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Constantin AT, Streata I, Covăcescu MS, Riza AL, Roșca I, Delia C, Tudor LM, Dorobanțu Ș, Dragoș A, Ristea D, Ioana M, Gherghina I. Genetic Testing for Familial Hypercholesterolemia in a Pediatric Group: A Romanian Showcase. Diagnostics (Basel) 2023; 13:1988. [PMID: 37370883 DOI: 10.3390/diagnostics13121988] [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: 05/16/2023] [Revised: 05/29/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
Familial hypercholesterolemia (FH) is a genetic disease marked by high levels of LDL-cholesterol. This condition has long-term clinical implications, such as cardiovascular events, that are evident during adult life. Here, we report on a single-center cross-sectional showcase study of genetic testing for FH in a Romanian pediatric group. Genetic testing for FH was performed on 20 Romanian pediatric patients, 10 boys and 10 girls, admitted with LDL-cholesterol levels over 130 mg/mL to the National Institute for Mother and Child Health "Alesssandrescu-Rusescu" in 2020. Genetic testing was performed using the Illumina TruSight Cardio panel. We identified pathogenic/likely pathogenic variants that could explain the phenotype in 5/20 cases. The involved genes were LDLR and APOB. Clinical signs that suggest the diagnosis of FH are scarce for the pediatric patient, although it can be diagnosed early during childhood by lipid panel screening. Prevention could prove lifesaving for some of these patients.
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Affiliation(s)
- Andreea Teodora Constantin
- Pediatrics Department, National Institute for Mother and Child Health "Alessandrescu-Rusescu", 020395 Bucharest, Romania
- Pediatrics Department, Faculty of Medicine, University of Medicine and Pharmacy "Carol Davila", 020021 Bucharest, Romania
| | - Ioana Streata
- Genetics Department, University of Medicine and Pharmacy, 200349 Craiova, Romania
- Regional Center for Medical Genetics Dolj, 200642 Craiova, Romania
| | - Mirela Silvia Covăcescu
- Pediatrics Department, National Institute for Mother and Child Health "Alessandrescu-Rusescu", 020395 Bucharest, Romania
- Pediatrics Department, Faculty of Medicine, University of Medicine and Pharmacy "Carol Davila", 020021 Bucharest, Romania
| | - Anca Lelia Riza
- Genetics Department, University of Medicine and Pharmacy, 200349 Craiova, Romania
- Regional Center for Medical Genetics Dolj, 200642 Craiova, Romania
| | - Ioana Roșca
- Faculty of Midwifery and Nursery, University of Medicine and Pharmacy "Carol Davila", 020021 Bucharest, Romania
- Neonatology Department, Clinical Hospital of Obstetrics and Gynecology "Prof. Dr. P.Sârbu", 060251 Bucharest, Romania
| | - Corina Delia
- Pediatrics Department, National Institute for Mother and Child Health "Alessandrescu-Rusescu", 020395 Bucharest, Romania
- Faculty of Biology, University of Bucharest, 030018 Bucharest, Romania
| | - Lucia Maria Tudor
- Pediatrics Department, National Institute for Mother and Child Health "Alessandrescu-Rusescu", 020395 Bucharest, Romania
- Pediatrics Department, Faculty of Medicine, University of Medicine and Pharmacy "Carol Davila", 020021 Bucharest, Romania
| | - Ștefania Dorobanțu
- Genetics Department, University of Medicine and Pharmacy, 200349 Craiova, Romania
- Regional Center for Medical Genetics Dolj, 200642 Craiova, Romania
| | - Adina Dragoș
- Genetics Department, University of Medicine and Pharmacy, 200349 Craiova, Romania
- Regional Center for Medical Genetics Dolj, 200642 Craiova, Romania
| | - Diana Ristea
- Regional Center for Medical Genetics Dolj, 200642 Craiova, Romania
| | - Mihai Ioana
- Genetics Department, University of Medicine and Pharmacy, 200349 Craiova, Romania
- Regional Center for Medical Genetics Dolj, 200642 Craiova, Romania
| | - Ioan Gherghina
- Pediatrics Department, Faculty of Medicine, University of Medicine and Pharmacy "Carol Davila", 020021 Bucharest, Romania
