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PubMed2005

Y-chromosome short tandem repeat (STR) haplotypes in a Campania population sample.

Given the lack of information about Y haplotypes for Campania (southern Italy), we analyzed eight Y short tandem repeats in a sample of males from this region with the aim of establishing a Y-haplotype database that can be used for forensic purposes. The eight Y short tandem repeats were amplified by two PCR multiplex reactions: multiplex A for loci DYS19, DYS385, DYS392 and DYS393, and multiplex B for DYS389 I and II, DYS390, DYS391 and DYS385. The proportion of unique haplotypes was 100% (108 Y-chromosome haplotypes in 108 unrelated males) and the haplotype diversity discrimination index was 0.99. These data reflect the high heterogeneity of male lineage in our population and are similar to those obtained in other regions of southern Italy.

Chromosome Mapping↗

PubMed2004

Simultaneous estimation of haplotype frequencies and quantitative trait parameters: applications to the test of association between phenotype and diplotype configuration.

The analysis of the haplotype-phenotype relationship has become more and more important. We have developed an algorithm, using individual genotypes at linked loci as well as their quantitative phenotypes, to estimate the parameters of the distribution of the phenotypes for subjects with and without a particular haplotype by an expectation-maximization (EM) algorithm. We assumed that the phenotype for a diplotype configuration follows a normal distribution. The algorithm simultaneously calculates the maximum likelihood (L0max) under the null hypothesis (i.e., nonassociation between the haplotype and phenotype), and the maximum likelihood (Lmax) under the alternative hypothesis (i.e., association between the haplotype and phenotype). Then we tested the association between the haplotype and the phenotype using a test statistic, -2 log(L0max/Lmax). The above algorithm along with some extensions for different modes of inheritance was implemented as a computer program, QTLHAPLO. Simulation studies using single-nucleotide polymorphism (SNP) genotypes have clarified that the estimation was very accurate when the linkage disequilibrium between linked loci was rather high. Empirical power using the simulated data was high enough. We applied QTLHAPLO for the analysis of the real data of the genotypes at the calpain 10 gene obtained from diabetic and control subjects in various laboratories.

Algorithms↗

PubMed2005

Linkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs.

Single nucleotide polymorphisms (SNPs) have been proposed to be grouped into haplotype blocks harboring a limited number of haplotypes. Within each block, the portion of haplotypes is expected to be tagged by a selected subset of SNPs; however, none of the proposed selection algorithms have been definitive. To address this issue, we developed a tag SNP selection algorithm based on grouping of SNPs by the linkage disequilibrium (LD) coefficient r(2) and examined five genes in three ethnic populations--the Japanese, African Americans, and Caucasians. Additionally, we investigated ethnic diversity by characterizing 979 SNPs distributed throughout the genome. Our algorithm could spare 60% of SNPs required for genotyping and limit the imprecision in allele-frequency estimation of nontag SNPs to 2% on average. We discovered the presence of a mosaic pattern of LD plots within a conventionally inferred haplotype block. This emerged because multiple groups of SNPs with strong intragroup LD were mingled in their physical positions. The pattern of LD plots showed some similarity, but the details of tag SNPs were not entirely concordant among three populations. Consequently, our algorithm utilizing LD grouping allows selection of a more faithful set of tag SNPs than do previous algorithms utilizing haplotype blocks.

Black or African American↗

PubMed2006

Assessing the relative ages of admixture in the bovine hybrid zones of Africa and the Near East using X chromosome haplotype mosaicism.

