: 33303403 DOI: 10.1016/j.jacl.2020.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/31/2020] [Accepted: 11/17/2020] [Indexed: 12/01/2022]
Abstract
BACKGROUND Susceptibility to severe hypertriglyceridemia (HTG), defined as plasma triglyceride (TG) levels ≥10 mmol/L (880 mg/dL), is conferred by both heterozygous rare variants in five genes involved in TG metabolism and numerous common single-nucleotide polymorphisms (SNPs) associated with TG levels. OBJECTIVE To date, these genetic susceptibility factors have been comprehensively assessed primarily in severe HTG patients of European ancestry. Here, we expand our analysis to HTG patients of East Asian and Hispanic ancestry. METHODS The genomic DNA of 336, 63 and 199 severe HTG patients of European, East Asian and Hispanic ancestry, respectively, was evaluated using a targeted next-generation sequencing panel to screen for: 1) rare variants in LPL, APOA5, APOC2, GPIHBP1 and LMF1; 2) common, small-to-moderate effect SNPs, quantified using a polygenic score; and 3) common, large-effect polymorphisms, APOA5 p.G185C and p.S19W. RESULTS While the proportion of individuals with high polygenic scores was similar, frequency of rare variant carriers varied across ancestries. Compared with ancestry-matched controls, Hispanic patients were the most likely to have a rare variant (OR = 5.02; 95% CI 3.07-8.21; p < 0.001), while European patients were the least likely (OR = 2.56; 95% CI 1.58-4.13; p < 0.001). The APOA5 p.G185C polymorphism, exclusive to East Asians, was significantly enriched in patients compared with controls (OR = 10.1; 95% CI 5.6-18.3; p < 0.001), showing the highest enrichment among the measured genetic factors. CONCLUSION While TG-associated rare variants and common SNPs are both found in statistical excess in severe HTG patients of different ancestral backgrounds, the overall genetic profiles of each ancestry group were distinct.
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Affiliation(s)
- Praneet K Gill
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada; Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Jacqueline S Dron
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada; Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Allison A Dilliott
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada; Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Adam D McIntyre
- Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Henian Cao
- Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Jian Wang
- Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Irina G Movsesyan
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mary J Malloy
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Clive R Pullinger
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - John P Kane
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Robert A Hegele
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada; Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada.
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19
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Gill PK, Dron JS, Berberich AJ, Wang J, McIntyre AD, Cao H, Hegele RA. Combined hyperlipidemia is genetically similar to isolated hypertriglyceridemia. J Clin Lipidol 2020; 15:79-87. [PMID: 33303402 DOI: 10.1016/j.jacl.2020.11.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/24/2020] [Accepted: 11/17/2020] [Indexed: 11/24/2022]
Abstract
BACKGROUND Combined hyperlipidemia (CHL) is a common disorder defined by concurrently elevated low-density lipoprotein cholesterol (LDL-C) and triglyceride (TG) levels. Despite decades of study, the genetic basis of CHL remains unclear. OBJECTIVE To characterize the genetic profiles of patients with CHL and compare them to those in patients with isolated hypercholesterolemia and isolated hypertriglyceridemia (HTG). METHODS DNA from 259, 379 and 124 patients with CHL, isolated hypercholesterolemia and isolated HTG, respectively, underwent targeted sequencing. We assessed: 1) rare variants disrupting canonical LDL-C or TG metabolism genes; and 2) two polygenic scores-for elevated LDL-C and TG-calculated using common trait-associated single-nucleotide polymorphisms (SNPs). Genetic profiles were compared against 1000 Genomes Project controls. RESULTS Both CHL and isolated HTG patients had significantly increased odds of a high polygenic score for TG: 2.50 (95% confidence interval [CI] 1.61-3.88; P < 0.001) and 3.72 (95% CI 2.24-6.19; P < 0.001), respectively. CHL patients had neither a significant accumulation of rare variants for LDL-C or TG, nor a high polygenic score for LDL-C. In contrast, patients with isolated hypercholesterolemia had a 3.03-fold increased odds (95% CI 2.22-4.13; P < 0.001) of carrying rare variants associated with familial hypercholesterolemia, while patients with isolated HTG had a 2.78-fold increased odds (95% CI 1.27-6.10; P = 0.0136) of carrying rare variants associated with severe HTG. CONCLUSION CHL is genetically similar to isolated HTG, a known polygenic trait. Both cohorts had a significant accumulation of common TG-raising variants. Elevated LDL-C levels in CHL are not associated with common or rare LDL-C-related genetic variants.
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Affiliation(s)
- Praneet K Gill
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada
| | - Jacqueline S Dron
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada; Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada
| | - Amanda J Berberich
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada; Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada; Department of Medicine, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada
| | - Jian Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada
| | - Adam D McIntyre
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada
| | - Henian Cao
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada
| | - Robert A Hegele
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada; Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada; Department of Medicine, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada.
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20
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Abstract
Familial hypercholesterolemia (FH) is considered the genetic cause of coronary heart disease and ischemic stroke. FH is mainly an autosomal codominant pattern-based disorder and is primarily determined by point mutations within the low-density lipoprotein receptor, apolipoprotein B, and proprotein convertase subtilisin/kexin type 9 genes, causing increased low-density lipoprotein cholesterol levels in the serum of untreated individuals. The accumulation will eventually lead to atherosclerotic cardiovascular disease. Although clinical criteria comprising several prognosis scores, such as the Simon Broome, Dutch Lipid Clinic Network, Make Early Diagnosis to Prevent Early Death, and the recently proposed Montreal-FH-SCORE, are the conventional basis of diagnosing FH, the genetic diagnosis made by single nucleotide polymorphism genotyping, multiplex ligation-dependent probe amplification analysis, and sequencing (both Sanger and Next-Generation sequencing) offers unequivocal diagnosis. Given the heterogeneity of known mutations, the genetic diagnosis of FH is often difficult to establish, despite the growing evidence of the causative mutations, as well as the polygenic aspect of this pathology and the importance of cascade screening of the FH patient’s healthy family members. This review article details different genetic techniques that can be used in FH identification when there is a clinical FH suspicion based on criteria comprised in prognosis scores, knowing that none of these are exhaustive in the diagnosis, yet they efficaciously overlap and complement each other for confirming the disease at the molecular level.
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21
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Next-generation sequencing verified by multiplex ligation-dependent probe amplification to detect a new copy number variations in a child with heterozygous familial hypercholesterolemia. Chin Med J (Engl) 2020; 134:840-841. [PMID: 33797469 PMCID: PMC8104201 DOI: 10.1097/cm9.0000000000001224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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22
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Raal FJ, Bahassi EM, Stevens B, Turner TA, Stein EA. Cascade Screening for Familial Hypercholesterolemia in South Africa: The Wits FIND-FH Program. Arterioscler Thromb Vasc Biol 2020; 40:2747-2755. [PMID: 32878475 DOI: 10.1161/atvbaha.120.315040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Due to gene founder effects, familial hypercholesterolemia (FH) has a prevalence of ≈1:80 in populations of Afrikaner ancestry and is a major contributor to premature atherosclerotic cardiovascular disease in South Africans of Jewish and Indian descent. No systematic program exists to identify these families. Furthermore, information regarding FH prevalence in Black Africans is sparse. The Wits FIND-FH program was initiated in late 2016 to address these issues. Approach and Results: Based on index subjects with definite or probable FH, first-degree relatives were contacted, informed consent obtained, and targeted medical history, physical examination, and blood samples collected. In patients with likely FH using the Simon Broome criteria, DNA analysis for LDLR (low-density lipoprotein receptor), APOB (apolipoprotein B), PCSK9 (proprotein convertase subtilisin/kexin type 9), and LDLRAP1 (LDLR adaptor protein 1) variants was analyzed by next-generation sequencing. Of the initial 700 subjects screened of whom 295 (42%) were index cases, 479 (68.4%) were clinically diagnosed with probable or definite FH. Genetic analysis confirmed 285 of 479 (59.5%) as having variants consistent with FH. Three subjects met the clinical diagnosis for homozygous FH, but DNA analysis revealed a further 34 patients, including 4 Black African subjects, with ≥2 FH-causing variants. CONCLUSIONS Using phenotype cascade screening, the Wits FIND-FH program has screened an average of 30 subjects monthly of whom 68% had a clinical diagnosis of FH with ≈60% genetically confirmed. The program is identifying a small but growing number of Black South Africans with FH. Interestingly, 37 subjects (7.7%) who underwent DNA testing were found to have ≥2 FH-causing variants.
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Affiliation(s)
- Frederick J Raal
- Department of Medicine, Stein Center for FH, Carbohydrate and Lipid Metabolism Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa (F.J.R., B.S.)
| | - El Mustapha Bahassi
- Medpace and Medpace Reference Laboratories, Cincinnati, OH (E.M.B., T.A.T., E.A.S.)
| | - Belinda Stevens
- Department of Medicine, Stein Center for FH, Carbohydrate and Lipid Metabolism Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa (F.J.R., B.S.)
| | - Traci A Turner
- Medpace and Medpace Reference Laboratories, Cincinnati, OH (E.M.B., T.A.T., E.A.S.)
| | - Evan A Stein
- Medpace and Medpace Reference Laboratories, Cincinnati, OH (E.M.B., T.A.T., E.A.S.)
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23
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Marmontel O, Rollat-Farnier PA, Wozny AS, Charrière S, Vanhoye X, Simonet T, Chatron N, Collin-Chavagnac D, Nony S, Dumont S, Mahl M, Jacobs C, Janin A, Caussy C, Poinsot P, Tauveron I, Bardel C, Millat G, Peretti N, Moulin P, Marçais C, Di Filippo M. Development of a new expanded next-generation sequencing panel for genetic diseases involved in dyslipidemia. Clin Genet 2020; 98:589-594. [PMID: 33111339 DOI: 10.1111/cge.13832] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022]
Abstract
The aim of this study was to provide an efficient tool: reliable, able to increase the molecular diagnosis performance, to facilitate the detection of copy number variants (CNV), to assess genetic risk scores (wGRS) and to offer the opportunity to explore candidate genes. Custom SeqCap EZ libraries, NextSeq500 sequencing and a homemade pipeline enable the analysis of 311 dyslipidemia-related genes. In the training group (48 DNA from patients with a well-established molecular diagnosis), this next-generation sequencing (NGS) workflow showed an analytical sensitivity >99% (n = 532 variants) without any false negative including a partial deletion of one exon. In the prospective group, from 25 DNA from patients without prior molecular analyses, 18 rare variants were identified in the first intention panel genes, allowing the diagnosis of monogenic dyslipidemia in 11 patients. In six other patients, the analysis of minor genes and wGRS determination provided a hypothesis to explain the dyslipidemia. Remaining data from the whole NGS workflow identified four patients with potentially deleterious variants. This NGS process gives a major opportunity to accede to an enhanced understanding of the genetic of dyslipidemia by simultaneous assessment of multiple genetic determinants.