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Vlad CE, Foia LG, Popescu R, Popa I, Aanicai R, Reurean-Pintilei D, Toma V, Florea L, Kanbay M, Covic A. Molecular Genetic Approach and Evaluation of Cardiovascular Events in Patients with Clinical Familial Hypercholesterolemia Phenotype from Romania. J Clin Med 2021; 10:jcm10071399. [PMID: 33807407 PMCID: PMC8036385 DOI: 10.3390/jcm10071399] [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] [Received: 03/04/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 12/13/2022] Open
Abstract
This study identifies the genetic background of familial hypercholesterolemia (FH) patients in Romania and evaluates the association between mutations and cardiovascular events. We performed a prospective observational study of 61 patients with a clinical diagnosis of FH selected based on Dutch Lipid Clinic Network (DLCN) and Simon Broome score between 2017 and 2020. Two techniques were used to identify mutations: multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing. The mutation rate was 37.7%, i.e., 23 patients with mutations were identified, of which 7 subjects had pathogenic mutations and 16 had polymorphisms. Moreover, 10 variants of the low-density lipoprotein receptor (LDLR) gene were identified in 22 patients, i.e., one variant of the proprotein convertase subtilisin/kexin type 9 (PCSK9) gene in six patients, and one variant of the apolipoprotein B (APOB) gene in three patients. Of the LDLR gene variants, four were LDLR pathogenic mutations (c.81C > G, c.502G > A, c.1618G > A mutations in exon 2, exon 4, exon 11, and exon 13–15 duplication). The PCSK9 and APOB gene variants were benign mutations. The pathogenic LDLR mutations were significant predictors of the new cardiovascular events, and the time interval for new cardiovascular events occurrence was significantly decreased, compared to FH patients without mutations. In total, 12 variants were identified, with four pathogenic variants identified in the LDLR gene, whereas 62.3% of the study population displayed no pathological mutations.
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Affiliation(s)
- Cristiana-Elena Vlad
- Faculty of Medicine, “Grigore T Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania; (C.-E.V.); (R.P.); (I.P.); (R.A.); (D.R.-P.); (V.T.); (L.F.); (A.C.)
- Department of Nephrology-Internal Medicine, “Dr. C.I. Parhon” Clinical Hospital, Carol I Street, No 50, 700503 Iasi, Romania
| | - Liliana Georgeta Foia
- Faculty of Medicine, “Grigore T Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania; (C.-E.V.); (R.P.); (I.P.); (R.A.); (D.R.-P.); (V.T.); (L.F.); (A.C.)
- Department of Biochemistry, “Sf. Spiridon” Clinical County Hospital, Independentei Street, 700111 Iasi, Romania
- Correspondence: ; Tel.: +40-744704452
| | - Roxana Popescu
- Faculty of Medicine, “Grigore T Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania; (C.-E.V.); (R.P.); (I.P.); (R.A.); (D.R.-P.); (V.T.); (L.F.); (A.C.)
| | - Ioana Popa
- Faculty of Medicine, “Grigore T Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania; (C.-E.V.); (R.P.); (I.P.); (R.A.); (D.R.-P.); (V.T.); (L.F.); (A.C.)
| | - Ruxandra Aanicai
- Faculty of Medicine, “Grigore T Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania; (C.-E.V.); (R.P.); (I.P.); (R.A.); (D.R.-P.); (V.T.); (L.F.); (A.C.)
| | - Delia Reurean-Pintilei
- Faculty of Medicine, “Grigore T Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania; (C.-E.V.); (R.P.); (I.P.); (R.A.); (D.R.-P.); (V.T.); (L.F.); (A.C.)
| | - Vasilica Toma
- Faculty of Medicine, “Grigore T Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania; (C.-E.V.); (R.P.); (I.P.); (R.A.); (D.R.-P.); (V.T.); (L.F.); (A.C.)
| | - Laura Florea
- Faculty of Medicine, “Grigore T Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania; (C.-E.V.); (R.P.); (I.P.); (R.A.); (D.R.-P.); (V.T.); (L.F.); (A.C.)
