Biomedical subjects

Emmanuelle Génin

Publications and source records attributed to Emmanuelle Génin.

17 recordsLinked to original sources

PubMed2006

ALTree: association detection and localization of susceptibility sites using haplotype phylogenetic trees.

Finding the genes involved in complex diseases susceptibility and among those genes, localizing the variant sites explaining this susceptibility is a major goal of genetic epidemiology. In this context, haplotypic methods that use the joint information on several markers may be of particular interest. When the number of haplotypes is large, a grouping may be required. Phylogenetic trees allow such groupings of haplotypes based on their evolutionary history and may help in the detection and localization of disease susceptibility sites. In this paper, we present a new software to perform phylogeny-based association and localization analysis.

Computational Biology↗

PubMed2006

Clustering of haplotypes based on phylogeny: how good a strategy for association testing?

Haplotypes are now widely used in association studies between markers and disease susceptibility locus. However, when a large number of markers are considered, the number of possible haplotypes increases leading to two problems: an increased number of degrees of freedom that may result in a lack of power and the existence of rare haplotypes that may be difficult to take into account in the statistical analysis. In a recent paper, Durrant et al proposed a method, CLADHC, to group haplotypes based on distance matrices and showed that this could considerably increase the power of the association test as compared to either single-locus analysis or haplotype analysis without prior grouping. Although the authors considered different one-disease-locus susceptibility models in their simulations, they did not study the impact of the linkage disequilibrium (LD) pattern and of the susceptibility allele frequency on their conclusions. Here, we show, using haplotype data from five regions of the genome of different lengths and with different LD patterns, that, when a single disease susceptibility locus is simulated, the prior grouping of haplotypes based on the algorithm of Durrant et al does not increase the power of association testing except in very particular situations of LD patterns and allele frequencies.

Computer Simulation↗

PubMed2005

Impact of the diagnosis definition on linkage detection.

Previous genome scan linkage analyses of the disease Kofendrerd Personality Disorder (KPD) with microsatellites led to detect some regions on chromosomes 1, 3, 5, and 9 that were identical for the three populations AI, KA, and DA but with large differences in significance levels. These differences in results may be explained by the different diagnosis definitions depending on the presence/absence of 12 traits that were used in the 3 populations AI, KA, and DA. Heterogeneity of linkage was thus investigated here according to the absence/presence of each of the 12 traits in the 3 populations. For this purpose, two methods, the triangle test statistic and the predivided sample test were applied to search for genetic heterogeneity. Three regions with a strong heterogeneity of linkage were detected: the region on chromosome 1 according to the presence/absence of the traits a and b, the region on chromosome 3 for the trait b, and the region on chromosome 9 for the traits k and l. These 3 regions were the same as those detected by linkage analyses. No novel region was detected by the heterogeneity tests. Concerning chromosome 1, linkage analyses showed a much stronger evidence of linkage for traits a and b and for a combination of these traits than for KPD. Moreover, there was no indication of linkage to any of the other traits used to define the diagnosis of KPD. A genetic factor located on the chromosome 1 may have been detected here which would be involved specifically in traits a and b or in a combination of these traits.

Chromosomes, Human, Pair 1↗

PubMed2005

On the use of haplotype phylogeny to detect disease susceptibility loci.

BACKGROUND: The cladistic approach proposed by Templeton has been presented as promising for the study of the genetic factors involved in common diseases. This approach allows the joint study of multiple markers within a gene by considering haplotypes and grouping them in nested clades. The idea is to search for clades with an excess of cases as compared to the whole sample and to identify the mutations defining these clades as potential candidate disease susceptibility sites. However, the performance of this approach for the study of the genetic factors involved in complex diseases has never been studied. RESULTS: In this paper, we propose a new method to perform such a cladistic analysis and we estimate its power through simulations. We show that under models where the susceptibility to the disease is caused by a single genetic variant, the cladistic test is neither really more powerful to detect an association nor really more efficient to localize the susceptibility site than an individual SNP testing. However, when two interacting sites are responsible for the disease, the cladistic analysis greatly improves the probability to find the two susceptibility sites. The impact of the linkage disequilibrium and of the tree characteristics on the efficiency of the cladistic analysis are also discussed. An application on a real data set concerning the CARD15 gene and Crohn disease shows that the method can successfully identify the three variant sites that are involved in the disease susceptibility. CONCLUSION: The use of phylogenies to group haplotypes is especially interesting to pinpoint the sites that are likely to be involved in disease susceptibility among the different markers identified within a gene.

