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PubMed2006

Fine mapping and positional candidate studies on chromosome 5p13 identify multiple asthma susceptibility loci.

BACKGROUND: Genome-wide linkage scans to identify asthma susceptibility loci have revealed many linked regions, including a broad region on chromosome 5p. OBJECTIVE: To identify a 5p-linked asthma or bronchial hyperresponsiveness (BHR) locus. METHODS: We performed fine mapping and positional candidate studies of this region in the Hutterites and an outbred case-control sample from Germany by genotyping 89 single nucleotide polymorphisms (SNPs) in 22 genes. SNP and haplotype analyses were performed. RESULTS: Three genes in a distal region (zinc finger RNA binding protein [ZFR], natriuretic peptide receptor C, and a disintegrin and metalloproteinase domain with thrombospondin type 1 motif [ADAMTS12]) were associated with BHR, whereas 4 genes in a proximal region (prolactin receptor, IL-7 receptor [IL7R], leukemia inhibitory factor receptor [LIFR], and prostaglandin E4 receptor [PTGER4]) were associated with asthma symptoms in the Hutterites. Furthermore, nearly the entire original linkage signal in the Hutterites was generated by individuals who had the risk-associated alleles in ZFR3, natriuretic peptide receptor C, ADAMTS12, LIFR, and PTGER4. Variation in ADAMTS12, IL7R, and PTGER4 were also associated with asthma in the outbred Germans, and the frequencies of long-range haplotypes composed of SNPs at ZFR, ADAMTS12, IL7R, LIFR, and PTGER4 were significantly different between both the German and Hutterite cases and controls. There is little linkage disequilbrium between alleles in these 2 regions in either population. CONCLUSION: These results suggest that a broad region on 5p, separated by >9 Mb, harbors at least 2 and possibly 5 asthma or BHR susceptibility loci. These findings are consistent with the hypothesis that regions providing evidence for linkage in multiple populations may, in fact, house more than 1 susceptibility locus, as appears to be the case for the linked region on 5p. CLINICAL IMPLICATIONS: Identifying asthma or BHR genes could lead to novel therapeutic approaches.

Asthma↗

PubMed2000

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.

Adult↗

PubMed2004

Are common disease susceptibility alleles the same in outbred and founder populations?

Founder populations have been the subjects of complex disease studies because of their decreased genetic heterogeneity, increased linkage disequilibrium and more homogeneous environmental exposures. However, it is possible that disease alleles identified in founder populations may not contribute significantly to susceptibility in outbred populations. In this study we examine the Hutterites, a founder population of European descent, for 103 polymorphisms in 66 genes that are candidates for cardiovascular or inflammatory diseases. We compare the frequencies of alleles at these loci in the Hutterites to their frequencies in outbred European-American populations and test for associations with cardiovascular disease-associated phenotypes in the Hutterites. We show that alleles at these loci are found at similar frequencies in the Hutterites and in outbred populations. In addition, we report associations between 39 alleles or haplotypes and cardiovascular disease phenotypes (P<0.05), with five loci remaining significant after adjusting for multiple comparisons. These data indicate that this founder population is informative and offers considerable advantages for genetic studies of common complex diseases.

Cardiovascular Diseases↗

PubMedDate not supplied

Studies of HLA, fertility and mate choice in a human isolate.

The role of human leukocyte antigen (HLA) genes in pregnancy and in human mate choice has been investigated in the Hutterites, an inbred population of European origins. High-resolution HLA haplotypes were defined by alleles at 16 loci in >1000 Hutterites. Prospective studies of pregnancy outcome previously demonstrated increased fetal loss rates among Hutterite couples matching for HLA-B antigens (P = 0.033) or for the entire 16-locus haplotype (P = 0.002). Among living children of couples matching for HLA-B or for the haplotype, there was a non-significant deficit of children who were heterozygous and compatible with the mother; the number of living children who were compatible and homozygous or incompatible and heterozygous was not different than expectations (HLA-B, P = 0.095; haplotype, P = 0.376). Mate choice among 411 couples was non-random with respect to the HLA haplotype, assessed by a variety of methods (P = 0.020 to <0.001). These combined data indicate a role for HLA region genes in both pregnancy outcome and mate choice, and suggest that selection acting on these genes occurs pre-conceptually as well as during pregnancy. This review outlines previously published studies on HLA, fertility and mate choice in the Hutterites.