- Department of Nephrology-Internal Medicine, “Dr. C.I. Parhon” Clinical Hospital, Carol I Street, No 50, 700503 Iasi, Romania
| | - Mehmet Kanbay
- Department of Medicine, Division of Nephrology, Koc University School of Medicine, 34450 Istanbul, Turkey;
| | - Adrian Covic
- Faculty of Medicine, “Grigore T Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania; (C.-E.V.); (R.P.); (I.P.); (R.A.); (D.R.-P.); (V.T.); (L.F.); (A.C.)
- Department of Nephrology-Internal Medicine, “Dr. C.I. Parhon” Clinical Hospital, Carol I Street, No 50, 700503 Iasi, Romania
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Huang CC, Charng MJ. Genetic Diagnosis of Familial Hypercholesterolemia in Asia. Front Genet 2020; 11:833. [PMID: 32793292 PMCID: PMC7393677 DOI: 10.3389/fgene.2020.00833] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/09/2020] [Indexed: 12/31/2022] Open
Abstract
Familial hypercholesterolemia (FH) is a common genetic disease with an incidence of about 1 in 200-500 individuals. Genetic mutations markedly elevate low-density lipoprotein cholesterol and atherosclerotic cardiovascular disease (ASCVD) in FH patients. With advances in clinical diagnosis and genetic testing, more genetic mutations have been detected, including those in low-density lipoprotein receptor (LDLR), apolipoprotein B (APOB), proprotein convertase subtilisin/kexin type 9 (PCSK9), and so on. Globally, most FH patients remain undiagnosed, untreated, or inappropriately treated. Recently, there was a Global Call to Action by the Global Familial Hypercholesterolemia Community to reduce the health burden of FH. Asia, despite being the most populous continent with half of the global population, has low FH detection rates compared to Western countries. Therefore, we aimed to review the current status of FH genetic diagnosis in Asia to understand the gaps in FH diagnosis and management in this region.
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Affiliation(s)
- Chin-Chou Huang
- Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan.,Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan
| | - Min-Ji Charng
- Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
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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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Benito-Vicente A, Siddiqi H, Uribe KB, Jebari S, Galicia-Garcia U, Larrea-Sebal A, Stef M, Ostolaza H, Palacios L, Martin C. p.(Asp47Asn) and p.(Thr62Met): non deleterious LDL receptor missense variants functionally characterized in vitro. Sci Rep 2018; 8:16614. [PMID: 30413722 PMCID: PMC6226515 DOI: 10.1038/s41598-018-34715-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/22/2018] [Indexed: 11/24/2022] Open
Abstract
Familial Hypercholesterolemia (FH) is a common genetic disorder caused most often by mutations in the Low Density Lipoprotein Receptor gene (LDLr) leading to high blood cholesterol levels, and ultimately to development of premature coronary heart disease. Genetic analysis and subsequent cascade screening in relatives allow diagnosis of FH at early stage, especially relevant to diagnose children. So far, more than 2300 LDLr variants have been described but only a minority of them have been functionally analysed to evaluate their pathogenicity in FH. Thus, identifying pathogenic mutations in LDLr is a long-standing challenge in the field. In this study, we investigated in vitro the activity p.(Asp47Asn) and p.(Thr62Met) LDLr variants, both in the LR1 region. We used CHO-ldlA7 transfected cells with plasmids carrying p.(Asp47Asn) or p.(Thr62Met) LDLr variants to analyse LDLr expression by FACS and immunoblotting, LDL binding and uptake was determined by FACS and analysis of mutation effects was assessed in silico. The in vitro activity assessment of p.(Asp47Asn) and p.(Thr62Met) LDLr variants shows a fully functional LDL binding and uptake activities. Therefore indicating that the three of them are non-pathogenic LDLr variants. These findings also emphasize the importance of in vitro functional LDLr activity studies to optimize the genetic diagnosis of FH avoiding the report of non-pathogenic variants and possible misdiagnose in relatives if cascade screening is carried out.
