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PubMed2005

A DNA pooling strategy for family-based association studies.

Genome-wide association scans for disease susceptibility genes of complex diseases require genotyping on a massive scale. A DNA pooling strategy for family-based association studies is described, which is robust to population stratification biases and to errors in pooling. It can achieve a statistical efficiency of 0.95 with approximately 1 of 8 or fewer genotyping efforts, and an efficiency of 0.90 with approximately 1 of 16 or fewer efforts compared with individual genotyping. The pooling method described in this article provides a tradeoff between genotyping efforts and subject recruitment efforts.

Alleles↗
PubMed2005

Alpha2-HS glycoprotein gene is associated with bone size at the hip in Chinese.

Bone size is an important risk factor, independent of bone mineral density (BMD), for osteoporotic fracture. Bone size has a high heritability. A better understanding of genetic factors regulating bone size will have important clinical implications. In this study, we explored the relationship between the alpha2-HS glycoprotein (AHSG) gene and bone size variation at the spine and hip in a Chinese population. The study sample comprised 1 260 subjects from 401 Chinese nuclear families (each including both parents and at least one female child). The Sac / polymorphism inside the exon 7 of the AHSG gene was genotyped and analyzed. This variant represents a nucleotide substitution of C to G at amino acid position 238 resulting in a translation polymorphism of threonine to serine and thus making a potential impact on gene function. We assessed population stratification but did not find significant evidence at any skeletal sites. We found significant association between the AHSG Sac / polymorphism and bone size at the intertrochanteric region (P = 0.019) and the total hip (P = 0.035). The polymorphisms explained 3.74% and 3.16% variations in bone size at the intertrochanteric region and total hip respectively. No significant evidence of linkage was detected, largely due to the limited number of sibpairs in this data set and less informative marker (AHSG Sac / polymorphism) (compared with microsatellite markers) for linkage analysis. Our results suggested that the AHSG gene may contribute to bone size variation at the hip in this Chinese population.

Asian People↗
PubMed2000

Using unaffected child trios to test for transmission distortion.

The transmission disequilibrium test (TDT), an alternative to case-control analysis that is not influenced by population stratification, focuses on affected child trios (ACTs) comprising affected cases and their parents. Unaffected child trios (UCTs) have also been proposed but mainly to rule out segregation distortion. To explore situations when UCTs are preferable to detect transmission distortion, we compared the number of UCTs and ACTs needed to achieve 80% power for a wide variety of scenarios. For a given genetic model, UCT sample size declined rapidly with increasing disease prevalence, whereas ACT sample size remained constant. Furthermore, at some prevalence value (40-60% depending on model parameters), detection of transmission distortion could be accomplished with fewer UCTs than ACTs. Such high prevalence may be found in special populations (diabetes among Pima Indians), secondary conditions (renal/retinal complications in diabetes), and pharmacogenetics (responders to treatment). Also, because exposure to an additional risk factor can increase the disease prevalence in an exposed sub-group, we explored how sample size requirements vary by exposure status. Whereas power differences between exposed and unexposed ACTs could be explained solely by genetic risk ratios, sub-group-specific disease prevalence also played an important role in UCTs. Finally, we considered the impact of including 5, 10, 20, or 30% misclassified ACTs in the UCT sample and found that a 24, 58, 180, or 550% larger sample would be required. In conclusion, UCTs can detect transmission distortion more effectively than ACTs when disease prevalence reaches 40-60%, although some efficiency may be lost owing to misclassification. Moreover, focusing on particular sub-groups defined by exposure status can potentially increase power, but such gains depend heavily on the nature of the gene-exposure interaction.

Child↗
PubMed1997

Survey of maximum CTG/CAG repeat lengths in humans and non-human primates: total genome scan in populations using the Repeat Expansion Detection method.