Adult↗

PubMed1989

Changes in completed family size and reproductive span in Anabaptist populations.

The Anabaptist Amish, Hutterite and Mennonite peoples trace their origins to the Reformation. Although they share certain beliefs, such as adult baptism and the separation of church and state, each group is culturally unique. The Hutterite and Amish are highly fertile and their populations exhibit stable rates of growth. These demographic characteristics reflect communal living among the Hutterites and labor intensive farming practices among the Amish. The Mennonites are the most receptive Anabaptist group to outside socioeconomic influences and provide a demographic contrast to the more conservative Amish and Hutterites. Demographic data collected during a study of aging in Mennonite population samples from Goessel and Meridian, Kansas, 1980, and Henderson, Nebraska, 1981, formed the basis of a cohort analysis in order to assess fertility change over time. Completed family size has decreased significantly in all three communities since 1870. Since the early 1900's the mean age of the mother at first birth has fluctuated but the mean age of mother at the birth of the last child is decreasing significantly for the communities of Goessel and Henderson, thus effectively shortening the reproductive span. The pattern is somewhat different for Meridian, the most conservative of the three communities.

Adolescent↗

PubMed1999

Effect of inbreeding avoidance on Hardy-Weinberg expectations: examples of neutral and selected loci.

Although all human populations avoid close inbreeding, the effect of inbreeding avoidance on genotype proportions has not been formally considered. This paper examines the expected proportions of genotype frequencies after adjusting the Hardy-Weinberg model for close inbreeding avoidance in an inbred population. This corrected model was used to evaluate genotype distributions for HLA haplotypes and haplotypes created from three microsatellite loci on human chromosome 13 in a sample of 315 married Hutterites. In this sample, there were five individuals who were homozygous for an HLA haplotype and 15 individuals who were homozygous for a chromosome 13 haplotype. The expected numbers of homozygotes were 21 for HLA and 26 for chromosome 13 haplotypes using a model adjusted for overall inbreeding (P = 0.00031 for HLA and P = 0.019 for chromosome 13) and 18 for HLA and 22 chromosome 13 haplotypes using a model adjusted for both overall inbreeding and close inbreeding avoidance (P = 0. 0016 for HLA and P = 0.099 for chromosome 13). The model that takes into account both overall inbreeding and inbreeding avoidance provided a better fit to the observed genotype distributions for chromosome 13 haplotypes (P = 0.099), suggesting that nonrandom aspects of Hutterite mating structure, other than inbreeding and inbreeding avoidance, have small effects on genotype distributions in the population. The fact that significant deficiencies of HLA homozygotes persist after taking into account inbreeding avoidance further suggests that factors related to the HLA haplotype per se influence the genotype proportions at HLA loci in the Hutterites.

Adult↗

PubMed2005

A locus for Bowen-Conradi syndrome maps to chromosome region 12p13.3.

Bowen-Conradi syndrome (BCS) is a lethal autosomal recessive disorder with an estimated incidence of 1 in 355 live births in the Hutterite population. A few cases have been reported in other populations. Here, we report the results of a genome-wide scan and fine mapping of the BCS locus in Hutterite families. By linkage and haplotype analysis the BCS locus was mapped to a 3.5 cM segment (1.9 Mbp) in chromosome region 12p13.3 bounded by F8VWF and D12S397. When genealogical relationships among the families were taken into account in the linkage analysis, the evidence for linkage was stronger and the number of potentially linked regions was reduced to one. Under the assumption that all the Hutterite patients were identical by descent for a disease-causing mutation, haplotype analysis was used to infer likely historical recombinants and thereby narrow the candidate region to a chromosomal segment shared in common by all the affected children. This study also demonstrates that BCS and cerebro-oculo-facial-skeletal syndrome (COFS) are genetically distinct.

Abnormalities, Multiple↗

PubMed2005

Commonality of TRIM32 mutation in causing sarcotubular myopathy and LGMD2H.

Sarcotubular myopathy (OMIM 268950) is a rare autosomal recessive myopathy first described in two Hutterite brothers from South Dakota and in two non-Hutterite brothers from Germany. We report that sarcotubular myopathy (STM) is caused by mutation in TRIM32, the gene encoding the tripartite motif-containing protein 32. TRIM32 was found to be the gene mutated in limb girdle muscular dystrophy type 2H (LGMD2H [OMIM 254110]), a disorder that has been confined to the Hutterite population. The TRIM32 mutation found in the STM patients is identical to the causative mutation for LGMD2H (D487N), Haplotype analysis shows that the disease chromosomes share common ancestry.

