Gene-centric genomewide association study via entropy

Genes are the functional units in most organisms. Compared to genetic variants located outside genes, genic variants are more likely to affect disease risk. The development of the human HapMap project provides an unprecedented opportunity for genetic association studies at the genomewide level for elucidating disease etiology. Currently, most association studies at the single-nucleotide polymorphism (SNP) or the haplotype level rely on the linkage information between SNP markers and disease variants, with which association findings are difficult to replicate. Moreover, variants in genes might not be sufficiently covered by currently available methods. In this article, we present a gene-centric approach via entropy statistics for a genomewide association study to identify disease genes. The new entropy-based approach considers genic variants within one gene simultaneously and is developed on the basis of a joint genotype distribution among genetic variants for an association test. A grouping algorithm based on a penalized entropy measure is proposed to reduce the dimension of the test statistic. Type I error rates and power of the entropy test are evaluated through extensive simulation studies. The results indicate that the entropy test has stable power under different disease models with a reasonable sample size. Compared to single SNP-based analysis, the gene-centric approach has greater power, especially when there is more than one disease variant in a gene. As the genomewide genic SNPs become available, our entropy-based gene-centric approach would provide a robust and computationally efficient way for gene-based genomewide association study.     

A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation

We conducted a multi-stage genome-wide association study of natural hair color in more than 10,000 men and women of European ancestry from the United States and Australia. An initial analysis of 528,173 single nucleotide polymorphisms (SNPs) genotyped on 2,287 women identified IRF4 and SLC24A4 as loci highly associated with hair color, along with three other regions encompassing known pigmentation genes. We confirmed these associations in 7,028 individuals from three additional studies. Across these four studies, SLC24A4 rs12896399 and IRF4 rs12203592 showed strong associations with hair color, with p=6.0×10⁻⁶² and p=7.46×10⁻¹²⁷, respectively. The IRF4 SNP was also associated with skin color (p=6.2×10⁻¹⁴), eye color (p=6.1×10⁻¹³), and skin tanning response to sunlight (p=3.9×10⁻⁸⁹). A multivariable analysis pooling data from the initial GWAS and an additional 1,440 individuals suggested that the association between rs12203592 and hair color was independent of rs1540771, a SNP between the IRF4 and EXOC2 genes previously found to be associated with hair color. After adjustment for rs12203592, the association between rs1540771 and hair color was not significant (p=0.52). One variant in the MATP gene was associated with hair color. A variant in the HERC2 gene upstream of the OCA2 gene showed the strongest and independent association with hair color compared with other SNPs in this region, including three previously reported SNPs. The signals detected in a region around the MC1R gene were explained by MC1R red hair color alleles. Our results suggest that the IRF4 and SLC24A4 loci are associated with human hair color and skin pigmentation.     

Iris pigmentation as a quantitative trait: variation in populations of European,East Asian and South Asian ancestry and association with candidate gene polymorphisms

In this study, we present a new quantitative method to measure iris colour based on high‐resolution photographs. We applied this method to analyse iris colour variation in a sample of individuals of East Asian, European and South Asian ancestry. We show that measuring iris colour using the coordinates of the CIELAB colour space uncovers a significant amount of variation that is not captured using conventional categorical classifications, such as ‘brown’, ‘blue’ or ‘green’. We tested the association of a selected panel of polymorphisms with iris colour in each population group. Six markers showed significant associations with iris colour in the European sample, three in the South Asian sample and two in the East Asian sample. We also observed that the marker HERC2 rs12913832, which is the main determinant of ‘blue’ versus ‘brown’ iris colour in European populations, is also significantly associated with central heterochromia in the European sample.     

