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Seselgyte R, Bryant D, Demetriou C, Ishida M, Peskett E, Moreno N, Morrogh D, Sell D, Lees M, Farrall M, Moore GE, Sommerlad B, Pauws E, Stanier P. Disruption of FOXF2 as a Likely Cause of Absent Uvula in an Egyptian Family. J Dent Res 2019; 98:659-665. [PMID: 30917284 DOI: 10.1177/0022034519837245] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
This study investigated the genetic basis of an unusual autosomal dominant phenotype characterized by familial absent uvula, with a short posterior border of the soft palate, abnormal tonsillar pillars, and velopharyngeal insufficiency. Cytogenetic analysis and single-nucleotide polymorphism-based linkage analysis were investigated in a 4-generation family with 8 affected individuals. Whole exome sequencing data were overlaid, and segregation analysis identified a single missense variant, p.Q433P in the FOXF2 transcription factor, that fully segregated with the phenotype. This was found to be in linkage disequilibrium with a small 6p25.3 tandem duplication affecting FOXC1 and GMDS. Notably, the copy number imbalances of this region are commonly associated with pathologies that are not present in this family. Bioinformatic predictions with luciferase reporter studies of the FOXF2 missense variant indicated a negative impact, affecting both protein stability and transcriptional activation. Foxf 2 is expressed in the posterior mouse palate, and knockout animals develop an overt cleft palate. Since mice naturally lack the structural equivalent of the uvula, we demonstrated FOXF2 expression in the developing human uvula. Decipher also records 2 individuals with hypoplastic or bifid uvulae with copy number variants affecting FOXF2. Nevertheless, given cosegregation with the 6p25.3 duplications, we cannot rule out a combined effect of these gains and the missense variant on FOXF2 function, which may account for the rare palate phenotype observed.
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Affiliation(s)
- R Seselgyte
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - D Bryant
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - C Demetriou
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - M Ishida
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - E Peskett
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - N Moreno
- 2 Developmental Biology and Cancer, UCL GOS Institute of Child Health, London, UK
| | - D Morrogh
- 3 NE Thames Regional Genetics Service Laboratory, Great Ormond Street Hospital NHS Trust, London, UK
| | - D Sell
- 4 North Thames Cleft Centre, St Andrew's Centre, Broomfield Hospital, Chelmsford, UK; Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - M Lees
- 4 North Thames Cleft Centre, St Andrew's Centre, Broomfield Hospital, Chelmsford, UK; Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,5 Department of Clinical Genetics, Great Ormond Street Hospital NHS Trust, London, UK
| | - M Farrall
- 6 Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - G E Moore
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - B Sommerlad
- 4 North Thames Cleft Centre, St Andrew's Centre, Broomfield Hospital, Chelmsford, UK; Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - E Pauws
- 2 Developmental Biology and Cancer, UCL GOS Institute of Child Health, London, UK
| | - P Stanier
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
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Hopewell JC, Seedorf U, Farrall M, Parish S, Kyriakou T, Goel A, Hamsten A, Collins R, Watkins H, Clarke R. Impact of lipoprotein(a) levels and apolipoprotein(a) isoform size on risk of coronary heart disease. J Intern Med 2014; 276:260-8. [PMID: 24372611 DOI: 10.1111/joim.12187] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Observational and genetic studies have shown that lipoprotein(a) [Lp(a)] levels and apolipoprotein(a) [apo(a)] isoform size are both associated with coronary heart disease (CHD) risk, but the relative independence of these risk factors remains unclear. Clarification of this uncertainty is relevant to the potential of future Lp(a)-lowering therapies for the prevention of CHD. METHODS Plasma Lp(a) levels and apo(a) isoform size, estimated by the number of kringle IV (KIV) repeats, were measured in 995 patients with CHD and 998 control subjects. The associations between CHD risk and fifths of Lp(a) levels were assessed before and after adjustment for KIV repeats and, conversely, the associations between CHD risk and fifths of KIV repeats were assessed before and after adjustment for Lp(a) levels. RESULTS Individuals in the top fifth of Lp(a) levels had more than a twofold higher risk of CHD compared with those in the bottom fifth, and this association was materially unaltered after adjustment for KIV repeats [odds ratio (OR) 2.05, 95% confidence interval (CI) 1.38-3.04, P < 0.001]. Furthermore, almost all of the excess risk was restricted to the two-fifths of the population with the highest Lp(a) levels. Individuals in the bottom fifth of KIV repeats had about a twofold higher risk of CHD compared with those in the top fifth, but this association was no longer significant after adjustment for Lp(a) levels (OR 1.13, 95% CI 0.77-1.66, P = 0.94). CONCLUSIONS The effect of KIV repeats on CHD risk is mediated through their impact on Lp(a) levels, suggesting that absolute levels of Lp(a), rather than apo(a) isoform size, are the main determinant of CHD risk.
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Affiliation(s)
- J C Hopewell
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
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Melén E, Granell R, Kogevinas M, Strachan D, Gonzalez JR, Wjst M, Jarvis D, Ege M, Braun-Fahrländer C, Genuneit J, Horak E, Bouzigon E, Demenais F, Kauffmann F, Siroux V, Michel S, von Berg A, Heinzmann A, Kabesch M, Probst-Hensch NM, Curjuric I, Imboden M, Rochat T, Henderson J, Sterne JAC, McArdle WL, Hui J, James AL, William Musk A, Palmer LJ, Becker A, Kozyrskyj AL, Chan-Young M, Park JE, Leung A, Daley D, Freidin MB, Deev IA, Ogorodova LM, Puzyrev VP, Celedón JC, Brehm JM, Cloutier MM, Canino G, Acosta-Pérez E, Soto-Quiros M, Avila L, Bergström A, Magnusson J, Söderhäll C, Kull I, Scholtens S, Marike Boezen H, Koppelman GH, Wijga AH, Marenholz I, Esparza-Gordillo J, Lau S, Lee YA, Standl M, Tiesler CMT, Flexeder C, Heinrich J, Myers RA, Ober C, Nicolae DL, Farrall M, Kumar A, Moffatt MF, Cookson WOCM, Lasky-Su J. Genome-wide association study of body mass index in 23 000 individuals with and without asthma. Clin Exp Allergy 2013; 43:463-74. [PMID: 23517042 DOI: 10.1111/cea.12054] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 09/28/2012] [Accepted: 10/22/2012] [Indexed: 12/20/2022]
Abstract
BACKGROUND Both asthma and obesity are complex disorders that are influenced by environmental and genetic factors. Shared genetic factors between asthma and obesity have been proposed to partly explain epidemiological findings of co-morbidity between these conditions. OBJECTIVE To identify genetic variants that are associated with body mass index (BMI) in asthmatic children and adults, and to evaluate if there are differences between the genetics of BMI in asthmatics and healthy individuals. METHODS In total, 19 studies contributed with genome-wide analysis study (GWAS) data from more than 23 000 individuals with predominantly European descent, of whom 8165 are asthmatics. RESULTS We report associations between several DENND1B variants (P = 2.2 × 10(-7) for rs4915551) on chromosome 1q31 and BMI from a meta-analysis of GWAS data using 2691 asthmatic children (screening data). The top DENND1B single nucleotide polymorphisms(SNPs) were next evaluated in seven independent replication data sets comprising 2014 asthmatics, and rs4915551 was nominally replicated (P < 0.05) in two of the seven studies and of borderline significance in one (P = 0.059). However, strong evidence of effect heterogeneity was observed and overall, the association between rs4915551 and BMI was not significant in the total replication data set, P = 0.71. Using a random effects model, BMI was overall estimated to increase by 0.30 kg/m(2) (P = 0.01 for combined screening and replication data sets, N = 4705) per additional G allele of this DENND1BSNP. FTO was confirmed as an important gene for adult and childhood BMI regardless of asthma status. CONCLUSIONS AND CLINICAL RELEVANCE DENND1B was recently identified as an asthma susceptibility gene in a GWAS on children, and here, we find evidence that DENND1B variants may also be associated with BMI in asthmatic children. However, the association was overall not replicated in the independent data sets and the heterogeneous effect of DENND1B points to complex associations with the studied diseases that deserve further study.
