26 results on '"Whittall RA"'
Search Results
2. DEVELOPMENT OF AN AFFORDABLE, SENSITIVE AND RAPID SCREENING METHOD FOR MUTATION DETECTION IN UK FH SUBJECTS
- Author
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Scartezini, M, Hubbart, C, Whittall, RA, Neil, HA, and Humphrics, SE
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Internal Medicine ,General Medicine ,Cardiology and Cardiovascular Medicine - Published
- 2008
3. Spectrum of LDL receptor gene mutations in heterozygous familial hypercholesterolemia
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Day, INM, primary, Whittall, RA, additional, O'Dell, SD, additional, Haddad, L, additional, Bolla, MK, additional, Gudnason, V, additional, and Humphries, SE, additional
- Published
- 1997
- Full Text
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4. Spectrum of LDL receptor gene mutations in heterozygous familial hypercholesterolemia
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Day, Inm, Whittall, Ra, Odell, Sd, Haddad, L., Bolla, Mk, Vilmundur Gudnason, and Humphries, Se
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Genetics ,Genetics (clinical)
5. Refinement of Variant Selection for the LDL Cholesterol Genetic Risk Score in the Diagnosis of the Polygenic Form of Clinical Familial Hypercholesterolemia and Replication in Samples from 6 Countries
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Mary Aderayo Bamimore, Jeanine E. Roeters van Lennep, Giuliana Fortunato, Vasiliki Mollaki, Eran Leitersdorf, Antonietta D'Angelo, Sonia Shah, Euridiki Drogari, Philippa J. Talmud, Steve E. Humphries, Albert Wiegman, Mahtab Sharifi, Małgorzata Waluś-Miarka, Maria Nicoletta D'Agostino, KaWah Li, Paolo Rubba, Monique T. Mulder, Ros Whittall, Jackie A. Cooper, Ronen Durst, Marta Futema, Olivia Goldberg, Robert A. Hegele, Eric J.G. Sijbrands, Joep C. Defesche, John C. Whittaker, Internal Medicine, Futema, M, Shah, S, Cooper, Ja, Li, K, Whittall, Ra, Sharifi, M, Goldberg, O, Drogari, E, Mollaki, V, Wiegman, A, Defesche, J, D'Agostino, MARIA NICOLETTA, D'Angelo, A, Rubba, PAOLO OSVALDO FEDERICO, Fortunato, Giuliana, Walu?? Miarka, M, Hegele, Ra, Aderayo Bamimore, M, Durst, R, Leitersdorf, E, Mulder, Mt, Roeters van Lennep, Je, Sijbrands, Ej, Whittaker, Jc, Talmud, Pj, Humphries, S. E., Paediatric Metabolic Diseases, ACS - Amsterdam Cardiovascular Sciences, and Experimental Vascular Medicine
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Adult ,Male ,Canada ,Multifactorial Inheritance ,Adolescent ,Clinical Biochemistry ,Single-nucleotide polymorphism ,Familial hypercholesterolemia ,Biology ,medicine.disease_cause ,Bioinformatics ,Polymorphism, Single Nucleotide ,Article ,Cohort Studies ,Hyperlipoproteinemia Type II ,Young Adult ,chemistry.chemical_compound ,Risk Factors ,Polymorphism (computer science) ,medicine ,Humans ,Israel ,Allele ,Child ,Gene ,Alleles ,Apolipoproteins B ,Genetics ,Mutation ,Cholesterol ,Serine Endopeptidases ,Biochemistry (medical) ,Case-control study ,Cholesterol, LDL ,Middle Aged ,medicine.disease ,Europe ,ROC Curve ,Receptors, LDL ,chemistry ,Case-Control Studies ,lipids (amino acids, peptides, and proteins) ,Female ,Proprotein Convertases ,Proprotein Convertase 9 - Abstract
BACKGROUND Familial hypercholesterolemia (FH) is an autosomal-dominant disorder caused by mutations in 1 of 3 genes. In the 60% of patients who are mutation negative, we have recently shown that the clinical phenotype can be associated with an accumulation of common small-effect LDL cholesterol (LDL-C)-raising alleles by use of a 12–single nucleotide polymorphism (12-SNP) score. The aims of the study were to improve the selection of SNPs and replicate the results in additional samples. METHODS We used ROC curves to determine the optimum number of LDL-C SNPs. For replication analysis, we genotyped patients with a clinical diagnosis of FH from 6 countries for 6 LDL-C-associated alleles. We compared the weighted SNP score among patients with no confirmed mutation (FH/M–), those with a mutation (FH/M+), and controls from a UK population sample (WHII). RESULTS Increasing the number of SNPs to 33 did not improve the ability of the score to discriminate between FH/M– and controls, whereas sequential removal of SNPs with smaller effects/lower frequency showed that a weighted score of 6 SNPs performed as well as the 12-SNP score. Metaanalysis of the weighted 6-SNP score, on the basis of polymorphisms in CELSR2 (cadherin, EGF LAG 7-pass G-type receptor 2), APOB (apolipoprotein B), ABCG5/8 [ATP-binding cassette, sub-family G (WHITE), member 5/8], LDLR (low density lipoprotein receptor), and APOE (apolipoprotein E) loci, in the independent FH/M– cohorts showed a consistently higher score in comparison to the WHII population (P < 2.2 × 10−16). Modeling in individuals with a 6-SNP score in the top three-fourths of the score distribution indicated a >95% likelihood of a polygenic explanation of their increased LDL-C. CONCLUSIONS A 6-SNP LDL-C score consistently distinguishes FH/M– patients from healthy individuals. The hypercholesterolemia in 88% of mutation-negative patients is likely to have a polygenic basis.
- Published
- 2015
6. Refinement of variant selection for the LDL cholesterol genetic risk score in the diagnosis of the polygenic form of clinical familial hypercholesterolemia and replication in samples from 6 countries.
