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Biomedical subjects

Alan F Wright

Publications and source records attributed to Alan F Wright.

At least 19 recordsLinked to original sources
PubMed2008

Runs of homozygosity in European populations.

Estimating individual genome-wide autozygosity is important both in the identification of recessive disease variants via homozygosity mapping and in the investigation of the effects of genome-wide homozygosity on traits of biomedical importance. Approaches have tended to involve either single-point estimates or rather complex multipoint methods of inferring individual autozygosity, all on the basis of limited marker data. Now, with the availability of high-density genome scans, a multipoint, observational method of estimating individual autozygosity is possible. Using data from a 300,000 SNP panel in 2618 individuals from two isolated and two more-cosmopolitan populations of European origin, we explore the potential of estimating individual autozygosity from data on runs of homozygosity (ROHs). Termed F(roh), this is defined as the proportion of the autosomal genome in runs of homozygosity above a specified length. Mean F(roh) distinguishes clearly between subpopulations classified in terms of grandparental endogamy and population size. With the use of good pedigree data for one of the populations (Orkney), F(roh) was found to correlate strongly with the inbreeding coefficient estimated from pedigrees (r = 0.86). Using pedigrees to identify individuals with no shared maternal and paternal ancestors in five, and probably at least ten, generations, we show that ROHs measuring up to 4 Mb are common in demonstrably outbred individuals. Given the stochastic variation in ROH number, length, and location and the fact that ROHs are important whether ancient or recent in origin, approaches such as this will provide a more useful description of genomic autozygosity than has hitherto been possible.

Adolescent↗
PubMed2007

Effects of genome-wide heterozygosity on a range of biomedically relevant human quantitative traits.

The dramatic changes in human population structure over the last 200 years have resulted in significant levels of outbreeding, which, in turn, is predicted to lead to increased levels of individual genetic diversity (genome-wide heterozygosity, h). To investigate possible effects of these large demographic changes on global health, we studied the effect of h, measured as relative heterozygosity, h(R), on 15 disease-related traits in four groups of individuals with widely differing ancestral histories (ranging from outbred to inbred) from the Dalmatian islands in Croatia. Higher levels of h(R), estimated using 1184 STR/indel markers, were found in the outbred group (P < 0.0001) and were associated with lower blood pressure (BP) and total/LDL cholesterol (P = 0.01 and 0.01, respectively) after controlling for other factors, with BP showing a strong sex effect (males P > 0.5 and females P = 0.002). These findings, if replicated, suggest that h(R) be considered as a genetic risk factor in genetic epidemiological studies on common disease traits. They are consistent with the well-known effects of heterosis (hybrid vigour) described when outcrossing animals and plants. Outbreeding resulting from urbanization and migration from traditional population subgroups may be leading to increasing h(R) and may have beneficial effects on a range of traits associated with human health and disease. Other traits, such as age at menarche, IQ and lifespan, which have been changing during the decades of urbanization, may also have been influenced by demographic factors.

Age Factors↗
PubMed2007

RPGR mutation analysis and disease: an update.

Mutations in the retinitis pigmentosa GTPase regulator (RPGR) gene are the most common single cause of retinitis pigmentosa, accounting for up to 15 to 20% of cases in Caucasians. A total of 240 different RPGR mutations have been reported, including 24 novel ones in this work, which are associated with X-linked retinitis pigmentosa (XLRP) (95%), cone, cone-rod dystrophy, or atrophic macular atrophy (3%), and syndromal retinal dystrophies with ciliary dyskinesia and hearing loss (2%). All disease-causing mutations occur in one or more RPGR isoforms containing the carboxyl-terminal exon open reading frame 15 (ORF15), which are widely expressed but show their highest expression in the connecting cilia of rod and cone photoreceptors. Of reported RPGR mutations, 55% occur in a glutamic acid-rich domain within exon ORF15, which accounts for only 31% of the protein. RPGR forms complexes with a variety of other proteins and appears to have a role in microtubular organization and transport between photoreceptor inner and outer segments.

Animals↗
PubMed2006

Molecular genetics of retinitis pigmentosa in two Romani (Gypsy) families.