Historical hybridization events between the two subspecies of cattle, Bos taurus and B. indicus, have occurred in several regions of the world, while other populations have remained nonadmixed. We typed closely linked X chromosome microsatellites in cattle populations with differing histories of admixture from Africa, Europe, the Near East, and India. Haplotype breakdown will occur as admixed populations age, and longer ancestral haplotypes will remain intact in more recently admixed populations compared to older ones. We genotyped male animals from these populations, obtaining unambiguous haplotypes, and measured levels of linkage disequilibrium (LD) and ancestral mosaicism. Extensive LD, likely to be the result of ongoing admixture, was discovered in hybrid cattle populations from the perimeter of the tsetse zone in West Africa. A Bayesian method to assign microsatellite allele ancestry was used to designate the likely origin of each chromosomal segment and assess the relative ages of admixture in the populations. A gradient of the age of admixture in the African continent emerged, where older admixture has produced more fragmented haplotypes in the south, and longer intact haplotypes, indicating more recent hybridization, feature in the northwest.

Africa↗

PubMed2006

Effects of introgression and recombination on haplotype structure and linkage disequilibrium surrounding a locus encoding Bymovirus resistance in barley.

We present a detailed analysis of linkage disequilibrium (LD) in the physical and genetic context of the barley gene Hv-eIF4E, which confers resistance to the barley yellow mosaic virus (BYMV) complex. Eighty-three SNPs distributed over 132 kb of Hv-eIF4E and six additional fragments genetically mapped to its flanking region were used to derive haplotypes from 131 accessions. Three haplogroups were recognized, discriminating between the alleles rym4 and rym5, which each encode for a spectrum of resistance to BYMV. With increasing map distance, haplotypes of susceptible genotypes displayed diverse patterns driven mainly by recombination, whereas haplotype diversity within the subgroups of resistant genotypes was limited. We conclude that the breakdown of LD within 1 cM of the resistance gene was generated mainly by susceptible genotypes. Despite the LD decay, a significant association between haplotype and resistance to BYMV was detected up to a distance of 5.5 cM from the resistance gene. The LD pattern and the haplotype structure of the target chromosomal region are the result of interplay between low recombination and recent breeding history.

Expressed Sequence Tags↗

PubMed2003

BetaS-haplotypes in sickle cell anemia patients from Salvador, Bahia, Northeastern Brazil.

BetaS-Globin haplotypes were studied in 80 (160 betaS chromosomes) sickle cell disease patients from Salvador, Brazil, a city with a large population of African origin resulting from the slave trade from Western Africa, mainly from the Bay of Benin. Hematological and hemoglobin analyses were carried out by standard methods. The betaS-haplotypes were determined by PCR and dot-blot techniques. A total of 77 (48.1%) chromosomes were characterized as Central African Republic (CAR) haplotype, 73 (45.6%) as Benin (BEN), 1 (0.63%) as Senegal (SEN), and 9 (5.63%) as atypical (Atp). Genotype was CAR/CAR in 17 (21.3%) patients, BEN/BEN in 17 (21.3%), CAR/BEN in 37 (46.3%), BEN/SEN in 1 (1.25%), BEN/Atp in 1 (1.25%), CAR/Atp in 6 (7.5%), and Atp/Atp in 1 (1.25%). Hemoglobin concentrations and hematocrit values did not differ among genotype groups but were significantly higher in 25 patients presenting percent fetal hemoglobin (%HbF) > or = 10% (P = 0.002 and 0.003, respectively). The median HbF concentration was 7.54+/-4.342% for the CAR/CAR genotype, 9.88 3.558% for the BEN/BEN genotype, 8.146 4.631% for the CAR/BEN genotype, and 4.180+/-2.250% for the CAR/Atp genotype (P = 0.02), although 1 CAR/CAR individual presented an HbF concentration as high as 15%. In view of the ethnic and geographical origin of this population, we did not expect a Hardy-Weinberg equilibrium for CAR/CAR and BEN/BEN homozygous haplotypes and a high proportion of heterozygous CAR/BEN haplotypes since the State of Bahia historically received more slaves from Western Africa than from Central Africa.

Anemia, Sickle Cell↗

PubMed1998

[Hemoglobin S haplotypes: their epidemiologic, anthropologic and clinical importance].