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Affiliation(s)
- Oriane Marmontel
- Service de Biochimie et Biologie moléculaire Grand Est, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Bron Cedex, France.,Univ-Lyon, CarMeN laboratory, Inserm U1060, INRA U1397, Université Claude Bernard Lyon 1, INSA Lyon, Villeurbanne, France
| | | | - Anne-Sophie Wozny
- Service de Biochimie et Biologie Moléculaire Sud, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Sybil Charrière
- Univ-Lyon, CarMeN laboratory, Inserm U1060, INRA U1397, Université Claude Bernard Lyon 1, INSA Lyon, Villeurbanne, France.,Fédération d'endocrinologie, maladies métaboliques, diabète et nutrition, GHE, Hospices Civils de Lyon, Bron Cedex, France
| | - Xavier Vanhoye
- Service de Biochimie et Biologie moléculaire Grand Est, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Bron Cedex, France
| | - Thomas Simonet
- Cellule BioInformatique, Hospices Civils de Lyon, Bron Cedex, France
| | | | - Delphine Collin-Chavagnac
- Service de Biochimie et Biologie Moléculaire Sud, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Séverine Nony
- Service de Biochimie et Biologie moléculaire Grand Est, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Bron Cedex, France
| | - Sabrina Dumont
- Service de Biochimie et Biologie moléculaire Grand Est, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Bron Cedex, France
| | - Muriel Mahl
- Service de Biochimie et Biologie Moléculaire Sud, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Chantal Jacobs
- Service de Biochimie et Biologie moléculaire Grand Est, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Bron Cedex, France
| | - Alexandre Janin
- Service de Biochimie et Biologie moléculaire Grand Est, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Bron Cedex, France
| | - Cyrielle Caussy
- Univ-Lyon, CarMeN laboratory, Inserm U1060, INRA U1397, Université Claude Bernard Lyon 1, INSA Lyon, Villeurbanne, France.,Département Endocrinologie, Diabète et Nutrition, Hospices Civils de Lyon, Hôpital Lyon Sud, Pierre-Bénite, France
| | - Pierre Poinsot
- Service de Gastroentérologie Hépatologie et Nutrition Pédiatrique, GHE, Hospices Civils de Lyon, Bron Cedex, France
| | - Igor Tauveron
- Service d'endocrinologie, CHU G. Montpied, Clermont-Ferrand, France
| | - Claire Bardel
- Cellule BioInformatique, Hospices Civils de Lyon, Bron Cedex, France
| | - Gilles Millat
- Service de Biochimie et Biologie moléculaire Grand Est, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Bron Cedex, France
| | - Noël Peretti
- Univ-Lyon, CarMeN laboratory, Inserm U1060, INRA U1397, Université Claude Bernard Lyon 1, INSA Lyon, Villeurbanne, France.,Service de Gastroentérologie Hépatologie et Nutrition Pédiatrique, GHE, Hospices Civils de Lyon, Bron Cedex, France
| | - Philippe Moulin
- Univ-Lyon, CarMeN laboratory, Inserm U1060, INRA U1397, Université Claude Bernard Lyon 1, INSA Lyon, Villeurbanne, France.,Fédération d'endocrinologie, maladies métaboliques, diabète et nutrition, GHE, Hospices Civils de Lyon, Bron Cedex, France
| | - Christophe Marçais
- Service de Biochimie et Biologie Moléculaire Sud, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Mathilde Di Filippo
- Service de Biochimie et Biologie moléculaire Grand Est, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Bron Cedex, France.,Univ-Lyon, CarMeN laboratory, Inserm U1060, INRA U1397, Université Claude Bernard Lyon 1, INSA Lyon, Villeurbanne, France
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24
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Abstract
Dyslipidemias include both rare single gene disorders and common conditions that have a complex underlying basis. In London, ON, there is fortuitous close physical proximity between the Lipid Genetics Clinic and the London Regional Genomics Centre. For >30 years, we have applied DNA sequencing of clinical samples to help answer scientific questions. More than 2000 patients referred with dyslipidemias have participated in an ongoing translational research program. In 2013, we transitioned to next-generation sequencing; our targeted panel is designed to concurrently assess both monogenic and polygenic contributions to dyslipidemias. Patient DNA is screened for rare variants underlying 25 mendelian dyslipidemias, including familial hypercholesterolemia, hepatic lipase deficiency, abetalipoproteinemia, and familial chylomicronemia syndrome. Furthermore, polygenic scores for LDL (low-density lipoprotein) and HDL (high-density lipoprotein) cholesterol, and triglycerides are calculated for each patient. We thus simultaneously document both rare and common genetic variants, allowing for a broad view of genetic predisposition for both individual patients and cohorts. For instance, among patients referred with severe hypertriglyceridemia, defined as ≥10 mmol/L (≥885 mg/dL), <1% have a mendelian disorder (ie, autosomal recessive familial chylomicronemia syndrome), ≈15% have heterozygous rare variants (a >3-fold increase over normolipidemic individuals), and ≈35% have an extreme polygenic score (a >3-fold increase over normolipidemic individuals). Other dyslipidemias show a different mix of genetic determinants. Genetic results are discussed with patients and can support clinical decision-making. Integrating DNA testing into clinical care allows for a bidirectional flow of information, which facilitates scientific discoveries and clinical translation.
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Affiliation(s)
- Robert A. Hegele
- From the Department of Medicine (R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Biochemistry (R.A.H., J.S.D.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Robarts Research Institute (R.A.H., J.S.D.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Jacqueline S. Dron
- Department of Biochemistry (R.A.H., J.S.D.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Robarts Research Institute (R.A.H., J.S.D.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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25
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Grzymski JJ, Elhanan G, Morales Rosado JA, Smith E, Schlauch KA, Read R, Rowan C, Slotnick N, Dabe S, Metcalf WJ, Lipp B, Reed H, Sharma L, Levin E, Kao J, Rashkin M, Bowes J, Dunaway K, Slonim A, Washington N, Ferber M, Bolze A, Lu JT. Population genetic screening efficiently identifies carriers of autosomal dominant diseases. Nat Med 2020; 26:1235-1239. [DOI: 10.1038/s41591-020-0982-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 06/12/2020] [Indexed: 01/10/2023]
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26
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Molecular mechanism linking a novel PCSK9 copy number variant to severe hypercholesterolemia. Atherosclerosis 2020; 304:39-43. [DOI: 10.1016/j.atherosclerosis.2020.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/14/2020] [Accepted: 05/20/2020] [Indexed: 11/16/2022]
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27
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Berberich AJ, Wang J, Cao H, McIntyre AD, Spaic T, Miller DB, Stock S, Huot C, Stein R, Knoll J, Yang P, Robinson JF, Hegele RA. Simplifying Detection of Copy-Number Variations in Maturity-Onset Diabetes of the Young. Can J Diabetes 2020; 45:71-77. [PMID: 33011132 DOI: 10.1016/j.jcjd.2020.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 11/30/2022]
Abstract
OBJECTIVES Copy-number variations (CNVs) are large-scale deletions or duplications of DNA that have required specialized detection methods, such as microarray-based genomic hybridization or multiplex ligation probe amplification. However, recent advances in bioinformatics have made it possible to detect CNVs from next-generation DNA sequencing (NGS) data. Maturity-onset diabetes of the young (MODY) 5 is a subtype of autosomal-dominant diabetes that is often caused by heterozygous deletions involving the HNF1B gene on chromosome 17q12. We evaluated the utility of bioinformatic processing of raw NGS data to detect chromosome 17q12 deletions in MODY5 patients. METHODS NGS data from 57 patients clinically suspected to have MODY but who were negative for pathogenic mutations using a targeted panel were re-examined using a CNV calling tool (CNV Caller, VarSeq version 1.4.3). Potential CNVs for MODY5 were then confirmed using whole-exome sequencing, cytogenetic analysis and breakpoint analysis when possible. RESULTS Whole-gene deletions in HNF1B, ranging from 1.46 to 1.85 million basepairs in size, were detected in 3 individuals with features of MODY5. These were confirmed by independent methods to be part of a more extensive 17q12 deletion syndrome. Two additional patients carrying a 17q12 deletion were subsequently diagnosed using this method. CONCLUSIONS Large-scale deletions are the most common cause of MODY5 and can be detected directly from NGS data, without the need for additional methods.
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Affiliation(s)
- Amanda J Berberich
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.
| | - Jian Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Henian Cao
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Adam D McIntyre
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Tamara Spaic
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - David B Miller
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Suzanne Stock
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Celine Huot
- Department of Pediatrics, CHU Sainte-Justine, University of Montreal, Montréal, Quebec, Canada
| | - Robert Stein
- Department of Pediatrics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Joan Knoll
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Ping Yang
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - John F Robinson
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Robert A Hegele
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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28
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Risk of Premature Atherosclerotic Disease in Patients With Monogenic Versus Polygenic Familial Hypercholesterolemia. J Am Coll Cardiol 2020; 74:512-522. [PMID: 31345425 DOI: 10.1016/j.jacc.2019.05.043] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/01/2019] [Accepted: 05/07/2019] [Indexed: 01/17/2023]
Abstract
BACKGROUND A pathogenic variant in LDLR, APOB, or PCSK9 can be identified in 30% to 80% of patients with clinically-diagnosed familial hypercholesterolemia (FH). Alternatively, ∼20% of clinical FH is thought to have a polygenic cause. The cardiovascular disease (CVD) risk associated with polygenic versus monogenic FH is unclear. OBJECTIVES This study evaluated the effect of monogenic and polygenic causes of FH on premature (age <55 years) CVD events in patients with clinically diagnosed FH. METHODS Targeted sequencing of genes known to cause FH as well as common genetic variants was performed to calculate polygenic scores in patients with "possible," "probable," or "definite" FH, according to Dutch Lipid Clinic Network Criteria (n = 626). Patients with a polygenic score ≥80th percentile were considered to have polygenic FH. We examined the risk of unstable angina, myocardial infarction, coronary revascularization, or stoke. RESULTS A monogenic cause of FH was associated with significantly greater risk of CVD (adjusted hazard ratio: 1.96; 95% confidence interval: 1.24 to 3.12; p = 0.004), whereas the risk of CVD in patients with polygenic FH was not significantly different compared with patients in whom no genetic cause of FH was identified. However, the presence of an elevated low-density lipoprotein cholesterol (LDL-C) polygenic risk score further increased CVD risk in patients with monogenic FH (adjusted hazard ratio: 3.06; 95% confidence interval: 1.56 to 5.99; p = 0.001). CONCLUSIONS Patients with monogenic FH and superimposed elevated LDL-C polygenic risk scores have the greatest risk of premature CVD. Genetic testing for FH provides important prognostic information that is independent of LDL-C levels.