Genome‐wide association study for pigmentation traits in Chinese Holstein population

With the Illumina BovineSNP50K BeadChip, we performed a genome‐wide association study (GWAS) for two pigmentation traits in a Chinese Holstein population: proportion of black (PB) and teat colour (TC). A case–control design was used. Cases were the cows with PB <0.30 (n = 129) and TC <2 points (n = 140); controls were those with PB >0.90 (n = 58) and TC >4 points (n = 281). The RM test of roadtrips (version 1.2) was applied to detect SNPs for the two traits with 42 883 and 42 741 SNPs respectively. A total of nine and 12 genome‐wide significant (P < 0.05) SNPs associated with PB and TC respectively were identified. Of these, two SNPs for PB were located within the KIT and IGFBP7 genes, and the other four SNPs were 23~212 kb away from the PDGFRA gene on BTA6; nine SNPs associated with TC were located within or 21~78.8 kb away from known genes on chromosomes 4, 11, 22, 23 and 24. By combing through our GWAS results and the biological functions of the genes, we suggest that the KIT, IGFBP7, PDGFRA, MITF, ING3 and WNT16 genes are promising candidates for PB and TC in Holstein cattle, providing a basis for further investigation on the genetic mechanism of pigmentation formation.     

Replication of genomewide association studies on age at menarche in the Korean population

Early menarche is associated with adverse health outcomes, including breast cancer, endometrial cancer, obesity, type 2 diabetes, and cardiovascular disease. Recently, a genomewide association study (GWAS) of age at menarche (AAM) in 104,533 individuals of European ancestry was reported by the ReproGen consortium. They identified 42 loci known and novel loci that were linked to age at menarche. Because age at menarche varies between ethnic groups, we decided to investigate if these results would be replicated in the Korean population. To this end, we examined the association of the SNPs reported in the ReproGen GWAS with AAM in 3,194 individuals from the Korean Genome and Epidemiology Study (KoGES) cohort. Genotype data for total 17 SNPs (6 genotyped SNPs and 11 imputed SNPs) were available for the association analysis using linear regression analysis for age at menarche with controlling current age, waist-to-hip ratio, and body mass index as the covariates. We found replication of the ReproGen study in two SNPs; one SNP (rs466639) in the retinoic acid receptor gamma gene (RXRG), showing a significant association with early menarche (beta = ?0.224 ± 0.065, p value = 5.2 × 10^?4, Bonferroni-corrected p value = 0.009), and the other (rs10899489), in GRB2 (growth factor receptor bound protein 2)-associated binding protein 2 (GAB2), linked to late menarche (beta = 0.140 ± 0.047, p value = 2.8 × 10^?3, Bonferroni-corrected p value = 0.049). This result possibly suggests that genetic factors governing AAM in the Korean population would be distinct from those in the Europeans, implying roles of modulating or interacting factors in determining AAM, including environmental factors such as nutritional status.     

A second-generation genomewide screen for asthma-susceptibility alleles in a founder population

A genomewide screen for asthma- and atopy-susceptibility loci was conducted, using 563 markers, in 693 Hutterites who are members of a single 15-generation pedigree, nearly doubling the sample size from the authors' earlier studies. The resulting increase in power led to the identification of 23 loci in 18 chromosomal regions showing evidence for linkage that is, in general, 10-fold more significant (P<.001 vs. P<.01) than the linkages reported previously in this population. Moreover, linkages to loci in 11 chromosomal regions were identified for the first time in the Hutterites in this report, including five regions (5p, 5q, 8p, 14q, and 16q) showing evidence both of linkage, by the likelihood ratio (LR) chi(2), and of disequilibrium, by the transmission/disequilibrium test. A region on chromosome 19 continues to show evidence for linkage, by both tests, in this study. Studies of 17 candidate genes provide evidence for association with variation in the IL4RA gene (16p12), the HLA class II genes (6p21), and the interferon-alpha gene cluster (9p22), but the lack of evidence for linkage in these regions by the LR chi(2) test suggests that these are minor susceptibility loci. A polymorphism in the CD14 gene is in linkage disequilibrium with an as yet unidentified susceptibility allele in the 5q cytokine cluster, a region showing evidence for linkage among the Hutterites. Finally, 10 of the regions showing evidence for linkage in the Hutterites have shown evidence of linkage to related phenotypes in other genome screens, suggesting that these regions may contain common alleles that have relatively large effects on asthma and atopy phenotypes in diverse populations.     