Crohn Disease↗

PubMed2005

ABCA2 is a strong genetic risk factor for early-onset Alzheimer's disease.

Recent epidemiological, biological and genetic data indicate a relationship between cholesterol and Alzheimer's disease (AD) including the association of polymorphisms of ABCA1 (a gene that is known to participate in cholesterol and phospholipid transport) with AD prevalence. Based on these data, we postulated that genetic variation in the related and brain-specific ABCA2 gene leads to increase risk of AD. A large case-control study was conducted where the sample was randomly divided into a hypothesis-testing sample (230 cases/286 controls) and a validation sample (210 cases/233 controls). Among the 45 SNPs we tested, one synonymous SNP (rs908832) was found significantly associated with AD in both samples. Additional analyses performed on the whole sample showed a very strong association between this marker and early-onset AD (OR = 3.82, 95% C.I. = [2.00 - 7.30], P = 5 x 10(-5)). Further research is needed to understand the functional role of this polymorphism. However, together with the reported associations of AD with APOE, CYP46A1 and ABCA1, the present result adds a very significant support for the role of cholesterol and phospholipid homeostasis in AD and a rationale for testing novel cholesterol homeostasis-related therapeutic strategies in AD.

ATP-Binding Cassette Transporters↗

PubMed2005

Complex trait mapping in isolated populations: Are specific statistical methods required?

In this paper, we review the statistical methods that can be used in isolated populations to map genes involved in complex diseases. Our intention is to highlight the fact that if the features of population isolates may help in the identification of susceptibility factors for complex traits, the choice and design of methods for statistical analysis in these populations deserve particular care. We show that methods designed for outbred samples are generally not appropriate for isolated populations and could lead to false conclusions.

Chromosome Mapping↗

PubMed2004

Handling missing values in population data: consequences for maximum likelihood estimation of haplotype frequencies.

Haplotype frequency estimation in population data is an important problem in genetics and different methods including expectation maximisation (EM) methods have been proposed. The statistical properties of EM methods have been extensively assessed for data sets with no missing values. When numerous markers and/or individuals are tested, however, it is likely that some genotypes will be missing. Thus, it is of interest to investigate the behaviour of the method in the presence of incomplete genotype observations. We propose an extension of the EM method to handle missing genotypes, and we compare it with commonly used methods (such as ignoring individuals with incomplete genotype information or treating a missing allele as any other allele). Simulations were performed, starting from data sets of haematopoietic stem cell donors genotyped at three HLA loci. We deleted some data to create incomplete genotype observations in various proportions. We then compared the haplotype frequencies obtained on these incomplete data sets using the different methods to those obtained on the complete data. We found that the method proposed here provides better estimations, both qualitatively and quantitatively, but increases the computation time required. We discuss the influence of missing values on the algorithm's efficiency and the advantages and disadvantages of deleting incomplete genotypes. We propose guidelines for missing data handling in routine analysis.

Computational Biology↗

PubMed2004

Robustness of case-control studies of genetic factors to population stratification: magnitude of bias and type I error.