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Futema M, Shah S, Cooper JA, Li K, Whittall RA, Sharifi M, Goldberg O, Drogari E, Mollaki V, Wiegman A, Defesche J, D'Agostino MN, D'Angelo A, Rubba P, Fortunato G, Waluś-Miarka M, Hegele RA, Aderayo Bamimore M, Durst R, Leitersdorf E, Mulder MT, Roeters van Lennep JE, Sijbrands EJ, Whittaker JC, Talmud PJ, and Humphries SE
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- Adolescent, Adult, Alleles, Apolipoproteins B genetics, Canada, Case-Control Studies, Child, Cholesterol, LDL genetics, Cohort Studies, Europe, Female, Humans, Hyperlipoproteinemia Type II blood, Israel, Male, Middle Aged, Mutation, Proprotein Convertase 9, Proprotein Convertases genetics, ROC Curve, Receptors, LDL genetics, Risk Factors, Serine Endopeptidases genetics, Young Adult, Cholesterol, LDL blood, Hyperlipoproteinemia Type II genetics, Multifactorial Inheritance genetics, Polymorphism, Single Nucleotide
- Abstract
Background: Familial hypercholesterolemia (FH) is an autosomal-dominant disorder caused by mutations in 1 of 3 genes. In the 60% of patients who are mutation negative, we have recently shown that the clinical phenotype can be associated with an accumulation of common small-effect LDL cholesterol (LDL-C)-raising alleles by use of a 12-single nucleotide polymorphism (12-SNP) score. The aims of the study were to improve the selection of SNPs and replicate the results in additional samples., Methods: We used ROC curves to determine the optimum number of LDL-C SNPs. For replication analysis, we genotyped patients with a clinical diagnosis of FH from 6 countries for 6 LDL-C-associated alleles. We compared the weighted SNP score among patients with no confirmed mutation (FH/M-), those with a mutation (FH/M+), and controls from a UK population sample (WHII)., Results: Increasing the number of SNPs to 33 did not improve the ability of the score to discriminate between FH/M- and controls, whereas sequential removal of SNPs with smaller effects/lower frequency showed that a weighted score of 6 SNPs performed as well as the 12-SNP score. Metaanalysis of the weighted 6-SNP score, on the basis of polymorphisms in CELSR2 (cadherin, EGF LAG 7-pass G-type receptor 2), APOB (apolipoprotein B), ABCG5/8 [ATP-binding cassette, sub-family G (WHITE), member 5/8], LDLR (low density lipoprotein receptor), and APOE (apolipoprotein E) loci, in the independent FH/M- cohorts showed a consistently higher score in comparison to the WHII population (P < 2.2 × 10(-16)). Modeling in individuals with a 6-SNP score in the top three-fourths of the score distribution indicated a >95% likelihood of a polygenic explanation of their increased LDL-C., Conclusions: A 6-SNP LDL-C score consistently distinguishes FH/M- patients from healthy individuals. The hypercholesterolemia in 88% of mutation-negative patients is likely to have a polygenic basis., (© 2014 American Association for Clinical Chemistry.)
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- 2015
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7. Whole exome sequencing of familial hypercholesterolaemia patients negative for LDLR/APOB/PCSK9 mutations.
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Futema M, Plagnol V, Li K, Whittall RA, Neil HA, Seed M, Bertolini S, Calandra S, Descamps OS, Graham CA, Hegele RA, Karpe F, Durst R, Leitersdorf E, Lench N, Nair DR, Soran H, Van Bockxmeer FM, and Humphries SE
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- Apolipoproteins B genetics, Genome-Wide Association Study, Humans, Mutation genetics, Proprotein Convertase 9, Proprotein Convertases genetics, Receptors, LDL genetics, Serine Endopeptidases genetics, Cholesterol, LDL genetics, Hyperlipoproteinemia Type II genetics
- Abstract
Background: Familial hypercholesterolaemia (FH) is an autosomal dominant disease of lipid metabolism, which leads to early coronary heart disease. Mutations in LDLR, APOB and PCSK9 can be detected in 80% of definite FH (DFH) patients. This study aimed to identify novel FH-causing genetic variants in patients with no detectable mutation., Methods and Results: Exomes of 125 unrelated DFH patients were sequenced, as part of the UK10K project. First, analysis of known FH genes identified 23 LDLR and two APOB mutations, and patients with explained causes of FH were excluded from further analysis. Second, common and rare variants in genes associated with low-density lipoprotein cholesterol (LDL-C) levels in genome-wide association study (GWAS) meta-analysis were examined. There was no clear rare variant association in LDL-C GWAS hits; however, there were 29 patients with a high LDL-C SNP score suggestive of polygenic hypercholesterolaemia. Finally, a gene-based burden test for an excess of rare (frequency <0.005) or novel variants in cases versus 1926 controls was performed, with variants with an unlikely functional effect (intronic, synonymous) filtered out., Conclusions: No major novel locus for FH was detected, with no gene having a functional variant in more than three patients; however, an excess of novel variants was found in 18 genes, of which the strongest candidates included CH25H and INSIG2 (p<4.3×10(-4) and p<3.7×10(-3), respectively). This suggests that the genetic cause of FH in these unexplained cases is likely to be very heterogeneous, which complicates the diagnostic and novel gene discovery process., (Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.)
- Published
- 2014
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8. Analysis of the frequency and spectrum of mutations recognised to cause familial hypercholesterolaemia in routine clinical practice in a UK specialist hospital lipid clinic.