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29
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Raal FJ, Kallend D, Ray KK, Turner T, Koenig W, Wright RS, Wijngaard PLJ, Curcio D, Jaros MJ, Leiter LA, Kastelein JJP. Inclisiran for the Treatment of Heterozygous Familial Hypercholesterolemia. N Engl J Med 2020; 382:1520-1530. [PMID: 32197277 DOI: 10.1056/nejmoa1913805] [Citation(s) in RCA: 402] [Impact Index Per Article: 100.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Familial hypercholesterolemia is characterized by an elevated level of low-density lipoprotein (LDL) cholesterol and an increased risk of premature atherosclerotic cardiovascular disease. Monoclonal antibodies directed against proprotein convertase subtilisin-kexin type 9 (PCSK9) have been shown to reduce LDL cholesterol levels by more than 50% but require administration every 2 to 4 weeks. In a phase 2 trial, a twice-yearly injection of inclisiran, a small interfering RNA, was shown to inhibit hepatic synthesis of PCSK9 in adults with heterozygous familial hypercholesterolemia. METHODS In this phase 3, double-blind trial, we randomly assigned, in a 1:1 ratio, 482 adults who had heterozygous familial hypercholesterolemia to receive subcutaneous injections of inclisiran sodium (at a dose of 300 mg) or matching placebo on days 1, 90, 270, and 450. The two primary end points were the percent change from baseline in the LDL cholesterol level on day 510 and the time-adjusted percent change from baseline in the LDL cholesterol level between day 90 and day 540. RESULTS The median age of the patients was 56 years, and 47% were men; the mean baseline level of LDL cholesterol was 153 mg per deciliter. At day 510, the percent change in the LDL cholesterol level was a reduction of 39.7% (95% confidence interval [CI], -43.7 to -35.7) in the inclisiran group and an increase of 8.2% (95% CI, 4.3 to 12.2) in the placebo group, for a between-group difference of -47.9 percentage points (95% CI, -53.5 to -42.3; P<0.001). The time-averaged percent change in the LDL cholesterol level between day 90 and day 540 was a reduction of 38.1% (95% CI, -41.1 to -35.1) in the inclisiran group and an increase of 6.2% (95% CI, 3.3 to 9.2) in the placebo group, for a between-group difference of -44.3 percentage points (95% CI, -48.5 to -40.1; P<0.001). There were robust reductions in LDL cholesterol levels in all genotypes of familial hypercholesterolemia. Adverse events and serious adverse events were similar in the two groups. CONCLUSIONS Among adults with heterozygous familial hypercholesterolemia, those who received inclisiran had significantly lower levels of LDL cholesterol than those who received placebo, with an infrequent dosing regimen and an acceptable safety profile. (Funded by the Medicines Company; ORION-9 ClinicalTrials.gov number, NCT03397121.).
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Affiliation(s)
- Frederick J Raal
- From the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa (F.J.R.); the Medicines Company, Zurich, Switzerland (D.K.); the Imperial Centre for Cardiovascular Disease Prevention, Department of Primary Care and Public Health, Imperial College, London (K.K.R.); Medpace Reference Laboratories, Cincinnati (T.T.); Deutsches Herzzentrum München, Technische Universität München, and German Center for Cardiovascular Research, Munich Heart Alliance, Munich (W.K.), and the Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm (W.K.) - all in Germany; the Division of Preventive Cardiology and the Department of Cardiology, Mayo Clinic, Rochester, MN (R.S.W.); the Medicines Company, Parsippany, NJ (P.L.J.W., D.C.); Summit Analytical, Denver (M.J.J.); Li Ka Shing Knowledge Institute, St. Michael's Hospital, University of Toronto, Toronto (L.A.L.); and the Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam (J.J.P.K.)
| | - David Kallend
- From the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa (F.J.R.); the Medicines Company, Zurich, Switzerland (D.K.); the Imperial Centre for Cardiovascular Disease Prevention, Department of Primary Care and Public Health, Imperial College, London (K.K.R.); Medpace Reference Laboratories, Cincinnati (T.T.); Deutsches Herzzentrum München, Technische Universität München, and German Center for Cardiovascular Research, Munich Heart Alliance, Munich (W.K.), and the Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm (W.K.) - all in Germany; the Division of Preventive Cardiology and the Department of Cardiology, Mayo Clinic, Rochester, MN (R.S.W.); the Medicines Company, Parsippany, NJ (P.L.J.W., D.C.); Summit Analytical, Denver (M.J.J.); Li Ka Shing Knowledge Institute, St. Michael's Hospital, University of Toronto, Toronto (L.A.L.); and the Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam (J.J.P.K.)
| | - Kausik K Ray
- From the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa (F.J.R.); the Medicines Company, Zurich, Switzerland (D.K.); the Imperial Centre for Cardiovascular Disease Prevention, Department of Primary Care and Public Health, Imperial College, London (K.K.R.); Medpace Reference Laboratories, Cincinnati (T.T.); Deutsches Herzzentrum München, Technische Universität München, and German Center for Cardiovascular Research, Munich Heart Alliance, Munich (W.K.), and the Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm (W.K.) - all in Germany; the Division of Preventive Cardiology and the Department of Cardiology, Mayo Clinic, Rochester, MN (R.S.W.); the Medicines Company, Parsippany, NJ (P.L.J.W., D.C.); Summit Analytical, Denver (M.J.J.); Li Ka Shing Knowledge Institute, St. Michael's Hospital, University of Toronto, Toronto (L.A.L.); and the Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam (J.J.P.K.)
| | - Traci Turner
- From the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa (F.J.R.); the Medicines Company, Zurich, Switzerland (D.K.); the Imperial Centre for Cardiovascular Disease Prevention, Department of Primary Care and Public Health, Imperial College, London (K.K.R.); Medpace Reference Laboratories, Cincinnati (T.T.); Deutsches Herzzentrum München, Technische Universität München, and German Center for Cardiovascular Research, Munich Heart Alliance, Munich (W.K.), and the Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm (W.K.) - all in Germany; the Division of Preventive Cardiology and the Department of Cardiology, Mayo Clinic, Rochester, MN (R.S.W.); the Medicines Company, Parsippany, NJ (P.L.J.W., D.C.); Summit Analytical, Denver (M.J.J.); Li Ka Shing Knowledge Institute, St. Michael's Hospital, University of Toronto, Toronto (L.A.L.); and the Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam (J.J.P.K.)
| | - Wolfgang Koenig
- From the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa (F.J.R.); the Medicines Company, Zurich, Switzerland (D.K.); the Imperial Centre for Cardiovascular Disease Prevention, Department of Primary Care and Public Health, Imperial College, London (K.K.R.); Medpace Reference Laboratories, Cincinnati (T.T.); Deutsches Herzzentrum München, Technische Universität München, and German Center for Cardiovascular Research, Munich Heart Alliance, Munich (W.K.), and the Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm (W.K.) - all in Germany; the Division of Preventive Cardiology and the Department of Cardiology, Mayo Clinic, Rochester, MN (R.S.W.); the Medicines Company, Parsippany, NJ (P.L.J.W., D.C.); Summit Analytical, Denver (M.J.J.); Li Ka Shing Knowledge Institute, St. Michael's Hospital, University of Toronto, Toronto (L.A.L.); and the Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam (J.J.P.K.)
| | - R Scott Wright
- From the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa (F.J.R.); the Medicines Company, Zurich, Switzerland (D.K.); the Imperial Centre for Cardiovascular Disease Prevention, Department of Primary Care and Public Health, Imperial College, London (K.K.R.); Medpace Reference Laboratories, Cincinnati (T.T.); Deutsches Herzzentrum München, Technische Universität München, and German Center for Cardiovascular Research, Munich Heart Alliance, Munich (W.K.), and the Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm (W.K.) - all in Germany; the Division of Preventive Cardiology and the Department of Cardiology, Mayo Clinic, Rochester, MN (R.S.W.); the Medicines Company, Parsippany, NJ (P.L.J.W., D.C.); Summit Analytical, Denver (M.J.J.); Li Ka Shing Knowledge Institute, St. Michael's Hospital, University of Toronto, Toronto (L.A.L.); and the Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam (J.J.P.K.)
| | - Peter L J Wijngaard
- From the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa (F.J.R.); the Medicines Company, Zurich, Switzerland (D.K.); the Imperial Centre for Cardiovascular Disease Prevention, Department of Primary Care and Public Health, Imperial College, London (K.K.R.); Medpace Reference Laboratories, Cincinnati (T.T.); Deutsches Herzzentrum München, Technische Universität München, and German Center for Cardiovascular Research, Munich Heart Alliance, Munich (W.K.), and the Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm (W.K.) - all in Germany; the Division of Preventive Cardiology and the Department of Cardiology, Mayo Clinic, Rochester, MN (R.S.W.); the Medicines Company, Parsippany, NJ (P.L.J.W., D.C.); Summit Analytical, Denver (M.J.J.); Li Ka Shing Knowledge Institute, St. Michael's Hospital, University of Toronto, Toronto (L.A.L.); and the Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam (J.J.P.K.)
| | - Danielle Curcio
- From the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa (F.J.R.); the Medicines Company, Zurich, Switzerland (D.K.); the Imperial Centre for Cardiovascular Disease Prevention, Department of Primary Care and Public Health, Imperial College, London (K.K.R.); Medpace Reference Laboratories, Cincinnati (T.T.); Deutsches Herzzentrum München, Technische Universität München, and German Center for Cardiovascular Research, Munich Heart Alliance, Munich (W.K.), and the Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm (W.K.) - all in Germany; the Division of Preventive Cardiology and the Department of Cardiology, Mayo Clinic, Rochester, MN (R.S.W.); the Medicines Company, Parsippany, NJ (P.L.J.W., D.C.); Summit Analytical, Denver (M.J.J.); Li Ka Shing Knowledge Institute, St. Michael's Hospital, University of Toronto, Toronto (L.A.L.); and the Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam (J.J.P.K.)
| | - Mark J Jaros
- From the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa (F.J.R.); the Medicines Company, Zurich, Switzerland (D.K.); the Imperial Centre for Cardiovascular Disease Prevention, Department of Primary Care and Public Health, Imperial College, London (K.K.R.); Medpace Reference Laboratories, Cincinnati (T.T.); Deutsches Herzzentrum München, Technische Universität München, and German Center for Cardiovascular Research, Munich Heart Alliance, Munich (W.K.), and the Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm (W.K.) - all in Germany; the Division of Preventive Cardiology and the Department of Cardiology, Mayo Clinic, Rochester, MN (R.S.W.); the Medicines Company, Parsippany, NJ (P.L.J.W., D.C.); Summit Analytical, Denver (M.J.J.); Li Ka Shing Knowledge Institute, St. Michael's Hospital, University of Toronto, Toronto (L.A.L.); and the Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam (J.J.P.K.)