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Affiliation(s)
- E Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
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Ganesh SK, Tragante V, Guo W, Guo Y, Lanktree MB, Smith EN, Johnson T, Castillo BA, Barnard J, Baumert J, Chang YPC, Elbers CC, Farrall M, Fischer ME, Franceschini N, Gaunt TR, Gho JMIH, Gieger C, Gong Y, Isaacs A, Kleber ME, Leach IM, McDonough CW, Meijs MFL, Mellander O, Molony CM, Nolte IM, Padmanabhan S, Price TS, Rajagopalan R, Shaffer J, Shah S, Shen H, Soranzo N, van der Most PJ, Van Iperen EPA, Van Setten J, Vonk JM, Zhang L, Beitelshees AL, Berenson GS, Bhatt DL, Boer JMA, Boerwinkle E, Burkley B, Burt A, Chakravarti A, Chen W, Cooper-DeHoff RM, Curtis SP, Dreisbach A, Duggan D, Ehret GB, Fabsitz RR, Fornage M, Fox E, Furlong CE, Gansevoort RT, Hofker MH, Hovingh GK, Kirkland SA, Kottke-Marchant K, Kutlar A, LaCroix AZ, Langaee TY, Li YR, Lin H, Liu K, Maiwald S, Malik R, Murugesan G, Newton-Cheh C, O'Connell JR, Onland-Moret NC, Ouwehand WH, Palmas W, Penninx BW, Pepine CJ, Pettinger M, Polak JF, Ramachandran VS, Ranchalis J, Redline S, Ridker PM, Rose LM, Scharnag H, Schork NJ, Shimbo D, Shuldiner AR, Srinivasan SR, Stolk RP, Taylor HA, Thorand B, Trip MD, van Duijn CM, Verschuren WM, Wijmenga C, Winkelmann BR, Wyatt S, Young JH, Boehm BO, Caulfield MJ, Chasman DI, Davidson KW, Doevendans PA, FitzGerald GA, Gums JG, Hakonarson H, Hillege HL, Illig T, Jarvik GP, Johnson JA, Kastelein JJP, Koenig W, Marz W, Mitchell BD, Murray SS, Oldehinkel AJ, Rader DJ, Reilly MP, Reiner AP, Schadt EE, Silverstein RL, Snieder H, Stanton AV, Uitterlinden AG, van der Harst P, van der Schouw YT, Samani NJ, Johnson AD, Munroe PB, de Bakker PIW, Zhu X, Levy D, Keating BJ, Asselbergs FW. Loci influencing blood pressure identified using a cardiovascular gene-centric array. Hum Mol Genet 2013. [DOI: 10.1093/hmg/ddt177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Chan K, Patel RS, Newcombe P, Nelson CP, Qasim A, Epstein SE, Burnett S, Vaccarino VL, Zafari AM, Shah SH, Anderson JL, Carlquist JF, Hartiala J, Allayee H, Hinohara K, Lee BS, Erl A, Ellis KL, Goel A, Schaefer AS, Mokhtari NE, Goldstein BA, Hlatky MA, Go AS, Shen GQ, Gong Y, Pepine C, Laxton RC, Wittaker JC, Tang WHW, Johnson JA, Wang QK, Assimes TL, Nöthlings U, Farrall M, Watkins H, Richards AM, Cameron VA, Muendlein A, Drexel H, Koch W, Park JE, Kimura A, Shen WF, Simpson IA, Hazen SL, Horne BD, Hauser ER, Quyyumi AA, Reilly MP, Samani NJ, Ye S. 126 CHROMOSOME 9P21 LOCUS AND ANGIOGRAPHIC CORONARY ARTERY DISEASE BURDEN: A COLLABORATIVE META-ANALYSIS. Heart 2013. [DOI: 10.1136/heartjnl-2013-304019.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Barbalic M, Narancic NS, Skaric-Juric T, Salihovic MP, Klaric IM, Lauc LB, Janicijevic B, Farrall M, Rudan I, Campbell H, Wright AF, Hastie ND, Rudan P. A quantitative trait locus for SBP maps near KCNB1 and PTGIS in a population isolate. Am J Hypertens 2009; 22:663-8. [PMID: 19265782 DOI: 10.1038/ajh.2009.46] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Population isolates are characterized by simplified genetic background and as such present promising opportunities for studying complex diseases. We performed a genome-wide linkage analysis for systolic (SBP) and diastolic blood pressure (DBP) followed up by the association analysis in the Croatian isolated island of Vis, where a very high prevalence of hypertension was reported (75%). METHODS Variance-components linkage analysis was used to map quantitative trait loci (QTL) for SBP and DBP in 125 families with 1,389 members. Follow-up association analysis was performed in a sample of 421 subjects from the island of Vis. The 15 top-ranking single nucleotide polymorphisms (SNPs) were selected and tested for the association by in silico replication in the British 1958 Birth Cohort DNA Collection. RESULTS Linkage results showed evidence for a QTL influencing DBP (lod = 1.89) on chromosome 7p14.2 and two QTL influencing SBP (lod = 2.03 on chromosome 1p36 and lod = 1.75 on chromosome 20q13). For the association results, the replication was observed for the rs237484 polymorphism on chromosome 20 that was associated with SBP with the effect size beta = -5.2 (P = 0.001; per A allele) in Vis population and beta = -1.1 (P = 0.04) in the British 1958 Birth Cohort. rs237484 is in proximity to the potassium voltage gate channel gene (KCNB1) and close to the prostaglandin I2 (prostacyclin) synthase gene (PTGIS). CONCLUSIONS These results provide evidence of a QTL influencing blood pressure (BP) variability in this region and support the notion that the isolated population of the island of Vis is a suitable population for conducting linkage and association analyses of cardiovascular-related phenotypes.
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Cunnington MS, Mayosi BM, Hall DH, Avery PJ, Farrall M, Vickers MA, Watkins H, Keavney B. Novel genetic variants linked to coronary artery disease by genome-wide association are not associated with carotid artery intima-media thickness or intermediate risk phenotypes. Atherosclerosis 2008; 203:41-4. [PMID: 18675980 PMCID: PMC2654912 DOI: 10.1016/j.atherosclerosis.2008.06.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Revised: 06/18/2008] [Accepted: 06/21/2008] [Indexed: 11/17/2022]
Abstract
Background It is uncertain whether the novel single nucleotide polymorphisms (SNPs) that have recently been associated with coronary artery disease (CAD) in genome-wide studies also influence carotid atheroma and stroke risk. The mechanisms of their association with CAD are unknown; relationships to other cardiovascular phenotypes may give mechanistic clues. Carotid artery intima-media thickness (CIMT) is a subclinical marker of atherosclerosis associated with stroke. We investigated association of reported CAD risk variants with CIMT, and with other intermediate phenotypes that may implicate causative pathways. Methods We studied 1425 members of 248 British Caucasian families ascertained through a hypertensive proband. We genotyped CAD risk SNPs on chromosomes 9 (rs1333049, rs7044859, rs496892, rs7865618), 6 (rs6922269) and 2 (rs2943634) using TaqMan. Merlin software was used for family-based association testing. Results No significant association was found between genotype at any SNP and CIMT in 846 individuals with acceptable measurements. Nor were SNPs significantly associated with blood pressure, obesity, cholesterol, CRP, interleukin-6, TNF-α, or leptin. Conclusions These novel CAD variants are not associated with CIMT and do not appear to mediate the risk of atherothrombosis through known risk factors.