Repeat Expansion Detection (RED) is an efficient and simple method for detecting repeat expansions in the human genome, including expansion mutations resulting in disease. Here we report the first population survey of CTG/CAG repeat lengths in humans using the RED method; we have determined maximum CTG/CAG repeat length in 244 individuals from six human populations: Danes, Chinese, Japanese, Rondonian Surui, Maya and Mbuti/Biaka Pygmies. We have also sampled a number of non-human primates including eight orang-utans (Pongo pygmaeus), seven gorillas (Gorilla gorilla), seven pygmy chimpanzees (Pan paniscus), 13 common chimpanzees (Pan troglodytes) and three Hylobatidae (one Hylobates lar, one H.klossii, and one H.syndactylus). Our results demonstrate the existence of significant variation in the sizes and frequencies of the longest CTG/CAG repeat length seen per individual both within and between human populations. The population differences argue that overall mutation rates at CTG/CAG repeat loci are sufficiently low that mutation does not obliterate the effect of random genetic drift and clearly indicate that population stratification could occur in disease association studies using the RED method. No significant differences were detected among the non-human primates sampled. Our results also show that both common chimpanzees and pygmy chimpanzees (bonobos) are polymorphic for maximum length of any CTG/CAG repeats while no variation was found for gorillas and orang-utans.

Animals↗
PubMed2003

Association between a functional catechol O-methyltransferase gene polymorphism and schizophrenia: meta-analysis of case-control and family-based studies.

OBJECTIVE: There is strong evidence for a genetic contribution to schizophrenia, but efforts to identify susceptibility genes have been largely unsuccessful because of the low power of individual studies. The authors' goal was to evaluate the collective evidence for an association between the Val158/108Met polymorphism of the catechol O-methyltransferase (COMT) gene and schizophrenia. METHOD: They performed separate meta-analyses of existing case-control and family-based association studies. RESULTS: Overall, case-control studies showed no indication of an association between either allele and schizophrenia, and family-based studies found modest evidence implicating the Val allele in schizophrenia risk. The pooled analyses of studies from diverse geographical regions may have obscured ethnic differences in patterns of genetic risk for schizophrenia. Stratification of the studies by ethnicity of the subjects yielded evidence for an association with the Val allele in case-control studies of European samples and, especially, in family-based studies of European samples. Case-control and family-based studies of Asian samples produced mixed results and, overall, little evidence for association. CONCLUSIONS: The results of the two types of association studies diverged somewhat, but the evidence from the family-based studies, although based on fewer reports, may be more accurate. The Val allele may be a small but reliable risk factor for schizophrenia for people of European ancestry, but the influence of this polymorphism on risk in Asian populations remains unclear. These results call for more family-based studies to confirm the association between COMT and schizophrenia in European samples and to clarify its contribution to risk in Asian samples. They also suggest that case-control studies should use methods of genomic control to avoid being confounded by population stratification.

Adult↗
PubMed2003

Measuring and using admixture to study the genetics of complex diseases.

Admixture is an important evolutionary force that can and should be used in efforts to apply genomic data and technology to the study of complex disease genetics. Admixture linkage disequilibrium (ALD) is created by the process of admixture and, in recently admixed populations, extends for substantial distances (of the order of 10 to 20 cM). The amount of ALD generated depends on the level of admixture, ancestry information content of markers and the admixture dynamics of the population, and thus influences admixture mapping (AM). The authors discuss different models of admixture and how these can have an impact on the success of AM studies. Selection of markers is important, since markers informative for parental population ancestry are required and these are uncommon. Rarely does the process of admixture result in a population that is uniform for individual admixture levels, but instead there is substantial population stratification. This stratification can be understood as variation in individual admixtures and can be both a source of statistical power for ancestry--phenotype correlation studies as well as a confounder in causing false-positives in gene association studies. Methods to detect and control for stratification in case/control and AM studies are reviewed, along with recent studies showing individual ancestry--phenotype correlations. Using skin pigmentation as a model phenotype, implications of AM in complex disease gene mapping studies are discussed. Finally, the article discusses some limitations of this approach that should be considered when designing an effective AM study.

Black or African American↗
PubMed2000

The common PPARgamma Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes.