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Affiliation(s)
- A Benito-Vicente
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, Apdo. 644, 48080, Bilbao, Spain
| | - H Siddiqi
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, Apdo. 644, 48080, Bilbao, Spain
| | - K B Uribe
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, Apdo. 644, 48080, Bilbao, Spain
| | - S Jebari
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, Apdo. 644, 48080, Bilbao, Spain
| | - U Galicia-Garcia
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, Apdo. 644, 48080, Bilbao, Spain
| | - A Larrea-Sebal
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, Apdo. 644, 48080, Bilbao, Spain
| | - M Stef
- Progenika Biopharma, a Grifols Company, Derio, Spain
| | - H Ostolaza
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, Apdo. 644, 48080, Bilbao, Spain
| | - L Palacios
- Progenika Biopharma, a Grifols Company, Derio, Spain
| | - C Martin
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, Apdo. 644, 48080, Bilbao, Spain.
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Chiou KR, Charng MJ. Detection of common sequence variations of familial hypercholesterolemia in Taiwan using DNA mass spectrometry. J Clin Lipidol 2017; 11:386-393.e6. [DOI: 10.1016/j.jacl.2016.12.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/21/2016] [Accepted: 12/30/2016] [Indexed: 01/18/2023]
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The use of targeted exome sequencing in genetic diagnosis of young patients with severe hypercholesterolemia. Sci Rep 2016; 6:36823. [PMID: 27830735 PMCID: PMC5103295 DOI: 10.1038/srep36823] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/18/2016] [Indexed: 12/17/2022] Open
Abstract
Familial hypercholesterolemia (FH) is an autosomal dominant disorder. Although genetic testing is an important tool for detecting FH-causing mutations in patients, diagnostic methods for young patients with severe hypercholesterolemia are understudied. This study compares the target exome sequencing (TES) technique with the DNA resequencing array technique on young patients with severe hypercholesterolemia. A total of 20 unrelated patients (mean age 14.8 years) with total cholesterol > 10 mmol/L were included. 12 patient samples were processed by DNA resequencing array, 14 patient samples were processed by TES, and 6 patient samples were processed by both methods. Functional characterization of novel mutations was performed by flow cytometry. The mutation detection rate (MDR) of DNA resequencing array was 75%, while the MDR of TES was 100%. A total of 27 different mutations in the LDLR were identified, including 3 novel mutations and 8 mutations with previously unknown pathogenicity. Functional characterization of c.673delA, c.1363delC, p.Leu575Phe and p.Leu582Phe variants found that all of them are pathogenic. Additionally, 7 patients were diagnosed with Heterozygous FH (HeFH) in which lipid levels were significantly higher than common HeFH patients. This data indicates that TES is a very efficient tool for genetic diagnosis in young patients with severe hypercholesterolemia.