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Freel EM, Ingram M, Friel EC, Fraser R, Brown M, Samani NJ, Caulfield M, Munroe P, Farrall M, Webster J, Clayton D, Dominiczak AF, Davies E, Connell JMC. Phenotypic consequences of variation across the aldosterone synthase and 11-beta hydroxylase locus in a hypertensive cohort: data from the MRC BRIGHT Study. Clin Endocrinol (Oxf) 2007; 67:832-8. [PMID: 17651452 DOI: 10.1111/j.1365-2265.2007.02971.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Aldosterone is an important cardiovascular hormone; 15% of hypertensive subjects have alteration in aldosterone regulation, defined by a raised ratio of aldosterone to renin (ARR). Studies of the aldosterone synthase gene (CYP11B2) have focused on a single nucleotide polymorphism in the 5'promoter region (-344 C/T). In normotensive subjects, the T allele associates with raised levels of the 11-deoxysteroids, deoxycorticosterone and 11-deoxycortisol which are substrates for 11beta-hydroxylase, encoded by the adjacent and homologous gene, CYP11B1. We have speculated that this altered 11beta-hydroxylase efficiency leads to increased ACTH drive to the adrenal gland to maintain cortisol production and reported herein the association between the -344 C/T single nucleotide polymorphism (SNP) and adrenal steroid production in subjects with essential hypertension. METHODS The CYP11B2-344 C/T polymorphism was genotyped and urinary excretion of adrenal steroid metabolites was measured (by GCMS) in 511 unrelated hypertensives from the Medical Research Council (MRC) British Genetics of Hypertension (BRIGHT) study. RESULTS Thirty-five per cent of subjects were homozygous for the -344T allele whilst 16% were CC homozygotes. There was no difference in cortisol excretion rate between the two genotype groups but the index of adrenal 11beta-hydroxylation (ratio of tetrahydrodeoxycortisol/total cortisol) was significantly higher in the TT group (P < 0.005) than in the CC group. Excretion rates of the major urinary metabolite of aldosterone (tetrahydroaldosterone) correlated strongly with the ACTH-regulated steroids, cortisol (r = 0.437, P < 0.0001) and total androgen metabolites (r = 0.4, P < 0.0001) in TT but not CC subjects. CONCLUSIONS Hypertensives homozygous for the -344 T allele of CYP11B2 demonstrate altered 11beta-hydroxylase efficiency (CYP11B1); this is consistent with the hypothesis of a genetically determined increase in adrenal ACTH drive in these subjects. The correlation between excretion of aldosterone and cortisol metabolites and suggests that, in TT subjects, ACTH exerts an important common regulatory influence on adrenal corticosteroid production in subjects with hypertension.
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Affiliation(s)
- E M Freel
- Glasgow Cardiovascular Research Centre, University of Glasgow, 126 University Place, Glasgow, UK.
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Wiltshire S, Bell JT, Groves CJ, Dina C, Hattersley AT, Frayling TM, Walker M, Hitman GA, Vaxillaire M, Farrall M, Froguel P, McCarthy MI. Epistasis between type 2 diabetes susceptibility Loci on chromosomes 1q21-25 and 10q23-26 in northern Europeans. Ann Hum Genet 2006; 70:726-37. [PMID: 17044847 DOI: 10.1111/j.1469-1809.2006.00289.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Characterisation of the interactions between susceptibility loci (epistasis) is central to a full understanding of the genetic aetiology and the molecular pathology of complex diseases. We have examined, in British and French pedigrees, evidence for epistasis between the type 2 diabetes susceptibility loci on chromosomes 1q21-25 and 10q23-26 using two complementary linkage-based approaches. Joint two-locus linkage analysis of 1q and 10q in British pedigrees provided significant evidence for interaction (P < or = 0.003) when comparing a general epistasis model with multiplicative or additive-effects-only models. Conditional linkage analysis (which models epistasis as a deviation from multiplicativity only) confirmed these findings, with significant LOD score increases at the 1q (P = 0.0002) and 10q (P = 0.0023) loci. These analyses provided sizeable reductions in the 1-LOD support intervals for both loci. Analyses of the British and French pedigrees together yielded comparable, but not enhanced, findings, with significant (P < or = 0.003) evidence for epistasis in joint two-locus linkage analysis, and during conditional linkage analysis significant increases in linkage evidence at the 1q (P = 0.0002) and 10q (P = 0.0036) loci. Our findings of epistasis nevertheless substantiate the evidence for genuine genetic effects at both loci, facilitate endeavours to fine-map these loci in population samples, and support further examination of this interaction at the nucleotide level by providing a robust prior hypothesis.
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Affiliation(s)
- S Wiltshire
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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Gaukrodger N, Mayosi BM, Imrie H, Avery P, Baker M, Connell JMC, Watkins H, Farrall M, Keavney B. A rare variant of the leptin gene has large effects on blood pressure and carotid intima-medial thickness: a study of 1428 individuals in 248 families. J Med Genet 2006; 42:474-8. [PMID: 15937081 PMCID: PMC1736073 DOI: 10.1136/jmg.2004.027631] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Rare mutations in the leptin (LEP) gene cause severe obesity. Common polymorphisms of LEP have been associated with obesity, but their association with cardiovascular disease has been little studied. We have examined the impact of both common and rare polymorphisms of the LEP gene on blood pressure (BP), subclinical atherosclerosis as measured by carotid intima-medial thickness (CIMT), and body mass index (BMI) in a large family study. METHODS Five polymorphisms spanning LEP were typed in 1428 individuals from 248 nuclear families. BP, CIMT, BMI, and plasma leptin were measured. RESULTS The polymorphisms typed captured all common haplotypes present at LEP. There was strong association between a rare polymorphism in the 3' untranslated region of LEP (C538T) and both pulse pressure (p = 0.0001) and CIMT (p = 0.008). C/T heterozygotes had a 22% lower pulse pressure and a 17% lower CIMT than C/C homozygotes. The polymorphism accounted for 3-5% of the population variation in pulse pressure and CIMT. There was no association between any LEP polymorphism and either BMI or plasma leptin level. CONCLUSIONS This large family study shows that the rare T allele at the C538T polymorphism of LEP substantially influences pulse pressure and CIMT, but does not appear to exert this effect through actions on plasma leptin level or BMI. This suggests that autocrine or paracrine effects in vascular tissue may be important physiological functions of leptin. This study also provides evidence that rare polymorphisms of particular genes may have substantial effects within the normal range of certain quantitative traits.
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Affiliation(s)
- N Gaukrodger
- Institute of Human Genetics, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
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Abstract
Genetic-association studies are widely expected to unravel the genetic basis of complex diseases. The population-based case-control study, a commonly used approach for association studies, is subject to the problem of population admixture. Consequently, evidence of disease-marker associations obtained from such studies is ideally confirmed by alternative methods. The Transmission/Disequilibrium Test (TDT) is suitable to assess evidence of association obtained from case-control studies. Since data are increasingly available from both case-control and TDT studies of the same disease-marker association, it is useful to obtain a combined estimate of disease-marker association. The odds ratio is a commonly used measure of the magnitude of a disease-marker association that can be easily obtained in case-control studies. Here we show how an odds ratio estimate and its' associated standard error can be obtained from TDT results. Furthermore, we suggest a method for integrating results from case-control studies and the TDT to provide a combined estimate of disease-marker association. Such combined estimates can be used to contrast the results of the two studies and provides an overall picture of the effect size attributable to such polymorphism. An illustrative application is made to a published data set on type 2 diabetes.
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Affiliation(s)
- G R Kazeem
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
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Mayosi BM, Keavney B, Kardos A, Davies CH, Ratcliffe PJ, Farrall M, Watkins H. Electrocardiographic measures of left ventricular hypertrophy show greater heritability than echocardiographic left ventricular mass. Eur Heart J 2002; 23:1963-71. [PMID: 12473259 DOI: 10.1053/euhj.2002.3288] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
AIMS To assess the heritability (i.e. relative contribution of genetic factors to the variability) of continuous measures of left ventricular hypertrophy determined by electrocardiography and echocardiography. METHODS AND RESULTS We studied 955 members of 229 Caucasian families, ascertained through a hypertensive proband. Electrocardiographic measurements were performed manually on resting 12-lead electrocardiograms, and echocardiographic measurements were made on M-mode images. Sex-specific residuals for the left ventricular phenotypes were calculated, adjusted for age, systolic blood pressure, weight, height, waist-hip ratio, and presence of diabetes. Heritability was estimated in two ways: firstly, from familial correlations with adjustment for spouse resemblance; and secondly by using variance components methods with ascertainment correction for proband status. The heritability estimates (given as a range derived from the two methods) were higher for Sokolow-Lyon voltage (39-41%) than for echocardiographic left ventricular mass (23-29%). Electrocardiographic left ventricular mass, Cornell voltage, and Cornell product had heritability estimates of 12-18%, 19-25%, and 28-32%, respectively. CONCLUSIONS Genetic factors may explain a substantial proportion of variability in quantitative electrocardiographic and echocardiographic measures of left ventricular hypertrophy. The greater heritability of Sokolow-Lyon voltage suggests that electrocardiographic phenotypes may be particularly important for the molecular investigation of the genetic susceptibility to cardiac hypertrophy.
