Wellcome Trust Centre for Human Genetics

About: Wellcome Trust Centre for Human Genetics is a facility organization based out in Oxford, United Kingdom. It is known for research contribution in the topics: Population & Genome-wide association study. The organization has 2122 authors who have published 4269 publications receiving 433899 citations.

Cholesterol activates the G-protein coupled receptor Smoothened to promote Hedgehog signaling.

Abstract: Cells must communicate with each other to coordinate the development of most tissues and organs. Damage to these communication systems is often seen in degenerative disorders and in cancer. The Hedgehog signaling pathway is one of a handful of these critical systems. Reduced Hedgehog signals can lead to birth defects, while excessive Hedgehog signals can lead to skin and brain cancers. Cells transmit the Hedgehog signal by releasing a protein into their surroundings, where it can influence neighboring cells. Despite years of study, it is not understood how the Hedgehog signal is transmitted from the outside to the inside of a receiving cell. Studies first done in flies and subsequently confirmed in humans have shown that a protein called Smoothened is needed to transmit the Hedgehog signal across the membrane of receiving cells. But it was not known how Smoothened carries out this critical signaling step to influence gene activation inside the cell and consequently to change cell behavior. Now, Luchetti, Sircar et al. find that cholesterol, an important component of the cell membrane, directly binds to Smoothened and changes its shape so that it can activate Hedgehog signaling components inside cells. The experiments made use of mouse cells, and the discovery shows that cholesterol may play a previously underappreciated role in cell-to-cell communication. This newly discovered role for cholesterol has implications for diseases, including a unique set of developmental disorders caused by abnormalities in pathways that produce cholesterol in human cells. Furthermore, this unexpected insight into Smoothened’s activity may be clinically important, because Smoothened can cause cancer when mutated and is the target of anti-cancer drugs that are being used in the clinic. Following on from these findings, a major step will be to uncover if and how Hedgehog signals regulate cholesterol to allow Smoothened to transmit these signals across the cell membrane.

Clinical utilisation of a rapid low-pass whole genome sequencing technique for the diagnosis of aneuploidy in human embryos prior to implantation

Abstract: Background The majority of human embryos created using in vitro fertilisation (IVF) techniques are aneuploid. Comprehensive chromosome screening methods, applicable to single cells biopsied from preimplantation embryos, allow reliable identification and transfer of euploid embryos. Recently, randomised trials using such methods have indicated that aneuploidy screening improves IVF success rates. However, the high cost of testing has restricted the availability of this potentially beneficial strategy. This study aimed to harness next-generation sequencing (NGS) technology, with the intention of lowering the costs of preimplantation aneuploidy screening. Methods Embryo biopsy, whole genome amplification and semiconductor sequencing. Results A rapid (<15 h) NGS protocol was developed, with consumable cost only two-thirds that of the most widely used method for embryo aneuploidy detection. Validation involved blinded analysis of 54 cells from cell lines or biopsies from human embryos. Sensitivity and specificity were 100%. The method was applied clinically, assisting in the selection of euploid embryos in two IVF cycles, producing healthy children in both cases. The NGS approach was also able to reveal specified mutations in the nuclear or mitochondrial genomes in parallel with chromosome assessment. Interestingly, elevated mitochondrial DNA content was associated with aneuploidy (p<0.05), a finding suggestive of a link between mitochondria and chromosomal malsegregation. Conclusions This study demonstrates that NGS provides highly accurate, low-cost diagnosis of aneuploidy in cells from human preimplantation embryos and is rapid enough to allow testing without embryo cryopreservation. The method described also has the potential to shed light on other aspects of embryo genetics of relevance to health and viability.

Insulin VNTR allele-specific effect in type 1 diabetes depends on identity of untransmitted paternal allele

Abstract: The IDDM2 type 1 diabetes susceptibility locus was mapped to and identified as allelic variation at the insulin gene (INS) VNTR regulatory polymorphism. In Caucasians, INS VNTR alleles divide into two discrete size classes. Class I alleles (26 to 63 repeats) predispose in a recessive way to type 1 diabetes, while class III alleles (140 to more than 200 repeats) are dominantly protective. The protective effect may be explained by higher levels of class III VNTR-associated INS mRNA in thymus such that elevated levels of preproinsulin protein enhance immune tolerance to preproinsulin, a key autoantigen in type 1 diabetes pathogenesis. The mode of action of IDDM2 is complicated, however, by parent-of-origin effects and possible allelic heterogeneity within the two defined allele classes. We have now analysed transmission of specific VNTR alleles in 1,316 families and demonstrate that a particular class I allele does not predispose to disease when paternally inherited, suggestive of polymorphic imprinting. But this paternal effect is observed only when the father's untransmitted allele is a class III. This allelic interaction is reminiscent of epigenetic phenomena observed in plants (for example, paramutation; ref. 17) and in yeast (for example, trans-inactivation; ref. 18). If untransmitted chromosomes can have functional effects on the biological properties of transmitted chromosomes, the implications for human genetics and disease are potentially considerable.