The link between beta s-gene haplotypes and sickle cell anemia has permitted a better understanding of the biological manifestations of this disease. The use of better laboratory methods can help rule out other hereditary factors that can camouflage the real hemoglobin genotype. The clinical heterogeneity of sickle cell disease, which is characterized by the presence of S hemoglobin, can be explained in terms of fetal hemoglobin (HbF) levels, ratio of G gamma chains to A gamma chains, 2,3-diphosphoglycerate levels, linked mutations, beta s haplotypes, coexistence of alpha-thalassemia, and environmental factors. The inheritance of Sen and Arab/Indian beta-gene cluster polymorphisms is associated with a milder clinical course, whereas the Central African Republic (CAR) or Bantu, Cameroon, and Benin haplotypes are linked with severe sickle cell disease. The CAR haplotype carries the worst prognosis of all (less than 12% HbF levels and adult-type G gamma:A gamma ratio). Once characterized, these DNA polymorphisms also assume great importance as anthropologic and genetic markers. In America, beta s haplotypes are contributing to a better understanding of Black American roots and their African ancestry. There is ample evidence of genetic variability not only between different Black populations in America, but also within the same country, as is the case in Costa Rica.

Analysis of Variance↗

PubMed2006

MDR1 haplotype frequencies in Japanese and Caucasian, and in Japanese patients with colorectal cancer and esophageal cancer.

The genotype frequencies of MDR1 T-129C, C1236T, G2677A,T and C3435T SNPs were compared in 154 healthy Japanese and 100 healthy Caucasians to provide basic information on the inter-ethnic differences of pharmacotherapeutic outcome. The variants were found at allelic frequencies of 5.5%, 65.6%, 16.6%, 40.6% and 40.6%, for T-129C, C1236T, G2677A, G2677T and C3435T, respectively, in Japanese, and at 5.1%, 45.9%, 3.6%, 46.4% and 56.6%, respectively, in Caucasians, with a statistically significant difference for C1236T, G2677A,T and C3435T (p<0.001). G2677A was about 5-fold more frequent in Japanese than Caucasians. These genotype frequencies were also investigated in 95 Japanese patients with colorectal cancer (CRC) and esophageal squamous cell carcinoma (ESCC), but no significant difference was detected, when compared with healthy Japanese subjects. The haplotype frequency reached a total of about 85% in Japanese with the following 4 major haplotypes; T(-129)-T1236-T2677-T3435 (36.1%), T(-129)-T1236-G2677-C3435 (22.5%), T(-129)-C1236-G2677-C3435 (14.2%) and T(-129)-C1236-A2677-C3435 (13.3%). The second and fourth haplotypes were hardly inferred in Caucasian, whereas T(-129)-C1236-G2677-T3435 (12.8%) was found to be Caucasian-specific. There was a tendency for higher frequencies of the T(-129)/C-(129)-C1236-A2677-C3435 haplotype in Japanese CRC patients and T(-129)-T1236-T2677-T3435 haplotype in Japanese ESCC patients, compared with that in healthy Japanese subjects.

Adult↗

PubMed2006

Molecular-based haplotype analysis of the beta 2-adrenergic receptor gene (ADRB2) in Japanese asthmatic and non-asthmatic subjects.

BACKGROUND: The beta2-adrenergic receptor gene (ADRB2) is a target molecule of beta2-agonists. Single nucleotide polymorphisms (SNPs) in the ADRB2 are related to the effectiveness of beta2-agonists. However, there are some discrepancies in the results of pharmacogenetic studies of ADRB2 among different ethnic groups. The aims of this study were to determine the ADRB2 haplotypes and diplotypes in Japanese asthmatic and non-asthmatic subjects and to examine their relation to asthma and to compare these results with previous studies done in other ethnic groups. METHODS: Complete sequences for 3 kb promoter and 1.2 kb structural regions of ADRB2 were analyzed in 48 Japanese asthmatics and 100 controls, and haplotypes and diplotypes of SNPs were analyzed. RESULTS: Fifteen SNPs including a novel one in -839 were observed. Allele frequencies for all SNPs were similar between asthmatics and controls. We also identified 42 haplotypes and 54 diplotypes of ADRB2 in a Japanese population. The frequencies were similar between the two groups. They were classified into 17 and 23 types, respectively, according to Drysdale's haplotype-organization system, and a significant ethnic difference was observed between the Japanese and Caucasian populations. CONCLUSIONS: The frequencies of SNPs and ADBR2 haplotypes in Japanese are different from those in Caucasians and African Americans. These divergences might imply the need for independent pharmacogenetic studies for ADBR2 in each ethnic group.