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Affiliation(s)
- B M Mayosi
- Department of Cardiovascular Medicine, John Radcliffe Hospital, Oxford, UK
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Lloyd SE, Onwuazor ON, Beck JA, Mallinson G, Farrall M, Targonski P, Collinge J, Fisher EM. Identification of multiple quantitative trait loci linked to prion disease incubation period in mice. Proc Natl Acad Sci U S A 2001; 98:6279-83. [PMID: 11353827 PMCID: PMC33459 DOI: 10.1073/pnas.101130398] [Citation(s) in RCA: 151] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Polymorphisms in the prion protein gene are known to affect prion disease incubation times and susceptibility in humans and mice. However, studies with inbred lines of mice show that large differences in incubation times occur even with the same amino acid sequence of the prion protein, suggesting that other genes may contribute to the observed variation. To identify these loci we analyzed 1,009 animals from an F2 intercross between two strains of mice, CAST/Ei and NZW/OlaHSd, with significantly different incubation periods when challenged with RML scrapie prions. Interval mapping identified three highly significantly linked regions on chromosomes 2, 11, and 12; composite interval mapping suggests that each of these regions includes multiple linked quantitative trait loci. Suggestive evidence for linkage was obtained on chromosomes 6 and 7. The sequence conservation between the mouse and human genome suggests that identification of mouse prion susceptibility alleles may have direct relevance to understanding human susceptibility to bovine spongiform encephalopathy (BSE) infection, as well as identifying key factors in the molecular pathways of prion pathogenesis. However, the demonstration of other major genetic effects on incubation period suggests the need for extreme caution in interpreting estimates of variant Creutzfeldt-Jakob disease epidemic size utilizing existing epidemiological models.
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Affiliation(s)
- S E Lloyd
- Medical Research Council Prion Unit and Department of Neurogenetics, Imperial College School of Medicine at St Mary's, Norfolk Place, London W2 1PG, United Kingdom
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15
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Abstract
Genome-wide searches for susceptibility genes using pairs of affected siblings are being undertaken to dissect out individual polygenes that contribute to human multifactorial disease. Efficient identity-by-descent (IBD)-based sibpair linkage tests are available that test individual markers or maps of linked markers for linkage to a single putative susceptibility gene. In order to assess the support for linkage to a second putative susceptibility gene that happens to map close to an established susceptibility gene, it is necessary to use a method that correctly allows for the IBD distortion that directly results from the linkage between the two genes. A maximum likelihood-based, multilocus linkage test is proposed, which accounts for this interdependency and evaluates the support for an interaction between constituent susceptibility genes. The size and power of a test for a second linked susceptibility gene is investigated by simulation studies.
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Affiliation(s)
- M Farrall
- Nuffield Department of Clinical Medicine, University of Oxford, Wellcome Trust Centre for Human Genetics, United Kingdom
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16
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Garner C, Tatu T, Reittie JE, Littlewood T, Darley J, Cervino S, Farrall M, Kelly P, Spector TD, Thein SL. Genetic influences on F cells and other hematologic variables: a twin heritability study. Blood 2000; 95:342-6. [PMID: 10607722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023] Open
Abstract
To assess the relative contribution of genetic factors in the variation of F cells (FC) and other hematologic variables, we conducted a classical twin study in unselected twins. The sample included 264 identical (monozygotic [MZ]) twin pairs and 511 nonidentical (dizygotic [DZ]) same-sex twin pairs (aged 20 to 80 years) from the St. Thomas' UK Adult Twin Register. The FC values were distributed continuously and positively skewed, with values ranging from 0.6% to 22%. FC values were higher in women than in men and decreased with age, with the variables accounting for 2% of the total FC variance. The intraclass correlations of FC values were higher in MZ (rMZ = 0.89) than in DZ (rDZ = 0.49) twins. The XmnI-(G)gamma polymorphism in the beta-globin gene cluster had a significant effect on FC levels, accounting for approximately 13% of the total FC variance. Variance components analysis showed that the FC values were accounted for predominantly by additive genetic and nonshared environmental influences, with an estimate of heritability of 0.89. Hemoglobin levels and red blood cell, white blood cell, and platelet numbers were also substantially heritable, with heritability estimates of 0.37, 0.42, 0.62, and 0.57, respectively. Previously, studies of sib pairs with sickle cell disease and isolated family studies showed that high levels of Hb F and FC tend to be inherited. Here, our classical twin study demonstrated that the variance of FC levels in healthy adults is largely genetically determined. (Blood. 2000;95:342-346)
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Affiliation(s)
- C Garner
- Wellcome Trust Centre for Human Genetics, Oxford, UK
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17
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Farrall M, Keavney B, McKenzie C, Delépine M, Matsuda F, Lathrop GM. Fine-mapping of an ancestral recombination breakpoint in DCP1. Nat Genet 1999; 23:270-1. [PMID: 10545941 DOI: 10.1038/15449] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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18
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Keavney B, McKenzie CA, Connell JM, Julier C, Ratcliffe PJ, Sobel E, Lathrop M, Farrall M. Measured haplotype analysis of the angiotensin-I converting enzyme gene. Hum Mol Genet 1998; 7:1745-51. [PMID: 9736776 DOI: 10.1093/hmg/7.11.1745] [Citation(s) in RCA: 150] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Linkage and segregation analysis have shown that circulating angiotensin-I converting enzyme (ACE) levels are influenced by a major quantitative trait locus that maps within or close to the ACE gene. The D variant of a 287 bp insertion/deletion (I/D) polymorphism in intron 16 of the gene is associated with high ACE levels and may also be related to increased risk of cardiovascular disease. Multiple variants that are in linkage disequilibrium with the I/D polymorphism have been described, but it is unknown if any of these are directly implicated, alone or in combination with as yet undiscovered variants, in the determination of ACE levels. An analysis of 10 polymorphisms spanning 26 kb of the ACE gene revealed a limited number of haplotypes in Caucasian British families due to strong linkage disequilibrium operating over this small chromosomal region. A haplotype tree (cladogram) was constructed with three main branches (clades A-C) which account for 90% of the observed haplotypes. Clade C is most likely derived from clades A and B following an ancestral recombination event. This evolutionary information was then used to direct a series of nested, measured haplotype analyses that excluded upstream sequences, including the ACE promoter, from harbouring the major ACE-linked variant that explains 36% of the total trait variability. Residual familial correlations were highly significant, suggesting the influence of additional unlinked genes. Our results demonstrate that a combined cladistic/measured haplotype analysis of polymorphisms within a gene provides a powerful means to localize variants that directly influence a quantitative trait.
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Affiliation(s)
- B Keavney
- The Wellcome Trust Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Windmill Road, Oxford OX3 7BN, UK
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19
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Munroe PB, Strautnieks SS, Farrall M, Daniel HI, Lawson M, DeFreitas P, Fogarty P, Gardiner RM, Caulfield M. Absence of linkage of the epithelial sodium channel to hypertension in black Caribbeans. Am J Hypertens 1998; 11:942-5. [PMID: 9715786 DOI: 10.1016/s0895-7061(98)00092-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Hypertensives of African origin have low-renin, sodium-sensitive blood pressure and respond poorly to treatment with angiotensin converting enzyme inhibitors. The epithelial sodium channel may be important in the pathogenesis of essential hypertension in this population. This is supported by the identification of mutations within this channel, which lead to excess sodium reabsorption and hypertension in Liddle's syndrome. In this study we tested whether there was linkage of the genes encoding the three subunits of the epithelial sodium channel to essential hypertension in 63 affected sibling pairs of West African origin from St. Vincent and the Grenadines. We found no support for linkage of the epithelial sodium channel to essential hypertension in this population. However, further studies will be needed in larger populations of African ancestry to exclude a contribution of the genes encoding the epithelial sodium channel to hypertension.