Adult↗

PubMed2001

Oligogenic approaches to the predisposition of asthma in ethnically diverse populations.

Using the genome-wide screening data of the Collaborative Study on the Genetics of Asthma (CSGA) (226 families, 1,461 genotyped subjects, 323 marker loci) and Hutterite studies (129 families, 690 genotyped subjects, 365 marker loci), we applied a genetic similarity function in order to quantify the inter-individual genetic distances d(xi,xj) between feature vectors xi, xj made up by the allelic patterns of subjects i,j with respect to loci li, l2,..., ln. Based on this similarity function, we structurally decomposed the genetic diversity of the CSGA population in order to address the question of ethnicity-related asthma vulnerability for genetically homogenous CSGA subgroups. The question of ethnicity-independent asthma vulnerability was investigated with all CSGA families as training and the Hutterite families as replication samples. We evaluated the between-sib similarities, which were expected to deviate from "0.5" in affected sib pairs if the region of interest contained markers close to disease-causing genes. The reference value 0.5 was derived by determining the parent-offspring similarities, which are always 0.5, irrespective of the affection status of parents and offspring. We found 18 vulnerability loci on chromosomes 1, 3, 4, 5, 6, 8, 12, 13, and 14, which were remarkably reproducible in the CSGA and the Hutterite data and constituted an ethnicity-independent oligogenic model.

Adult↗

PubMed2006

Variation in the type I interferon gene cluster on 9p21 influences susceptibility to asthma and atopy.

A genome-wide screen for asthma and atopy susceptibility alleles conducted in the Hutterites, a founder population of European descent, reported evidence of linkage with a short tandem repeat polymorphism (STRP) within the type I interferon (IFN) gene cluster on chromosome 9p21. The goal of this study was to identify variation within the IFN gene cluster that influences susceptibility to asthma and atopic phenotypes. We screened approximately 25 kb of sequence, including the flanking sequence of all 15 functional genes and the single coding exon in 12, in Hutterites representing different IFNA-STRP genotypes. We identified 78 polymorphisms, and genotyped 40 of these (in 14 genes) in a large Hutterite pedigree. Modest associations (0.003<P<0.05) with asthma, bronchial hyper-responsiveness (BHR), and atopy were observed with individual variants or genes, spanning the entire 400 kb region. However, pairwise combinations of haplotypes between genes showed highly significant associations with different phenotypes (P<10(-5)) that were localized to specific pairs of genes or regions of this cluster. These results suggest that variation in multiple genes in the type I IFN cluster on 9p22 contribute to asthma and atopy susceptibility, and that not all genes contribute equally to all phenotypes.

Adolescent↗

PubMed1999

Inbreeding effects on fertility in humans: evidence for reproductive compensation.

The effects of inbreeding on prereproductive mortality have been demonstrated in many natural populations, including humans. However, little is known about the effects in inbred individuals who survive to adulthood. We have investigated the effects of inbreeding on fertility among inbred adult Hutterites and demonstrate significantly reduced fecundity among the most inbred Hutterite women, as evidenced by longer interbirth intervals (P=.024) and longer intervals to a recognized pregnancy (P=.010) but not by increased rates of fetal loss (P>.50). These data suggest the presence of recessive alleles that adversely affect fecundity among the population. In contrast, completed family sizes do not differ among the more and the less-inbred Hutterite women who were born after 1920, suggesting that reproductive compensation is occurring among the more-inbred and less-fecund women. This recent reproductive strategy would facilitate the maintenance of recessive alleles and contribute to an overall decline in fertility in the population.

Adult↗

PubMed2000

Variation in the interleukin 4-receptor alpha gene confers susceptibility to asthma and atopy in ethnically diverse populations.

After a genomewide screen in the Hutterites was completed, the IL4RA gene was examined as the 16p-linked susceptibility locus for asthma and atopy. Seven known variants and one novel variant, representing all nonsynonymous substitutions in the mature protein, were examined in the Hutterites; on the basis of studies in the Hutterites, outbred white, black, and Hispanic families were genotyped for selected markers. All population samples showed evidence of association to atopy or to asthma (P values.039-.0044 for atopy and. 029-.0000061 for asthma), but the alleles or haplotypes showing the strongest evidence differed between the groups. Overall, these data suggest that the IL4RA gene is an atopy- and asthma-susceptibility locus but that variation outside the coding region of the gene influences susceptibility.