Genome-wide association studies of pigmentation and skin cancer: a review and meta-analysis

Recent genome-wide association studies (GWAS) identified genetic loci associated with pigmentation, nevi, and skin cancer. We performed a review and meta-analysis of GWAS results, grouping them into four categories: (i) loci associated with pigmentation (hair, eye, and/or skin color), cutaneous UV-response (sun sensitivity and/or freckling), and skin cancer; (ii) loci associated with nevi and melanoma; (iii) loci associated with pigmentation and/or cutaneous UV-response but not skin cancer; and (iv) loci associated distinctly with skin cancer, mostly basal cell carcinoma, but not pigmentation or cutaneous UV-response. These findings suggest at least two pathways for melanoma development (via pigmentation and via nevi), and two pathways for basal cell carcinoma development (via pigmentation and independent of pigmentation). However, further work is necessary to separate the association with skin cancer from the association with pigmentation. As with any GWAS, the identified loci may not include the causal variants and may need confirmation by direct genome sequencing.     

Coverage and power in genomewide association studies

The ability of genomewide association studies to decipher genetic traits is driven in part by how well the measured single-nucleotide polymorphisms "cover" the unmeasured causal variants. Estimates of coverage based on standard linkage-disequilibrium measures, such as the average maximum squared correlation coefficient (r2), can lead to inaccurate and inflated estimates of the power of genomewide association studies. In contrast, use of the "cumulative r2 adjusted power" measure presented here gives more-accurate estimates of power for genomewide association studies.     

A genomewide screen for late-onset Alzheimer disease in a genetically isolated Dutch population

Alzheimer disease (AD) is the most common cause of dementia. We conducted a genome screen of 103 patients with late-onset AD who were ascertained as part of the Genetic Research in Isolated Populations (GRIP) program that is conducted in a recently isolated population from the southwestern area of The Netherlands. All patients and their 170 closely related relatives were genotyped using 402 microsatellite markers. Extensive genealogy information was collected, which resulted in an extremely large and complex pedigree of 4,645 members. The pedigree was split into 35 subpedigrees, to reduce the computational burden of linkage analysis. Simulations aiming to evaluate the effect of pedigree splitting on false-positive probabilities showed that a LOD score of 3.64 corresponds to 5% genomewide type I error. Multipoint analysis revealed four significant and one suggestive linkage peaks. The strongest evidence of linkage was found for chromosome 1q21 (heterogeneity LOD [HLOD]=5.20 at marker D1S498). Approximately 30 cM upstream of this locus, we found another peak at 1q25 (HLOD=4.0 at marker D1S218). These two loci are in a previously established linkage region. We also confirmed the AD locus at 10q22-24 (HLOD=4.15 at marker D10S185). There was significant evidence of linkage of AD to chromosome 3q22-24 (HLOD=4.44 at marker D3S1569). For chromosome 11q24-25, there was suggestive evidence of linkage (HLOD=3.29 at marker D11S1320). We next tested for association between cognitive function and 4,173 single-nucleotide polymorphisms in the linked regions in an independent sample consisting of 197 individuals from the GRIP region. After adjusting for multiple testing, we were able to detect significant associations for cognitive function in four of five AD-linked regions, including the new region on chromosome 3q22-24 and regions 1q25, 10q22-24, and 11q25. With use of cognitive function as an endophenotype of AD, our study indicates the that the RGSL2, RALGPS2, and C1orf49 genes are the potential disease-causing genes at 1q25. Our analysis of chromosome 10q22-24 points to the HTR7, MPHOSPH1, and CYP2C cluster. This is the first genomewide screen that showed significant linkage to chromosome 3q23 markers. For this region, our analysis identified the NMNAT3 and CLSTN2 genes. Our findings confirm linkage to chromosome 11q25. We were unable to confirm SORL1; instead, our analysis points to the OPCML and HNT genes.     