| | - Lawrence A Leiter
- From the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa (F.J.R.); the Medicines Company, Zurich, Switzerland (D.K.); the Imperial Centre for Cardiovascular Disease Prevention, Department of Primary Care and Public Health, Imperial College, London (K.K.R.); Medpace Reference Laboratories, Cincinnati (T.T.); Deutsches Herzzentrum München, Technische Universität München, and German Center for Cardiovascular Research, Munich Heart Alliance, Munich (W.K.), and the Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm (W.K.) - all in Germany; the Division of Preventive Cardiology and the Department of Cardiology, Mayo Clinic, Rochester, MN (R.S.W.); the Medicines Company, Parsippany, NJ (P.L.J.W., D.C.); Summit Analytical, Denver (M.J.J.); Li Ka Shing Knowledge Institute, St. Michael's Hospital, University of Toronto, Toronto (L.A.L.); and the Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam (J.J.P.K.)
| | - John J P Kastelein
- From the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa (F.J.R.); the Medicines Company, Zurich, Switzerland (D.K.); the Imperial Centre for Cardiovascular Disease Prevention, Department of Primary Care and Public Health, Imperial College, London (K.K.R.); Medpace Reference Laboratories, Cincinnati (T.T.); Deutsches Herzzentrum München, Technische Universität München, and German Center for Cardiovascular Research, Munich Heart Alliance, Munich (W.K.), and the Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm (W.K.) - all in Germany; the Division of Preventive Cardiology and the Department of Cardiology, Mayo Clinic, Rochester, MN (R.S.W.); the Medicines Company, Parsippany, NJ (P.L.J.W., D.C.); Summit Analytical, Denver (M.J.J.); Li Ka Shing Knowledge Institute, St. Michael's Hospital, University of Toronto, Toronto (L.A.L.); and the Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam (J.J.P.K.)
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30
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Trinder M, Francis GA, Brunham LR. Association of Monogenic vs Polygenic Hypercholesterolemia With Risk of Atherosclerotic Cardiovascular Disease. JAMA Cardiol 2020; 5:390-399. [PMID: 32049305 PMCID: PMC7042820 DOI: 10.1001/jamacardio.2019.5954] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/01/2019] [Indexed: 12/13/2022]
Abstract
Importance Monogenic familial hypercholesterolemia (FH) is associated with lifelong elevations in low-density lipoprotein cholesterol (LDL-C) levels and increased risk of atherosclerotic cardiovascular disease (CVD). However, many individuals with hypercholesterolemia have a polygenic rather than a monogenic cause for their condition. It is unclear if a genetic variant for hypercholesterolemia alters the risk of CVD. Objectives To assess whether a genetic variant for hypercholesterolemia alters the risk of atherosclerotic CVD and to evaluate how this risk compares with that of nongenetic hypercholesterolemia. Design, Setting, and Participants In this genetic-association, case-control, cohort study, individuals aged 40 to 69 years were recruited by the UK Biobank from across the United Kingdom between March 13, 2006, and October 1, 2010, and followed up until March 31, 2017. Genotyping array and exome sequencing data from the UK Biobank cohort were used to identify individuals with monogenic (LDLR, APOB, and PCSK9) or polygenic hypercholesterolemia (LDL-C polygenic score >95th percentile based on 223 single-nucleotide variants in the entire cohort). The data were analyzed from July 1, 2019, to December 30, 2019. Main Outcomes and Measures The study investigated the association of genotype with the risk of coronary and carotid revascularization, myocardial infarction, ischemic stroke, and all-cause mortality among the overall study population and among participants with monogenic FH (n = 277), polygenic hypercholesterolemia (n = 2379), or hypercholesterolemia with undetermined cause (n = 2232) at comparable levels of LDL-C measured at study enrollment. Results For the 48 741 individuals with genotyping array and exome sequencing data, the mean (SD) age was 56.6 (8.0) years, and 54.5% were female (n = 26 541 of 48 741). A monogenic FH variant for hypercholesterolemia was found in 277 individuals (0.57%, 1 in 176 individuals). Participants with monogenic FH were significantly more likely than those without monogenic FH to experience an atherosclerotic CVD event at 55 years or younger (17 of 277 [6.1%] vs 988 of 48 464 [2.0%]; P < .001). Compared with the general population, both monogenic and polygenic hypercholesterolemia were associated with an increased risk of CVD events. Moreover, among individuals with comparable levels of LDL-C, both monogenic (hazard ratio, 1.93; 95% CI, 1.34-2.77; P < .001) and polygenic hypercholesterolemia (hazard ratio, 1.26; 95% CI, 1.03-1.55; P = .03) were significantly associated with an increased risk of CVD events compared with the risk of such events in individuals with hypercholesterolemia without an identified genetic cause. Conclusions and Relevance The findings of this study suggest that among individuals with hypercholesterolemia, genetic determinants of LDL-C levels may impose additional risk of CVD. Thus, understanding the possible genetic cause of hypercholesterolemia may provide important prognostic information to treat patients.
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Affiliation(s)
- Mark Trinder
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
- Experimental Medicine Program, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gordon A. Francis
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Liam R. Brunham
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
- Experimental Medicine Program, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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31
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Tada H, Hori M, Nomura A, Hosomichi K, Nohara A, Kawashiri MA, Harada-Shiba M. A catalog of the pathogenic mutations of LDL receptor gene in Japanese familial hypercholesterolemia. J Clin Lipidol 2020; 14:346-351.e9. [PMID: 32331935 DOI: 10.1016/j.jacl.2020.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 03/16/2020] [Accepted: 03/16/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND Little data exist on the pathogenic mutations of LDL receptor in Japanese familial hypercholesterolemia (FH). OBJECTIVE We aimed to catalog the pathogenic mutations of LDL receptor gene in the 2 major Japanese FH-care centers (Kanazawa University and National Cerebral and Cardiovascular Center Research Institute), where genetic testing of FH has been performed centrally on requests from institutes all over Japan during more than past 2 decades. METHODS 796 FH subjects from 472 families who had nonsynonymous mutations in LDL receptor gene were included in this study. Genetic mutations were analyzed for mutations by Sanger sequencing as well as by multiplex ligation probe dependent amplification technique for large rearrangements. Pathogenic mutations were defined either as 1) protein truncated variants, 2) registered as pathogenic in ClinVar, or Human Gene Mutation Database (HGMD), or meet the criteria of American College of Medical Genetics and Genomics guideline, or 3) CADD score > 10. RESULTS We found 138 different mutations. Among them, 132 mutations were considered as pathogenic, including 19 large rearrangement mutations. However, 6 missense mutations were classified as variants of unknown significance. A single mutation accounted for as much as 41% of the FH subjects recruited from Kanazawa University mainly due to founder gene effect, whereas many singleton mutations were found from National Cerebral and Cardiovascular Center Research Institute located in Osaka. CONCLUSIONS We provided the largest catalog of pathogenic mutations of LDL receptor gene in Japanese FH. This could aid to determine the pathogenicity of the LDL receptor genetic mutations not only in Japanese but also in other ethnicities.
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Affiliation(s)
- Hayato Tada
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Mika Hori
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Akihiro Nomura
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa, Japan
| | - Atsushi Nohara
- Department of Genetics, Ishikawa Prefectural Central Hospital, Kanazawa, Japan
| | - Masa-Aki Kawashiri
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan.
| | - Mariko Harada-Shiba
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
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Dron JS, Wang J, McIntyre AD, Iacocca MA, Robinson JF, Ban MR, Cao H, Hegele RA. Six years' experience with LipidSeq: clinical and research learnings from a hybrid, targeted sequencing panel for dyslipidemias. BMC Med Genomics 2020; 13:23. [PMID: 32041611 PMCID: PMC7011550 DOI: 10.1186/s12920-020-0669-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 01/23/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND In 2013, our laboratory designed a targeted sequencing panel, "LipidSeq", to study the genetic determinants of dyslipidemia and metabolic disorders. Over the last 6 years, we have analyzed 3262 patient samples obtained from our own Lipid Genetics Clinic and international colleagues. Here, we highlight our findings and discuss research benefits and clinical implications of our panel. METHODS LipidSeq targets 69 genes and 185 single-nucleotide polymorphisms (SNPs) either causally related or associated with dyslipidemia and metabolic disorders. This design allows us to simultaneously evaluate monogenic-caused by rare single-nucleotide variants (SNVs) or copy-number variants (CNVs)-and polygenic forms of dyslipidemia. Polygenic determinants were assessed using three polygenic scores, one each for low-density lipoprotein cholesterol, triglyceride, and high-density lipoprotein cholesterol. RESULTS Among 3262 patient samples evaluated, the majority had hypertriglyceridemia (40.1%) and familial hypercholesterolemia (28.3%). Across all samples, we identified 24,931 unique SNVs, including 2205 rare variants predicted disruptive to protein function, and 77 unique CNVs. Considering our own 1466 clinic patients, LipidSeq results have helped in diagnosis and improving treatment options. CONCLUSIONS Our LipidSeq design based on ontology of lipid disorders has enabled robust detection of variants underlying monogenic and polygenic dyslipidemias. In more than 50 publications related to LipidSeq, we have described novel variants, the polygenic nature of many dyslipidemias-some previously thought to be primarily monogenic-and have uncovered novel mechanisms of disease. We further demonstrate several tangible clinical benefits of its use.
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Affiliation(s)
- Jacqueline S. Dron
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street, London, ON N6A 5B7 Canada
| | - Jian Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
| | - Adam D. McIntyre
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
| | - Michael A. Iacocca
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street, London, ON N6A 5B7 Canada
- Department of Biomedical Data Science, Stanford School of Medicine, Stanford University, 450 Serra Mall, Stanford, CA 94305 USA
| | - John F. Robinson
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
| | - Matthew R. Ban
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
| | - Henian Cao
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
| | - Robert A. Hegele
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street, London, ON N6A 5B7 Canada
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
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Dron JS, Wang J, McIntyre AD, Cao H, Hegele RA. The polygenic nature of mild-to-moderate hypertriglyceridemia. J Clin Lipidol 2020; 14:28-34.e2. [PMID: 32033914 DOI: 10.1016/j.jacl.2020.01.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/01/2020] [Accepted: 01/06/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Patients with mild-to-moderate hypertriglyceridemia (HTG) are thought to share specific genetic susceptibility factors that are also present in patients with severe HTG, but no data have been reported on this issue. OBJECTIVE The objective of this study was to characterize genetic profiles of patients with mild-to-moderate HTG and compare them to patients with severe HTG. METHODS DNA from patients with mild-to-moderate HTG was sequenced using our targeted sequencing panel, "LipidSeq". For each patient, we assessed 1) rare variants disrupting five TG metabolism genes and 2) the accumulation of 16 common single-nucleotide polymorphisms (SNPs) using a polygenic risk score. The genetic profiles for these patients were then compared with normolipidemic controls from the 1000 Genomes Project and with patients with severe HTG. RESULTS Across 134 patients with mild-to-moderate HTG, 9.0% carried heterozygous rare variants and 26.9% had an excess accumulation of common SNPs. Patients with mild-to-moderate HTG were 2.38 times (95% CI [1.13-4.99]; P = .021) more likely to carry a rare variant and 3.26 times (95% CI [2.02-5.26]; P < .0001) more likely to have an extreme polygenic risk score compared with the 1000 Genomes Project. In addition, patients with severe HTG were 1.86 times (95% CI [0.98-3.51]; P = .032) more likely to carry a rare variant and 1.63 times (95% CI [1.07-2.48]; P = .013) more likely to have an extreme polygenic risk score than patients with mild-to-moderate HTG. CONCLUSIONS We report an increased prevalence of genetic determinants in patients with an increased severity of the HTG phenotype when considering either rare variants disrupting TG metabolism genes or an excess accumulation of common SNPs. As well, the findings confirm that the most prevalent genetic contributor to HTG, regardless of severity, is polygenic SNP accumulation.