PURPOSE: To identify the disease-causing mutations in two large Bulgarian Romani (Gypsy) pedigrees: one with autosomal dominant retinitis pigmentosa (adRP) with partial penetrance and the other with severe X-linked RP (xlRP). METHODS: Detailed clinical investigations were undertaken and genomic DNA was extracted from blood samples. DNA was analyzed by PCR amplification with gene-specific primers and direct genomic sequencing. RESULTS: Analysis of the complete coding sequence of PRPF31 in the adRP family led to the identification of a new heterozygous splice site mutation IVS6+1G>T. RPGR mutation screening in affected male individuals in the X-linked RP family identified a hemizygous c.ORF15+652_653delAG mutation. Interestingly this mutation was found in a homozygous state in one severely affected female from the family. CONCLUSIONS: In this first report of molecular genetic analysis of retinitis pigmentosa in Romani families, we describe a novel PRPF31 mutation and present the first case of a homozygous mutation in the RPGR gene in a female individual.

Adolescent↗
PubMed2006

Disease mechanisms in late-onset retinal macular degeneration associated with mutation in C1QTNF5.

Late-onset retinal macular degeneration (L-ORMD) is an autosomal dominant condition resembling age-related macular degeneration (AMD) in which a key pathological feature is a thick extracellular sub-retinal pigment epithelial (RPE) deposit. L-ORMD is caused by mutation in the C1QTNF5 (CTRP5) short-chain collagen gene, but the disease mechanism is unknown. Here, we first show that wild-type C1QTNF5 is secreted, whereas mutant C1QTNF5 is misfolded and retained within the endoplasmic reticulum (ER). Secondly, the ER retained mutant protein has a shorter half-life than wild-type C1QTNF5 and is preferentially degraded by proteasomes. Thirdly, C1QTNF5 is shown to interact with the membrane-type frizzled related protein (MFRP), on the basis of yeast two-hybrid, protein pull-down and co-immunoprecipitation assays and RPE co-localization. These data suggest that L-ORMD is due to insufficient levels of secreted C1QTNF5, compromised RPE cell function resulting from ER retention of the mutant protein or both mechanisms.

Age of Onset↗
PubMed2006

A microdeletion in Xp11.3 accounts for co-segregation of retinitis pigmentosa and mental retardation in a large kindred.

In a previous report, Aldred et al. [1994] described a 5-generation family in which severe retinitis pigmentosa (RP) co-segregates with mild-moderate mental retardation as an X-linked recessive phenotype mapping to the broad interval between Xp21-q21. We re-examined this family, initially analyzing RP2, a gene in the disease interval that was identified as a cause of RP after the initial report of this family. We found that the male propositus lacked the 5' three exons of RP2 and that RP2 marks the centromeric boundary of a 1.27 Mb deletion that includes two other annotated genes (SLC9A7, CHST7), one predicted transcript encoding a zinc finger protein (FLJ20344) and two highly conserved miRNAs (mir221, mir222). We conclude that this family is segregating a contiguous gene deletion and that the absence of a functional RP2 accounts, at least in part, for the retinal degeneration while deletion of one or more of the other genes is likely responsible for the mental retardation phenotype.

Antiporters↗
PubMed2006

Developmental and tissue expression of Xenopus laevis RPGR.

PURPOSE: The present study examined the developmental and tissue expression of the retinitis pigmentosa GTPase regulator (RPGR) gene in Xenopus laevis. METHODS: The cDNA for X. laevis RPGR (XRPGR) was isolated from adult eye mRNA by reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends. The deduced peptide sequence was aligned with RPGR orthologues. Gene expression was examined by whole-mount in situ hybridization and RT-PCR. The localization of XRPGR in X. laevis photoreceptor cells and XTC-2 cells was determined by immunostaining. RESULTS: The XRPGR(ex1-19) isoform encodes a protein of 727 amino acids containing an RCC1 domain and a C-terminal isoprenylation anchorage motif. It shares 33% to 41% amino acid identity with human, mouse, and dog RPGR. The C-terminal exon of the alternatively spliced RPGR(ORF15) isoform is also conserved across species. XRPGR is expressed at the earliest stages of X. laevis development and persists into adulthood, where expression is highest in the eye. XRPGR is expressed in presumptive eye fields (stages 18 to 22), becoming largely restricted to the central retina (stages 28 to 40). XRPGR protein colocalizes with beta-tubulin at the X. laevis ciliary axoneme and with gamma-tubulin at centrosomes in XTC-2 cells. CONCLUSIONS: XRPGR is widely expressed throughout development but shows highest expression after the appearance of the eye primordium and persists in the eye into adulthood. The data are consistent with XRPGR expression in a single microtubular organelle-the centriole or basal body and associated ciliary transitional zone found in modified sensory cilia of photoreceptors and motile cilia.