Case-control studies of genetic factors are prone to a special form of confounding called population stratification, whenever the existence of one or more subpopulations may lead to a false association, be it positive or negative. We quantify both the bias (in terms of confounding risk ratio) and the probability of false association (type I error) in the most unfavorable situation in which only one high-risk subpopulation is hidden within the studied population, considering different scenarios of population structuring and varying sample sizes. In accord with previous work, we find that the bias is likely to be small in most cases. In addition, we show that the same applies to the associated type I error whenever the subpopulation is small in proportion. For instance, when the hidden subpopulation makes up 5% of the entire population, with an allelic frequency of 0.25 (versus 0.10) and a disease rate that is double, then the estimated bias is 1.07 and the type I error associated with a sample of 500 cases and 500 controls is 8% (instead of 5%). We also show that the type I error is substantially greater for a rare allele (frequency of 0.1) than for a common allele (frequency of 0.5) and analyze the pattern of increase of vulnerability to stratification bias with sample size. Based on our findings, we may therefore conclude that with moderate sample sizes the type I error associated with population stratification remains very limited in most realistic scenarios.

Bias↗

PubMed2003

No replication of the association between the Nicastrin gene and familial early-onset Alzheimer's disease.

Polymorphisms in the Nicastrin (NCSTN) gene have recently been associated with familial early-onset Alzheimer's disease (AD). The authors genotyped four NCTSN polymorphisms in a large cohort of 489 AD cases (including 158 sporadic early-onset AD cases and 95 familial early-onset AD cases) and 386 controls but failed to replicate the association between NCSTN haplotype B and AD.

Age of Onset↗

PubMed2003

Estimation of the inbreeding coefficient through use of genomic data.

Many linkage studies are performed in inbred populations, either small isolated populations or large populations with a long tradition of marriages between relatives. In such populations, there exist very complex genealogies with unknown loops. Therefore, the true inbreeding coefficient of an individual is often unknown. Good estimators of the inbreeding coefficient (f) are important, since it has been shown that underestimation of f may lead to false linkage conclusions. When an individual is genotyped for markers spanning the whole genome, it should be possible to use this genomic information to estimate that individual's f. To do so, we propose a maximum-likelihood method that takes marker dependencies into account through a hidden Markov model. This methodology also allows us to infer the full probability distribution of the identity-by-descent (IBD) status of the two alleles of an individual at each marker along the genome (posterior IBD probabilities) and provides a variance for the estimates. We simulate a full genome scan mimicking the true autosomal genome for (1) a first-cousin pedigree and (2) a quadruple-second-cousin pedigree. In both cases, we find that our method accurately estimates f for different marker maps. We also find that the proportion of genome IBD in an individual with a given genealogy is very variable. The approach is illustrated with data from a study of demyelinating autosomal recessive Charcot-Marie-Tooth disease.

Charcot-Marie-Tooth Disease↗

PubMed2003

A risk for early-onset Alzheimer's disease associated with the APBB1 gene (FE65) intron 13 polymorphism.

Alzheimer's disease (AD) is a genetically complex neurodegenerative disorder and the leading cause of dementia of the elderly. Recently, Hu et al. suggested that a trinucleotide deletion in intron 13 of the APBB1 gene was a factor protecting against late-onset AD. We report here the results of a case/control study aimed at replicating this association. Our study included 461 AD patients and 397 matched controls. We compared the allele and genotype frequencies of the polymorphism between the two groups but did not find any statistically significant difference (P=0.08 and P=0.09, respectively). By contrast, adjusting for age and sex, we found a slight risk associated with the deletion (odds ratio=1.47, 95% confidence interval=1.05-2.04). Stratification by age showed that the risk effect associated with the deletion concerned subjects aged less than 65 years.

Age Factors↗

PubMed2003

Genetic analysis of multiple sclerosis in Europeans: French data.

We report the results of a genome-wide screen for linkage disequilibrium (LD) in multiple sclerosis (MS) performed on 200 cases, 200 controls and 200 case-parent trios from France employing pooled DNA methodology. A total of 3510 microsatellite markers supplied through the GAMES collaborative were analysed and ranked according to their evidence for association. The most promising 117 markers were then followed up in a two-step validation process. In the first step, additional PCR of the DNA pools was performed in order to refine the ranking order. In the second step, markers were genotyped in individual cases and parents from the trio families. Seven markers showing nominally significant allele frequency differences between affected and unaffected emerged-D6S265, D12S1064, TNFa, D7S1824, D14S1426, D14S605 and D21S2051. These potential associations will require confirmation in further studies.