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Affiliation(s)
- Jacqueline S Dron
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Jian Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Adam D McIntyre
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Henian Cao
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Robert A Hegele
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.
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Abstract
Loss-of-function variants in PCSK9 (proprotein convertase subtilisin-kexin type 9) are associated with lower lifetime risk of atherosclerotic cardiovascular disease) events. Confirmation of these genetic observations in large, prospective clinical trials in participants with atherosclerotic cardiovascular disease has provided guidance on risk stratification and enhanced our knowledge on hitherto unresolved and contentious issues concerning the efficacy and safety of markedly lowering LDL-C (low-density lipoprotein cholesterol). PCSK9 has a broad repertoire of molecular effects. Furthermore, clinical trials with PCSK9 inhibitors demonstrate that reductions in atherosclerotic cardiovascular disease events are more effective in patients with recent myocardial infarction, multiple myocardial infarctions, multivessel coronary artery disease, and lower extremity arterial disease. The potent LDL-C lowering efficacy of PCSK9 inhibitors provides the opportunity for more aggressive LDL-lowering strategies in high-risk patients with atherosclerotic cardiovascular disease and supports the notion that there is no lower limit for LDL-C. Aggressive LDL-C lowering with fully human PCSK9 monoclonal antibodies has been associated by a safety profile superior to that of other classes of LDL-lowering agents. These clinical trials provide evidence that LDL lowering with PCSK9 inhibitors is an effective therapy for lowering cardiovascular events in high-risk patients with LDL-C levels ≥70 mg/dL on maximally tolerated oral therapies, including statins and ezetimibe.
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Affiliation(s)
- Robert S Rosenson
- From the Zena and Michael A. Wiener Cardiovascular Institute and Marie-Josee and Henry R. Kravis Center for Cardiovascular Health, Mount Sinai Hospital, Icahn School of Medicine at Mount Sinai, New York, NY (R.S.R.)
| | - Robert A Hegele
- Department of Medicine and Robarts Research Institute, Schulich School of Medicine, Western University, London, Ontario, Canada
| | - Wolfgang Koenig
- Deutsches Herzzentrum München, Technische Universität München, Munich, Germany (W.K.).,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany (W.K.).,Institute of Epidemiology and Biostatistics, University of Ulm, Germany (W.K.)
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35
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Cao YX, Zhou BY, Sun D, Li S, Guo YL, Zhu CG, Wu NQ, Gao Y, Xu RX, Liu G, Dong Q, Li JJ. Differences in phenotype, genotype and cardiovascular events between patients with probable and definite heterozygous familial hypercholesterolemia. Per Med 2019; 16:467-478. [PMID: 31691639 DOI: 10.2217/pme-2018-0135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: To investigated the potential differences between probable and definite heterozygous familial hypercholesterolemia (HeFH) patients diagnosed by Dutch Lipid Clinic Network criteria. Methods: Clinical characteristics, lipid profile, severity of coronary artery stenosis and gene mutations were compared. Kaplan-Meier curve was performed to evaluate the cardiovascular events. Results: Overall, 325 participants were included and divided into two groups: probable (n = 233) and definite HeFH (n = 92). Definite HeFH patients had higher low-density lipoprotein cholesterol (LDL-C), oxidized-LDL and proprotein convertase subtilisin/kexin 9 levels, and higher prevalence of tendon xanthomas. The incidence of genetic mutations was statistically higher in definite HeFH than probable HeFH patients. The coronary stenosis calculated by Gensini score was statistically severer in definite HeFH patients. The best LDL-C threshold for predicting mutations was 5.14 mmol/l. Definite HeFH had lower event-free survival rates. Conclusion: Definite HeFH patients had higher severity of phenotype and genotype, and higher risk of cardiovascular events.
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Affiliation(s)
- Ye-Xuan Cao
- Division of Dyslipidemia, State Key Laboratory of Cardiovascular Disease, Fu Wai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, BeiLiShi Road 167, Beijing 100037, China
| | - Bing-Yang Zhou
- Department of Cardiology, Tianjin Chest Hospital, Tianjin Institute of Cardiovascular Diseases, Tianjin 300222, China
| | - Di Sun
- Division of Dyslipidemia, State Key Laboratory of Cardiovascular Disease, Fu Wai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, BeiLiShi Road 167, Beijing 100037, China
| | - Sha Li
- Division of Dyslipidemia, State Key Laboratory of Cardiovascular Disease, Fu Wai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, BeiLiShi Road 167, Beijing 100037, China
| | - Yuan-Lin Guo
- Division of Dyslipidemia, State Key Laboratory of Cardiovascular Disease, Fu Wai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, BeiLiShi Road 167, Beijing 100037, China
| | - Cheng-Gang Zhu
- Division of Dyslipidemia, State Key Laboratory of Cardiovascular Disease, Fu Wai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, BeiLiShi Road 167, Beijing 100037, China
| | - Na-Qiong Wu
- Division of Dyslipidemia, State Key Laboratory of Cardiovascular Disease, Fu Wai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, BeiLiShi Road 167, Beijing 100037, China
| | - Ying Gao
- Division of Dyslipidemia, State Key Laboratory of Cardiovascular Disease, Fu Wai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, BeiLiShi Road 167, Beijing 100037, China
| | - Rui-Xia Xu
- Division of Dyslipidemia, State Key Laboratory of Cardiovascular Disease, Fu Wai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, BeiLiShi Road 167, Beijing 100037, China
| | - Geng Liu
- Division of Dyslipidemia, State Key Laboratory of Cardiovascular Disease, Fu Wai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, BeiLiShi Road 167, Beijing 100037, China
| | - Qian Dong
- Division of Dyslipidemia, State Key Laboratory of Cardiovascular Disease, Fu Wai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, BeiLiShi Road 167, Beijing 100037, China
| | - Jian-Jun Li
- Division of Dyslipidemia, State Key Laboratory of Cardiovascular Disease, Fu Wai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, BeiLiShi Road 167, Beijing 100037, China
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Hsiung YC, Lin PC, Chen CS, Tung YC, Yang WS, Chen PL, Su TC. Identification of a novel LDLR disease-causing variant using capture-based next-generation sequencing screening of familial hypercholesterolemia patients in Taiwan. Atherosclerosis 2019; 277:440-447. [PMID: 30270083 DOI: 10.1016/j.atherosclerosis.2018.08.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 08/10/2018] [Accepted: 08/21/2018] [Indexed: 12/30/2022]
Abstract
BACKGROUND AND AIMS Familial hypercholesterolemia (FH) is an autosomal dominant disorder with paramount health impacts. However, less than 1% FH patients in Taiwan were formally diagnosed, partly due to the lack of reliable cost-effective genetic testing. We aimed at using a next-generation sequencing (NGS) platform as the clinical genetic testing method for FH. METHODS We designed probes to capture the whole LDLR gene and all coding sequences of APOB and PCSK9, and then sequenced with Illumina MiSeq platform (2 × 300 bps). The entire pipeline was tested on 13 DNA samples with known causative variants (including 3 large duplications and 2 large deletions). Then we enrolled a new cohort of 28 unrelated FH patients with Dutch Lipid Clinic Network score ≥5. Relatives were included in the cascade screening. RESULTS From the 13 DNA samples, we correctly identify all the variants, including big duplications and deletions. From the new cohort, we identified the causative variants in 21 of the 28 unrelated probands; five of them carrying a novel splice site variant c.1186+2T>G in LDLR. Among the family members, the concentration of LDL cholesterol was 7.82 ± 2.13 mmol/l in LDLR c.1186+2T>G carrier group (n = 26), and was significantly higher than 3.18 ± 1.36 mmol/l in the non-carrier group (n = 25). CONCLUSIONS This is the first capture-based NGS testing for FH to cover the whole LDLR genomic region, and therefore making reliable structural variation detection. This panel can comprehensively detect disease-causing variants in LDLR, APOB, and PCSK9 for FH patients.
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Affiliation(s)
- Yun-Chieh Hsiung
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Po-Chih Lin
- Department of Internal Medicine and Cardiovascular Center, National Taiwan University Hospital, Taipei, Taiwan
| | - Chih-Shan Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yi-Ching Tung
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wei-Shiung Yang
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan; Department of Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Pei-Lung Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.
| | - Ta-Chen Su
- Department of Internal Medicine and Cardiovascular Center, National Taiwan University Hospital, Taipei, Taiwan; Institute of Occupational Medicine and Industrial Hygiene, National Taiwan University College of Public Health, Taipei, Taiwan.
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37
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Zhang M, Dilliott AA, Khallaf R, Robinson JF, Hegele RA, Comishen M, Sato C, Tosto G, Reitz C, Mayeux R, George-Hyslop PS, Freedman M, Rogaeva E. Genetic and epigenetic study of an Alzheimer's disease family with monozygotic triplets. Brain 2019; 142:3375-3381. [PMID: 31580390 PMCID: PMC6821163 DOI: 10.1093/brain/awz289] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 06/26/2019] [Accepted: 07/29/2019] [Indexed: 12/14/2022] Open
Abstract
Age at onset of Alzheimer's disease is highly variable, and its modifiers (genetic or environmental) could act through epigenetic changes, such as DNA methylation at CpG sites. DNA methylation is also linked to ageing-the strongest Alzheimer's disease risk factor. DNA methylation age can be calculated using age-related CpGs and might reflect biological ageing. We conducted a clinical, genetic and epigenetic investigation of a unique Ashkenazi Jewish family with monozygotic triplets, two of whom developed Alzheimer's disease at ages 73 and 76, while the third at age 85 has no cognitive complaints or deficits in daily activities. One of their offspring developed Alzheimer's disease at age 50. Targeted sequencing of 80 genes associated with neurodegeneration revealed that the triplets and the affected offspring are heterozygous carriers of the risk APOE ε4 allele, as well as rare substitutions in APP (p.S198P), NOTCH3 (p.H1235L) and SORL1 (p.W1563C). In addition, we catalogued 52 possibly damaging rare variants detected by NeuroX array in affected individuals. Analysis of family members on a genome-wide DNA methylation chip revealed that the DNA methylation age of the triplets was 6-10 years younger than chronological age, while it was 9 years older in the offspring with early-onset Alzheimer's disease, suggesting accelerated ageing.