Amino Acid Sequence↗
PubMed2006

Strategy for mapping quantitative trait loci (QTL) by using human metapopulations.

AIM: To present a novel strategy for mapping quantitative trait loci (QTL), using human metapopulations. The strategy is based on the expectation that in geographic clusters of small and distinct human isolates, a combination of founder effect and genetic drift can dramatically increase population frequency of rare QTL variants with large effect. In such cases, the distribution of QT measurements in an (affected) isolate is expected to deviate from that observed in neighboring isolates. METHODS: We tested this hypothesis in 9 villages from a larger Croatian isolate resource, where 7 Mendelian disorders have been previously reported. The values of 10 physiological and biochemical QTs were measured in a random sample of 1001 individuals (100 inhabitants of each of 9 villages and 101 immigrant controls). RESULTS: Significant over- or under- representation of individuals from specific villages in extreme ends of standardized QT measurement distribution was found 10 times more frequently than expected by chance. The large majority of such clusters of individuals with extreme QT values (34/36, 94.4%) originated from the 6 villages with the most pronounced geographic isolation and endogamy. CONCLUSION: Early epidemiological assessment supports the feasibility of the proposed strategy. Clusters of individuals with extreme QT values responsible for over-representation of single villages can usually be linked to a larger pedigree and may be useful for further QTL mapping, using linkage analysis.

Body Height↗
PubMed2005

Mortality and cancer incidence in women with extra X chromosomes: a cohort study in Britain.

About one woman in 1,000 has an extra X chromosome, but such women have no recognised characteristic somatic features and little is known about their long-term health and cancer risks. We conducted a cohort study of mortality and cancer incidence in 542 women diagnosed with X polysomy at 25 cytogenetic centres in Britain since 1959. Fifty-nine deaths occurred during follow-up to mid-2004. Mortality was significantly raised (standardised mortality ratio (SMR) = 2.5 (95% confidence interval (CI) 1.9-3.2)), with excess deaths due particularly to cardiovascular disease (SMR = 2.5 (95% CI 1.5-3.8)) and respiratory disease (SMR = 4.0 (95% CI 1.7-7.9)). Risks of cancer incidence and cancer mortality overall were not raised, but there was significantly raised mortality from non-Hodgkin's lymphoma (NHL) (SMR = 10.4 (95% CI 1.3-37.6); based on 2 cases). The data indicate that mortality in women diagnosed with X polysomy is considerably raised. The raised risk of NHL is seen also in males with more than one X chromosome, and hence although unexpected and based on small numbers, it might indicate the action of a gene on the X chromosome, possibly in the pseudoautosomal region, that escapes X-inactivation.

Adolescent↗
PubMed2005

Mortality in patients with Klinefelter syndrome in Britain: a cohort study.

CONTEXT: Klinefelter syndrome is characterized by hypogonadism and infertility, consequent on the presence of extra X chromosome(s). There is limited information about long-term mortality in this syndrome because there have been no large cohort studies. OBJECTIVE: Our objective was to investigate mortality in men with Klinefelter syndrome. DESIGN AND SETTING: We obtained data about patients diagnosed with Klinefelter syndrome at almost all cytogenetics centers in Britain, as far back as records were available, and conducted a cohort study of their mortality, overall and by karyotype. PATIENTS: We assessed 3518 patients diagnosed since 1959, followed to mid-2003. OUTCOME MEASURE: The outcome measure was standardized mortality ratio (SMR). RESULTS: A total of 461 deaths occurred. There was significantly raised mortality overall [SMR, 1.5; 95% confidence interval (CI), 1.4-1.7] and from most major causes of death including cardiovascular disease (SMR, 1.3; 95% CI, 1.1-1.5), nervous system disease (SMR, 2.8; 95% CI, 1.6-4.6), and respiratory disease (SMR, 2.3; 95% CI, 1.8-2.9). Mortality was particularly raised from diabetes (SMR, 5.8; 95% CI, 3.4-9.3), epilepsy (SMR, 7.2; 95% CI, 3.1-14.1), pulmonary embolism (SMR, 5.7; 95% CI, 2.5-11.3), peripheral vascular disease (SMR, 7.9; 95% CI, 2.9-17.2), vascular insufficiency of the intestine (SMR, 12.3; 95% CI, 4.0-28.8), renal disease (SMR, 5.0; 95% CI, 2.0-10.3), and femoral fracture (SMR, 39.4; 95% CI, 4.8-142.3). Mortality from ischemic heart disease was significantly decreased (SMR, 0.7; 95% CI, 0.5-0.9). CONCLUSIONS: Patients diagnosed with Klinefelter syndrome have raised mortality from several specific causes. This may reflect hormonal and genetic mechanisms.