Meta-analysis and a large association study confirm a role for calpain-10 variation in type 2 diabetes susceptibility.

Abstract: To the Editor: Variation in the calpain-10 gene (CAPN10 [MIM 605286]) was recently linked and associated with type 2 diabetes mellitus (T2DM) susceptibility (Horikawa et al. 2000). The initial linkage of T2DM to chromosome 2 was found in a population of Mexican Americans from Starr County, Texas (Hanis et al. 1996). Specific combinations of three intronic variants, designated “SNP-43,” “SNP-19,” and “SNP-63,” that capture most of the haplotype diversity at CAPN10 were associated with a three-fold increased risk of T2DM in this population and could account for the observed linkage (Horikawa et al. 2000). Subsequent association and linkage studies of these three polymorphisms in other populations have produced conflicting results, with association being observed in some populations (Baier et al. 2000 [Pima Indian]; Cassell et al. 2002 [South Indian]; Garant et al. 2002 [African American]; Malecki et al. 2002 [Polish]; Orho-Melander et al. 2002 [Finnish/Botnia]), but not others (Evans et al. 2001 [British]; Hegele et al. 2001 [Oji-Cree Indians]; Tsai et al. 2001 [Samoan]; Xiang et al. 2001 [Chinese]; Daimon et al. 2002 [Japanese]; Elbein et al. 2002 [whites from Utah]; Fingerlin et al. 2002 [Finnish]; Rasmussen et al. 2002 [Danish and Swedish]; Horikawa et al. 2003 [Japanese]). We previously reported that another variant, SNP-44 (designated “CAPN10-g4841T→C”; minor allele frequency 16%), located in intron 3 and 11 bp from SNP-43, was independently associated with T2DM in whites from the United Kingdom (Evans et al. 2001). Further studies have provided tentative support for a role of SNP-44 in T2DM and related traits: associations with polycystic ovary syndrome (Gonzalez et al. 2002) and with measures of oral glucose tolerance (Wang et al. 2002; Tschritter et al. 2003) have been reported. Functional studies suggest that SNP-44 is located in an enhancer element and might affect CAPN10 expression (Horikawa et al. 2000). Also, in the U.K., German, Japanese, and South Indian populations, SNP-44 is in perfect linkage disequilibrium (r2=1) with a missense mutation Thr504Ala (SNP-110) and two polymorphisms in the 5′-UTR (SNP-134 and SNP-135) (Evans et al. 2001; Cassell et al. 2002; Y. Horikawa and P. E. Schwarz, unpublished data). To assess the association of SNP-44 with T2DM more comprehensively, we performed a meta-analysis of all published SNP-44/T2DM association study data. To identify all relevant published studies, we searched PubMed using the keywords “calpain 10,” “diabetes,” “44,” “SNP 44,” “CAPN10,” and “type 2,” in different combinations. When necessary, authors were contacted to obtain exact genotype numbers, so that precise odds ratios (ORs) from each study could be calculated. Our search identified 10 published case/control studies, consisting of 3,303 subjects. The studies were spread across a number of ethnic groups: British (three studies, Evans et al. 2001); Chinese (Wang et al. 2002); Japanese (Daimon et al. 2002; Horikawa et al. 2003); Finnish/Botnia (two studies, Orho-Melander et al. 2002); South Indian (Cassell et al. 2002); and Mexican American (Horikawa et al. 2000). The frequency of the T2DM-associated SNP-44 C allele (allele 2) ranged from 6% in Mexican Americans to 25% in the Botnia I control population. There was no evidence for OR heterogeneity (Q test P=.27), and, although these studies are only a small sample from the many existing T2DM genetic resources, a funnel-plot analysis (Egger et al. 1997) suggested an absence of publication bias (P=.44). A Mantel-Haenszel meta-analysis of these studies showed that the C allele was associated with increased risk of T2DM (OR 1.17 [1.02–1.34], P=.02). Three transmission/disequilibrium tests (TDT) had been performed (Evans et al. 2001; Cassell et al. 2002; Orho-Melander et al. 2002). The combined TDT results demonstrated that the C allele was significantly overtransmitted (117 transmitted vs. 77 not transmitted, P=.004) from heterozygous parents to diabetic offspring. Although this result cannot be considered independent replication, as proband data was included in the case/control meta-analysis from two of the TDT studies (Evans et al. 2001; Cassell et al. 2002), it provides evidence that the association is not due to population stratification. Of the 10 studies in the meta-analysis, only 1 reported a significant (P<.05) association (Evans et al. 2001). However, these studies were small and the mean power to detect an OR of 1.17 at P<.05 was ∼11% (range 5%–14%). In the context