Black or African American↗

PubMed2006

A haplotype-based analysis of the PTPN22 locus in type 1 diabetes.

A recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp). However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T. In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests. The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)). After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P < 0.05). Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk.

Diabetes Mellitus, Type 1↗

PubMed1992

HLA haplotype sharing in rheumatoid arthritis sibships: risk estimates in siblings.

The distribution of the number of parental HLA haplotypes shared by sibs with rheumatoid arthritis (RA) has been used to obtain information on the genetics of the disease. Thirty-four RA sibships (25 sib-pairs, 9 sib-trios) were ascertained, all of which were HLA typed and which satisfied the 1958 American Rheumatism Association criteria for "definite" RA. These were combined with other published but nonoverlapping data from the literature; thus, 143 sib-pairs, 36 sib-trios and 4 sibquads were identified. The affected RA sibs shared two, one and zero parental HLA haplotypes in a ratio of 40: 45: 15 which was significantly different from random expectations (p less than 0.05). Risk estimates for sibs of probands for those sharing two, one and zero parental HLA haplotypes were 6.2%, 3.5% and 2.3% respectively. Risks subdivided by DR genotype of the proband are also calculated, the highest (8.7%) being for sibs sharing two haplotypes with a proband carrying at least one DR4 allele. The manuscript also considers genetic information in relatives other than siblings; an extension of the affected relative pair haplotype sharing method to second and third degree kinships is presented.

Arthritis, Rheumatoid↗

PubMed1991

Sickle cell anemia in the Tunisian population: haplotyping and HB F expression.

Thirty-three Tunisian patients, homozygous for Hb S, were examined. Haplotyping using nine restriction sites in the beta-globin gene cluster revealed that the most common type is the Benin type [---- + - + - +] which occurs at a frequency of 0.94% (31 cases); only one patient was homozygous for an atypical haplotype which shows some differences with the Benin haplotype at sites 1, 5, 6, and 8 [+ ---- + + + +]; the two remaining patients were assumed to be double heterozygotes for the Benin and atypical haplotypes. The presence of the atypical haplotype suggested a double origin of the beta S gene in Tunisia. Moreover, a heterogeneity in the Hb F production was observed, ranging between 2 to 16%, whereas the G gamma-globin expression was remarkably homogeneous in our patients with a normal amount approaching 40%. These results suggested the presence of a combination of several control factors.

Adolescent↗

PubMed1997

The insulin gene region and susceptibility to insulin-dependent diabetes mellitus in four races; new insights from Afro-Caribbean race-specific haplotypes.

The IDDM2 component of the genetic susceptibility to insulin-dependent diabetes mellitus (IDDM) has been mapped to chromosome 11p15.5. The exact identity of IDDM2 remains uncertain. It has been suggested that IDDM2 maps within the 5' VNTR (variable number tandem repeat) polymorphism upstream of the insulin gene (INS). This has not been confirmed and a contribution from other INS gene region polymorphisms cannot be excluded. We present INS region genotype data from four racial groups: the Japanese, Hong Kong Chinese, North Indian Asians and Afro-Caribbeans (two groups; one born and resident in the UK, one in Jamaica). These races have not been previously studied with the range of INS region polymorphisms included here. No INS polymorphism was associated with IDDM across all races. These data from this study thus do not identify any INS polymorphism as IDDM2. The Afro-Caribbean race showed a very different distribution of INS genotypes from the other races and novel race-specific INS haplotypes were identified. Analysis of these excluded a contribution to susceptibility to IDDM from the- 23HphI INS polymorphism. An Afro-Caribbean INS haplotype which differed only at the VNTR from the very protective INS haplotype (VPH) identified in white Caucasians was detected. Population analysis of this haplotype will allow direct assessment of the role of the VNTR in susceptibility to IDDM. In conclusion, the diverse Afro-Caribbean TH/INS/IGF2 haplotypes identified in this study will be valuable in mapping IDDM2 more precisely.