- Author
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Futema M, Whittall RA, Kiley A, Steel LK, Cooper JA, Badmus E, Leigh SE, Karpe F, Neil HA, and Humphries SE
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- Adult, Aged, Cholesterol blood, Cohort Studies, Female, Genetic Testing, Humans, Male, Middle Aged, Mutation, Outpatient Clinics, Hospital, Proprotein Convertase 9, Triglycerides blood, United Kingdom, Apolipoproteins B genetics, Hyperlipoproteinemia Type II genetics, Proprotein Convertases genetics, Receptors, LDL genetics, Serine Endopeptidases genetics
- Abstract
Aim: To determine the frequency and spectrum of mutations causing Familial Hypercholesterolaemia (FH) in patients attending a single UK specialist hospital lipid clinic in Oxford and to identify characteristics contributing to a high mutation detection rate., Methods: 289 patients (272 probands) were screened sequentially over a 2-year period for mutations in LDLR, APOB and PCSK9 using standard molecular genetic techniques. The Simon Broome (SB) clinical diagnostic criteria were used to classify patients and a separate cohort of 409 FH patients was used for replication., Results: An FH-causing mutation was found in 101 unrelated patients (LDLR = 54 different mutations, APOB p.(Arg3527Gln) = 10, PCSK9 p.(Asp374Tyr) = 0). In the 60 SB Definite FH patients the mutation detection rate was 73% while in the 142 with Possible FH the rate was significantly lower (27%, p < 0.0001), but similar (14%, p = 0.06) to the 70 in whom there was insufficient data to make a clinical diagnosis. The mutation detection rate varied significantly (p = 9.83 × 10(-5)) by untreated total cholesterol (TC) levels (25% in those <8.1 mmol/l and 74% in those >10.0 mmol/l), and by triglyceride levels (20% in those >2.16 mmol/l and 60% in those <1.0 mmol/l (p = 0.0005)), with both effects confirmed in the replication sample (p for trend = 0.0001 and p = 1.8 × 10(-6) respectively). There was no difference in the specificity or sensitivity of the SB criteria versus the Dutch Lipid Clinic Network score in identifying mutation carriers (AROC respectively 0.73 and 0.72, p = 0.68)., Conclusions: In this genetically heterogeneous cohort of FH patients the mutation detection rate was significantly dependent on pre-treatment TC and triglyceride levels., (Copyright © 2013 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.)
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- 2013
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9. Use of targeted exome sequencing as a diagnostic tool for Familial Hypercholesterolaemia.
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Futema M, Plagnol V, Whittall RA, Neil HA, and Humphries SE
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- Adaptor Proteins, Signal Transducing genetics, Apolipoproteins B genetics, Computational Biology methods, DNA Copy Number Variations, Humans, Mutation, Proprotein Convertase 9, Proprotein Convertases genetics, Receptors, LDL genetics, Serine Endopeptidases genetics, Exome, High-Throughput Nucleotide Sequencing, Hyperlipoproteinemia Type II diagnosis, Hyperlipoproteinemia Type II genetics
- Abstract
Background: Familial Hypercholesterolaemia (FH) is an autosomal dominant disease, caused by mutations in LDLR, APOB or PCSK9, which results in high levels of LDL-cholesterol (LDL-C) leading to early coronary heart disease. An autosomal recessive form of FH is also known, due to homozygous mutations in LDLRAP1. This study assessed the utility of an exome capture method and deep sequencing in FH diagnosis., Methods: Exomes of 48 definite FH patients, with no mutation detected by current methods, were captured by Agilent Human All Exon 50Mb assay and sequenced on the Illumina HiSeq 2000 platform. Variants were called by GATK and SAMtools., Results: The mean coverage of FH genes varied considerably (PCSK9=23x, LDLRAP1=36x, LDLR=56x and APOB=93x). Exome sequencing detected 17 LDLR mutations, including three copy number variants, two APOB mutations, missed by the standard techniques, two LDLR novel variants likely to be FH-causing, and five APOB variants of uncertain effect. Two variants called in PCSK9 were not confirmed by Sanger sequencing. One heterozygous mutation was found in LDLRAP1., Conclusions: High-throughput DNA sequencing demonstrated its efficiency in well-covered DNA regions, in particular LDLR. This highly automated technology is proving to be effective for heterogeneous diseases and may soon replace laborious conventional methods. However, the poor coverage of gene promoters and repetitive, or GC-rich sequences, remains problematic, and validation of all identified variants is currently required.
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- 2012
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10. Low-density lipoprotein receptor gene familial hypercholesterolemia variant database: update and pathological assessment.
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Usifo E, Leigh SE, Whittall RA, Lench N, Taylor A, Yeats C, Orengo CA, Martin AC, Celli J, and Humphries SE
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- Humans, Mutation, Protein Isoforms, Databases as Topic, Genetic Variation, Hyperlipoproteinemia Type II genetics, Receptors, LDL genetics
- Abstract
Familial hypercholesterolemia (FH) is caused predominately by variants in the low-density lipoprotein receptor gene (LDLR). We report here an update of the UCL LDLR variant database to include variants reported in the literature and in-house between 2008 and 2010, transfer of the database to LOVDv.2.0 platform (https://grenada.lumc.nl/LOVD2/UCL-Heart/home.php?select_db=LDLR) and pathogenicity analysis. The database now contains over 1288 different variants reported in FH patients: 55% exonic substitutions, 22% exonic small rearrangements (<100 bp), 11% large rearrangements (>100 bp), 2% promoter variants, 10% intronic variants and 1 variant in the 3' untranslated sequence. The distribution and type of newly reported variants closely matches that of the 2008 database, and we have used these variants (n= 223) as a representative sample to assess the utility of standard open access software (PolyPhen, SIFT, refined SIFT, Neural Network Splice Site Prediction Tool, SplicePort and NetGene2) and additional analyses (Single Amino Acid Polymorphism database, analysis of conservation and structure and Mutation Taster) for pathogenicity prediction. In combination, these techniques have enabled us to assign with confidence pathogenic predictions to 8/8 in-frame small rearrangements and 8/9 missense substitutions with previously discordant results from PolyPhen and SIFT analysis. Overall, we conclude that 79% of the reported variants are likely to be disease causing., (© 2012 The Authors Annals of Human Genetics © 2012 Blackwell Publishing Ltd/University College London.)
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- 2012
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11. Novel and recurrent LDLR gene mutations in Pakistani hypercholesterolemia patients.