of genetic association studies, which test many polymorphisms in numerous candidate genes, a P value of .02 can only be considered evidence suggestive of a real association. We therefore genotyped SNP-44 in an additional 4,213 subjects: 3,274 white European subjects from four case/control studies (one British, two German, and one Czech); 691 Japanese subjects from two case/control studies; and 248 Mexican (mestizo) subjects from Mexico City and Orizaba City from one case/control study. Overall, this provided 2,056 subjects with T2DM and 2,157 controls, and a power of ∼80% to detect an OR of 1.17. Clinical details of the study subjects are presented in table 1; further details are available as supplementary information from the authors. All studies were approved by the relevant ethics committee, and all subjects gave their informed consent. Table 1 Clinical Characteristics of Subjects in Study[Note] When all the studies were combined, there was no evidence for between-studies OR heterogeneity (Q test P=.23); a Mantel-Haenszel fixed-effects model was therefore used for subsequent analysis. Meta-analysis of the new studies gave an OR for the SNP-44 C allele of 1.18 (1.04–1.34), P=.01 (fig. 1). A combined meta-analysis of all previously published data and our new data gave an OR of 1.17 (1.07–1.29), P=.0007. All study populations were in Hardy-Weinberg equilibrium except the T2DM cohort of Horikawa et al. 2003 (P=.005) and the control population of the third Japanese study (P=.02). Although these deviations may be due to random fluctuation and multiple-hypothesis testing, they contributed a large amount to heterogeneity (27% of the Q statistic); excluding these studies, the SNP-44 C allele OR for the new studies was 1.23 (1.07–1.40), P=.003; the overall OR was 1.19 (1.08–1.31), P=.0005. This OR is of similar magnitude to that of E23K (Gloyn et al. 2003; Love-Gregory et al. 2003; Nielsen et al. 2003) and Pro12Ala (Altshuler et al. 2000), the other common variants confirmed as T2DM-susceptibility polymorphisms. An OR of 1.17 is low and may help explain why there is little evidence for linkage of the CAPN10 region to T2DM in most populations. The haplotypes responsible for the CAPN10 linkage seen in the Mexican American population were associated with a higher T2DM OR (∼3.0) and were more likely to be detected by linkage analysis (Horikawa et al. 2000). These haplotypes are less common in other populations. Figure 1 Mantel-Haenszel OR meta-analysis plot (fixed effects) for SNP-44 association with T2DM. Point estimates and 95% CLs for each previously published, new, and combined case/control study. SNP-44 is in perfect linkage disequilibrium (r2=1) with the missense mutation, Thr504Ala, and two SNPs (SNP-134 and SNP-135) in the 5′-UTR and therefore may not be the causal variant. Further haplotype and functional analyses are required to confirm which of these polymorphisms contribute to T2DM susceptibility. In conclusion, our results have confirmed that a CAPN10 haplotype defined by the SNP-44 polymorphism predisposes to T2DM. Meta-analyses of published genetic associations, combined with large replication studies, are a powerful approach to detecting susceptibility variants in common disease.

Genetic Susceptibility for Human Familial Essential Hypertension in a Region of Homology with Blood Pressure Linkage on Rat Chromosome 10

Abstract: Hypertension is a significant risk factor for heart attack and stroke and represents a major public health burden because of its high prevalence (e.g. 15-20% of the European and American populations). Although blood pressure is known to have a strong genetic determination, the genes responsible for susceptibility to essential hypertension are mostly unknown. Loci involved in blood pressure regulation have been found by linkage in experimental hereditary hypertensive rat strains, but their relationship to human hypertension has not been extensively investigated. One of the principal blood pressure loci has been mapped to rat chromosome 10 and we have undertaken an investigation of the homologous region on human chromosome 17 in familial essential hypertension. Affected sib-pair analysis and parametric analysis with ascertainment correction gave significant evidence of linkage ( P <0.0001 in some analyses) near two closely linked microsatellite markers, D17S183 and D17S934, that reside 18 cM proximal to the ACE locus in the homology region. Our results indicate that chromosome 17q could contain a susceptibility locus for human hypertension and show that comparative mapping may be a useful approach for identification of such loci in humans.