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Pandey S, Leider M, Khan M, Grammatopoulos DK. Cascade Screening for Familial Hypercholesterolemia: PCR Methods with Melting-Curve Genotyping for the Targeted Molecular Detection of Apolipoprotein B and LDL Receptor Gene Mutations to Identify Affected Relatives. J Appl Lab Med 2016; 1:109-118. [PMID: 33626794 DOI: 10.1373/jalm.2016.020610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 06/30/2016] [Indexed: 11/06/2022]
Abstract
BACKGROUND A key objective of the UK National Institute for Health and Care Excellence (NICE) pathway for diagnosis of familial hypercholesterolemia (FH) is the identification of affected relatives of index cases through cascade screening. At present, there is no systematic appraisal of available methodological options to identify the appropriate diagnostic testing protocol that would allow cost-effective cascade genetic screening. The majority of FH-causing mutations identified in the LDL receptor (LDLR) or apolipoprotein B (APOB) genes are single-nucleotide changes. This pattern of mutations suggests that PCR methods using melting curve-based genotyping might offer a convenient methodological approach for screening relatives. METHODS We developed and validated one-tube PCR methods for the mutations APOB c.10580G>A (p.Arg3527Gln), LDLR c.1474G>A (p.Asp492Asn), and c.2054C>T (p.Pro685Leu) and 3 novel LDLR mutations identified in the Coventry and Warwickshire population: LDLR c.1567G>C (p.Val523Leu), c.487dupC (p.Gln163Profs17), and c.647G>C (p.Cys216Ser). RESULTS These methods successfully amplified target sequence from genomic DNA extracted from either peripheral blood or saliva. They also demonstrated acceptable analytical performance characteristics (specificity of amplification, repeatability, and reproducibility) over a wide range of DNA concentrations and purity. This approach was used for cascade testing of relatives of index FH cases with confirmed mutations and identified family members with high plasma LDL cholesterol as heterozygous for disruptive alleles. CONCLUSIONS Our study generates proof-of-concept evidence of methods suitable for detecting single nucleotide substitutions and insertions that can deliver reliable, easy, low-cost, and rapid family screening of FH patients and can be adopted by nonspecialist molecular diagnostic laboratories.
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Affiliation(s)
- Sarojini Pandey
- Department of Clinical Biochemistry, University Hospital Coventry and Warwickshire, Coventry, UK
| | | | - Mike Khan
- Department of Endocrinology and Diabetes, University Hospital Coventry and Warwickshire, Coventry, UK
| | - Dimitris K Grammatopoulos
- Department of Clinical Biochemistry, University Hospital Coventry and Warwickshire, Coventry, UK.,Division of Translational and Systems Medicine, Warwick Medical School, Coventry, UK
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9
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Genetic diagnosis of familial hypercholesterolemia in Han Chinese. J Clin Lipidol 2016; 10:490-6. [DOI: 10.1016/j.jacl.2016.01.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 01/22/2016] [Accepted: 01/26/2016] [Indexed: 12/26/2022]
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10
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Wang Y, Cui Y, Zhou X, Han J. Development of a high-throughput resequencing array for the detection of pathogenic mutations in osteogenesis imperfecta. PLoS One 2015; 10:e0119553. [PMID: 25742658 PMCID: PMC4350936 DOI: 10.1371/journal.pone.0119553] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 01/30/2015] [Indexed: 01/29/2023] Open
Abstract
Objective Osteogenesis imperfecta (OI) is a rare inherited skeletal disease, characterized by bone fragility and low bone density. The mutations in this disorder have been widely reported to be on various exonal hotspots of the candidate genes, including COL1A1, COL1A2, CRTAP, LEPRE1, and FKBP10, thus creating a great demand for precise genetic tests. However, large genome sizes make the process daunting and the analyses, inefficient and expensive. Therefore, we aimed at developing a fast, accurate, efficient, and cheaper sequencing platform for OI diagnosis; and to this end, use of an advanced array-based technique was proposed. Method A CustomSeq Affymetrix Resequencing Array was established for high-throughput sequencing of five genes simultaneously. Genomic DNA extraction from 13 OI patients and 85 normal controls and amplification using long-range PCR (LR-PCR) were followed by DNA fragmentation and chip hybridization, according to standard Affymetrix protocols. Hybridization signals were determined using GeneChip Sequence Analysis Software (GSEQ). To examine the feasibility, the outcome from new resequencing approach was validated by conventional capillary sequencing method. Result Overall call rates using resequencing array was 96–98% and the agreement between microarray and capillary sequencing was 99.99%. 11 out of 13 OI patients with pathogenic mutations were successfully detected by the chip analysis without adjustment, and one mutation could also be identified using manual visual inspection. Conclusion A high-throughput resequencing array was developed that detects the disease-associated mutations in OI, providing a potential tool to facilitate large-scale genetic screening for OI patients. Through this method, a novel mutation was also found.