Adolescent↗
PubMed2005

Genetic influences on oxidative stress and their association with normal cognitive ageing.

Oxidative stress is hypothesised to play a major role in ageing processes. Reactive oxygen species produced during normal aerobic metabolism damage cellular macromolecules. The brain is particularly susceptible to oxidative stress due to its high rate of aerobic metabolism. We hypothesised that polymorphisms in genes contributing to antioxidant defences are associated with variation in normal cognitive ageing in the absence of dementia. We examined associations between two SNPs (rs2073495 and rs743658) in Lactotransferrin (LTF), a gene involved in iron absorption, and the common M129V SNP in the prion protein gene, PRNP (rs1799990), with cognitive ability and cognitive ageing in a cohort of non-demented individuals born in 1921. All had cognitive ability measured at age 11 in the Scottish Mental Survey of 1932, and again at age 79. No association was identified with LTF. PRNP M129V was significantly related to Moray House Test (MHT) IQ scores at age 79, adjusted for sex and age 11 IQ (p=0.006). Individuals homozygous for the methionine allele performed significantly better than heterozygotes. This study supports the hypothesis that genetic variations in antioxidant defence genes, specifically PRNP, are important influences on the trajectory of normal cognitive ageing. An interaction between PRNP and klotho (KL) genotypes was also identified (p=0.015), highlighting the importance of analysing gene interactions when investigating associations with quantitative traits.

Aged↗
PubMed2005

The functional COMT polymorphism, Val 158 Met, is associated with logical memory and the personality trait intellect/imagination in a cohort of healthy 79 year olds.

A polymorphism (Val 158 Met) in the gene for catechol-O-methyl transferase (COMT) was previously associated with differences in cognitive ability and personality. Here we examine associations between this polymorphism and cognitive ability, cognitive aging, personality and mood in 460 relatively healthy people born in 1921. All had cognitive ability measured at age 11 in the Scottish Mental Survey of 1932, and again at age 79. COMT genotype was not associated with childhood IQ. At age 79, COMT genotype was significantly related to differences in verbal declarative memory (scores on the Logical Memory test; p=0.028) and to scores on the personality trait of intellect/imagination (p=0.023), adjusted for sex and childhood IQ. In both cases the Val/Met heterozygotes had higher scores than both homozygous groups. There were trends toward the heterozygotes having higher scores on the personality traits of agreeableness and conscientiousness. The effect of COMT genotype on Logical Memory scores was independent of the effect of APOE genotype, and similar in effect size. Therefore, COMT genotype may contribute to differences in normal cognitive aging and to differences in some of the major personality traits in old age.

Aged↗
PubMed2005

Cancer incidence and mortality in men with Klinefelter syndrome: a cohort study.

BACKGROUND: Men with Klinefelter syndrome have one or more extra X chromosomes and have endocrine abnormalities. Case reports have led to suggestions that men with Klinefelter syndrome have elevated risks of several cancers, but published cohort studies have been relatively small. We conducted a nationwide cohort study to examine these risks. METHODS: We followed a cohort of 3518 men who had been cytogenetically diagnosed with Klinefelter syndrome in Britain from 1959 through 2002 and compared their cancer incidence and mortality with that of men in the national population. All statistical tests were two-sided. RESULTS: The standardized mortality ratio (SMR) for all cancers was 1.2 (95% confidence interval [CI] = 1.0 to 1.4). Compared with the general population, men with Klinefelter syndrome had higher mortality from lung cancer (SMR = 1.5, 95% CI = 1.0 to 2.0), breast cancer (SMR = 57.8, 95% CI = 18.8 to 135.0), and non-Hodgkin lymphoma (SMR = 3.5, 95% CI = 1.6 to 6.6) and lower mortality from prostate cancer (SMR = 0, 95% CI = 0 to 0.7). The standardized mortality ratios were particularly high for breast cancer among men with 47,XXY mosaicism (SMR = 222.8, 95% CI = 45.9 to 651.0) and for non-Hodgkin lymphoma among men with a 48,XXYY constitution (SMR = 36.7, 95% CI = 4.4 to 132.5). The cancer incidence data corroborated these associations. CONCLUSIONS: These results support a hormonal etiology for breast cancer in men and for prostate cancer and suggest that men with Klinefelter syndrome may be at substantially elevated risks for non-Hodgkin lymphoma, breast cancer, and, perhaps, lung cancer.