Religion and economic activity in the South Asian population

Anthropological and sociological literature points to the importance of religion as a basis for understanding the diverse nature of Britain's South Asian population. Using a rare quantitative source, the 1994 National Survey of Ethnic Minorities, and against a backdrop of relative neglect by quantitative social scientists, this article considers the religious dimension to observed differences in economic activity among South Asians. The analysis reports substantial differences between religious sub-groups (by age and sex) across a range of key measures, including: differences in the proportion who are economically active; differences in the proportion of the economically active who successfully gain employment; among the employed, differences in the type of jobs held and in reported income. The analysis suggests a more complex picture than the Muslim/non-Muslim dichotomy often inferred from analysis using conventional ethnic group classifications, with notable differences between Indian Sikhs and Hindus, and between Indian Muslims and Pakistani and Bangladeshi Muslims.     

A mixed two-stage method for detecting interactions in genomewide association studies

Genomewide association studies (GWAS) are being conducted to unravel the genetic etiology of complex diseases, in which complex epistasis may play an important role. One-stage method in which interactions are tested using all samples at one time may be computationally problematic, may have low power as the number of markers tested increases and may not be cost-efficient. A common two-stage method may be a reasonable and powerful approach for detecting interacting genes using all samples in both two stages. In this study, we introduce an alternative two-stage method, in which some promising markers are selected using a proportion of samples in the first stage and interactions are then tested using the remaining samples in the second stage. This two-stage method is called mixed two-stage method. We then investigate the power of both one-stage method and mixed two-stage method to detect interacting disease loci for a range of two-locus epistatic models in a case-control study design. Our results suggest that mixed two-stage method may be more powerful than one-stage method if we choose about 30% of samples for single-locus tests in the first stage, and identify less than and equal to 1% of markers for follow-up interaction tests. In addition, we compare both two-stage methods and find that our two-stage method will lose power because we only use part of samples in both two stages.     

A weighted-Holm procedure accounting for allele frequencies in genomewide association studies

In the context of genomewide association studies where hundreds of thousand of polymorphisms are tested, stringent thresholds on the raw association test P-values are generally used to limit false-positive results. Instead of using thresholds based on raw P-values as in Bonferroni and sequential Sidak (SidakSD) corrections, we propose here to use a weighted-Holm procedure with weights depending on allele frequency of the polymorphisms. This method is shown to substantially improve the power to detect associations, in particular by favoring the detection of rare variants with high genetic effects over more frequent ones with lower effects.     

Mechanism of skin pigmentation

Melanin is a pigment that plays an important role in providing coloration and protecting human skin from the harmful effects of UV light radiation. Human skin color is determined by the type and amount of melanins that are synthesized and deposited within the melanosomes. In addition, the transfer of these specialized membrane-bound organelles from melanocytes to surrounding keratinocytes also plays a role in dictating human skin color. In order to investigate the principle features of skin pigmentation, the origin, function, and production ability of melanin should be highly understood in terms of biological and pathophysiological aspects. Furthermore, a deep understanding of melanin synthesis will also contribute to cosmetics and drugs development. In this review, the processes of melanin biosynthesis, such as survival, proliferation, and differentiation of melanin cells, as well as the biological regulation of human pigmentation were described.     

Evaluating statistical significance in two-stage genomewide association studies

Genomewide association studies are being conducted to unravel the genetic etiology of complex human diseases. Because of cost constraints, these studies typically employ a two-stage design, under which a large panel of markers is examined in a subsample of subjects, and the most-promising markers are then examined in all subjects. This report describes a simple and efficient method to evaluate statistical significance for such genome studies. The proposed method, which properly accounts for the correlated nature of polymorphism data, provides accurate control of the overall false-positive rate and is substantially more powerful than the standard Bonferroni correction, especially when the markers are in strong linkage disequilibrium.     

Genome-wide association study identifies TNFSF13 as a susceptibility gene for IgA in a South Chinese population in smokers