Genetic association studies are viewed as problematic and plagued by irreproducibility. Many associations have been reported for type 2 diabetes, but none have been confirmed in multiple samples and with comprehensive controls. We evaluated 16 published genetic associations to type 2 diabetes and related sub-phenotypes using a family-based design to control for population stratification, and replication samples to increase power. We were able to confirm only one association, that of the common Pro12Ala polymorphism in peroxisome proliferator-activated receptor-gamma(PPARgamma) with type 2 diabetes. By analysing over 3,000 individuals, we found a modest (1.25-fold) but significant (P=0.002) increase in diabetes risk associated with the more common proline allele (85% frequency). Moreover, our results resolve a controversy about common variation in PPARgamma. An initial study found a threefold effect, but four of five subsequent publications failed to confirm the association. All six studies are consistent with the odds ratio we describe. The data implicate inherited variation in PPARgamma in the pathogenesis of type 2 diabetes. Because the risk allele occurs at such high frequency, its modest effect translates into a large population attributable risk-influencing as much as 25% of type 2 diabetes in the general population.

Adult↗
PubMed2005

Obstacles and opportunities in meta-analysis of genetic association studies.

Genetic association studies have the potential to advance our understanding of genotype-phenotype relationships, especially for common, complex diseases where other approaches, such as linkage, are less powerful. Unfortunately, many reported studies are not replicated or corroborated. This lack of reproducibility has many potential causes, relating to study design, sample size, and power issues, and from sources of true variability among populations. Genetic association studies can be considered as more similar to randomized trials than other types of observational epidemiological studies because of "Mendelian randomization" (Mendel's second law). The rationale and methodology for synthesizing randomized trials is highly relevant to the meta-analysis of genetic association studies. Nevertheless, there are a number of obstacles to overcome when performing such meta-analyses. In this review, the impacts of Type I error, lack of power, and publication and reporting biases are explored, and the role of multiple testing is discussed. A number of special features of association studies are especially pertinent, because they may lead to true variability among study results. These include population dynamics and structure, linkage disequilibrium, conformity to Hardy-Weinberg Equilibrium, bias, population stratification, statistical heterogeneity, epistatic and environmental interactions, and the choice of statistical models used in the analysis. Approaches to dealing with these issues are outlined. The supreme importance of complete and consistent study reporting and of making data readily available is also highlighted as a prerequisite for sound meta-analysis. We believe that systematic review and meta-analysis has an important role to play in understanding genetic association studies and should help us to separate the wheat from the chaff.

Epistasis, Genetic↗
PubMed2004

Case-control association studies with matching and genomic controlling.

Family-based association studies have gained in popularity for mapping disease-susceptibility gene(s) of complex diseases. However, recruiting family controls is often more difficult than recruiting unrelated controls. The author proposes a case-control study, where the possible biases due to population stratification are controlled by matching in the design stage and by genomic controlling in the data-analytic stage. The matching is based on a set of "stratum-delineating variables," such as, race, ethnicity, nationality, ancestry, and birthplace; and the genomic controlling is based on typing a number of null markers across the genome and applying the principle of multiplicative scaling of chi-square distribution. It pays to match carefully to have a higher proportion of correctly matched sets, as computer simulation showed that this would increase the power of the study. If matching is crude, one loses power but still has the correct type I error rate after genomic controlling. Power studies showed that the numbers of affected subjects required for the pair-matched study are comparable to those required by the case-parents design, if the study was conducted in a homogeneous population. As the (control-to-case) matching ratio increases, the number of affected subjects required decreases. With matching ratio tending toward infinity, the number required shrinks roughly by half. The case-control study with matching and genomic controlling frees us from family bondage, and the genetic problem as complicated as mapping genes can now be studied using simple epidemiologic methods.

Case-Control Studies↗
PubMed2001

Family-based association study of serotonin transporter promoter in suicidal adolescents: no association with suicidality but possible role in violence traits.