Adolescent↗
PubMed2005

RPGR-ORF15, which is mutated in retinitis pigmentosa, associates with SMC1, SMC3, and microtubule transport proteins.

Mutations in the retinitis pigmentosa GTPase regulator (RPGR) gene account for almost 20% of patients with retinitis pigmentosa. Most mutations are detected in alternatively spliced RPGR-ORF15 isoform(s), which are primarily but not exclusively expressed in the retina. We show that, in addition to the axoneme, the RPGR-ORF15 protein is localized to the basal bodies of photoreceptor connecting cilium and to the tip and axoneme of sperm flagella. Mass spectrometric analysis of proteins that were immunoprecipitated from the retinal axoneme-enriched fraction using an anti-ORF15 antibody identified two chromosome-associated proteins, structural maintenance of chromosomes (SMC) 1 and SMC3. Using pulldown assays, we demonstrate that the interaction of RPGR with SMC1 and SMC3 is mediated, at least in part, by the RCC1-like domain of RPGR. This interaction was not observed with phosphorylation-deficient mutants of SMC1. Both SMC1 and SMC3 localized to the cilia of retinal photoreceptors and Madin-Darby canine kidney cells, suggesting a broader physiological relevance of this interaction. Additional immunoprecipitation studies revealed the association of RPGR-ORF15 isoform(s) with the intraflagellar transport polypeptide IFT88 as well as microtubule motor proteins, including KIF3A, p150Glued, and p50-dynamitin. Inhibition of dynein function by overexpressing p50 abrogated the localization of RPGR-ORF15 to basal bodies. Taken together, these results provide novel evidence for the possible involvement of RPGR-ORF15 in microtubule organization and regulation of transport in primary cilia.

Animals↗
PubMed2005

Increased level of linkage disequilibrium in rural compared with urban communities: a factor to consider in association-study design.

Few studies have investigated genetic differentiation within nonisolate European populations, despite the initiation of large national sample collections such as U.K. Biobank. Here, we used short tandem repeat markers to explore fine-scale genetic structure and to examine the extent of linkage disequilibrium (LD) within national subpopulations. We studied 955 unrelated individuals of local ancestry from nine Scottish rural regions and the urban center of Edinburgh, as well as 96 unrelated individuals from the general U.K. population. Despite little overall differentiation on the basis of allele frequencies, there were clear differences among subpopulations in the extent of pairwise LD, measured between a subset of X-linked markers, that reflected presumed differences in the depths of the underlying genealogies within these subpopulations. Therefore, there are strategic advantages in studying rural subpopulations, in terms of increased power and reduced cost, that are lost by sampling across regions or within urban populations. Similar rural-urban contrasts are likely to exist in many other populations with stable rural subpopulations, which could influence the design of genetic association studies and national biobank data collections.

Genetics, Population↗
PubMed2005

KLOTHO genotype and cognitive ability in childhood and old age in the same individuals.

This study examined the influence of a variation in the KLOTHO gene on cognitive ability at age 11 and age 79 in 464 people from the Lothian Birth Cohort 1921 (LBC1921), and at age 11 and age 64 in 451 people in the Aberdeen Birth Cohort 1936 (ABC1936). In the LBC1921, people with the KLOTHO V/V genotype had lower verbal reasoning ability at age 11 and age 79, and lower non-verbal reasoning at age 79, than those with the F/F genotype, or heterozygotes. The effect of the KLOTHO polymorphism on cognition at age 79 was non-significant when adjusted for IQ at age 11. In this sample, KLOTHO V allele status accounts for about 2% of the variance in life-long traits related to verbal and non-verbal reasoning, but not to age-related cognitive change. These results were not replicated in the ABC1936 sample. In a combined analysis of the LBC1921 and the ABC1936 cohorts there was a significant KLOTHOxsex interaction: women with the V/V genotype had lower non-verbal reasoning scores at age 79, after adjustment for cognitive ability at age 11. Variation in the KLOTHO gene is a possible contributor to life-long reasoning differences in humans and/or to the ageing of non-verbal reasoning, especially in women.

Aged↗