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Affiliation(s)
- P B Munroe
- Department of Paediatrics, University College London Medical School, The Rayne Institute, England
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20
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Farrall M. The Book of Man: The Human Genome Project and the Quest to Discover Our Genetic Heritage. J Med Genet 1998. [DOI: 10.1136/jmg.35.8.703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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21
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Garner C, Mitchell J, Hatzis T, Reittie J, Farrall M, Thein SL. Haplotype mapping of a major quantitative-trait locus for fetal hemoglobin production, on chromosome 6q23. Am J Hum Genet 1998; 62:1468-74. [PMID: 9585587 PMCID: PMC1377138 DOI: 10.1086/301859] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Fetal hemoglobin (Hb F) and fetal cell (FC) levels in adults show considerable variation and are influenced by several genetic variants; the major determinants appear to be unlinked to the beta-globin gene cluster. Recently, a trans-acting locus controlling Hb F and FC production has been mapped to chromosome 6q23 in an Asian Indian kindred that includes individuals with heterocellular hereditary persistence of Hb F (HPFH) associated with beta thalassemia. We have extended the kindred by 57 members, bringing the total studied to 210, and have saturated the region with 26 additional markers. Linkage analysis showed tight linkage of the quantitative-trait locus (QTL) to the anonymous markers D6S976 (LOD score 11.3; recombination fraction .00) and D6S270 (LOD score 7.4; recombination fraction .00). Key recombination events now place this QTL within a 1-2-cM interval spanning approximately 1.5 Mb between D6S270 and D6S1626. Furthermore, haplotype analysis has led to a reevaluation of the genealogy and to the identification of additional relationships in the kindred.
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Affiliation(s)
- C Garner
- Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom
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22
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Farrall M, Weeks DE. Mutational mechanisms for generating microsatellite allele-frequency distributions: an analysis of 4,558 markers. Am J Hum Genet 1998; 62:1260-2. [PMID: 9545399 PMCID: PMC1377086 DOI: 10.1086/301829] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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23
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Rubio JP, Danek A, Stone C, Chalmers R, Wood N, Verellen C, Ferrer X, Malandrini A, Fabrizi GM, Manfredi M, Vance J, Pericak-Vance M, Brown R, Rudolf G, Picard F, Alonso E, Brin M, Németh AH, Farrall M, Monaco AP. Chorea-acanthocytosis: genetic linkage to chromosome 9q21. Am J Hum Genet 1997; 61:899-908. [PMID: 9382101 PMCID: PMC1715977 DOI: 10.1086/514876] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Chorea-acanthocytosis (CHAC) is a rare autosomal recessive disorder characterized by progressive neurodegeneration and unusual red-cell morphology (acanthocytosis), with onset in the third to fifth decade of life. Neurological impairment with acanthocytosis (neuroacanthocytosis) also is seen in abetalipoproteinemia and X-linked McLeod syndrome. Whereas the molecular etiology of McLeod syndrome has been defined (Ho et al. 1994), that of CHAC is still unknown. In the absence of cytogenetic rearrangements, we initiated a genomewide scan for linkage in 11 families, segregating for CHAC, who are of diverse geographical origin. We report here that the disease is linked, in all families, to a 6-cM region of chromosome 9q21 that is flanked by the recombinant markers GATA89a11 and D9S1843. A maximum two-point LOD score of 7.1 (theta = .00) for D9S1867 was achieved, and the linked region has been confirmed by homozygosity-by-descent, in offspring from inbred families. These findings provide strong evidence for the involvement of a single locus for CHAC and are the first step in positional cloning of the disease gene.
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Affiliation(s)
- J P Rubio
- The Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
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24
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Farrall M. LOD wars: the affected-sib-pair paradigm strikes back! Am J Hum Genet 1997; 60:735-8. [PMID: 9042936 PMCID: PMC1712522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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25
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Bonyadi M, Rusholme SA, Cousins FM, Su HC, Biron CA, Farrall M, Akhurst RJ. Mapping of a major genetic modifier of embryonic lethality in TGF beta 1 knockout mice. Nat Genet 1997; 15:207-11. [PMID: 9020852 DOI: 10.1038/ng0297-207] [Citation(s) in RCA: 133] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The transforming growth factor beta 1 (TGF beta 1) signalling pathway is important in embryogenesis and has been implicated in hereditary haemorrhagic telangiectasia (HHT), atherosclerosis, tumorigenesis and immunomodulation. Therefore, identification of factors which modulate TGF beta 1 bioactivity in vivo is important. On a mixed genetic background, approximately 50% Tgfb1-/- conceptuses die midgestation from defective yolk sac vasculogenesis. The other half are developmentally normal but die three weeks postpartum. Intriguingly, the vascular defects of Tgfb1-/- mice share histological similarities to lesions seen in HHT patients. It has been suggested that dichotomy in Tgfb1-/- lethal phenotypes is due to maternal TGF beta 1 rescue of some, but not all, Tgfb1-/- embryos12. Here we show that the Tgfb1-/- phenotype depends on the genetic background of the conceptus. In NIH/Ola, C57BL/6J/Ola and F1 conceptuses, Tgfb1-/- lethality can be categorized into three developmental classes. A major codominant modifier gene of embryo lethality was mapped to proximal mouse chromosome 5, using a genome scan for non-mendelian distribution of alleles in Tgfb1-/- neonatal animals which survive prenatal lethality. This gene accounts for around three quarters of the genetic effect between mouse strains and can, in part, explain the distribution of the three lethal phenotypes. This approach, using neonatal DNA samples, is generally applicable to identification of loci that influence the effect of early embryonic lethal mutations, thus furthering knowledge of genetic interactions that occur during early mammalian development in vivo.
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Affiliation(s)
- M Bonyadi
- Department of Medical Genetics, Glasgow University, Duncan Guthrie Institute, Yorkhill, UK
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26
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Hughes DC, Allen J, Morley G, Sutherland K, Ahmed W, Prosser J, Lettice L, Allan G, Mattei MG, Farrall M, Hill RE. Cloning and sequencing of the mouse Gli2 gene: localization to the Dominant hemimelia critical region. Genomics 1997; 39:205-15. [PMID: 9027508 DOI: 10.1006/geno.1996.4468] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The GLI family of zinc finger genes has been implicated in both neoplastic and developmental disorders. We have cloned and sequenced the mouse homolog of the zinc finger gene Gli2 and demonstrated significant similarity to the human GLI3 gene. We have also localized Gli2 to mouse chromosome 1, in the vicinity of the morphogenetic mutation Dominant hemimelia (Dh), which is characterized by tibial hemimelia, poly/oligodactyly, and a number of visceral abnormalities, most strikingly absence of the spleen. Using a Gli2-associated microsatellite, we demonstrated no recombination between Dh and Gli2 in a Dh intraspecific backcross. Gli2 is expressed in Dh heterozygotes and homozygotes. However, using a combination of mismatch analysis and direct sequencing, we have failed to identify any mutations in the coding sequence of Gli2 from Dh. We have also demonstrated that it is unlikely that there are any Gli genes in the mouse genome in addition to the previously described Gli, Gli2, and Gli3.
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Affiliation(s)
- D C Hughes
- MRC Human Genetics Unit, Western General Hospital, Edinburgh, United Kingdom.
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27
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Affiliation(s)
- M Farrall
- Wellcome Trust Centre for Human Genetics, University of Oxford, UK
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28
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Abstract
The candidacy of angiotensinogen for a role in the genetic basis of hypertension is supported by the observation that plasma angiotensinogen levels track with raised blood pressure through families. In addition, transgenic mice with overexpression of a rat angiotensinogen gene develop hypertension, and knockout mice with a disrupted gene and absent angiotensinogen production develop low blood pressure. There are now two studies in populations of white European origin and one in African Caribbeans providing support for a role of the angiotensinogen gene locus in human essential hypertension.