The serotonin transporter-linked promoter region polymorphism (5-HTTLPR) is thought to be associated with some serotonin dysfunction-related psychopathologies such as depression and anxiety disorders. Suicide and suicide-related behaviors such as violence, aggression, and impulsivity have been reproducibly associated with serotonin dysfunction and are partially genetic. This study examined the association of 5-HTTLPR with suicidal behavior and related traits in Israeli suicidal adolescent inpatients using the haplotype relative risk (HRR) method that controls for artifacts caused by population stratification. Forty-eight inpatient adolescents who recently attempted suicide were assessed by structured interviews for detailed clinical history, diagnoses, suicide intent, suicide risk, impulsivity, violence, and depression. Blood samples were collected and DNA extracted from patients and their biological parents. The 5-HTTLPR allele frequencies were tested for association with suicidality by the HRR method. In addition, the relationship between genotypes and phenotypic severity of several clinical parameters was analyzed. No significant allelic association of the 5-HTTLPR polymorphism with suicidal behavior was found (chi square = 0.023; P = 0.88). Analysis of variance of the suicide-related trait measures for the three genotypes demonstrated a significant difference in violence measures between patients carrying the LL and LS genotypes (9.50+/-4.04 vs. 5.36+/-4.03; P = 0.029). This study suggests that the 5-HTTLPR polymorphism is unlikely to have major relevance to the pathogenesis of suicidal behavior in adolescence but may contribute to violent behavior in this population.

Adolescent↗
PubMed2026

National genomic projects in Asia and Africa: a review.

National genome projects (NGPs) are increasingly shaping precision medicine by improving representation of population-specific genetic diversity. This review compiles findings from NGPs across Asia and Africa, regions that remain underrepresented in global genomic databases despite their extensive demographic and genetic diversity. A total of 53 studies from 24 countries were identified to understand (1) the genomic approach utilized, (2) novel findings that have emerged, and (3) strategies for improving research in these regions. The NGPs implement population-based variome databases (20 NGPs), linear reference genome assemblies (8 NGPs), and graph-based pangenome assemblies (1 NGP). Novel variants ranged between 0.28% (China) and 19.6% (Iran), whereas rare variants accounted for up to 88.9% of the detected variants in the Chinese population. Each NGP documents its country's evolutionary and migration history, which impacts disease frequency and pharmacogenomic variants. Clinically, NGPs revealed strong population stratification in disease-associated and pharmacogenomic variants. For example, the GJB2 rs72474224 hearing-loss variant ranged from 13% in Vietnam and 12% in Hong Kong to 0.0894% in Turkey, while the VKORC1 rs9923231 pharmacogenomic variant reached 89.2% in Taiwan but was 20%-25% in European-related Russian subpopulations. These findings demonstrate that clinically relevant allele frequencies, pathogenicity assessments, and drug-response markers differ substantially across ancestries. This review highlights ongoing efforts and strategies to enhance the representativeness of genomic data through NGPs in Asia and Africa. We also suggest future directions for national projects, including integrating family-based studies, multi-omic data, and standardized pipelines to accelerate discovery and support the equitable implementation of precision medicine.

Humans↗
PubMed2004

HLA and susceptibility to juvenile idiopathic arthritis: a study of affected sibpairs in an isolated Finnish population.

OBJECTIVE: To determine the effects of class I (A, B, and C) and II (DRB1 and DQB1) HLA loci alleles and DRB1-DQB1 haplotypes on genetic susceptibility to juvenile idiopathic arthritis (JIA) in families with 2 or more affected siblings. METHODS: A total of 83 affected siblings belonging to 38 families and corresponding to 50 affected sibpairs, their parents, and 45 healthy sibs were typed for HLA in A, C, B, DRB1, and DQB1 loci. Two study designs were used to explore linkage and association: a case-population control design and a family design using the linkage method: identical-by-descent (IBD) allele-sharing and the association analysis methods. Associations in family data were analyzed using the independent transmission disequilibrium test (TDT) for linkage in the presence of association. This was supplemented by the family-based association test (FBAT) to look for association in the presence of linkage, and is robust for population stratification and phenotype-based selection of data. RESULTS: Significantly increased HLA allele frequencies among the affected siblings compared to Finnish bone marrow donors were observed for HLA alleles Cw4 (odds ratio, OR, 1.7), B27 (1.8), B35 (1.7), and DR8 (3.7). The observed ratio of sharing 0, 1, and 2 HLA haplotypes (A, C, B, DRB1, and DQB1) among affected sibpairs (ASP) was 10:23:17, significantly different from expected (p < 0.001), using a formula that takes into account disease prevalence and the sibling recurrence risk. In the univariate association analysis, both independent TDT and FBAT found significantly increased transmission of the DRB1*0801 and DQB1*0402 alleles and Cw*0401. Independent positive allele effects of Cw*0401, DRB1*0801, and DQB1*0402 as well as negative effects of Cw*0701 and DQB1*0302 were shown by the family-based association analysis of the joint allele main effects. Multi-allelic test for association of each locus confirmed significant associations of the DRB1 and DQB1 loci in the risk of JIA. We found DRB1*0801/DQB1*0402 haplotype to be strongly associated (p < 0.001) with JIA, supporting findings of the haplotype associations-based ASP design. CONCLUSION: Both linkage analysis of the affected sibpairs and association analysis of nuclear families with JIA provided overwhelming evidence of the major contribution of HLA to genetic susceptibility to JIA. The association analysis of HLA-A, C, B, DRB1, and DQB1 alleles by both TDT and FBAT tests confirmed in the Finnish population that the most significant associations prevailed for DRB1*0801, DQB1*0402, as expected from previous observations, and supported the independent role of Cw*0401.

