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PubMed2000

Beta-globin gene haplotypes and alpha-thalassemia analysis in Babinga pygmies from Congo-Brazzaville.

We analyzed beta-globin gene cluster haplotypes and deletional alpha+-thalassemia (-alpha3.7kb) in 54 Babinga pygmy subjects from Congo-Brazzaville. The beta(S)-globin gene frequency was 0.065 and that of the deletional alpha-globin gene (-alpha3.7kb) was 0.29. Eighty-five percent of the beta(S) chromosomes and 13% of the beta(A) chromosomes were associated with the Bantu haplotype, 10% of beta(A) chromosomes with the Senegal haplotype, and the remaining beta chromosomes with atypical haplotypes. None of the chromosomes were of the Benin haplotype. These results are clearly of anthropological and evolutionary interest. They also support earlier observations that alpha+-thalassemia is prevalent at a high frequency in African populations.

Cluster Analysis↗

PubMed2000

Improved haplotype analysis of human myelin basic protein short tandem repeat loci.

We report an improved haplotype analysis of the human myelin basic protein gene (MBP) short tandem repeat (STR) polymorphism. The polymorphic G-->A transition and 2 conventional STR polymorphisms, MBPA and MBPB, were simultaneously determined by an amplified product length polymorphism technique. After the MBPC fragments containing MBPA and MBPB were amplified, the linkage of these 2 STR loci was determined by a second amplification, using polymerase chain reaction (PCR) technique, of the isolated MBPC fragments. The present haplotype analysis dispensed with family studies for the haplotyping of MBPA and MBPB. Polymorphisms of the MBP loci studied in German and Japanese populations showed a high genomic variation. Haplotype analysis of the MBP loci showed distinct differences between the German and the Japanese populations. Consequently, haplotype analysis of the MBP loci promises to be useful in forensic identification and paternity testing.

Alleles↗

PubMed2000

A study of C4AQ0 and MHC haplotypes in Icelandic multicase families with systemic lupus erythematosus.

OBJECTIVE: To study MHC haplotypes and C4AQ0 in Caucasian multicase systemic lupus erythematosus (SLE) families from Iceland. METHODS: Eight families with 26 SLE patients, 98 non-SLE first-degree relatives, and a control group were studied. For statistical analysis one SLE patient and one first-degree relative were randomly chosen from each family. C4 allotyping was performed by protein electrophoresis, HLA typing of class I by the lymphocytotoxicity test, and typing of class II alleles with polymerase chain reaction with sequence specific primers. RESULTS: Six of the 8 families showed a high background of C4A protein deficiency (C4AQ0) and a significant increase was seen in C4AQ0 in the randomly chosen group of patients. A similar tendency that was statistically nonsignificant was seen in first-degree relatives. In the SLE patients C4AQ0 was found on several MHC haplotypes. Half the patients with C4A protein deficiency carry C4AQ0 on the classical C4A deletion haplotype B8-C4AQ0-C4B1-DR3 or variants of it, and the remaining C4A deficient patients on other non-DR3 carrying haplotypes. The transmission of C4AQ0 from parents to patients was in most cases through the family line, although in some instances it originates from outside the multicase SLE family through spouses married into the family. CONCLUSION: In these Caucasian multicase SLE families from Iceland, C4AQ0 shows weaker linkage disequilibrium with DR3 than reported in studies on other white populations, emphasizing the role of ethnicity. The common factor in the MHC haplotypes studied is C4AQ0, supporting a hypothesis that C4AQ0 may be an independent risk factor for SLE.

Complement C4a↗

PubMed2002

Online Y-chromosomal short tandem repeat haplotype reference database (YHRD) for U.S. populations.

We describe here an online Y-chromosomal short tandem repeat haplotype reference database (YHRD) for U.S. populations, which represents 9-locus Y-STR haplotypes for 1705 African-Americans, European-Americans and Hispanics as of October 2001. This database is available online (http://www.ystr. org/usa/), free to access and was generated in order to supply the U.S. forensic DNA community with a valuable resource for frequencies of complete or incomplete 9-locus Y-STR haplotypes, as well as information about typing protocols and population genetic analyses. Pairwise R(ST)-statistics derived from the Y-STR haplotypes indicate no significant substructure among African-American populations from different regions of the U.S., nor (usually) among European-American and Hispanic populations. Thus, pooling of Y-STR haplotype data from regional populations within these three major groups is appropriate in order to obtain larger sample sizes. However, pooling of different major populations is generally not recommended due to statistically significant differences between African-American populations and all European-American/Hispanic populations, as well as between some European-American and Hispanic populations.