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Affiliation(s)
- M Caulfield
- Department of Clinical Pharmacology, St Bartholomew's Hospital, London, UK
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29
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30
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Abstract
Genome-wide scans for linkage of chromosome regions to type 1 diabetes in affected sib pair families have revealed that the major susceptibility locus resides within the major histocompatibility complex (MHC) on chromosome 6p21 (lambda S = 2.4). It is recognized that the MHC contains multiple susceptibility loci (referred to collectively as IDDM1), including the class II antigen receptor genes, which control the major pathological feature of the disease: T-lymphocyte-mediated autoimmune destruction of the insulin-producing pancreatic beta cells. However, the MHC genes, and a second locus, the insulin gene minisatellite on chromosome 11p15 (IDDM2; lambda S = 1.25), cannot account for all of the observed clustering of disease in families (lambda S = 15), and the scans suggested the presence of other susceptibility loci scattered throughout the genome. There are four additional loci for which there is currently sufficient evidence from linkage and association studies to justify fine mapping experiments: IDDM4 (FGF3/11q13), IDDM5 (ESR/6q22), IDDM8 (D6S281/6q27) and IDDM12 (CTLA-4/2q33). IDDM4, 5 and 8 were detected by genome scanning, and IDDM12 by a candidate gene strategy. Seven other named loci are not discounted but remain to be replicated widely. Multiple susceptibility loci were expected as genome-wide scans of the mouse model of type 1 diabetes had shown that although the MHC is the major mouse locus, at least 13 genes unlinked to the MHC are involved in the development of disease. Genome-wide scans using 1000 affected sibpair families will be required to be confident that all genes with effects on familial clustering equivalent to the insulin gene locus (lambda S = 1.25) have been detected. The identification of aetiological determinants requires exclusion of hitchhiking polymorphisms in regions of linkage disequilibrium, as demonstrated for the MHC and the insulin gene loci, and functional studies implicating the disease-associated variant in pathogenesis. Ultimately, targeting of specific candidate mutations in mice by homologous recombination and replacement will be necessary to prove the primary role of any candidate mutation.
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Affiliation(s)
- J A Todd
- Wellcome Trust Centre for Human Genetics, Nuffield Departments of Surgery, University of Oxford, Headington, UK
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31
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McKenzie CA, Julier C, Forrester T, McFarlane-Anderson N, Keavney B, Lathrop GM, Ratcliffe PJ, Farrall M. Segregation and linkage analysis of serum angiotensin I-converting enzyme levels: evidence for two quantitative-trait loci. Am J Hum Genet 1995; 57:1426-35. [PMID: 8533773 PMCID: PMC1801409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Human serum angiotensin I-converting enzyme (ACE) levels vary substantially between individuals and are highly heritable. Segregation analysis in European families has shown that more than half of the total variability in ACE levels is influenced by quantitative-trait loci (QTL). One of these QTLs is located within or close to the ACE locus itself. Combined segregation/linkage analysis in a series of African Caribbean families from Jamaica shows that the ACE insertion-deletion polymorphism is in moderate linkage disequilibrium with an ACE-linked QTL. Linkage analysis with a highly informative polymorphism at the neighboring growth-hormone gene (GH) shows surprisingly little support for linkage (LOD score [Z] = 0.12). An extended analysis with a two-QTL model, where an ACE-linked QTL interacts additively with an unlinked QTL, significantly improves both the fit of the model (P = .002) and the support for linkage between the ACe-linked QTL interacts additively with an unlinked QTL, significantly improves both the fit of the model (P = .002) and the support for linkage between the ACe-linked QTL and GH polymorphism (Z = 5.0). We conclude that two QTLs jointly influence serum ACE levels in this population. One QTL is located within or close to the ACE locus and explains 27% of the total variability; the second QTL is unlinked to the ACE locus and explains 52% of the variability. The identification of the molecular mechanisms underlying both QTLs is necessary in order to interpret the role of ACE in cardiovascular disease.
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Affiliation(s)
- C A McKenzie
- Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom
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32
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Abstract
The Maximum Lod Score method for affected relative-pair analysis, introduced by Risch, is a powerful method for detecting linkage between an autosomal marker locus and disease. In order to use the method to detect linkage to markers on the X-chromosome, some modification is necessary. Here we extend the method to be applicable to X-chromosomal data, and derive genetic restrictions on the haplotype-sharing probabilities analogous to the 'possible triangle' restrictions described by Holmans for the autosomal case. Size criteria are derived using asymptotic theory and simulation, and the power is calculated for a number of possible underlying models. The method is applied to data from 284 type 1 diabetic families and evidence is found for the presence of one or more diabetogenic loci on the X-chromosome.
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Affiliation(s)
- H J Cordell
- Nuffield Department of Surgery, Wellcome Trust Centre for Human Genetics, University of Oxford
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33
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Cordell HJ, Todd JA, Bennett ST, Kawaguchi Y, Farrall M. Two-locus maximum lod score analysis of a multifactorial trait: joint consideration of IDDM2 and IDDM4 with IDDM1 in type 1 diabetes. Am J Hum Genet 1995; 57:920-34. [PMID: 7573054 PMCID: PMC1801514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
To investigate the genetic component of multifactorial diseases such as type 1 (insulin-dependent) diabetes mellitus (IDDM), models involving the joint action of several disease loci are important. These models can give increased power to detect an effect and a greater understanding of etiological mechanisms. Here, we present an extension of the maximum lod score method of N. Risch, which allows the simultaneous detection and modeling of two unlinked disease loci. Genetic constraints on the identical-by-descent sharing probabilities, analogous to the "triangle" restrictions in the single-locus method, are derived, and the size and power of the test statistics are investigated. The method is applied to affected-sib-pair data, and the joint effects of IDDM1 (HLA) and IDDM2 (the INS VNTR) and of IDDM1 and IDDM4 (FGF3-linked) are assessed with relation to the development of IDDM. In the presence of genetic heterogeneity, there is seen to be a significant advantage in analyzing more than one locus simultaneously. Analysis of these families indicates that the effects at IDDM1 and IDDM2 are well described by a multiplicative genetic model, while those at IDDM1 and IDDM4 follow a heterogeneity model.
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Affiliation(s)
- H J Cordell
- Nuffield Department of Surgery, Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom
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34
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Caulfield M, Lavender P, Newell-Price J, Farrall M, Kamdar S, Daniel H, Lawson M, De Freitas P, Fogarty P, Clark AJ. Linkage of the angiotensinogen gene locus to human essential hypertension in African Caribbeans. J Clin Invest 1995; 96:687-92. [PMID: 7635961 PMCID: PMC185250 DOI: 10.1172/jci118111] [Citation(s) in RCA: 135] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The renin-angiotensin system regulates blood pressure and sodium balance. The angiotensinogen gene which encodes the key substrate within this system has been linked to essential hypertension in White Europeans. It has been suggested that people of West African ancestry may have a different genetic basis for hypertension. In this study we have tested whether there is linkage of the angiotensinogen gene to essential hypertension in African Caribbeans from St. Vincent and the Grenadines. DNA from 63 affected sibling pairs with hypertension was tested for linkage by analyzing whether there was excess allele sharing among siblings genotyped using an angiotensinogen dinucleotide repeat sequence. There was significant support for linkage (T = 3.07, P = 0.001) and association of this locus to hypertension (chi 2 = 50.2, 12 degrees of freedom, P << 0.001). A DNA polymorphism which alters methionine to threonine at position 235 (M235T) within the angiotensinogen peptide has been associated previously with hypertension. However, we found no association of this variant with hypertension in this study. These findings provide support for linkage and association of the angiotensinogen locus to hypertension in African Caribbeans and suggest some similarities in the genetic basis of essential hypertension in populations of different ethnicity.
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Affiliation(s)
- M Caulfield
- Department of Clinical Pharmacology, St. Bartholomew's Hospital, London, United Kingdom
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35
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Munroe PB, Daniel HI, Farrall M, Lawson M, Bouloux PM, Caulfield MJ. Absence of genetic linkage between polymorphisms of the insulin receptor gene and essential hypertension. J Hum Hypertens 1995; 9:669-70. [PMID: 8523386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This study evaluated whether hypertensive siblings had excess sharing of RsaI and SstI alleles of the insulin receptor gene compared with a random population. Thirty families consisting of 60 affected individuals with established hypertension were genotyped for the RsaI and SstI restriction fragment length polymorphisms and the resulting genotype data was analysed using the affected pedigree member method of linkage analysis. The hypertensive siblings were found to have increased sharing of INSR alleles; however, this linkage could not be confirmed using a maximum LOD score method. Thus, the results from this study do not support a role for the INSR gene in the genesis of essential hypertension in the population studied.