IgA is an important factor in our immune system. There are many diseases associated with it, such as IgA nephropathy, IgA deficiency, and so on. In order to describe the relationship between the genes and the IgA level, we performed a genome-wide association study of serum IgA with 1,999 healthy Chinese men in the first stage and replicated on an independent Chinese sample with 1,496 subjects in the second stage. Association between each SNP with IgA was estimated by multivariate linear regression analysis conditioned on age and smoke. Haplotype analysis for the block around the top SNP was performed. In the first stage, one genomic locus was identified to be significantly associated with IgA. The loci is TNFSF13 (17p13.1; rs3803800; P?=?6.26?×?10(-8)). In smoke-specific analysis, rs3803800 was approximately significantly associated with IgA levels in smokers (P?=?3.96?×?10(-7)), while no association was observed in nonsmokers (P?=?2.28?×?10(-1)). In addition, we performed the haplotype analysis on chromosome 17 with the SNPs around rs3803800. Although the total P value for the haplotype did not acquire significant difference, three haplotypes (TGAG, CACG, and CACA) reached significant (P?相似文献   

Pathway-based approaches for analysis of genomewide association studies

Published genomewide association (GWA) studies typically analyze and report single-nucleotide polymorphisms (SNPs) and their neighboring genes with the strongest evidence of association (the “most-significant SNPs/genes” approach), while paying little attention to the rest. Borrowing ideas from microarray data analysis, we demonstrate that pathway-based approaches, which jointly consider multiple contributing factors in the same pathway, might complement the most-significant SNPs/genes approach and provide additional insights into interpretation of GWA data on complex diseases.     

Epidemiological profiles between equol producers and nonproducers: a genomewide association study of the equol-producing phenotype

Equol is a daidzein (a phytoestrogen isoflavone) metabolite of gut bacteria, and the ability to produce equol varies between individuals and reduces the risks of several diseases. We tested the effects of equol production on health in Koreans and identified the genetic factors that determine the equol-producing phenotype. In 1391 subjects, the equol-producing phenotype was determined, based on measurements of serum equol concentrations. The anthropometric and blood biochemical measurements between equol producers and nonproducers were analyzed by LC-MS/MS. Genetic factors were identified in a genomewide association study (GWAS), and the interaction between genetic factors and the equol-producing phenotype was examined. We observed that 70.1 % of the study population produced equol. Blood pressure was significantly lower in equol producers (beta ± SE = −1.35 ± 0.67, p = 0.045). In our genomewide association study, we identified 5 single-nucleotide polymorphisms (p < 1 × 10⁻⁵) in HACE1. The most significant SNP was rs6927608, and individuals with a minor allele of rs6927608 did not produce equol (odds ratio = 0.57 (95 % CI 0.45–0.72), p value = 2.5 × 10⁻⁶). Notably, the interaction between equol production and the rs6927608 HACE1 SNP was significantly associated with systolic blood pressure (p value = 1.3 × 10⁴). Equol production is linked to blood pressure, and HACE1, identified in our (GWAS), might be a determinant of the equol-producing phenotype.

Electronic supplementary material

The online version of this article (doi:10.1007/s12263-012-0292-8) contains supplementary material, which is available to authorized users.     

Recent developments in genomewide association scans: a workshop summary and review

With the imminent availability of ultra-high-volume genotyping platforms (on the order of 100,000-1,000,000 genotypes per sample) at a manageable cost, there is growing interest in the possibility of conducting genomewide association studies for a variety of diseases but, so far, little consensus on methods to design and analyze them. In April 2005, an international group of >100 investigators convened at the University of Southern California over the course of 2 days to compare notes on planned or ongoing studies and to debate alternative technologies, study designs, and statistical methods. This report summarizes these discussions in the context of the relevant literature. A broad consensus emerged that the time was now ripe for launching such studies, and several common themes were identified--most notably the considerable efficiency gains of multistage sampling design, specifically those made by testing only a portion of the subjects with a high-density genomewide technology, followed by testing additional subjects and/or additional SNPs at regions identified by this initial scan.     

Current opportunities and challenges: genome-wide association studies on pigmentation and skin cancer

Genome-wide association studies (GWAS) have become a widely used approach for genetic association studies of various human traits. A few GWAS have been conducted with the goal of identifying novel loci for pigmentation traits, melanoma, and non-melanoma skin cancer. Nevertheless, the phenotype variation explained by the genetic markers identified so far is limited. In this review, we discuss the GWAS study design and its application in pigmentation and skin cancer research. Furthermore, we summarize recent developments in post-GWAS activities such as meta-analysis, pathway analysis, and risk prediction.