Black People↗

PubMed1992

Friedreich ataxia in Louisiana Acadians: demonstration of a founder effect by analysis of microsatellite-generated extended haplotypes.

Eleven Acadian families with Friedreich ataxia (FA) who were from southwest Louisiana were studied with a series of polymorphic markers spanning 310 kb in the D9S5-D9S15 region previously shown to be tightly linked to the disease locus. In particular, three very informative microsatellites were tested. Evidence for a strong founder effect was found, since a specific extended haplotype spanning 230 kb from 26P (D9S5) to MCT112 (D9S15) was present on 70% of independent FA chromosomes and only once (6%) on the normal ones. There was no evident correlation between haplotypes and clinical expression. The typing of an additional microsatellite (GS4) located 80 kb from MCT112 created a divergence of the main FA-linked haplotype, generating four minor and one major haplotype. A similar split was observed with GS4 in a patient homozygous for a rare 26P-to-MCT112 haplotype. These results suggest that GS4 is flanking marker for the disease locus, although other interpretations are possible.

Adolescent↗

PubMed1992

[Analysis of RFLP haplotypes in the beta-globin gene cluster and the identification of beta-thalassemia genes in patients from Guangdong Province].

RFLP haplotypes of 69 chromosomes from members of 18 families affected with beta-thalassemia (beta T) in Guangdong Province were analyzed. 17 haplotypes were found. Haplotypes 1, 2 and 3 accounted for most of them and 4 new haplotypes were identified, three of which were associated with beta T genes. In 9 families, the haplotype data could be used for definitive prenatal diagnosis. In 7 families, 50% exclusive diagnosis could be achieved. In order to know the frequencies of various beta T genes in Guangdong Province and to improve prenatal diagnosis, we identified the beta T genes of 46 affected children in Guangdong Province by amplifying beta-globin gene sequences with the polymerase chain reaction (PCR) and hybridization with allele specific oligonucleotide (ASO) probes. 82 beta T genes hybridized with 6 probes. The most common beta T mutations were frameshift 41/42-TCTT, -28 A----G and IVS-2 nt654 G----T, accounting for 80% of the total. In 36 families PCR combined with hybridization using 6 ASO probes could provide definitive prenatal diagnosis.

Globins↗

PubMed2003

The factor V HR2 haplotype and the risk of venous thrombosis: a meta-analysis.

BACKGROUND AND OBJECTIVES: A complex haplotype of factor V gene (FV HR2) has been recently reported. FVHR2 possesses decreased co-factor activity to APC in the degradation of FVIIIa, and an increased ratio of the more procoagulant isoform FV1 compared to FV2. Contrasting results on whether the haplotype induces a significant risk of venous thromboembolism (VTE) have been reported. DESIGN AND METHODS: It has been surmised that FVHR2 enhances the risk of VTE carried by FV Leiden. We carried out a meta-analysis of the reported studies on the role of HR2 haplotype in inducing a risk of VTE and the influence of the polymorphism on the risk carried by patients with FV Leiden. RESULTS: Eight studies were analyzed for the estimation of the risk of VTE. A total of 338 out of 2,696 cases (12.5%; range 7.8 to 18.5%) and 885 out of 7,710 controls (11.5%; range 8.1 to 12.1%) were HR2 positive. The odds ratio for VTE associated with HR2 haplotype was not statistically significant (OR 1.15; 95% C.I. 0.98-1.36). The OR for the association between FV Leiden and FV HR2 and the risk of VTE in cases and controls was largely heterogeneous as to OR and 95% C.I. and no statistical significant difference was observed. INTERPRETATION AND CONCLUSIONS: The data from the present meta-analysis suggests that FVHR2 could be a very mild prothrombotic factor. The association of FV Leiden and HR2 haplotype seems not to increase significantly the risk of VTE carried by isolated heterozygosity for FV Leiden. However, well-designed clinical studies are needed to clarify this issue definitely.