Arthritis, Juvenile↗
PubMed2006

Family-based versus unrelated case-control designs for genetic associations.

The most simple and commonly used approach for genetic associations is the case-control study design of unrelated people. This design is susceptible to population stratification. This problem is obviated in family-based studies, but it is usually difficult to accumulate large enough samples of well-characterized families. We addressed empirically whether the two designs give similar estimates of association in 93 investigations where both unrelated case-control and family-based designs had been employed. Estimated odds ratios differed beyond chance between the two designs in only four instances (4%). The summary relative odds ratio (ROR) (the ratio of odds ratios obtained from unrelated case-control and family-based studies) was close to unity (0.96 [95% confidence interval, 0.91-1.01]). There was no heterogeneity in the ROR across studies (amount of heterogeneity beyond chance I(2) = 0%). Differences on whether results were nominally statistically significant (p < 0.05) or not with the two designs were common (opposite classification rates 14% and 17%); this reflected largely differences in power. Conclusions were largely similar in diverse subgroup analyses. Unrelated case-control and family-based designs give overall similar estimates of association. We cannot rule out rare large biases or common small biases.

Case-Control Studies↗
PubMed2005

Robust genomic control for association studies.

Population-based case-control studies are a useful method to test for a genetic association between a trait and a marker. However, the analysis of the resulting data can be affected by population stratification or cryptic relatedness, which may inflate the variance of the usual statistics, resulting in a higher-than-nominal rate of false-positive results. One approach to preserving the nominal type I error is to apply genomic control, which adjusts the variance of the Cochran-Armitage trend test by calculating the statistic on data from null loci. This enables one to estimate any additional variance in the null distribution of statistics. When the underlying genetic model (e.g., recessive, additive, or dominant) is known, genomic control can be applied to the corresponding optimal trend tests. In practice, however, the mode of inheritance is unknown. The genotype-based chi (2) test for a general association between the trait and the marker does not depend on the underlying genetic model. Since this general association test has 2 degrees of freedom (df), the existing formulas for estimating the variance factor by use of genomic control are not directly applicable. By expressing the general association test in terms of two Cochran-Armitage trend tests, one can apply genomic control to each of the two trend tests separately, thereby adjusting the chi (2) statistic. The properties of this robust genomic control test with 2 df are examined by simulation. This genomic control-adjusted 2-df test has control of type I error and achieves reasonable power, relative to the optimal tests for each model.

Case-Control Studies↗
PubMed1976

Histocompatibility (HL-A) factors in familial multiple sclerosis. Is multiple sclerosis susceptibility inherited via the HL-A chromosome?

In order to study a possible hereditary factor leading to multiple sclerosis (MS) susceptibility, histocompatibility (HL-A) types were studied in families where two or more first-degree relatives had MS. Neither the inheritance of a particular parental HL-A chromosome, nor the occurrence of any specific HL-A antigens, could be shown to be necessary or sufficient for the development of MS in family members. The distribution of HL-A chromosomes was essentially the same for affected and unaffected family members. An excess of 3,7 haplotype and W21 antigen was demonstrated, both in affected patients and in unaffected family members, in equal proportions. We conclude that the HL-A chromosome has no direct causal relationship to MS susceptibility, although it may be indirectly associated by population stratification, maternal factors, or some other mechanism.