Alleles↗

PubMed2001

Broad and narrow heritabilities of quantitative traits in a founder population.

Estimation of the components of variance for a quantitative trait allows one to evaluate both the degree to which genetics influences the trait and the trait's underlying genetic architecture. For particular traits, the estimates also may have implications for discriminating between potential models of selection and for choosing an appropriate model for linkage analysis. Using a recently developed method, we estimate the additive and dominance components of variance--or, equivalently, the narrow and broad sense heritabilities--of several traits in the Hutterites, a founder population with extensive genealogical records. As a result of inbreeding and because Hutterite individuals are typically related through multiple lines of descent, we expect that power to detect dominance variance will be increased relative to that in outbred studies. Furthermore, the communal lifestyle of the Hutterites allows us to evaluate the genetic influences in a relatively homogeneous environment. Four phenotypes had a significant dominance variance, resulting in a relatively high broad heritability. We estimated the narrow and broad heritabilities as being, respectively,.36 and.96 for LDL,.51 and 1.0 for serotonin levels, and.45 and.76 for fat free mass (FFM). There was no significant additive component for systolic blood pressure (SBP), resulting in a narrow heritability of 0 and a broad heritability of.45. There were several traits for which we found no significant dominance component, resulting in equal broad and narrow heritability estimates. These traits and their heritabilities are as follows: HDL,.63; triglycerides,.37; diastolic blood pressure,.21; immunoglobulin E,.63; lipoprotein(a),.77; and body-mass index,.54. The large difference between broad and narrow heritabilities for LDL, serotonin, FFM, and SBP are indicative of strong dominance effects in these phenotypes. To our knowledge, this is the first study to report an estimate of heritability for serotonin and to detect a dominance variance for LDL, FFM, and SBP.

Blood Pressure↗

PubMed1997

HLA and mate choice in humans.

Evidence from studies in rodents suggests that mate selection is influenced by major-histocompatibility-complex haplotypes, with preferences for dissimilar partners. This study was initiated to determine whether avoidance of a mate with the same HLA haplotype as one's own might be occurring in the Hutterites, a North American reproductive isolate of European ancestry, notable for their large sibships, communal lifestyle, and limited number of five-locus HLA haplotypes (HLA-A, -B, -C, -DR, and -DQ). HLA haplotypes were known for 411 Hutterite couples. The number of couples expected to match for a haplotype was calculated in two ways: first, from population genotype frequencies, with account being taken of the nonrandom mating pattern with respect to colony lineages, and, second, from computer simulations using conservative founder assumptions and the exact genealogy of the 411 couples. We observed fewer matches for HLA haplotypes between spouses than expected (first method, P = .005; second method, P = .020-.067). Among couples who did match for a haplotype, the matched haplotype was inherited from the mother in 29 cases and from the father in 50 cases (P = .018). These results are consistent with the conclusion that Hutterite mate choice is influenced by HLA haplotypes, with an avoidance of spouses with haplotypes that are the same as one's own.

Adult↗

PubMed1995

A polymorphism of the paraoxonase gene associated with variation in plasma lipoproteins in a genetic isolate.

The Hutterite Brethren are a genetic isolate characterized by high indices of relatedness and a communal agrarian lifestyle. We hypothesized that variation of the paraoxonase (PON) gene that underlies the interindividual variation in plasma PON activity would be associated with variation in fasting plasma lipoprotein variables in this group. In 793 Hutterites, we measured plasma lipids, lipoproteins, and apolipoproteins and analyzed DNA for genotypes of the protein polymorphism at amino acid residue 192 of PON. We observed that genotypes of PON were significantly associated with variation in plasma concentrations of total, HDL, non-HDL, and LDL cholesterol, total triglycerides, and apolipoprotein (apo) B. Homozygotes for the low-activity variant of PON had significantly lower levels of plasma apoB-related biochemical variables than heterozygotes and homozygotes for the high-activity variant of PON. Homozygotes for the low-activity variant of PON also had significantly lower ratios of total cholesterol/HDL cholesterol, LDL cholesterol/HDL cholesterol, and apoB/apoA-I than heterozygotes and homozygotes for the high-activity variant of PON. We found no evidence for a gene-gender interaction for any plasma lipoprotein variable. The PON polymorphism accounted for about 1% of the variation in total cholesterol and related lipoprotein traits in the Hutterites. These observations suggest that PON is a significant genetic determinant of plasma lipoprotein levels.