Factor V↗

PubMed2003

[Killer Ig-like receptor gene content diversity and haplotype analysis in Chinese Han population in Shanghai].

OBJECTIVE: To detect the diversity of killer Ig-like receptor(KIR) gene content and the combination of haplotypes in Chinese Han population in Shanghai area. METHODS: DNA samples from 87 randomly unrelated healthy individuals in Shanghai Han population were genotyped with SSP/PCR method. RESULTS: (1) Frequencies of KIR genes: All of 18 known KIRs genes, such as 2DL1-5, 2DS1-5, 3DL1-3, 3DS1, KIR1D and the pseudogenes X, Xv and Z(KIR2DP1) were observed in Shanghai Hans. All individuals contain 3DL3, 2DL4, 3DL2 and 3DL1; the most common genes were 2DL3, Z, 2DL1 and X; the following were 2DS4, 1D, 2DL5, 2DS1, 3DS1 and 2DS5; the next were 2DS2, 2DL2, 2DS3 and Xv. (2) Frequencies of KIR gene haplotypes; there were 13 haplotypes detected in 87 Han individuals, among them, the most frequent one was type 2 (haplotypeA-2DS4). (3) Frequencies of KIR genotypes: 18 kinds of the combinations of the haplotypes were observed; the most frequent ones were AJ(2,2), AF (1,2). Also, In this study were identified five new genotypes FZ1 2 9 , FZ2 1 16 , FZ3 6 17 , FZ4 4 13 and FZ5 2 6 ,which had not been observed in Caucasians so far. CONCLUSION: These findings suggest that there are distinctive frequencies of KIR gene content, haplotype as well as genotype in Chinese Han population in Shanghai area.

China↗

PubMed2004

[The study on the haplotype of MICA and MICB microsatellite locus in Guangzhou Han population].

This study is to investigate genetic polymorphisms and haplotypes of microsatellite locus in the exon 5 of the MICA gene and intron 1 of the MICB gene based on 106 samples of Guangzhou Han Population by polymerase chain reaction and fluorescent technique (6-FAM). The corresponding haplotype frequencies, linkage disequilibria values and relative linkage disequilibria values were estimated based on population data. The results show that the genotype distributions of MICA and MICB microsatellite meet Hardy-Weinberg equilibrium in Guangdong Han population. In total, 5 alleles of MICA microsatellite locus and 14 alleles of MICB microsatellite locus were observed. MICA A5 was the most common allele (0.2877), whereas A4 was the least popular one (0.1321). MICB CA14 was the most common allele (0.3255), and CA19 and CA28 were the least popular ones (0.0047). CA27 was not observed. Twenty-one kinds of MICA-MICB haplotypes occurred at frequencies of more than 1% (linkage disequilibria value>0). The common MICA-MICB haplotypes were A5-CA14 (16.73%) , A5.1- CA18 (8.75%), A4- CA26(3.76%),A9-CA15(3.66%) and A6-CA21(2.61%) (chi(2)>3.84, P<0.05) , and they were strong linkage disequilibria. The polymorphisms and haplotypes distributions of MICA and MICB microsatellite locus in Guangzhou Han population have their own genetic characteristics. The microsatellite locus of the exon5 of the MICA gene and intron 1 of the MICB gene could be used as the genetic markers in the studies of anthropology, linkage analysis of genetic disease genes, individual identification and paternity test in forensic medicine.

Asian People↗

PubMed2004

[Haplotypes extending across AGT are associated essential hypertension].

Present studies examined the DNA polymorphisms in the AGT genes in a Chinese population in Henan province of central China. By using PCR-RFLP and maximum likelihood estimation (MLE), we estimated the pattern of intragenic linkage disequilibrium and the haplotype structure and explored the possible association between the polymorphisms of AGT gene and essential hypertension in a case-control study. Seven polymorphic sites (SNPs) and seven major haplotypes of AGT gene were analyzed. Among the individual SNP pairs examined, the A-6G, C+31T and M235T are nearly completely disequilibrium. All those single polymorphism loci were individually not associated with hypertension. But we found the frequency of haplotype H2 (-217: G, -152: G, -20: A, -6: G, +31: T, 174: T, 235: M) was significantly higher in controls than patients (P=0.010). Our study suggested that few haplotypes derived seven polymorphism loci could account for the most of the variation in AGT gene in Chinese Hans. The haplotype H2 of AGT gene might represent or be in disequilibrium with a genetic protective factor against EH.