Adolescent↗
PubMed1997

Population genetics of a functional variant of the dopamine beta-hydroxylase gene (DBH).

Dopamine beta-hydroxylase (E.C. 1.14.17.1; protein abbreviation: DbetaH) catalyzes conversion of dopamine to norepinephrine. Previous work identified two expressed alleles of the gene encoding DbetaH (locus symbol DBH), containing either G or T at nucleotide position 910, resulting in specification by codon 304 of alanine (DBH*304A) or serine (DBH*304S), respectively. The current study employed denaturing gradient gel electrophoresis to identify these alleles, and after developing a PCR RFLP for rapid genotyping, estimated the frequencies of the alleles in African-Americans, European-Americans, and in several geographically dispersed populations (Mbuti, Danes, Adygei, Chinese, Japanese, Surui, Maya, and Nasioi). DBH*304A was the most common allele in all populations tested, with allele frequencies greater than 0.80 in each case. There was significant heterogeneity in allele frequency across population groups. The DBH*304S allele was most common in subjects of African descent, and least common in East Asians and individuals from indigenous populations of North and South America. The frequency of DBH*304S was significantly higher in African-Americans (0.16) than in European-Americans (0.06; P < 0.004). Of the four DBH*304S homozygotes observed, all were Europeans and three of the four were Danes. Based on empirical P-values generated by computer simulation, the observed proportions of DBH*304S homozygotes did not differ significantly from Hardy-Weinberg expectations in any of the populations after Bonferroni correction for multiple comparisons. The observation of significant heterogeneity in DBH*304S allele frequency across different population samples demonstrates the importance of controlling for population stratification in future studies testing for associations between DBH*304S and clinical phenotypes.

Alleles↗
PubMed1997

Genetic association between monoamine oxidase and manic-depressive illness: comparison of relative risk and haplotype relative risk data.

There have been several conflicting reports of association of monoamine oxidase (MAO) A gene polymorphisms and bipolar affective disorder. In order to determine the possible role of the MAO region in susceptibility to affective disorders in an independent sample, we have genotyped 83 probands of bipolar affective disorder families, 56 sets of parents of bipolar probands, and 84 normal controls for intronic simple sequence repeat polymorphisms of the MAO-A and MAO-B genes. For MAO-A there were no significant differences in allele frequencies between bipolar and normal control groups for both genders. However, for MAO-B there were significant differences between groups for both genders. In contrast, allele-wise haplotype relative risk analysis for the 56 bipolar proband-parent trios found no significant differences between transmitted and non-transmitted allele frequencies for MAO-A or B. These data do not support the association of MAO-A or B with bipolar affective disorder but do demonstrate that undetected population stratification can be an important source of bias in case-control studies.

Alleles↗
PubMed2000

Family-based study of the association of the dopamine D2 receptor gene (DRD2) with habitual smoking.

A recent study showed an association between the dopamine D2 receptor gene (DRD2) and smoking. The purpose of this study was to determine if the familial transmission of smoking is linked to variation at the DRD2 locus in a genetically informative sample. Subjects were identified in alcohol treatment centers and their relatives were recruited for study. All subjects were interviewed to assess alcohol dependence, smoking habits, and psychiatric disorders. Two polymorphisms within the DRD2 gene were analyzed, including the TaqIA polymorphism. The sample consisted of 138 nuclear families with at least one offspring with habitual smoking, and analysis was by the transmission disequilibrium test (TDT), which avoids problems due to population stratification. There was no significant difference in the frequency between DRD2 alleles transmitted and not transmitted to habitual smokers. There also was no evidence for unequal transmission of DRD2 alleles for the phenotypes "ever smoker" or comorbid alcohol dependence and habitual smoking. This study does not support linkage of the DRD2 with smoking.

Chromosome Mapping↗