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Affiliation(s)
- Ming Zhang
- First Rehabilitation Hospital, School of Medicine, Tongji University, Shanghai, China
- Collaborative Innovation Center for Brain Science, Tongji University, Shanghai, China
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Ave, Toronto, ON, Canada
| | - Allison A Dilliott
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Roaa Khallaf
- Department of Medicine, Division of Neurology, Baycrest Health Sciences, and University of Toronto, Toronto, ON, Canada
| | - John F Robinson
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Robert A Hegele
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Michael Comishen
- Department of Medicine, Division of Neurology, Baycrest Health Sciences, and University of Toronto, Toronto, ON, Canada
| | - Christine Sato
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Ave, Toronto, ON, Canada
| | - Giuseppe Tosto
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, USA
| | - Christiane Reitz
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY, USA
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, 710 West 168th Street, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY, USA
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University. 1051 Riverside Drive, New York, NY, USA
| | - Peter St George-Hyslop
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Ave, Toronto, ON, Canada
| | - Morris Freedman
- Department of Medicine, Division of Neurology, Baycrest Health Sciences, Mt. Sinai Hospital, and University of Toronto, Toronto, ON, Canada
- Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Ave, Toronto, ON, Canada
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Dron JS, Wang J, McIntyre AD, Cao H, Robinson JF, Duell PB, Manjoo P, Feng J, Movsesyan I, Malloy MJ, Pullinger CR, Kane JP, Hegele RA. Partial LPL deletions: rare copy-number variants contributing towards severe hypertriglyceridemia. J Lipid Res 2019; 60:1953-1958. [PMID: 31519763 DOI: 10.1194/jlr.p119000335] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/09/2019] [Indexed: 01/31/2023] Open
Abstract
Severe hypertriglyceridemia (HTG) is a relatively common form of dyslipidemia with a complex pathophysiology and serious health complications. HTG can develop in the presence of rare genetic factors disrupting genes involved in the triglyceride (TG) metabolic pathway, including large-scale copy-number variants (CNVs). Improvements in next-generation sequencing technologies and bioinformatic analyses have better allowed assessment of CNVs as possible causes of or contributors to severe HTG. We screened targeted sequencing data of 632 patients with severe HTG and identified partial deletions of the LPL gene, encoding the central enzyme involved in the metabolism of TG-rich lipoproteins, in four individuals (0.63%). We confirmed the genomic breakpoints in each patient with Sanger sequencing. Three patients carried an identical heterozygous deletion spanning the 5' untranslated region (UTR) to LPL exon 2, and one patient carried a heterozygous deletion spanning the 5'UTR to LPL exon 1. All four heterozygous CNV carriers were determined to have multifactorial severe HTG. The predicted null nature of our identified LPL deletions may contribute to relatively higher TG levels and a more severe clinical phenotype than other forms of genetic variation associated with the disease, particularly in the polygenic state. The identification of novel CNVs in patients with severe HTG suggests that methods for CNV detection should be included in the diagnostic workup and molecular genetic evaluation of patients with high TG levels.
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Affiliation(s)
- Jacqueline S Dron
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada.,Departments of Biochemistry Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
| | - Jian Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
| | - Adam D McIntyre
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
| | - Henian Cao
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
| | - John F Robinson
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
| | - P Barton Duell
- Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR 97239
| | - Priya Manjoo
- Department of Medicine, Gordon and Leslie Diamond Centre, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - James Feng
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158
| | - Irina Movsesyan
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158
| | - Mary J Malloy
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158
| | - Clive R Pullinger
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158
| | - John P Kane
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158
| | - Robert A Hegele
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada .,Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada.,Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
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39
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Zhao PJ, Ban MR, Iacocca MA, McIntyre AD, Wang J, Hegele RA. Genetic Determinants of Myocardial Infarction Risk in Familial Hypercholesterolemia. CJC Open 2019; 1:225-230. [PMID: 32159113 PMCID: PMC7063643 DOI: 10.1016/j.cjco.2019.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/05/2019] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Familial hypercholesterolemia (FH) is an inherited condition of elevated serum low-density lipoprotein (LDL) cholesterol leading to premature coronary heart disease. We evaluated whether FH mutations are independently associated with the development of myocardial infarction (MI), after adjusting for LDL cholesterol level and clinical risk factors. METHODS In 182 unrelated patients from different families referred with clinically suspected FH, targeted next-generation DNA sequencing was performed on 73 lipid-related genes and 178 single nucleotide polymorphisms, at 300-times mean read depth, to identify monogenic mutations and high-risk single nucleotide polymorphisms. RESULTS Pathogenic FH mutations were identified in 27% of patients. Patients with mutations, compared with those without, were 12 years younger when referred to the lipid clinic (P < 0.001) and had higher baseline and post-treatment LDL cholesterol by 1.11 mmol/L (P < 0.001) and 0.62 mmol/L (P = 0.01), respectively. The hazard ratio for premature MI with respect to having an FH mutation, controlling for sex, hypertension, body mass index, diabetes, LDL cholesterol, and smoking, was 4.51 (P = 0.002). CONCLUSION FH is a genetically diverse condition. FH mutations are independently associated with higher risk of premature MI in patients referred for hypercholesterolemia. Therefore, genotyping could guide cardiovascular risk stratification in the personalized treatment of FH.
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Affiliation(s)
- Pei Jun Zhao
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Matthew R. Ban
- Robarts Research Institute, Western University, London, Ontario, Canada
| | | | - Adam D. McIntyre
- Robarts Research Institute, Western University, London, Ontario, Canada
| | - Jian Wang
- Robarts Research Institute, Western University, London, Ontario, Canada
| | - Robert A. Hegele
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
- Robarts Research Institute, Western University, London, Ontario, Canada
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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40
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Iacocca MA, Chora JR, Carrié A, Freiberger T, Leigh SE, Defesche JC, Kurtz CL, DiStefano MT, Santos RD, Humphries SE, Mata P, Jannes CE, Hooper AJ, Wilemon KA, Benlian P, O'Connor R, Garcia J, Wand H, Tichy L, Sijbrands EJ, Hegele RA, Bourbon M, Knowles JW. ClinVar database of global familial hypercholesterolemia-associated DNA variants. Hum Mutat 2019; 39:1631-1640. [PMID: 30311388 PMCID: PMC6206854 DOI: 10.1002/humu.23634] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 08/02/2018] [Accepted: 08/28/2018] [Indexed: 12/14/2022]
Abstract
Accurate and consistent variant classification is imperative for incorporation of rapidly developing sequencing technologies into genomic medicine for improved patient care. An essential requirement for achieving standardized and reliable variant interpretation is data sharing, facilitated by a centralized open-source database. Familial hypercholesterolemia (FH) is an exemplar of the utility of such a resource: it has a high incidence, a favorable prognosis with early intervention and treatment, and cascade screening can be offered to families if a causative variant is identified. ClinVar, an NCBI-funded resource, has become the primary repository for clinically relevant variants in Mendelian disease, including FH. Here, we present the concerted efforts made by the Clinical Genome Resource, through the FH Variant Curation Expert Panel and global FH community, to increase submission of FH-associated variants into ClinVar. Variant-level data was categorized by submitter, variant characteristics, classification method, and available supporting data. To further reform interpretation of FH-associated variants, areas for improvement in variant submissions were identified; these include a need for more detailed submissions and submission of supporting variant-level data, both retrospectively and prospectively. Collaborating to provide thorough, reliable evidence-based variant interpretation will ultimately improve the care of FH patients.
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Affiliation(s)
- Michael A Iacocca
- Robarts Research Institute, Western University, London, Ontario, Canada
| | - Joana R Chora
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal.,BioISI, University of Lisbon, Lisbon, Portugal
| | - Alain Carrié
- Hôpitaux Universitaires Pitié-Salpêtrière/Charles-Foix, Molecular and Chromosomal Genetics Center, Obesity and Dyslipidemia Genetics Unit, Assistance Publique-Hôpitaux de Paris, Paris, France.,Inserm, Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié, Sorbonne Université, Paris, France
| | - Tomáš Freiberger
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic.,Ceitec and Medical Faculty, Masaryk University, Brno, London
| | | | - Joep C Defesche
- Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - C Lisa Kurtz
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | | | | | - Steve E Humphries
- Centre for Cardiovascular Genetics, University College of London, London, United Kingdom
| | - Pedro Mata
- Fundacion Hipercolesterolemia Familiar, Madrid, Spain
| | | | - Amanda J Hooper
- PathWest Laboratory Medicine, University of Western Australia, Perth, Australia
| | | | - Pascale Benlian
- CNRS, CHU Lille, UMR 8199 - Integrative Genomics and Metabolic Diseases Modeling, University of Lille, Lille, France
| | | | - John Garcia
- Invitae Corporation, San Francisco, California
| | - Hannah Wand
- Center for Inherited Cardiovascular Disease, Stanford University, Palo Alto, California
| | - Lukáš Tichy
- Center of Molecular Biology and Gene Therapy, University Hospital Brno, Brno, Czech Republic
| | - Eric J Sijbrands
- University Medical Center, Erasmus University, Rotterdam, Netherlands
| | - Robert A Hegele
- Robarts Research Institute, Western University, London, Ontario, Canada
| | - Mafalda Bourbon
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal.,BioISI, University of Lisbon, Lisbon, Portugal
| | - Joshua W Knowles
- FH Foundation, Pasadena, California.,Center for Inherited Cardiovascular Disease, Stanford University, Palo Alto, California
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41
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Berberich AJ, Huot C, Cao H, McIntyre AD, Robinson JF, Wang J, Hegele RA. Copy Number Variation in GCK in Patients With Maturity-Onset Diabetes of the Young. J Clin Endocrinol Metab 2019; 104:3428-3436. [PMID: 30912798 PMCID: PMC6594302 DOI: 10.1210/jc.2018-02574] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/20/2019] [Indexed: 12/20/2022]
Abstract
PURPOSE Next generation sequencing (NGS) methods to diagnose maturity-onset diabetes of the young (MODY), a monogenic autosomal dominant cause of diabetes, do not typically detect large-scale copy number variations (CNVs). New techniques may allow assessment for CNVs using output data from targeted NGS, without requiring additional sequencing. Using this technique, two kindreds of patients presenting with features of MODY were found to bear the same heterozygous large-scale deletion in GCK. METHODS Patients suspected of having MODY but with negative targeted NGS pathogenic variant calling were reanalyzed using the CNV caller tool (VarSeq v1.4.3). Two patients were identified as having a possible heterozygous whole exon deletion affecting exon 1 of GCK. For confirmation and determination of the exact breakpoints, whole exome sequencing followed by Sanger sequencing were used. Familial samples from both affected and nonaffected first-degree relatives were then analyzed for each proband. RESULTS A heterozygous whole-exon deletion spanning 4763 bp affecting the entire exon 1 of GCK was detected in two apparently unrelated patients with clinical features of MODY. This deletion showed segregation concordance across generations in affected and nonaffected family members. CONCLUSIONS Our findings confirm the utility of applying the CNV caller tool to screen for CNVs in GCK from NGS data. In so doing, we identified a deletion of exon 1 of GCK as likely causal for MODY. Our data indicate that incorporating CNV analysis routinely when assessing for MODY via targeted NGS may increase diagnostic yield and reduce false negative genetic testing rates.