Adult↗

PubMed2005

[Gene frequencies and haplotypes of nine Y-short tandem repeat loci in four minority populations of China].

OBJECTIVE: To investigate the polymorphism of nine Y-short tandem repeat loci in 117 male individuals from four minority populations of China, and to obtain the polymorphism information in these populations. METHODS: Nine loci in all samples were amplified by PCR. Products were electrophoresed on ABI PRISM 377 DNA sequencer. The electrophoresis result was analyzed by Genotyper 2.0 software. Allele frequencies, diversities and genetic distance were calculated. RESULTS: Forty-three alleles and 32 haplotypes were found in Manchu population, 43 alleles and 33 haplotypes in Uygur population, 31 alleles and 15 haplotypes in Kirgiz population and 34 alleles and 23 haplotypes in Zhuang population. The closest genetic distance is 0.02530 between Manchu and Uygur, the highest genetic distance is 0.34590 between Kirgiz and Zhuang. CONCLUSION: High haplotype diversities were found in four populations. The study of genetic diversity among different populations is useful in research of their origins, migrations and their relationships.

China↗

PubMed2005

[Haplotype and linkage analysis in Chinese hereditary mixed polyposis syndrome].

OBJECTIVE: To investigate if hereditary mixed polyposis syndrome (HMPS) locus of two Singapore Chinese HMPS families is identical with the Ashkenazi families. METHODS: Genomic DNA was extracted, multiplex polymerase chain reaction (PCR) was used to amplify 4 microsatellite markers D15S1010, D15S1007, ACTC and D15S118 in 31 individuals from two families. The HMPS locus cosecretion of the markers on 15q13 over a region of 2.8 cM was confirmed by Haplotype and linkage analysis. RESULTS: The disease of haplotype identified in one pedigree was not co-segregated with an affected individual while no definitive disease haplotype could be assigned for the second pedigree. The maximum two-point and multi-point LOD scores at ACTC for the two Chinese families are 0.20 (theta = 0.3) and -5.0 respectively. CONCLUSIONS: Haplotype and linkage analysis indicate that the Ashkenazi haplotypes is not associated with HMPS in Singapore Chinese families, which suggests genetic heterogeneity.

Adenomatous Polyposis Coli↗

PubMedDate not supplied

Identification of an ancestral haplotype of the 35delG mutation in the GJB2 (connexin 26) gene responsible for autosomal recessive non-syndromic hearing loss in families from the Eastern Black Sea Region in Turkey.

Mutations in the GJB2 gene have been shown to be the major cause of autosomal recessively inherited, prelingual, non-syndromic hearing loss. 35delG was found to be the most frequent mutation among Caucasians. In this study, we performed haplotype analysis of two large families with autosomal recessive non-syndromic hearing loss (totally 33 affected, 37 unaffected) from Trabzon (a city from the Eastern Black Sea region) by using polymorphic markers close to the 35delG mutation region, and identified a common haplotype, "2-6-4". The frequency of the mutant chromosomes having the 2-6-4 haplotype was compared between the Eastern Black Sea region and the other regions of Turkey and the difference was found to be significant (chi squared = 5.13/df = 1/p = 0.023). Also, when the frequency of mutant and wild type chromosomes having the 2-6-4 haplotype was compared in the Eastern Black Sea region, a statistically significant difference was observed in the mutant chromosomes (chi squared = 7.46/df = 1/p < or = 0.01). The results of this study demonstrate that the ancestral haplotype of the chromosomes bearing 35delG mutation in the Eastern Black Sea region is "2-6-4".

Connexin 26↗

PubMed2005

Mutational risk in highly repetitive exon ORF15 of the RPGR multidisease gene is not associated with haplotype background.