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Affiliation(s)
- P B Munroe
- Department of Clinical Pharmacology, St. Bartholomew's Hospital, London, UK
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36
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Dunnill MG, Richards AJ, Milana G, Mollica F, Atherton D, Winship I, Farrall M, al-Imara L, Eady RA, Pope FM. Genetic linkage to the type VII collagen gene (COL7A1) in 26 families with generalised recessive dystrophic epidermolysis bullosa and anchoring fibril abnormalities. J Med Genet 1994; 31:745-8. [PMID: 7837248 PMCID: PMC1050118 DOI: 10.1136/jmg.31.10.745] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
To strengthen the evidence for genetic linkage to COL7A1, we have studied 26 generalised recessive dystrophic epidermolysis bullosa (EB) families of British, Italian, Irish, and South African origin. We chose two linkage markers, a COL7A1 PvuII intragenic polymorphism and a highly informative anonymous microsatellite marker, D3S1100, which maps close to the COL7A1 locus at 3p21.1-3. Diagnosis was established by family history, clinical examination, immunofluorescence, and ultrastructural studies. The PvuII marker was informative in 16 families with a maximum lod score (Zmax) of 3.51 at recombination fraction (theta) = 0. The D3S1100 microsatellite was informative in 24 out of 25 families with Zmax = 6.8 at theta = 0.05 (Z = 4.94 at theta = 0) and no obligatory recombination events. These data strongly suggest that COL7A1 mutations cause EB in these families and, combined with previous studies, indicate locus homogeneity. The importance of anchoring fibrils for dermal-epidermal adhesion is further underlined. D3S1100 may later prove useful in prenatal diagnosis of this disease, if used in combination with other markers.
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Affiliation(s)
- M G Dunnill
- MRC Clinical Research Centre, Northwick Park Hospital, Middlesex, UK
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37
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Cullen P, Farren B, Scott J, Farrall M. Complex segregation analysis provides evidence for a major gene acting on serum triglyceride levels in 55 British families with familial combined hyperlipidemia. Arterioscler Thromb 1994; 14:1233-49. [PMID: 8049184 DOI: 10.1161/01.atv.14.8.1233] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Familial combined hyperlipidemia (FCHL) was first described as an autosomal dominant inherited trait with primary action on triglyceride levels and secondary effects on cholesterol metabolism. This conclusion has since been questioned by several groups despite subsequent supportive biochemical and metabolic studies. To reexplore the genetics of FCHL, we assembled 55 families from the United Kingdom comprising 559 persons ascertained through probands with both hypercholesterolemia and hypertriglyceridemia. The results of univariate complex segregation analysis were consistent with a major gene acting on triglyceride and explaining two thirds of the genetic variability and 20% of the phenotypic variance in triglyceride levels. Univariate analysis did not identify a major genetic component acting on cholesterol levels. Bivariate segregation analysis rejected a major gene model. We also reexamined the original FCHL pedigrees collected by Goldstein et al and obtained results similar to those in the UK families. The prospects for mapping putative major genes determining triglyceride levels in FCHL patients by linkage analysis are discussed.
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Affiliation(s)
- P Cullen
- MRC Molecular Medicine Group, Royal Postgraduate Medical School, Hammersmith Hospital, London, England, UK
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38
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Abstract
BACKGROUND The renin-angiotensin system is a powerful pressor system with a major influence on salt and water homeostasis. Angiotensinogen (also called renin substrate) is a key component of this system; it is cleaved by renin to yield angiotensin I, which is then cleaved by angiotensin-converting enzyme to yield angiotensin II. The observation that plasma angiotensinogen levels correlate with blood pressure and track through families suggests that angiotensinogen may have a role in essential hypertension. We therefore investigated whether there is linkage between the angiotensinogen gene on chromosome 1q42-43 and essential hypertension. METHODS Samples of DNA from 63 white European families in which two or more members had essential hypertension were tested for linkage of the angiotensinogen gene to this disorder. Affected cousins, nephews, nieces, and half-siblings were included when possible. To test for linkage, we used as a marker a dinucleotide-repeat sequence flanking this gene, and we employed the affected-pedigree-member method of linkage analysis. Two molecular variants of the angiotensinogen gene, one encoding threonine instead of methionine at position 235 (M235T) and the other encoding methionine rather than threonine at position 174 (T174M), were also tested for possible association with essential hypertension. RESULTS We found significant linkage (t = 5.00, P < 0.001) and association (chi-square = 53.3, P < 0.001) of the angiotensinogen-gene locus to essential hypertension in the 63 multiplex families. This linkage was consistently maintained in the subgroup of subjects with diastolic pressure above 100 mm Hg and in the subgroups classified according to sex. It has been proposed previously that T174M and M235T are associated with essential hypertension. However, we found no association in our population between either polymorphism and this disorder. CONCLUSIONS This study provides strong and consistent support for the linkage to essential hypertension of regions within or close to the angiotensinogen gene. Precisely how mutations in this region may result in hypertension remains to be determined.
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Affiliation(s)
- M Caulfield
- Department of Clinical Pharmacology, St. Bartholomew's Hospital, London, United Kingdom
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39
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Newton R, Stanier P, Loughna S, Henderson DJ, Forbes SA, Farrall M, Jensson O, Moore GE. Linkage analysis of 62 X-chromosomal loci excludes the X chromosome in an Icelandic family showing apparent X-linked recessive inheritance of neural tube defects. Clin Genet 1994; 45:241-9. [PMID: 8076409 DOI: 10.1111/j.1399-0004.1994.tb04149.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We report here the findings of a linkage analysis, involving numerous markers from the human X chromosome, in an attempt to localise a putative gene causing apparent X-linked spina bifida and anencephaly (SBA) in a large Icelandic pedigree. Two-point linkage analysis was performed using markers from 62 informative loci in this family. Although small positive lod scores were found at a number of these loci, none reached the significance level for linkage. Haplotypes were extensively analysed and found to exclude linkage to the X chromosome.
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Affiliation(s)
- R Newton
- Action Research Laboratory for the Molecular Biology of Fetal Development, Royal Postgraduate Medical School, London, UK
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40
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Twells R, Yenchitsomanus PT, Sirinavin C, Allotey R, Poungvarin N, Viriyavejakul A, Cemal C, Weber J, Farrall M, Rodprasert P. Autosomal dominant cerebellar ataxia with dementia: evidence for a fourth disease locus. Hum Mol Genet 1994; 3:177-80. [PMID: 8162021 DOI: 10.1093/hmg/3.1.177] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The autosomal dominant cerebellar ataxias have proved particularly difficult to classify due to the lack of phenotypic concordance both within and between families. Genetic heterogeneity has been established, and disease loci for spinal cerebellar ataxia have been assigned to chromosomes 6 (SCA1), 12 (SCA2) and 14 (Machado Joseph disease (MJD)). Genetic analysis performed on a large Thai kindred with autosomal dominant cerebellar ataxia, in which frontal lobe signs and dementia are commonly observed in affected family members, exclude linkage to the SCA1, SCA2 and MJD loci. This demonstrates that mutation in at least one further locus can cause spinal cerebellar ataxia, indicating the need for caution in the use of markers for predictive testing or prenatal diagnosis these disorders.
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Affiliation(s)
- R Twells
- Department of Biochemistry and Molecular Genetics, St Mary's Hospital Medical School, Imperial College, London, UK
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41
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FitzPatrick D, Farrall M. An estimation of the number of susceptibility loci for isolated cleft palate. J Craniofac Genet Dev Biol 1993; 13:230-235. [PMID: 8288730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The existence of a major gene (or genes) that contributes significantly to the familial clustering of cleft lip with or without cleft palate (CL(P)) has been suggested by genetic epidemiology studies and supported by patient-control genotype association studies with a candidate gene. Here we present an analysis of the familial recurrence risk data for isolated cleft palate (CP) and show that an oligogenic model with six genes of equal effect fits the data best. The discrimination between alternative models is, however, poor and a major locus that explains half of the familial recurrence is plausible. The prospects for identification of susceptibility loci for CP are discussed.