Diabetes Mellitus, Type 1↗

PubMed2004

Effects of casein haplotypes on milk production traits in Italian Holstein and Brown Swiss cattle.

The objective of this study was to estimate the effects of different haplotypes of the casein genes on milk production traits in Italian dairy cattle. Traits of interest were yields of milk, fat, and protein, and percentages of fat and protein in milk. The data included 728 multiparous records from 347 Holsteins and 773 records from 298 Brown Swiss cows. Records were preadjusted for effects of age and parity, season of calving, and region, and expressed as deviations from herdmate averages. Twenty half-sib families were represented in each breed. Haplotype probabilities were estimated for each animal and phenotypes were regressed on these probabilities. Nine haplotypes were observed in Holsteins and 17 were identified among the Brown Swiss. For Holsteins, significant effects were observed for protein percentage, with some indication of an effect for fat percentage. For the Brown Swiss, effects of haplotypes were significant for milk yield and fat and protein percentages. Effects were strongest for protein percentage. Correlation coefficients of solutions across breeds tended to be strong and positive, indicating that the same haplotypes had similar estimated effects in the 2 breeds. Although the data were limited (<350 cows in each study), this latter result may suggest that genes in the casein complex itself are responsible for the effects observed, rather than loci that are physically linked on either side of the casein cluster.

Animals↗

PubMed2026

Integrative haplotype and SNP-based GWAS supports the identification of stable genomic loci controlling yield-related traits in soybean.

Soybean yield is vulnerable to environmental variation, therefore, it is important to detect and implement stable genomic regions associated with yield-related traits in soybean breeding programs. In this study, SNP and haplotype-based GWAS were conducted to reveal important candidate genomic regions and putative candidate genes associated with soybean yield-related traits. This study demonstrates that the integration of haplotype and SNP-based GWAS could improve the detection of genomic regions associated with complex traits, enhance statistical power, and facilitate the identification of biologically relevant candidate genes. Ten stable haplotype blocks and six stable SNPs were detected based on the integration of haplotype and SNP-based GWAS, respectively. Furthermore, multiple candidate genes associated with the yield-related traits were identified. For instance, six genes were identified as transporters, including Glyma.15G092800, encoding serine-type endopeptidase activity, Glyma.15G203300 encoding a major facilitator superfamily (MFS) sugar transporter, Glyma.04G163000, transmembrane transporter, and Glyma.04G164100, leucine-rich repeat receptor-like protein kinase (LRR-RLK), as the most promising candidate genes. Additionally, three genes involved in signaling and pathways of various phytohormones can be promising candidates for increasing seed yield through improving plant architecture in soybean plants. The identified superior haplotypes with favourable alleles will be useful for marker-assisted selection in future breeding programs in soybean.

DArT markers↗

PubMed2006

[Association of single nucleotide polymorphisms and haplotypes in DNA repair gene XRCC1 with susceptibility of breast cancer].

OBJECTIVE: To examine the contribution of the three most common single nucleotide polymorphisms (SNPs) in XRCC1 gene, C26304T, G27466A and G28152A, to susceptibility of breast cancer in Chinese Han population. METHODS: In this population-based case control study, 84 cases with breast cancer and 252 controls, matched to the cases in terms of habitation and age (5 years), were genotyped for the XRCC1 C26304T, G27466A and G28152A polymorphisms by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methods. The haplotype distribution was estimated and compared by EH linkage software 1. 2. RESULT: The distribution of basic characteristics, such as age, alcohol drinking, the family history of malignancy in first and second relatives except cigarette smoking, were not significantly different between cases and controls. However, the percentage of ever or current smokers was significantly higher in cases (7.1%) than that in controls (2.0%). The distributions of allelotype and genotype of C26304T, G27466A and G28152A polymorphisms were also not significantly different between cases and controls. There was no significant association between the risk of breast cancer and these three SNPs of XRCC1 gene. The genetic linkage disequilibrium existed in these three polymorphic sites both in cases and controls, in which the CGG, CGA, CAG and TGG haplotypes were the most common. There was also no significant association of XRCC1 haplotype with risk of breast cancer. CONCLUSION: XRCC1 C26304T, G27466A and G28152A SNPs may not be associated with the susceptibility of breast cancer. The CGG, CGA, CAG and TGG haplotypes might be the most common haplotypes in Chinese Han population.