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Ahmed W, Ajmal M, Sadeque A, Whittall RA, Rafiq S, Putt W, Khawaja A, Imtiaz F, Ahmed N, Azam M, Humphries SE, and Qamar R
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- Adult, Amino Acid Sequence, Female, Humans, Hyperlipoproteinemia Type II diagnosis, Male, Middle Aged, Molecular Sequence Data, Mutation, Pakistan, Pedigree, Protein Structure, Secondary, Receptors, LDL chemistry, Young Adult, Hyperlipoproteinemia Type II genetics, Receptors, LDL genetics
- Abstract
The majority of patients with the autosomal dominant disorder familial hypercholesterolemia (FH) carry novel mutations in the low density lipoprotein receptor (LDLR) that is involved in cholesterol regulation. In different populations the spectrum of mutations identified is quite different and to date there have been only a few reports of the spectrum of mutations in FH patients from Pakistan. In order to identify the causative LDLR variants the gene was sequenced in a Pakistani FH family, while high resolution melting analysis followed by sequencing was performed in a panel of 27 unrelated sporadic hypercholesterolemia patients. In the family a novel missense variant (c.1916T > G, p.(V639G)) in exon 13 of LDLR was identified in the proband. The segregation of the identified nucleotide change in the family and carrier status screening in a group of 100 healthy subjects was done using restriction fragment length polymorphism analysis. All affected members of the FH family carried the variant and none of the non-affected members nor any of the healthy subjects. In one of the sporadic cases, two sequence changes were detected in exon 9, one of these was a recurrent missense variant (c.1211C > T; p.T404I), while the other was a novel substitution mutation (c.1214 A > C; N405T). In order to define the allelic status of this double heterozygous individual, PCR amplified fragments were cloned and sequenced, which identified that both changes occurred on the same allele. In silico tools (PolyPhen and SIFT) were used to predict the effect of the variants on the protein structure, which predicted both of these variants to have deleterious effect. These findings support the view that there will be a novel spectrum of mutations causing FH in patients with hypercholesterolaemia from Pakistan.
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- 2012
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12. Development of a high-resolution melting method for mutation detection in familial hypercholesterolaemia patients.
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Whittall RA, Scartezini M, Li K, Hubbart C, Reiner Z, Abraha A, Neil HA, Dedoussis G, and Humphries SE
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- Adolescent, Adult, Aged, Child, Preschool, Female, Genetic Testing methods, Heterozygote, Homozygote, Humans, Hyperlipoproteinemia Type II diagnosis, Infant, Male, Middle Aged, Mutation, Polymerase Chain Reaction methods, Polymorphism, Single Nucleotide, Sensitivity and Specificity, DNA Mutational Analysis methods, Hyperlipoproteinemia Type II genetics, Nucleic Acid Denaturation
- Abstract
Aims: Current screening methods, such as single strand conformational polymorphism (SSCP) and denaturing high performance liquid chromatography (dHPLC) that are used for detecting mutations in familial hypercholesterolaemia (FH) subjects are time consuming, costly and only 80-90% sensitive. Here we have tested high-resolution melt (HRM) analysis for mutation detection using the Rotor-Gene(6000) realtime rotary analyser. Methods and subjects Polymerase chain reaction and melt conditions (HRM) for 23 fragments of the LDL-receptor gene, a region of exon 26 in the APOB gene (including p.R3527Q) and exon 7 of the PCSK9 gene (including p.D374Y) were optimized. Two double stranded DNA saturating dyes, LC-Green and Syto9, were compared for sensitivity. Eighty-two samples with known mutations were used as positive controls. Twenty-eight Greek FH heterozygous patients and two homozygous patients from the UK and Croatia were screened., Results: HRM was able to identify all the positive control mutations tested, with similar results with either dye. Eight different variations were found in 17 of the 28 Greek FH patients for an overall detection rate of 61%: c.41delT (1), p.W165X (1), p.C173R (3), p.S286R (2), p.V429M (4), p.G549D (4), p.V613I (1), and a previously unreported mutation p.F694V (1) which is predicted to be FH-causing by functional algorithms. Mutations were found in both the homozygous patients; p.Q92X (Croatia) and p.Y489C (UK); both patients were homozygous for their respective mutations., Conclusions: HRM is a sensitive, robust technique that could significantly reduce the time and cost of screening for mutations in a clinical setting.
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- 2010
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13. Healthy individuals carrying the PCSK9 p.R46L variant and familial hypercholesterolemia patients carrying PCSK9 p.D374Y exhibit lower plasma concentrations of PCSK9.
- Author
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Humphries SE, Neely RD, Whittall RA, Troutt JS, Konrad RJ, Scartezini M, Li KW, Cooper JA, Acharya J, and Neil A
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- Apolipoproteins B genetics, Heterozygote, Humans, Hydroxymethylglutaryl-CoA Reductase Inhibitors therapeutic use, Hyperlipoproteinemia Type II drug therapy, Male, Middle Aged, Mutation, Proprotein Convertase 9, Proprotein Convertases, Receptors, LDL genetics, Reference Values, Serine Endopeptidases blood, Hyperlipoproteinemia Type II genetics, Serine Endopeptidases genetics
- Abstract
Background: We measured plasma PCSK9 concentrations in healthy men with a PCSK9 (proprotein convertase subtilisin/kexin type 9) loss-of-function variant (p.R46L), in statin-treated patients with a clinical diagnosis of familial hypercholesterolemia (FH) and carrying a PCSK9 gain-of-function mutation (p.D374Y), and in statin-treated patients with FH due to different genetic causes., Methods: PCSK9 was measured with a previously described ELISA., Results: In 81 healthy middle-aged Caucasian men, the PCSK9 concentration was significantly associated with the concentrations of total cholesterol (r = 0.42; P < 0.0001), LDL cholesterol (r = 0.34; P = 0.01), and triglycerides (r = 0.25; P = 0.02). In p.R46L carriers, mean (SD) concentrations of PCSK9 were 15% lower than in RR individuals [65.5 microg/L (21.6 microg/L) vs 77.5 microg/L (18.2 microg/L); P = 0.03]. In patients with the p.D374Y variant (n = 7), the mean PCSK9 concentration was significantly lower than in the combined group of patients with an LDLR (low density lipoprotein receptor) mutation (n = 25), an APOB [apolipoprotein B (including Ag(x) antigen)] variant encoding p.R3527Q (n = 6), or no detectable mutation (n = 14) [96.4 microg/L (42.5 microg/L) vs 151.6 microg/L (69.6 microg/L); P = 0.02]. Two of the 14 patients with no mutation had PCSK9 concentrations below the mean for p.D374Y carriers; sequencing of the PCSK9 gene and promoter revealed no mutations. Among 409 FH patients, we identified 6 carriers of the promoter variant -287G>A (1.5%), a frequency similar to that (1.0%) previously reported for 2772 healthy men in the UK. In neither group was the -287G>A variant associated with differences in lipid traits., Conclusions: The loss-of-function p.R46L variant is associated with the expected lower concentrations of circulating PCSK9; the gain-of-function p.D374Y mutation is also associated with lower concentrations, presumably because of the higher affinity of this variant for the LDL receptor and its more rapid clearance. In treated FH patients, a low plasma PCSK9 concentration does not appear to be a useful screening tool for identifying novel PCSK9 mutations.