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Affiliation(s)
- Yao Wang
- Shandong Academy of Medical Sciences, Shandong Medical Biotechnological Center, Key Laboratory for Biotech Drugs of the Ministry of Health, Ji’nan, Shandong, China
- Shandong Institute of Endocrine and Metabolic Diseases, Shandong Academy of Medical Sciences, Ji’nan, Shandong, China
| | - Yazhou Cui
- Shandong Academy of Medical Sciences, Shandong Medical Biotechnological Center, Key Laboratory for Biotech Drugs of the Ministry of Health, Ji’nan, Shandong, China
| | - Xiaoyan Zhou
- Shandong Academy of Medical Sciences, Shandong Medical Biotechnological Center, Key Laboratory for Biotech Drugs of the Ministry of Health, Ji’nan, Shandong, China
| | - Jinxiang Han
- Shandong Academy of Medical Sciences, Shandong Medical Biotechnological Center, Key Laboratory for Biotech Drugs of the Ministry of Health, Ji’nan, Shandong, China
- * E-mail:
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Halcox J, Misra A. Type 2 diabetes mellitus, metabolic syndrome, and mixed dyslipidemia: how similar, how different, and how to treat? Metab Syndr Relat Disord 2014; 13:1-21. [PMID: 25402738 DOI: 10.1089/met.2014.0049] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Individuals with mixed atherogenic dyslipidemia, type 2 diabetes mellitus (T2DM), and metabolic syndrome are at high risk of developing cardiovascular disease (CVD) and can often benefit greatly from preventive lifestyle and medical interventions. These conditions typically co-exist in an individual, and the lipid profiles associated with them have several features in common. The worldwide prevalence of T2DM, atherogenic dyslipidemia, and metabolic syndrome is increasing, particularly in southern Asia and the Middle East. Statins can lower low-density lipoprotein-cholesterol and reduce the risk of CVD in these high-risk individuals, but there is a residual risk of CVD associated with additional lipid abnormalities, such as high levels of triglycerides and low levels of high-density lipoprotein cholesterol. These abnormalities are commonly found in patients with T2DM and metabolic syndrome. Additional lipid-modifying therapies that target these abnormalities, such as fibrates and omega-3 polyunsaturated fatty acids, may be able to improve lipid profiles and further reduce the risk of CVD in these patients.
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Affiliation(s)
- Julian Halcox
- 1 University of Swansea , Singleton Park, Swansea, United Kingdom
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Faiz F, Nguyen LT, van Bockxmeer FM, Hooper AJ. Genetic screening to improve the diagnosis of familial hypercholesterolemia. ACTA ACUST UNITED AC 2014. [DOI: 10.2217/clp.14.32] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Bengtson HN, Kolpashchikov DM. A differential fluorescent receptor for nucleic acid analysis. Chembiochem 2014; 15:228-31. [PMID: 24339354 PMCID: PMC4066444 DOI: 10.1002/cbic.201300657] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Indexed: 01/28/2023]
Abstract
Differential receptors use an array of sensors to recognize analytes. Each sensor in the array can recognize not one, but several analytes with different rates, so a single analyte triggers a response of several sensors in the array. The receptor thus produces a pattern of signals that is unique for each analyte, thereby enabling identification of a specific analyte by producing a "fingerprint" pattern. We applied this approach for the analysis of DNA sequences of Mycobacterium tuberculosis strains that differ by single nucleotide substitutions in the 81-bp hot-spot region that imparts rifampin resistance. The technology takes advantage of the new multicomponent, selfassembling sensor, which produces a fluorescent signal in the presence of specific DNA sequences. A differential fluorescent receptor (DFR) contained an array of three such sensors and differentiated at least eight DNA sequences. The approach requires only one molecular-beacon-like fluorescent reporter, which can be used by all three sensors. The DFR developed in this study represents a cost-efficient alternative to molecular diagnostic technologies that use fluorescent hybridization probes.