Alleles↗

PubMed2002

Linkage of one gene for familial glucocorticoid deficiency type 2 (FGD2) to chromosome 8q and further evidence of heterogeneity.

In several cases of familial glucocorticoid deficiency (FGD), referred to as FGD type 1, mutations have been described in the coding exon of the adrenocorticotropin receptor (melanonocortin receptor type 2, MC2R) gene. However, for the majority of cases (FGD type 2), no mutations were found in this gene. In the more informative families, the involvement of the MC2R locus could be excluded by linkage or sequencing analysis and, as there was no obvious candidate gene, a genome linkage scan was performed. Fourteen families were studied in this report. Evidence of linkage was found with markers on chromosome 8q in three out of the 14 families (maximum heterogeneity LOD score of 2.81 at D8S1763). These three families were consanguineous and the gene could be located by homozygosity mapping between markers D8S285 and D8S1718 in a 8.8-cM region. No potential candidate genes were apparent in the region. Linkage to this region could be excluded in some families from our sample giving highly negative LOD scores with the markers of the region. This result suggests that at least one other gene, located on a different region, must be responsible for FGD in these families and provides new evidence of genetic heterogeneity of this disorder.

Adrenal Cortex Diseases↗

PubMed2002

Absence of association of thrombophilia polymorphisms with intrauterine growth restriction.

BACKGROUND: Previous data have demonstrated associations between thrombophilia polymorphisms in pregnant women and an increased risk of intrauterine growth restriction in their offspring, but this finding remains uncertain. METHODS: We performed a hospital-based case-control study and a family-based study including 493 newborns with intrauterine growth restriction (defined by birth weight below the 10th percentile for gestational age and sex according to Canadian norms) and 472 controls (with birth weight at or above the 10th percentile). We determined the presence or absence in newborns and their parents of the following polymorphisms: methylenetetrahydrofolate reductase (MTHFR) C677T and A1298C, factor V Leiden G1691A, and prothrombin G20210A. Mothers were interviewed to obtain information on other risk factors for intrauterine growth restriction. RESULTS: The risk of intrauterine growth restriction was not increased among mothers carrying a polymorphism associated with thrombophilia. In the case-control study, the odds ratios associated with two copies of the variant, after adjustment for newborn genotype and other risk factors, were 1.55 for MTHFR C677T (95 percent confidence interval, 0.83 to 2.90) and 0.49 for MTHFR A1298C (95 percent confidence interval, 0.25 to 0.93); heterozygotes for factor V Leiden had an odds ratio of 1.18 (95 percent confidence interval, 0.54 to 2.55), and heterozygotes for prothrombin G20210A had an odds ratio of 0.92 (95 percent confidence interval, 0.36 to 2.35). These polymorphisms in the newborn were not associated with an increased risk. Newborns who were homozygous for the MTHFR C677T variant had a decreased risk of intrauterine growth restriction (odds ratio after adjustment for mother's genotype and other confounders, 0.52 [95 percent confidence interval, 0.29 to 0.94]). The results of the family-based study supported those of the case-control study. CONCLUSIONS: Our findings do not indicate that there are associations between maternal or newborn polymorphisms associated with thrombophilia and an increased risk of intrauterine growth restriction.

Adult↗

PubMed2002

Properties of the transmission-disequilibrium test in the presence of inbreeding.

Family-based association tests such as the transmission-disequilibrium test (TDT), which compare alleles transmitted and non-transmitted from parents to affected offspring, are widely used to detect the role of genetic risk factors in diseases. These methods have the advantage of being robust to population stratification and are thus believed to be valid whatever the population context. In different studies of the statistical properties of the TDT, parents of affected offspring are typically assumed to be neither inbred nor related. In many human populations, however, this assumption is false and parental alleles are then no longer independent. It is thus of interest to determine whether the TDT is a valid test of linkage and association in the presence of inbreeding. We present a method to derive the expected value of the TDT statistic under different disease models and for any relationship between the parents of affected offspring. Using this method, we show that in the presence of inbreeding, the TDT is still a valid test for linkage but not for association. The power of the test to detect linkage may, however, be increased in the presence of inbreeding under different modes of inheritance.