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- 2009
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14. Update and analysis of the University College London low density lipoprotein receptor familial hypercholesterolemia database.
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Leigh SE, Foster AH, Whittall RA, Hubbart CS, and Humphries SE
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- Amino Acid Substitution, Animals, Evolution, Molecular, Gene Rearrangement, Humans, Medicine in Literature, Polymorphism, Genetic, Databases, Genetic standards, Hyperlipoproteinemia Type II genetics, Receptors, LDL genetics
- Abstract
Familial hypercholesterolemia (FH) (OMIM 143890) is most commonly caused by variations in the LDLR gene which encodes the receptor for Low Density Lipoprotein (LDL) cholesterol particles. We have updated the University College London (UCL) LDLR FH database (http://www.ucl.ac.uk/ldlr) by adding variants reported in the literature since 2001, converting existing entries to standard nomenclature, and transferring the database to the Leiden Open Source Variation Database (LOVD) platform. As of July 2007 the database listed 1066 unique LDLR gene events. Sixty five percent (n = 689) of the variants are DNA substitutions, 24% (n = 260) small DNA rearrangements (<100bp) and 11% (n = 117) large DNA rearrangements (>100bp), proportions which are similar to those reported in the 2001 database (n = 683, 62%, 24% and 14% respectively). The DNA substitutions and small rearrangements occur along the length of the gene, with 24 in the promoter region, 86 in intronic sequences and 839 in the exons (93 nonsense variants, 499 missense variants and 247 small rearrangements). These occur in all exons, with the highest proportion (20%) in exon 4 (186/949); this exon is the largest and codes for the critical ligand binding region, where any missense variant is likely to be pathogenic. Using the PolyPhen and SIFT prediction computer programmes 87% of the missense variants are predicted to have a deleterious effect on LDLR activity, and it is probable that at least 48% of the remainder are also pathogenic, but their role in FH causation requires confirmation by in vitro or family studies.
- Published
- 2008
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15. The PCSK9 gene R46L variant is associated with lower plasma lipid levels and cardiovascular risk in healthy U.K. men.
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Scartezini M, Hubbart C, Whittall RA, Cooper JA, Neil AH, and Humphries SE
- Subjects
- Cholesterol blood, Cholesterol, LDL blood, Coronary Disease blood, Female, Gene Frequency, Genetic Predisposition to Disease, Genotype, Humans, Hyperlipoproteinemia Type II genetics, Male, Middle Aged, Polymorphism, Genetic, Proprotein Convertase 9, Proprotein Convertases, Risk Factors, Coronary Disease genetics, Lipids blood, Serine Endopeptidases genetics
- Abstract
In the present study, we have determined the relative frequency of the R46L, I474V and E670G variants in the PCSK9 (protein convertase subtilisin/kexin type 9) gene and its association with plasma lipid levels and CHD (coronary heart disease) in healthy U.K. men and patients with clinically defined definite FH (familial hypercholesterolaemia). Genotypes were determined using PCR and restriction enzyme digestion in 2444 healthy middle-aged (50-61 years) men from the prospective NPHSII (Second Northwick Park Heart Study), with 275 CHD events (15 years of follow-up), and in 597 U.K. FH patients from the Simon Broome Register. In the NPHSII healthy men, the R46L genotype distribution was in Hardy-Weinberg equilibrium and the frequency of 46L was 0.010 [95% CI (confidence interval), 0.007-0.013], with one man homozygous for the 46L allele. There was significant association of the 46L allele with lower mean (S.D.) total cholesterol [5.74 (1.01) mmol/l for RR compared with 5.26+/-1.03 mmol/l for RL; P=0.001], apolipoprotein B [0.87 (0.24) g/l for RR compared with 0.75 (0.26) g/l for RL; P<0.0001] and low-density lipoprotein cholesterol [4.01 (0.95) mmol/l for RR compared with 3.62 (0.97) mmol/l for RL; P=0.02]) levels, after adjustment for age, general medical practice, smoking, body mass index and systolic blood pressure. As expected, 46L carriers had a low risk of definite or possible CHD [hazard ratio, 0.46 (95% CI, 0.11-1.84)], but this was not statistically significant (P=0.27). Two other common PCSK9 variants I474V [V allele frequency, 0.179 (95% CI, 0.17-0.19)] and E670G [G allele frequency, 0.034 (CI, 0.03-0.04)] were not associated with any significant effects on lipid levels or CHD risk. In FH patients, the frequency of 46L was 0.003 (95% CI, 0.00-0.01), which was significantly lower (P=0.037) than the healthy subjects. In the four FH patients carrying 46L, mean untreated total cholesterol levels were not different (P=0.91) in carriers and non-carriers (median, 10.3 mmol/l compared with 10.2 mmol/l respectively, after adjustment for age, gender and mutation type). In conclusion, the PCSK9 46L allele is more frequent in healthy U.K. men than in FH patients and is strongly associated with a protective plasma lipid profile risk for CHD. Its low frequency (approx. 2% carriers) means that it does not make a major contribution to determining population CHD risk in the U.K.
- Published
- 2007
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16. Genetic causes of familial hypercholesterolaemia in patients in the UK: relation to plasma lipid levels and coronary heart disease risk.