Adult↗

PubMed1995

Genetic variation on chromosome 1 associated with variation in body fat distribution in men.

BACKGROUND: Interindividual variation in fat deposition in swine is determined by loci on porcine chromosome 4, which are contained in a region that is syntenic with part of the long arm of human chromosome 1. We hypothesized that genomic variation of chromosome 1q would be associated with variation in the ratio of waist-to-hip circumference in male North American Hutterites, a genetic isolate characterized by significant relatedness and sharing of environmental factors. METHODS AND RESULTS: In 316 male Hutterites, we tested for phenotype-genotype association of two DNA polymorphisms on chromosome 1q and the ratio of waist-to-hip circumference. We included control loci on 10 other chromosomes in the multivariate model. We observed that DNA variation on chromosome 1q was significantly associated with variation in the ratio of waist-to-hip circumference in men (P = .0029). CONCLUSIONS: The association of DNA variation chromosome 1q with the ratio of waist-to-hip circumference in male Hutterites suggests that there are important structural elements in this genomic region that have a functional impact on body fat distribution.

Adipose Tissue↗

PubMed2005

Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy.

BACKGROUND: Evolutionarily conserved sequences likely have biological function. METHODS: To determine whether variation in conserved sequences in non-coding DNA contributes to risk for human disease, we studied six conserved non-coding elements in the Th2 cytokine cluster on human chromosome 5q31 in a large Hutterite pedigree and in samples of outbred European American and African American asthma cases and controls. RESULTS: Among six conserved non-coding elements (> 100 bp, > 70% identity; human-mouse comparison), we identified one single nucleotide polymorphism (SNP) in each of two conserved elements and six SNPs in the flanking regions of three conserved elements. We genotyped our samples for four of these SNPs and an additional three SNPs each in the IL13 and IL4 genes. While there was only modest evidence for association with single SNPs in the Hutterite and European American samples (P < 0.05), there were highly significant associations in European Americans between asthma and haplotypes comprised of SNPs in the IL4 gene (P < 0.001), including a SNP in a conserved non-coding element. Furthermore, variation in the IL13 gene was strongly associated with total IgE (P = 0.00022) and allergic sensitization to mold allergens (P = 0.00076) in the Hutterites, and more modestly associated with sensitization to molds in the European Americans and African Americans (P < 0.01). CONCLUSION: These results indicate that there is overall little variation in the conserved non-coding elements on 5q31, but variation in IL4 and IL13, including possibly one SNP in a conserved element, influence asthma and atopic phenotypes in diverse populations.

Asthma↗

PubMed2005

Sex differences in the genetic basis of morning serum cortisol levels: genome-wide screen identifies two novel loci specific to women.

CONTEXT: Relatively little is known about the influence of specific genes on cortisol levels, particularly morning cortisol levels. OBJECTIVE: The objective of this study was to identify quantitative trait loci associated with morning serum cortisol levels. DESIGN: We carried out a genome screen for morning serum cortisol using linkage and association methods tailored for use in large pedigrees. We conducted these analyses both in the whole sample and partitioned by sex. SETTING: This study was conducted on nine communal Hutterite farms in South Dakota. PARTICIPANTS: The Hutterites are a young founder population who practice a communal, farming lifestyle in the western United States and in Canada. Hutterites (n = 504, 53% female) aged 11-89 yr from a single pedigree participated in this study. MAIN OUTCOME MEASURES: The main outcome measures were markers significantly linked or associated with variation in morning serum cortisol levels. RESULTS: One genome-wide significant association was identified in the whole sample on 11p (D11S1981, P = 0.000092). Results of sex-partitioned analyses indicated that this association was restricted to females (females, P = 0.000084; males, P = 0.20). The 146-bp allele at this locus accounted for 7% of the variance in morning cortisol values in females, and females homozygous for the allele had an 89% increase in morning cortisol levels compared with female noncarriers. A second genome-wide significant association in females was identified on 14q (D14S74, P = 0.000091). CONCLUSIONS: Our results suggest that the genetic determinants of morning cortisol levels may be different for men and women and that loci on 11p and 14q influence morning cortisol levels in women.

Adolescent↗