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Affiliation(s)
- D FitzPatrick
- Duncan Guthrie Institute of Medical Genetics, Yorkhill, Glasgow, U.K
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42
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43
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Farrall M. Inheritance of chronic inflammatory bowel disease. BMJ 1993; 306:651. [PMID: 8461833 PMCID: PMC1676929 DOI: 10.1136/bmj.306.6878.651-b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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44
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Farrall M, Buetow KH, Murray JC. Resolving an apparent paradox concerning the role of TGFA in CL/P. Am J Hum Genet 1993; 52:434-7. [PMID: 8094269 PMCID: PMC1682186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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45
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Chamberlain S, Farrall M, Shaw J, Wilkes D, Carvajal J, Hillerman R, Doudney K, Harding AE, Williamson R, Sirugo G. Genetic recombination events which position the Friedreich ataxia locus proximal to the D9S15/D9S5 linkage group on chromosome 9q. Am J Hum Genet 1993; 52:99-109. [PMID: 8434613 PMCID: PMC1682111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The absence of recombination between the mutation causing Friedreich ataxia and the two loci which originally assigned the disease locus to chromosome 9 has slowed attempts to isolate and characterize the genetic defect underlying this neurodegenerative disorder. A proximity of less than 1 cM to the linkage group has been proved by the generation of high maximal lod score (Z) to each of the two tightly linked markers D9S15 (Z = 96.69; recombination fraction [theta] = .01) and D9S5 (Z = 98.22; theta = .01). We report here recombination events which indicate that the FRDA locus is located centromeric to the D9S15/D9S5 linkage group, with the most probable order being cen-FRDA-D9S5-D9S15-qter. However, orientation of the markers with respect to the centromere, critical to the positional cloning strategy, remains to be resolved definitively.
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Affiliation(s)
- S Chamberlain
- Department of Biochemistry and Molecular Genetics, St. Mary's Hospital Medical School, London, England
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46
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Ramsay M, Colman MA, Stevens G, Zwane E, Kromberg J, Farrall M, Jenkins T. The tyrosinase-positive oculocutaneous albinism locus maps to chromosome 15q11.2-q12. Am J Hum Genet 1992; 51:879-84. [PMID: 1415228 PMCID: PMC1682821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Tyrosinase-positive oculocutaneous albinism (ty-pos OCA), an autosomal recessive disorder of the melanin biosynthetic pathway, is the most common type of albinism occurring worldwide. In southern African Bantu-speaking negroids it has an overall prevalence of about 1/3,900. Since the basic biochemical defect is unknown, a linkage study with candidate loci, candidate chromosomal regions, and random loci was undertaken. The ty-pos OCA locus was found to be linked to two arbitrary loci, D15S10 and D15S13, in the Prader-Willi/Angelman chromosomal region on chromosome 15q11.2-q12. The pink-eyed dilute locus, p, on mouse chromosome 7, maps close to a region of homology on human chromosome 15q, and we postulate that the ty-pos OCA and p loci are homologous.
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Affiliation(s)
- M Ramsay
- Department of Human Genetics, School of Pathology, South African Institute for Medical Research, Johannesburg
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47
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al-Imara L, Richards AJ, Eady RA, Leigh IM, Farrall M, Pope FM. Linkage of autosomal dominant dystrophic epidermolysis bullosa in three British families to the marker D3S2 close to the COL7A1 locus. J Med Genet 1992; 29:381-2. [PMID: 1377750 PMCID: PMC1015986 DOI: 10.1136/jmg.29.6.381] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Linkage of the anonymous marker D3S2 at 3p21 has been shown in three British families with dominant dystrophic epidermolysis bullosa with a combined lod score of 6.75 at theta = 0. This locus is close to the collagen type VII locus implying that abnormalities of this gene cause dominant dystrophic epidermolysis bullosa.
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Affiliation(s)
- L al-Imara
- Dermatology Research Group, Northwick Park Hospital, Harrow, Middlesex
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48
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Farrall M, Holder S. Familial recurrence-pattern analysis of cleft lip with or without cleft palate. Am J Hum Genet 1992; 50:270-7. [PMID: 1346481 PMCID: PMC1682459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023] Open
Abstract
Cleft lip with or without cleft palate (CL/P) is a common congenital malformation with an incidence in European white populations of about 1/1,000. The familial clustering of CL/P has been extensively characterized, and epidemiological studies have proposed monogenic models (with reduced penetrance), multifactorial/threshold models, and mixed major-gene/multifactorial models to explain its inheritance. The recognition of an association between two RFLPs at the transforming growth factor alpha (TGFA) locus and CL/P supports a major-gene component to the etiology of CL/P. Risch has shown that the recurrence risk ratio lambda R (risk to relatives, vs. population prevalence) is a useful pointer to the mode of inheritance. Here we further develop the use of lambda R to analyze recurrence-risk data for CL/P. Recurrence risks for first-, second-, and third-degree relatives equate well with oligogenic models with as few as four loci. A monogenic/additive model is strongly rejected. The limited available twin data are also consistent with this model. A "major gene" interacting epistatically with an oligogenic background is shown to be a plausible alternative. Power calculations for a linkage study to map the CL/P major-risk locus suggest that a sample of 50 affected sib pairs will be adequate, but linkage to minor-risk loci will require very much larger samples.
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Affiliation(s)
- M Farrall
- Division of Molecular Medicine, Medical Research Council Clinical Research Centre, Harrow, England
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49
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Dorin JR, Emslie E, Hanratty D, Farrall M, Gosden J, Porteous DJ. Gene targeting for somatic cell manipulation: rapid analysis of reduced chromosome hybrids by Alu-PCR fingerprinting and chromosome painting. Hum Mol Genet 1992; 1:53-9. [PMID: 1363778 DOI: 10.1093/hmg/1.1.53] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The techniques of reverse genetics rely heavily on parasexual methods for manipulating the human genome. However, the application of somatic cell genetics is severely limited by the availability of suitable endogenous selectable markers in the genome. We have addressed this problem by targeting a universally selectable marker into a predetermined region of the genome, using a stringent selection for homologous recombination. Correct gene targeting to human chromosome 7q11 was screened for by Southern blotting and confirmed by fluorescent in situ hybridization. Reduced chromosome 7 hybrids were generated by chromosome mediated gene transfer and selection for the neo gene. The resultant transgenomes were characterized by a combination of L1 fingerprinting, locus specific marker analysis, Alu-PCR and chromosome 'painting'. Alu-PCR and L1 'fingerprints' are complementary and mutually consistent. Chromosome 'painting' reflects and extends the results obtained for specific marker co-transfer. Thus Alu-PCR 'fingerprinting' and 'painting' combine to rapidly provide an accurate picture of transgenome content and complexity. Gene targeting, chromosome tagging and subsequent isolation can be applied to any region of the genome for which a molecular probe is available.
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Affiliation(s)
- J R Dorin
- Human Genetics Unit, Western General Hospital, Edinburgh, UK
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50
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Dixon MJ, Haan E, Baker E, David D, McKenzie N, Williamson R, Mulley J, Farrall M, Callen D. Association of Treacher Collins syndrome and translocation 6p21.31/16p13.11: exclusion of the locus from these candidate regions. Am J Hum Genet 1991; 48:274-80. [PMID: 1671319 PMCID: PMC1683002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Treacher Collins syndrome (TCS) is an autosomal dominant defect of craniofacial development which has not been chromosomally localized. We have identified a mother and two children who have TCS and also a balanced translocation t(6;16)(p21.31;p13.11), which suggested the possibility that the TCS locus might be located at one of the translocation breakpoints. These were defined by in-situ hybridization as 6p21.31 (by using loci in the HLA complex defined by the probes p45.1DP beta 003/HLA-DPB2 and pRS5.10/HLA class I chain) and 16p13.11 (by using probes pACHF1.3.2/D16S8 and VK45/D16S131). Pairwise and multipoint linkage analysis using localized chromosome 6 probes and chromosome 16 probes in 12 unrelated TCS families with multiple affected siblings excluded the TCS locus from proximity to both translocation breakpoints. These data were confirmed when a third affected child, who did not exhibit the translocation, was born to the mother.
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Affiliation(s)
- M J Dixon
- Department of Cell and Structural Biology, University of Manchester, England
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