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Humphries SE, Whittall RA, Hubbart CS, Maplebeck S, Cooper JA, Soutar AK, Naoumova R, Thompson GR, Seed M, Durrington PN, Miller JP, Betteridge DJ, and Neil HA
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- Adult, Apolipoproteins B genetics, Cholesterol, HDL blood, Cholesterol, LDL blood, Coronary Disease blood, DNA Mutational Analysis, Female, Gene Frequency, Humans, Hyperlipoproteinemia Type II blood, Linkage Disequilibrium, Male, Middle Aged, Mutation genetics, Odds Ratio, Polymorphism, Single-Stranded Conformational, Proprotein Convertase 9, Proprotein Convertases, Receptors, LDL genetics, Risk Factors, Serine Endopeptidases genetics, United Kingdom, Coronary Disease genetics, Hyperlipoproteinemia Type II genetics, Lipids blood
- Abstract
Aims: To determine the relative frequency of mutations in three different genes (low-density lipoprotein receptor (LDLR), APOB, PCSK9), and to examine their effect in development of coronary heart disease (CHD) in patients with clinically defined definite familial hypercholesterolaemia in UK., Patients and Methods: 409 patients with familial hypercholesterolaemia patients (158 with CHD) were studied. The LDLR was partially screened by single-strand conformational polymorphism (SSCP) (exons 3, 4, 6-10 and 14) and by using a commercial kit for gross deletions or rearrangements. APOB (p.R3500Q) and PCSK9 (p.D374Y) were detected by specific assays. Coding exons of PCSK9 were screened by SSCP., Results: Mutations were detected in 253 (61.9%), Patients: 236 (57.7%) carried LDLR, 10 (2.4%) carried APOB p.Q3500 and 7 (1.7%) PCSK9 p.Y374. No additional mutations were identified in PCSK9. After adjusting for age, sex, smoking and systolic blood pressure, compared to those with no detectable mutation, the odds ratio of having CHD in those with an LDLR mutation was 1.84 (95% CI 1.10 to 3.06), for APOB 3.40 (0.71 to 16.36), and for PCSK9 19.96 (1.88 to 211.5; p = 0.001 overall). The high risk in patients carrying LDLR and PCSK9 p.Y374 was partly explained by their higher pretreatment cholesterol levels (LDLR, PCSK9 and no mutation, 10.29 (1.85), 13.12 and 9.85 (1.90) mmol/l, respectively, p = 0.001). The post-statin treatment lipid profile in PCSK9 p.Y374 carriers was worse than in patients with no identified mutation (LDL-C, 6.77 (1.82) mmol/l v 4.19 (1.26) mmol/l, p = 0.001, HDL-C 1.09 (0.27) mmol/l v 1.36 (0.36) mmol/l, p = 0.03)., Conclusions: The higher CHD risk in patients carrying PCSK9 p.Y347 or a detected LDLR mutation supports the usefulness of DNA testing in the diagnosis and management of patients with familial hypercholesterolaemia. Mutations in PCSK9 appear uncommon in patients with familial hypercholesterolaemia in UK.
- Published
- 2006
- Full Text
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17. The A370T variant (StuI polymorphism) in the LDL receptor gene is not associated with plasma lipid levels or cardiovascular risk in UK men.
- Author
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Vieira JR, Whittall RA, Cooper JA, Miller GJ, and Humphries SE
- Subjects
- Body Mass Index, Coronary Disease diagnosis, Coronary Disease genetics, Deoxyribonucleases, Type II Site-Specific, Genotype, Homozygote, Humans, Hyperlipoproteinemia Type II blood, Hyperlipoproteinemia Type II diagnosis, Hyperlipoproteinemia Type II genetics, Lipids analysis, Male, Middle Aged, Risk Factors, Stroke diagnosis, Stroke genetics, United Kingdom, Coronary Disease epidemiology, Lipids blood, Polymorphism, Single Nucleotide, Receptors, LDL genetics
- Abstract
Over 800 different missense mutations in the low density lipoprotein (LDL) receptor gene (LDLR) have been identified in patients with familial hypercholesterolaemia (FH). Only two of them, including the Alanine to Threonine change at position 370 (A370T), have been discovered in FH patients but do not cause FH. The frequency of the 370T allele has been reported worldwide to be between 0.022 and 0.070, with no clear association with high cholesterol levels or risk for coronary heart disease (CHD) and stroke. To explore this relationship in more detail we have determined this genotype in 2,659 healthy middle-aged (50-61 years) men participating in the prospective Second Northwick Park Heart Study, with 236 CHD and 67 stroke incident events. The genotype distribution was in Hardy-Weinberg equilibrium and in the no-event group the frequency of 370T was 0.046 (95% CI 0.040-0.052). Overall, there was no significant association of the 370T allele with any measured plasma lipid trait, and there was no difference in genotype distribution or allele frequency between the no-event and CHD (0.059; 95% CI 0.040-0.085) or stroke (0.037; 95% CI 0.012-0.085) groups ( p= 0.18 and 0.65, respectively). There was evidence for significant interaction ( p= 0.006) between body mass index (BMI) and genotype on CHD risk, with 370A homozygotes showing the expected higher CHD risk for those with higher BMI, whilst risk for 370T allele carriers was highest in men in the lowest tertile of BMI. The explanation for this association is unclear, and may simply be chance. Thus, these data confirm the absence of a significant impact of the A370T polymorphism on LDL receptor function, at least as measured by the effect on plasma lipid levels and CHD risk.
- Published
- 2006
- Full Text
- View/download PDF
18. Mutation scanning by meltMADGE: validations using BRCA1 and LDLR, and demonstration of the potential to identify severe, moderate, silent, rare, and paucimorphic mutations in the general population.