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Affiliation(s)
- Amanda J Berberich
- Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Céline Huot
- Department of Pediatrics, CHU Sainte-Justine, University of Montreal, Montreal, Quebec, Canada
| | - Henian Cao
- Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Adam D McIntyre
- Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - John F Robinson
- Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Jian Wang
- Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Robert A Hegele
- Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
- Correspondence and Reprint Requests: Robert A. Hegele, MD, FRCPC, FACP, Robarts Research Institute, 4288A-1151 Richmond Street North, London, Ontario N6A 5B7, Canada. E-mail:
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42
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Gulilat M, Lamb T, Teft WA, Wang J, Dron JS, Robinson JF, Tirona RG, Hegele RA, Kim RB, Schwarz UI. Targeted next generation sequencing as a tool for precision medicine. BMC Med Genomics 2019; 12:81. [PMID: 31159795 PMCID: PMC6547602 DOI: 10.1186/s12920-019-0527-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/13/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Targeted next-generation sequencing (NGS) enables rapid identification of common and rare genetic variation. The detection of variants contributing to therapeutic drug response or adverse effects is essential for implementation of individualized pharmacotherapy. Successful application of short-read based NGS to pharmacogenes with high sequence homology, nearby pseudogenes and complex structure has been previously shown despite anticipated technical challenges. However, little is known regarding the utility of such panels to detect copy number variation (CNV) in the highly polymorphic cytochrome P450 (CYP) 2D6 gene, or to identify the promoter (TA)7 TAA repeat polymorphism UDP glucuronosyltransferase (UGT) 1A1*28. Here we developed and validated PGxSeq, a targeted exome panel for pharmacogenes pertinent to drug disposition and/or response. METHODS A panel of capture probes was generated to assess 422 kb of total coding region in 100 pharmacogenes. NGS was carried out in 235 subjects, and sequencing performance and accuracy of variant discovery validated in clinically relevant pharmacogenes. CYP2D6 CNV was determined using the bioinformatics tool CNV caller (VarSeq). Identified SNVs were assessed in terms of population allele frequency and predicted functional effects through in silico algorithms. RESULTS Adequate performance of the PGxSeq panel was demonstrated with a depth-of-coverage (DOC) ≥ 20× for at least 94% of the target sequence. We showed accurate detection of 39 clinically relevant gene variants compared to standard genotyping techniques (99.9% concordance), including CYP2D6 CNV and UGT1A1*28. Allele frequency of rare or novel variants and predicted function in 235 subjects mirrored findings from large genomic datasets. A large proportion of patients (78%, 183 out of 235) were identified as homozygous carriers of at least one variant necessitating altered pharmacotherapy. CONCLUSIONS PGxSeq can serve as a comprehensive, rapid, and reliable approach for the detection of common and novel SNVs in pharmacogenes benefiting the emerging field of precision medicine.
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Affiliation(s)
- Markus Gulilat
- Division of Clinical Pharmacology, Department of Medicine, Western University, London Health Sciences Centre - University Hospital, 339 Windermere Road, London, ON, N6A 5A5, Canada.,Department of Physiology and Pharmacology, Western University, Medical Sciences Building, Room 216, London, ON, N6A 5C1, Canada
| | - Tyler Lamb
- Department of Physiology and Pharmacology, Western University, Medical Sciences Building, Room 216, London, ON, N6A 5C1, Canada
| | - Wendy A Teft
- Division of Clinical Pharmacology, Department of Medicine, Western University, London Health Sciences Centre - University Hospital, 339 Windermere Road, London, ON, N6A 5A5, Canada
| | - Jian Wang
- Robarts Research Institute, Western University, 1151 Richmond St. N, London, ON, N6A 5B7, Canada
| | - Jacqueline S Dron
- Robarts Research Institute, Western University, 1151 Richmond St. N, London, ON, N6A 5B7, Canada
| | - John F Robinson
- Robarts Research Institute, Western University, 1151 Richmond St. N, London, ON, N6A 5B7, Canada
| | - Rommel G Tirona
- Division of Clinical Pharmacology, Department of Medicine, Western University, London Health Sciences Centre - University Hospital, 339 Windermere Road, London, ON, N6A 5A5, Canada.,Department of Physiology and Pharmacology, Western University, Medical Sciences Building, Room 216, London, ON, N6A 5C1, Canada
| | - Robert A Hegele
- Robarts Research Institute, Western University, 1151 Richmond St. N, London, ON, N6A 5B7, Canada
| | - Richard B Kim
- Division of Clinical Pharmacology, Department of Medicine, Western University, London Health Sciences Centre - University Hospital, 339 Windermere Road, London, ON, N6A 5A5, Canada.,Department of Physiology and Pharmacology, Western University, Medical Sciences Building, Room 216, London, ON, N6A 5C1, Canada
| | - Ute I Schwarz
- Division of Clinical Pharmacology, Department of Medicine, Western University, London Health Sciences Centre - University Hospital, 339 Windermere Road, London, ON, N6A 5A5, Canada.
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43
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Rodríguez-Contreras FJ, Marbán-Calzón M, Vallespín E, Del Pozo Á, Solís-López M, Lobato-Vidal N, Fernández-Elvira M, Del Valle Rex-Romero M, Heath KE, González-Casado I, Campos-Barros Á. Loss of function BMP4 mutation supports the implication of the BMP/TGF-β pathway in the etiology of combined pituitary hormone deficiency. Am J Med Genet A 2019; 179:1591-1597. [PMID: 31120642 DOI: 10.1002/ajmg.a.61201] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 04/23/2019] [Accepted: 04/27/2019] [Indexed: 12/19/2022]
Abstract
Despite BMP4 signaling being critical to Rathke's pouch induction and maintenance during early stages of pituitary development, its implication in the etiology of combined pituitary hormone deficiency (CPHD) and other clinical presentations of congenital hypopituitarism has not yet been definitely demonstrated. We report here the first CPHD patient with a de novo pathogenic loss-of-function variant in BMP4. A 6-year-old boy, with macrocephaly, myopia/astigmatism, mild psychomotor retardation, anterior pituitary hypoplasia and ectopic posterior pituitary, clinically diagnosed with growth hormone deficiency, and central hypothyroidism, was referred for genetic analysis of CPHD. Targeted NGS analysis with a custom panel (n = 310 genes) identified a novel heterozygous de novo nonsense variant, NM_001202.5:c.794G > A, p.(Trp265*) in BMP4, which introduces a premature stop codon in the BMP4 pro-domain, impairing the transcription of the TGF-β mature peptide domain. Additional relevant variants in other genes implicated in pituitary development signaling pathways such as SMAD4 and E2F4 (BMP/TGF-pathway), ALMS1 (NOTCH-pathway), and TSHZ1 (Prokineticin-pathway), were also identified. Our results support the implication of the BMP/TGF-β signaling pathway in the etiology of CPHD and suggest that oligogenic contribution of additional inherited variants may modify the phenotypic expressivity of BMP4 pathogenic variants.
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Affiliation(s)
- Francisco J Rodríguez-Contreras
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain.,Department of Pediatrics, Centro de Salud Galapagar, Madrid, Spain
| | | | - Elena Vallespín
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER; U753), Instituto de Salud Carlos III, Madrid, Spain
| | - Ángela Del Pozo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER; U753), Instituto de Salud Carlos III, Madrid, Spain
| | - Mario Solís-López
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain
| | - Nerea Lobato-Vidal
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain
| | - María Fernández-Elvira
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain
| | - María Del Valle Rex-Romero
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain
| | - Karen E Heath
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER; U753), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Ángel Campos-Barros
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER; U753), Instituto de Salud Carlos III, Madrid, Spain
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Abstract
PURPOSE OF REVIEW DNA copy number variations (CNVs) are large-scale mutations that include deletions and duplications larger than 50 bp in size. In the era when single-nucleotide variations were the major focus of genetic technology and research, CNVs were largely overlooked. However, CNVs clearly underlie a substantial proportion of clinical disorders. Here, we update recent progress in identifying CNVs in dyslipidemias. RECENT FINDINGS Until last year, only the LDLR and LPA genes were appreciated as loci within which clinically relevant CNVs contributed to familial hypercholesterolemia and variation in Lp(a) levels, respectively. Since 2017, next-generation sequencing panels have identified pathogenic CNVs in at least five more genes underlying dyslipidemias, including a PCSK9 whole-gene duplication in familial hypercholesterolemia; LPL, GPIHBP1, and APOC2 deletions in hypertriglyceridemia; and ABCA1 deletions in hypoalphalipoproteinemia. SUMMARY CNVs are an important class of mutation that contribute to the molecular genetic heterogeneity underlying dyslipidemias. Clinical applications of next-generation sequencing technologies need to consider CNVs concurrently with familiar small-scale genetic variation, given the likely implications for improved diagnosis and treatment.