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Affiliation(s)
- Hillary N. Bengtson
- Chemistry Department and Burnett School of Biomedical Sciences University of Central Florida 4000 Central Florida Blvd, Orlando, FL 32816 (USA)
| | - Dmitry M. Kolpashchikov
- Chemistry Department and Burnett School of Biomedical Sciences University of Central Florida 4000 Central Florida Blvd, Orlando, FL 32816 (USA)
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Faiz F, Allcock RJ, Hooper AJ, van Bockxmeer FM. Detection of variations and identifying genomic breakpoints for large deletions in the LDLR by Ion Torrent semiconductor sequencing. Atherosclerosis 2013; 230:249-55. [PMID: 24075752 DOI: 10.1016/j.atherosclerosis.2013.07.050] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 07/24/2013] [Accepted: 07/29/2013] [Indexed: 01/16/2023]
Abstract
OBJECTIVES The aims of this study were to 1) compare LDLR variant detection between Ion Torrent Personal Genome Machine (PGM) sequencing and conventional methods used for familial hypercholesterolaemia (FH) diagnosis i.e. exon-by-exon sequence analysis and multiplex ligation-dependent probe amplification (MLPA) and 2) identify genomic breakpoints for 12 cases of large deletions in LDLR previously identified by MLPA. METHODS Thirty FH patient samples were selected, 22 with mutations previously determined. Primers were designed and optimised to generate six amplicons covering the entire LDLR and sequenced on a PGM. An additional twelve samples carrying MLPA variants were sequenced on the PGM followed by Sanger sequencing to establish the breakpoints. RESULTS A total of 2179 LDLR variants were identified in the 30 samples, with 383 variants in the region sequenced that was common to both PGM and Sanger methods. Three discrepancies were identified; two of these were identified by visual inspection of the BAM files, whilst the remaining discrepancy was likely an artefact of the PCR approach. Approximate genomic breakpoints for the 12 MLPA variants were identified using PGM sequencing, and Sanger sequencing of these regions established causative breakpoints. Eleven different rearrangements/mutational events were found, with eight out of eleven occurring in Alus. Two of the three samples with exons 2-6del had identical breakpoints. Two samples with exons 11-12del had unique breakpoints, indicating separate ancestral origin or mutational events. CONCLUSIONS This study showed that Ion Torrent PGM sequencing is an accurate and efficient method to detect LDLR variants while providing additional information such as genomic breakpoints.
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Affiliation(s)
- Fathimath Faiz
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, Australia
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Feddersen S, Overgaard M, Nybo M. Duplication of exon 7-12 in the low-density lipoprotein receptor gene in three Danish patients with familial hypercholesterolemia. J Clin Lipidol 2013; 7:174-7. [PMID: 23415438 DOI: 10.1016/j.jacl.2012.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 11/02/2012] [Accepted: 11/19/2012] [Indexed: 11/18/2022]
Abstract
Familial hypercholesterolemia (FH) is one of the most frequent single-gene disorders; nevertheless, it is commonly underdiagnosed and undertreated. To increase the number of individuals diagnosed and treated for FH, an ongoing discovery of novel FH mutations is necessary as a prerequisite to implement good nationwide genetic FH screening strategies. Here we report on the finding of a seldom exon 7-12 duplication in the low-density lipoprotein receptor gene of three Danish patients with FH.
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Affiliation(s)
- Søren Feddersen
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark.
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Abstract
PURPOSE OF REVIEW Familial hypercholesterolemia is an underdiagnosed autosomal codominant genetic condition associated with significantly increased risk of early cardiovascular disease when untreated. Early diagnosis and treatment decrease the excess risk, and strategies for identification of affected individuals are being developed worldwide. This review will discuss, from a clinician's perspective, some of the issues involved in identifying people with familial hypercholesterolemia. RECENT FINDINGS Several sets of recommendations have been published outlining the strategies for identification of people with familial hypercholesterolemia in various countries and regions. These include Australasia, Europe, and the USA. SUMMARY Continuing efforts to find the best methods for identification of people with familial hypercholesterolemia are needed to ensure that this very treatable inherited condition is diagnosed early enough to prevent the development of atherosclerotic vascular disease.