- Author
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Alharbi KK, Aldahmesh MA, Spanakis E, Haddad L, Whittall RA, Chen XH, Rassoulian H, Smith MJ, Sillibourne J, Ball NJ, Graham NJ, Briggs PJ, Simpson IA, Phillips DI, Lawlor DA, Ye S, Humphries SE, Cooper C, Smith GD, Ebrahim S, Eccles DM, and Day IN
- Subjects
- Breast Neoplasms genetics, Electrophoresis, Polyacrylamide Gel methods, Female, Genes, BRCA1, Humans, Hyperlipoproteinemia Type II genetics, Male, Polymorphism, Genetic, Population Surveillance, Receptors, LDL genetics, Sensitivity and Specificity, DNA Mutational Analysis methods, Mutation
- Abstract
We have developed a mutation-scanning approach suitable for whole population screening for unknown mutations. The method, meltMADGE, combines thermal ramp electrophoresis with MADGE to achieve suitable cost efficiency and throughput. The sensitivity was tested in blind trials using 54 amplicons representing the BRCA1 coding region and a panel of 94 unrelated family breast cancer risk consultands previously screened in a clinical diagnostic laboratory. All 10 common polymorphisms, 15/15 previously identified disease-causing mutations, and three previously untested single base changes were identified. Assays of LDLR exons 3 and 8 were validated in 460 familial hypercholesteremics and detected 8/9 known variants. We then applied the exon 3 assay in several DNA banks representing approximately 8000 subjects with known cholesterol values and applied both assays in one DNA bank (n = 3600). In exon 3 we identified one previously reported moderate mutation, P84S (n = 1), also associated with moderate hypercholesteremia in this subject; an unreported silent variant, N76N (n = 1); and known severe hypercholesteremia splice mutation 313+1G-->A (n = 2). Around exon 8 we identified a paucimorphism (n = 35) at the splice site 1061-8T-->C (known to be in complete linkage disequilibrium with T705I) and unreported sequence variants 1186+11G-->A (n = 1) and D335N G-->A (n = 1). The cholesterol value for D335N was on the 96.2 percentile and for T705I, 2/35 carriers were above the 99th percentile. Thus, variants with predicted severe, moderate, and no effect were identified at the population level. In contrast with case collections, CpG mutations predominated. MeltMADGE will enable definition of the full population spectrum of rare, paucimorphic, severe, moderate (forme fruste), and silent mutations and effects.
- Published
- 2005
- Full Text
- View/download PDF
19. Three novel mutations in the apolipoprotein E gene in a sample of individuals with type 2 diabetes mellitus.
- Author
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Stephens JW, Sozen MM, Whittall RA, Caslake MJ, Bedford D, Acharya J, Hurel SJ, and Humphries SE
- Subjects
- Apolipoproteins E blood, Genotype, Humans, Isoelectric Focusing, Mutation, Phenotype, Sequence Analysis, DNA, Apolipoproteins E genetics, Diabetes Mellitus, Type 2 genetics
- Abstract
Background: Apolipoprotein E (apoE) is found in association with triglyceride-rich lipoproteins and is the ligand for the removal of these particles from the plasma. Genetic variations in exon 4 lead to three common gene variants: E2, E3, and E4., Methods: We performed apoE genotyping in 765 individuals with type 2 diabetes., Results: We identified three new variant heteroduplex patterns. Sequencing of these variants revealed three novel mutations that were related to biochemical and clinical characteristics. One mutation produced a frameshift at amino acid position 166, which predicted termination of protein synthesis. This individual had a heteroduplex pattern and sequence of E3E3, which was associated with a change in the plasma isoelectric focusing pattern and a 70% lower plasma concentration of apoE compared with healthy individuals. The other mutations were both single base changes. A CGC>CAC change at amino acid position 150 predicted a substitution of Arg>His. This individual had a heteroduplex pattern and sequence of E2E2, which was not associated with major changes in plasma lipids or apoE concentration. The third individual had a CGC>CCC base change at amino acid position 114, which predicted an Arg>Pro change. This person had a heteroduplex pattern and sequence of E3E3, higher plasma total cholesterol, and moderately decreased plasma apoE., Conclusions: The frequency of new mutations in this sample (1 in 255) is higher than that of a healthy population (1 in 7900). Further screening for common apoE gene variants in individuals at risk for dyslipidemia may reveal abnormal heteroduplex patterns and uncover further mutations in this important lipid-regulating gene.
- Published
- 2005
- Full Text
- View/download PDF
20. R643G polymorphism in PECAM-1 influences transendothelial migration of monocytes and is associated with progression of CHD and CHD events.
- Author
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Elrayess MA, Webb KE, Bellingan GJ, Whittall RA, Kabir J, Hawe E, Syvänne M, Taskinen MR, Frick MH, Nieminen MS, Kesäniemi YA, Pasternack A, Miller GJ, and Humphries SE
- Subjects
- Cells, Cultured, Disease Progression, Endothelium, Vascular cytology, Humans, Platelet Aggregation, Risk Factors, Cell Movement physiology, Coronary Disease genetics, Monocytes physiology, Platelet Endothelial Cell Adhesion Molecule-1 genetics, Polymorphism, Genetic
- Abstract
The 643R allele of R643G polymorphism (also known as R670G in the premature protein) in PECAM-1 has been associated with risk of myocardial infarction (MI), while the 643G allele has been associated with risk of coronary artery stenosis (CAS). The aim of this study was to investigate this apparently conflicting association. The association of R643G with risk of MI was determined in the second Northwick Park Heart study (2037 men with 138 CHD events; mean age: 56 years). Smokers homozygous for the 643R allele showed increased risk of MI with a hazard ratio of 2.47 (95% CI: 1.23-4.97; P=0.01) compared to smokers homozygous for the 643G allele. Progression of disease was determined in the Lopid Coronary Angiography Trial (279 men; mean age: 58.9 years). The 643G homozygotes showed greater focal (-0.08 +/- 0.02 mm) and diffuse (-0.01 +/- 0.01 mm) progression of CAS compared to 643R homozygotes (-0.02 +/- 0.02 mm and 0.001 +/- 0.01 mm, respectively; P=0.04). While there was no genotype effect on platelet aggregation, PECAM-1 tyrosine phosphorylation in HUVECs of GG genotype was 2.4-fold greater (P <0.01) than cells of RR genotype, and the level of transendothelial migration of monocytes of GG genotype was greater than that of monocytes of RR genotype following stimulation with either IL-1beta (12% higher, P <0.01) or TNF-alpha (10% higher, P=0.05). These data confirm the association of the R643G polymorphism with MI and CAS and suggest that greater influx of monocytes in individuals homozygous for the 643G may explain the association with CAS.