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Affiliation(s)
- Michael A Iacocca
- Robarts Research Institute, and Department of Biochemistry, Schulich School of Medicine and Dentistry
| | - Jacqueline S Dron
- Robarts Research Institute, and Department of Biochemistry, Schulich School of Medicine and Dentistry
| | - Robert A Hegele
- Robarts Research Institute, and Department of Biochemistry, Schulich School of Medicine and Dentistry
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily G, Member 5/blood
- ATP Binding Cassette Transporter, Subfamily G, Member 5/genetics
- ATP Binding Cassette Transporter, Subfamily G, Member 8/blood
- ATP Binding Cassette Transporter, Subfamily G, Member 8/genetics
- Adaptor Proteins, Signal Transducing/blood
- Adaptor Proteins, Signal Transducing/genetics
- Apolipoprotein B-100/blood
- Apolipoprotein B-100/genetics
- Apolipoproteins E/blood
- Apolipoproteins E/genetics
- Cholesterol, LDL/blood
- Databases, Genetic
- Gene Expression
- Genomics/methods
- Humans
- Hyperlipoproteinemia Type II/blood
- Hyperlipoproteinemia Type II/genetics
- Hyperlipoproteinemia Type II/pathology
- Lipid Metabolism/genetics
- Lipoproteins/blood
- Lipoproteins/genetics
- Mutation
- Proprotein Convertase 9/blood
- Proprotein Convertase 9/genetics
- Receptors, LDL/blood
- Receptors, LDL/genetics
- Sterol Esterase/blood
- Sterol Esterase/genetics
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Affiliation(s)
- Ana C Alves
- Unidade de I&D, Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Joana R Chora
- Unidade de I&D, Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Mafalda Bourbon
- Unidade de I&D, Grupo de Investigação Cardiovascular, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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Affiliation(s)
- Robert A Hegele
- Departments of Medicine and Biochemistry, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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Di Filippo M, Collardeau Frachon S, Janin A, Rajan S, Marmontel O, Decourt C, Rubio A, Nony S, Dumont S, Cuerq C, Charrière S, Moulin P, Lachaux A, Hussain MM, Bozon D, Peretti N. Normal serum ApoB48 and red cells vitamin E concentrations after supplementation in a novel compound heterozygous case of abetalipoproteinemia. Atherosclerosis 2019; 284:75-82. [PMID: 30875496 DOI: 10.1016/j.atherosclerosis.2019.02.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/16/2019] [Accepted: 02/19/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS Abetalipoproteinemia (ABL) is a rare recessive monogenic disease due to MTTP (microsomal triglyceride transfer protein) mutations leading to the absence of plasma apoB-containing lipoproteins. Here we characterize a new ABL case with usual clinical phenotype, hypocholesterolemia, hypotriglyceridemia but normal serum apolipoprotein B48 (apoB48) and red blood cell vitamin E concentrations. METHODS Histology and MTP activity measurements were performed on intestinal biopsies. Mutations in MTTP were identified by Sanger sequencing, quantitative digital droplet and long-range PCR. Functional consequences of the variants were studied in vitro using a minigene splicing assay, measurement of MTP activity and apoB48 secretion. RESULTS Intestinal steatosis and the absence of measurable lipid transfer activity in intestinal protein extract supported the diagnosis of ABL. A novel MTTP c.1868G>T variant inherited from the patient's father was identified. This variant gives rise to three mRNA transcripts: one normally spliced, found at a low frequency in intestinal biopsy, carrying the p.(Arg623Leu) missense variant, producing in vitro 65% of normal MTP activity and apoB48 secretion, and two abnormally spliced transcripts resulting in a non-functional MTP protein. Digital droplet PCR and long-range sequencing revealed a previously described c.1067+1217_1141del allele inherited from the mother, removing exon 10. Thus, the patient is compound heterozygous for two dysfunctional MTTP alleles. The p.(Arg623Leu) variant may maintain residual secretion of apoB48. CONCLUSIONS Complex cases of primary dyslipidemia require the use of a cascade of different methodologies to establish the diagnosis in patients with non-classical biological phenotypes and provide better knowledge on the regulation of lipid metabolism.
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Affiliation(s)
- Mathilde Di Filippo
- Laboratoire de Biologie Médicale Multi Sites, Centre de Biologie et de Pathologie Est, Service de Biochimie et Biologie Moléculaire Grand Est, Hospices Civils de Lyon, Bron cedex, F-69677, France; INSERM U1060, Laboratoire Carmen, Université Lyon 1, INRA U1235, INSA de Lyon, CENS, Centre de Recherche en Nutrition Humaine Rhône Alpes, Villeurbanne F-69621, Oullins cedex, F-69921, France.
| | - Sophie Collardeau Frachon
- INSERM U1060, Laboratoire Carmen, Université Lyon 1, INRA U1235, INSA de Lyon, CENS, Centre de Recherche en Nutrition Humaine Rhône Alpes, Villeurbanne F-69621, Oullins cedex, F-69921, France; Laboratoire de Biologie Médicale Multi Sites, Centre de Biologie et de Pathologie Est, Institut de Pathologie, Hospices Civils de Lyon, Bron cedex, F-69677, France.
| | - Alexandre Janin
- Laboratoire de Biologie Médicale Multi Sites, Centre de Biologie et de Pathologie Est, Service de Biochimie et Biologie Moléculaire Grand Est, Hospices Civils de Lyon, Bron cedex, F-69677, France; Université de Lyon, Université Claude Bernard Lyon 1, Institut NeuroMyoGène, CNRS UMR5310, INSERM U1217, Lyon, F-69622, France.
| | - Sujith Rajan
- NYU Winthrop Hospital, 101 Mineola Blvd, Mineola, USA.
| | - Oriane Marmontel
- Laboratoire de Biologie Médicale Multi Sites, Centre de Biologie et de Pathologie Est, Service de Biochimie et Biologie Moléculaire Grand Est, Hospices Civils de Lyon, Bron cedex, F-69677, France; INSERM U1060, Laboratoire Carmen, Université Lyon 1, INRA U1235, INSA de Lyon, CENS, Centre de Recherche en Nutrition Humaine Rhône Alpes, Villeurbanne F-69621, Oullins cedex, F-69921, France.
| | - Charlotte Decourt
- Laboratoire de Biologie Médicale Multi Sites, Centre de Biologie et de Pathologie Est, Service de Biochimie et Biologie Moléculaire Grand Est, Hospices Civils de Lyon, Bron cedex, F-69677, France.
| | - Amandine Rubio
- Gastroentérologie et Nutrition Pédiatrique Hôpital Couple Enfant, CHU de Grenoble Alpes, Grenoble, F-38043, France; Laboratoire de Bioénergétique Fondamentale et Appliquée, INSERM U1055, Univ. Grenoble Alpes, F-38000, France.
| | - Séverine Nony
- Laboratoire de Biologie Médicale Multi Sites, Centre de Biologie et de Pathologie Est, Service de Biochimie et Biologie Moléculaire Grand Est, Hospices Civils de Lyon, Bron cedex, F-69677, France.
| | - Sabrina Dumont
- Laboratoire de Biologie Médicale Multi Sites, Centre de Biologie et de Pathologie Est, Service de Biochimie et Biologie Moléculaire Grand Est, Hospices Civils de Lyon, Bron cedex, F-69677, France.
| | - Charlotte Cuerq
- INSERM U1060, Laboratoire Carmen, Université Lyon 1, INRA U1235, INSA de Lyon, CENS, Centre de Recherche en Nutrition Humaine Rhône Alpes, Villeurbanne F-69621, Oullins cedex, F-69921, France; Laboratoire de Biologie Médicale Multi Sites, Centre de Biologie et de Pathologie Sud, Service de Biochimie et Biologie Moléculaire, Hospices Civils de Lyon, Pierre, Benite cedex, F-69495, France.
| | - Sybil Charrière
- INSERM U1060, Laboratoire Carmen, Université Lyon 1, INRA U1235, INSA de Lyon, CENS, Centre de Recherche en Nutrition Humaine Rhône Alpes, Villeurbanne F-69621, Oullins cedex, F-69921, France; Fédération d'endocrinologie, maladies métaboliques, diabète et nutrition, Hôpital Louis Pradel, Hospices Civils de Lyon, Bron cedex, F-69677, France.
| | - Philippe Moulin
- INSERM U1060, Laboratoire Carmen, Université Lyon 1, INRA U1235, INSA de Lyon, CENS, Centre de Recherche en Nutrition Humaine Rhône Alpes, Villeurbanne F-69621, Oullins cedex, F-69921, France; Fédération d'endocrinologie, maladies métaboliques, diabète et nutrition, Hôpital Louis Pradel, Hospices Civils de Lyon, Bron cedex, F-69677, France.
| | - Alain Lachaux
- Service de Nutrition Pediatrique, Gastroenterologie and Hepatologie, Hôpital Femme Mère Enfants, Hospices Civils de Lyon, Bron cedex, F-69677, France.
| | | | - Dominique Bozon
- Laboratoire de Biologie Médicale Multi Sites, Centre de Biologie et de Pathologie Est, Service de Biochimie et Biologie Moléculaire Grand Est, Hospices Civils de Lyon, Bron cedex, F-69677, France.
| | - Noël Peretti
- INSERM U1060, Laboratoire Carmen, Université Lyon 1, INRA U1235, INSA de Lyon, CENS, Centre de Recherche en Nutrition Humaine Rhône Alpes, Villeurbanne F-69621, Oullins cedex, F-69921, France; Service de Nutrition Pediatrique, Gastroenterologie and Hepatologie, Hôpital Femme Mère Enfants, Hospices Civils de Lyon, Bron cedex, F-69677, France.
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48
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Schwarz UI, Gulilat M, Kim RB. The Role of Next-Generation Sequencing in Pharmacogenetics and Pharmacogenomics. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a033027. [PMID: 29844222 DOI: 10.1101/cshperspect.a033027] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Inherited genetic variations in pharmacogenetic loci are widely acknowledged as important determinants of phenotypic differences in drug response, and may be actionable in the clinic. However, recent studies suggest that a considerable number of novel rare variants in pharmacogenes likely contribute to a still unexplained fraction of the observed interindividual variability. Next-generation sequencing (NGS) represents a rapid, relatively inexpensive, large-scale DNA sequencing technology with potential relevance as a comprehensive pharmacogenetic genotyping platform to identify genetic variation related to drug therapy. However, many obstacles remain before the clinical use of NGS-based test results, including technical challenges, functional interpretation, and strict requirements for diagnostic tests. Advanced computational analyses, high-throughput screening methodologies, and generation of shared resources with cell-based and clinical information will facilitate the integration of NGS data into candidate genotyping approaches, likely enhancing future drug phenotype predictions in patients.
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Affiliation(s)
- Ute I Schwarz
- Division of Clinical Pharmacology, Department of Medicine, Western University, London, Ontario N6A 5A5, Canada.,Department of Physiology and Pharmacology, Western University, London, Ontario N6A 5A5, Canada
| | - Markus Gulilat
- Department of Physiology and Pharmacology, Western University, London, Ontario N6A 5A5, Canada
| | - Richard B Kim
- Division of Clinical Pharmacology, Department of Medicine, Western University, London, Ontario N6A 5A5, Canada.,Department of Physiology and Pharmacology, Western University, London, Ontario N6A 5A5, Canada
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49
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Berberich AJ, Hegele RA. The role of genetic testing in dyslipidaemia. Pathology 2019; 51:184-192. [DOI: 10.1016/j.pathol.2018.10.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 01/28/2023]
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50
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Severe hypertriglyceridemia is primarily polygenic. J Clin Lipidol 2019; 13:80-88. [DOI: 10.1016/j.jacl.2018.10.006] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 10/13/2018] [Accepted: 10/16/2018] [Indexed: 12/22/2022]
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