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Affiliation(s)
- Annie Haase
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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Abstract
Familial hypercholesterolaemia (FH) is an autosomal dominant disorder characterised by increased plasma concentrations of low density lipoprotein (LDL) cholesterol leading to atherosclerosis and premature coronary heart disease (CHD) and death. The clinical diagnosis of FH is based on a personal and family history, physical examination findings and LDL-cholesterol concentrations. FH is primarily caused by mutations in the LDL-receptor gene (LDLR), and less frequently by mutations in genes for APOB and the more recently identified PCSK9. Lifestyle modification and pharmacotherapy can delay or prevent the onset of CHD in FH. It is estimated that only 20% of cases have been diagnosed in Australia and that the majority are inadequately treated. Screening options for FH include population screening (of children or adults), targeted screening of patients with premature CHD and their relatives, or opportunistic screening such as flagging laboratory lipid reports. Cascade screening, a form of targeted screening, is an ethically acceptable, cost-effective strategy for the identification of FH. However, for screening to be successful, medical practitioners need to be aware of the signs and diagnosis of FH and the benefits of early treatment.
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Phan JH, Quo CF, Wang MD. Cardiovascular genomics: a biomarker identification pipeline. ACTA ACUST UNITED AC 2012; 16:809-22. [PMID: 22614726 DOI: 10.1109/titb.2012.2199570] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Genomic biomarkers are essential for understanding the underlying molecular basis of human diseases such as cardiovascular disease. In this review, we describe a biomarker identification pipeline for cardiovascular disease, which includes 1) high-throughput genomic data acquisition, 2) preprocessing and normalization of data, 3) exploratory analysis, 4) feature selection, 5) classification, and 6) interpretation and validation of candidate biomarkers. We review each step in the pipeline, presenting current and widely used bioinformatics methods. Furthermore, we analyze several publicly available cardiovascular genomics datasets to illustrate the pipeline. Finally, we summarize the current challenges and opportunities for further research.
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Affiliation(s)
- John H Phan
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA.
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Sakai H, Suzuki S, Mizuguchi T, Imoto K, Yamashita Y, Doi H, Kikuchi M, Tsurusaki Y, Saitsu H, Miyake N, Masuda M, Matsumoto N. Rapid detection of gene mutations responsible for non-syndromic aortic aneurysm and dissection using two different methods: resequencing microarray technology and next-generation sequencing. Hum Genet 2011; 131:591-9. [PMID: 22001912 DOI: 10.1007/s00439-011-1105-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 10/04/2011] [Indexed: 12/15/2022]
Abstract
Aortic aneurysm and/or dissection (AAD) is a life-threatening condition, and several syndromes are known to be related to AAD. In this study, two new technologies, resequencing array technology (ResAT) and next-generation sequencing (NGS), were used to analyze eight genes associated with syndromic AAD in 70 patients with non-syndromic AAD. Eighteen sequence variants were detected using both ResAT and NGS. In addition one of these sequence variants was detected by ResAT only and two additional variants by NGS only. Three of the 18 variants are likely to be pathogenic (in 4.3% of AAD patients and in 8.6% of a subset of patients with thoracic AAD), highlighting the importance of genetic analysis in non-syndromic AAD. ResAT and NGS similarly detected most, but not all, of the variants. Resequencing array technology was a rapid and efficient method for detecting most nucleotide substitutions, but was unable to detect short insertions/deletions, and it is impractical to update custom arrays frequently. Next-generation sequencing was able to detect almost all types of mutation, but requires improved informatics methods.
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Affiliation(s)
- Haruya Sakai
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Yokohama, Japan
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