- Published
- 2004
- Full Text
- View/download PDF
21. Serum homocysteine concentrations, gemfibrozil treatment, and progression of coronary atherosclerosis.
- Author
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Syvänne M, Whittall RA, Turpeinen U, Nieminen MS, Frick MH, Kesäniemi YA, Pasternack A, Humphries SE, and Taskinen MR
- Subjects
- Cholesterol, HDL blood, Coronary Angiography, Coronary Artery Disease diagnostic imaging, Coronary Artery Disease genetics, Disease Progression, Double-Blind Method, Humans, Male, Methylenetetrahydrofolate Reductase (NADPH2) genetics, Triglycerides blood, Coronary Artery Disease blood, Coronary Artery Disease drug therapy, Gemfibrozil therapeutic use, Homocysteine blood, Hypolipidemic Agents therapeutic use
- Abstract
The present study aimed to assess the effect of gemfibrozil on serum total homocysteine (tHcy) concentration and to evaluate the influence of tHcy on the angiographically determined progression of coronary atherosclerosis in a randomised, placebo-controlled trial of 395 post-coronary bypass men with low HDL cholesterol levels. The baseline levels of tHcy and those after 16 months of randomised therapy were measured by high-pressure liquid chromatography. Patients were genotyped for the thermolabile variant of N5,N10-methylenetetrahydrofolate reductase (MTHFR) (677C > T substitution). Gemfibrozil therapy was associated with a median 18% increase in tHcy levels (P < 0.01). In the gemfibrozil group increases in tHcy and HDL cholesterol were related (r = 0.217, P = 0.004), but changes in tHcy and triglycerides were not. Levels of tHCy were not associated with baseline extent or progression of coronary-artery disease. Subjects homozygous for the rare MTHFR T allele had 34% higher median tHcy concentrations than CC homozygotes or CT heterozygotes, but responses to gemfibrozil did not differ significantly among genotypes. The MTHFR genotype was not associated with extent or progression of coronary atherosclerosis. We conclude that gemfibrozil causes a significant elevation in tHcy levels, but the clinical relevance of this is unknown at present.
- Published
- 2004
- Full Text
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22. The intron 14 2140+5G>A variant in the low density lipoprotein receptor gene has no effect on plasma cholesterol levels.
- Author
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Whittall RA, Matheus S, Cranston T, Miller GJ, and Humphries SE
- Subjects
- DNA Mutational Analysis, Humans, Hyperlipoproteinemia Type II blood, Male, Middle Aged, Cholesterol blood, Hyperlipoproteinemia Type II genetics, Introns genetics, Point Mutation, Receptors, LDL genetics
- Published
- 2002
- Full Text
- View/download PDF
23. Low-density lipoprotein receptor gene (LDLR) world-wide website in familial hypercholesterolaemia: update, new features and mutation analysis.
- Author
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Heath KE, Gahan M, Whittall RA, and Humphries SE
- Subjects
- Databases as Topic, Humans, Hyperlipoproteinemia Type II genetics, Internet, Mutation genetics, Receptors, LDL genetics
- Abstract
Mutations in the low density lipoprotein receptor gene (LDLR) cause familial hypercholesterolaemia (FH). The FH website (http://www.ucl. ac.uk/fh) has been updated to provide various functions enabling the analysis of the large number of LDLR mutations. To date, 683 LDLR mutations have been reported; of these 58.9% are missense mutations, 21.1% minor rearrangements, 13.5% major rearrangements and 6.6% splice site mutations. Of the 402 missense mutations, only 11.4% occurred at CpG sites. The majority of mutations were found in two functional domains, the ligand binding domain (42%) and the epidermal growth factor (EGF) precursor-like domain (47%). This report describes new features of the FH website and assesses the spectrum of mutations reported to date.
- Published
- 2001
- Full Text
- View/download PDF
24. A World Wide Web site for low-density lipoprotein receptor gene mutations in familial hypercholesterolemia: sequence-based, tabular, and direct submission data handling.
- Author
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Wilson DJ, Gahan M, Haddad L, Heath K, Whittall RA, Williams RR, Humphries SE, and Day IN
- Subjects
- Amino Acid Sequence, Base Sequence, Databases as Topic, Humans, Molecular Sequence Data, United States, Hyperlipoproteinemia Type II genetics, Medical Informatics, Mutation, Receptors, LDL genetics
- Abstract
Familial hypercholesterolemia is an autosomal dominant inherited condition characterized by a mutation in the low-density lipoprotein receptor (LDLR) gene. A database has been set up on the World Wide Web for mutations in the LDLR gene.
- Published
- 1998
- Full Text
- View/download PDF
25. Identification of a common low density lipoprotein receptor mutation (R329X) in the south of England: complete linkage disequilibrium with an allele of microsatellite D19S394.
- Author
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Day IN, Haddad L, O'Dell SD, Day LB, Whittall RA, and Humphries SE
- Subjects
- Alleles, England, Humans, Hypercholesterolemia genetics, Linkage Disequilibrium, Microsatellite Repeats, Mutation, Receptors, LDL genetics
- Abstract
Familial hypercholesterolaemia is commonly caused by mutations in the low density lipoprotein receptor (LDLR) gene and more than 300 different mutations have been described worldwide. Some mutations occur at relatively higher frequency in certain populations, reflecting both chance and demography, most evident in founder populations. As part of a study of kindreds of 78 probands from Southampton and south west Hampshire, we identified the same mutation (R329X) in 9/78 (11.5%) probands. In all (100%) of these probands, length allele 259nt of the 17 allele microsatellite D19S394, sited approximately 250 kilobases telomeric and 5' to the LDLR gene, was observed, although in the general population this allele has a prevalence of only 16.1%. A simple diagnostic assay for R329X was constructed in conjunction with more detailed family studies. Both the R329X and linked D19S394 allele also cosegregated with the FH phenotype within each kindred. Although R329X involves a CpG site, it is highly likely that the families are identical by descent for R329X, we surmise with a common ancestor within 500 to 1000 years, although the mutation is not restricted to this geographical area. This relationship illustrates that the linkage disequilibrium of gene LDLR with marker D19S394 will enable rapid recognition using D19S394 genotype of possible common FH mutation(s) within a cohort of FH patients from a particular locality or ethnic group.
- Published
- 1997
- Full Text
- View/download PDF
26. Health of juvenile delinquents.
- Author
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Weindling AM, Bamford FN, and Whittall RA
- Subjects
- Adolescent, England, Family Characteristics, Hearing Disorders epidemiology, Humans, Male, Vision Disorders epidemiology, Juvenile Delinquency, Morbidity
- Published
- 1986
- Full Text
- View/download PDF
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