Adult↗

PubMed2000

Duplicated DQ haplotypes increase the complexity of restriction element usage in cattle.

The MHC of cattle encodes two distinct isotypes of class II molecules, DR and DQ. Unlike humans, cattle lack the DP locus and about half the common haplotypes express duplicated DQ genes. The number and frequency of DQA and DQB alleles means that most cattle are heterozygous. If inter- and/or intrahaplotype pairing of DQA and DQB molecules occurs, cattle carrying DQ-duplicated haplotypes may express more restriction elements than would be predicted by the number of expressed alleles. We are investigating whether duplicated haplotypes cause differences in immune response, particularly in terms of generating protective immunity. We have analyzed the Ag-presenting function of DQ molecules in two heterozygous animals, one of which carries a duplicated haplotype. We compared the class II isotype specificity of T cell clones recognizing a putative vaccinal peptide from foot-and-mouth disease virus (FMDV15). We show for the first time that bovine T cells can recognize Ag in the context of DQ molecules. We also present evidence that interhaplotype pairings of DQA and DQB molecules form functional restriction elements. Both animals showed distinct biases to usage of particular restriction elements. Mainly DQ-restricted clones were derived from the animal with duplicated DQ genes, whereas the majority of clones from the animal with a single DQ gene pair were DR restricted. Furthermore, haplotype bias was observed with both animals. These experiments show that understanding of class II chain pairing in addition to knowledge of the genotype may be important in vaccine design where effective epitope selection is essential.

Animals↗

PubMed1995

Utility of a "swish and spit" technique for the collection of buccal cells for TAP haplotype determination.

OBJECTIVE: To demonstrate the utility of a "swish and spit" technique as a nucleated cell source for transporter associated with antigen processing (TAP) haplotype determination by molecular methods in large-scale clinical trials. DESIGN: Twenty normal volunteers were recruited for this prospective feasibility study. From each subject, buccal or blood cells (or both) were collected for use in TAP haplotype assignment by molecular methods and subjected to various storage conditions. MATERIAL AND METHODS: As an alternative to use of lymphocytes obtained by venipuncture, we developed a swish and spit technique for collecting buccal cells for assigning TAP haplotype. For this technique, the subject vigorously swishes isotonic saline in the mouth and expectorates it into a collection container. DNA is extracted from the buccal cells by proteinase K digestion, phenol-chloroform extraction, and ethanol precipitation. In addition, we compared DNA extracted from mouthwash specimens stored under various conditions to which a specimen might be exposed if mailed. RESULTS: DNA extracted from buccal cells obtained by the swish and spit technique provided excellent templates for the polymerase chain reaction (PCR), and subject acceptance of this method was universal. In all cases, assigning TAP haplotype by PCR amplification of specific alleles with use of buccal or blood-derived specimens was successful. The integrity of the specimens was unaffected by storage at -20 degrees C, 4 degrees C, 25 degrees C, or 37 degrees C, and we were able to use the DNA from cells stored under any of these conditions for TAP haplotying. CONCLUSION: We conclude that DNA from buccal cells collected by the swish and spit technique for TAP haplotype assignment is an excellent substitute for DNA obtained from nucleated blood cells, and the technique is useful for large-scale clinical studies that require DNA from subjects geographically distant from the research site.

DNA↗