Consanguinity↗

PubMed2002

Impact of parental relationships in maximum lod score affected sib-pair method.

Many studies are done in small isolated populations and populations where marriages between relatives are encouraged. In this paper, we point out some problems with applying the maximum lod score (MLS) method (Risch, [1990] Am. J. Hum. Genet. 46:242-253) in these populations where relationships exist between the two parents of the affected sib-pairs. Characterizing the parental relationships by the kinship coefficient between the parents (f), the maternal inbreeding coefficient (alpha(m), and the paternal inbreeding coefficient (alpha(p)), we explored the relationship between the identity by descent (IBD) vector expected under the null hypothesis of no linkage and these quantities. We find that the expected IBD vector is no longer (0.25, 0.5, 0.25) when f, alpha(m), and alpha(p) differ from zero. In addition, the expected IBD vector does not always follow the triangle constraints recommended by Holmans ([1993] Am. J. Hum. Genet. 52:362-374). So the classically used MLS statistic needs to be adapted to the presence of parental relationships. We modified the software GENEHUNTER (Kruglyak et al. [1996] Am. J. Hum. Genet. 58: 1347-1363) to do so. Indeed, the current version of the software does not compute the likelihood properly under the null hypothesis. We studied the adapted statistic by simulating data on three different family structures: (1) parents are double first cousins (f=0.125, alpha(m)=alpha(p)=0), (2) each parent is the offspring of first cousins (f=0, alpha(m)=alpha(p)=0.0625), and (3) parents are related as in the pedigree from Goddard et al. ([1996] Am. J. Hum. Genet. 58:1286-1302) (f=0.109, alpha(m)=alpha(p)=0.0625). The appropriate threshold needs to be derived for each case in order to get the correct type I error. And using the classical statistic in the presence of both parental kinship and parental inbreeding almost always leads to false conclusions.

Computer Simulation↗

PubMed2001

Inherited interleukin-12 deficiency: IL12B genotype and clinical phenotype of 13 patients from six kindreds.

Interleukin-12 (IL12) is a cytokine that is secreted by activated phagocytes and dendritic cells and that induces interferon-gamma production by natural-killer and T lymphocytes. It consists of two subunits, p35 and p40, which are encoded by IL12A and IL12B, respectively. The first reported patient with a genetic cytokine disorder was a Pakistani child, who was homozygous for a large loss-of-function deletion (g.482+82_856-854del) in IL12B. This IL12-deficient child suffered from infections caused by bacille Calmette-Guérin (BCG) and Salmonella enteritidis. We herein report 12 additional patients from five other kindreds. In one kindred from India, the same large deletion that was described elsewhere (g.482+82_856-854del) was identified. In four kindreds from Saudi Arabia, a recessive loss-of-function frameshift insertion (g.315_316insA) was found. A conserved haplotype encompassing the IL12B gene suggested that a founder effect accounted for the recurrence of each mutation. The two founder mutational events-g.482+82_856-854del and g.315_316insA-were estimated to have occurred approximately 700 and approximately 1,100 years ago, respectively. Among a total of 13 patients with IL12 deficiency, 1 child had salmonellosis only and 12 suffered from clinical disease due to BCG or environmental nontuberculous mycobacteria. One patient also had clinical disease caused by virulent Mycobacterium tuberculosis, five patients had clinical disease caused by Salmonella serotypes, and one patient had clinical disease caused by Nocardia asteroides. The clinical outcome varies from case to case, since five patients (aged 2-11 years) died of overwhelming infection, whereas eight patients (aged 3-12 years) are still in good health and are not currently taking antibiotics. In conclusion, IL12 deficiency is not limited to a single kindred, shows significant variability of outcome, and should be considered in the genetic diagnosis of patients with mycobacteriosis and/or salmonellosis. To date, two founder IL12B mutations have been identified, accounting for the recurrence of a large deletion and a small insertion within populations from the Indian subcontinent and from the Arabian Peninsula, respectively.

Adolescent↗