Exon ORF15 is an alternative exon in the retinitis pigmentosa GTPase regulator (RPGR) gene containing a highly repetitive, purine-rich internal region. It constitutes a mutational hot spot giving rise to a group of heterogeneous X-linked retinal disorders. We sought to determine whether non-pathogenic substitutions and sequence length variations in the repetitive sequence have an influence on the risk of pathogenic exon ORF15 mutations. The type and distribution of exon ORF15 polymorphisms were assessed by genotyping 107 healthy German males using standard procedures. Polymorphisms were grouped into haplotypes and their frequencies determined in normal controls and previously analyzed patients with X-linked retinitis pigmentosa (XLRP). In the control group we identified 6 complex variants of the most common, ancestral exon ORF15 allele corresponding to the GenBank reference sequence (accession no. AF286472). Exon ORF15 mutations in XLRP patients were associated with the ancestral allele in 75% of affected cases. Four of the most recent founder haplotypes termed H3, H4, H6 and H7 were not identified in the patient samples. Our analysis and review of polymorphism data from the published literature suggests the presence of common exon ORF15 haplotypes in the European population. While the mutational risk in the RPGR gene appears not to be altered by the haplotype background, exon ORF15 haplotype analysis may be useful for tracing the evolutionary history of RP3-associated diseases.

Exons↗

PubMed2003

Haplotype motifs: an algorithmic approach to locating evolutionarily conserved patterns in haploid sequences.

The promise of plentiful data on common human genetic variations has given hope that we will be able to uncover genetic factors behind common diseases that have proven difficult to locate by prior methods. Much recent interest in this problem has focused on using haplotypes (contiguous regions of correlated genetic variations), instead of the isolated variations, in order to reduce the size of the statistical analysis problem. In order to most effectively use such variation data, we will need a better understanding of haplotype structure, including both the general principles underlying haplotype structure in the human population and the specific structures found in particular genetic regions or sub-populations. This paper presents a probabilistic model for analyzing haplotype structure in a population using conserved motifs found in statistically significant sub-populations. It describes the model and computational methods for deriving the predicted motif set and haplotype structure for a population. It further presents results on simulated data, in order to validate the method, and on two real datasets from the literature, in order to illustrate its practical application.

Algorithms↗

PubMed2006

[Association of haplotype formed on HLA-DRB1 and HLA-DQA1 alleles with outcomes of hepatitis B virus infection].

OBJECTIVE: To assess the association of haplotype of HLA-DRB1 and HLA-DQA1 alleles with outcomes of hepatitis B virus infection in Han population of north China. METHODS: Two hundred and seven chronic hepatitis B (HB) patients, two hundred and twelve chronic asymptomatic hepatitis B virus (HBV) carriers (HBV carrier) and one hundred and forty-eight self-limited HBV infection were investigated for HLA-DRB1 and HLA-DQA1 alleles by sequence specific-polymerase chain reaction (PCR-SSP). RESULTS: The frequency of DRB1*04-DQA1*0301 haplotype was 10.03% in self-limited HBV infection subjects, significantly higher than that in chronic HB patients (3.66%) (P=0.0005)ûthe frequency of DRB1*15/*16-DQA1*0102 haplotype was 6.80% in self-limited HBV infection subjects, significantly higher than 1.94% in chronic HB patients (P=0.0012) and 1.65% in asymptomatic HBV carriers (P=0.0004)ûwhile the frequency of DRB1*04-DQA1*0302 haplotype was 3.10% in chronic HB patients, higher than that in self-limited HBV infection subjects (0.39%) (P=0.0077). CONCLUSION: Individuals with different haplotypes composed of HLA-DRB1 and HLA-DQA1 might have different outcomes of HBV infection.

Adolescent↗

PubMed1991

Haplotyping by double PCR amplification of specific alleles.

Haplotypes are useful in population genetics and medicine. Determining haplotypes in the absence of DNA samples from appropriate family members can be difficult and laborious. We have developed a rapid and reproducible method for haplotyping an individual in the absence of relatives. The method utilizes pairs of allele-specific PCR primers to differentially amplify each haplotype. Four amplifications can distinguish the haplotypes produced by two biallelic polymorphisms.

Alleles↗

PubMed1991

Sickle cell anemia: beta s-gene-cluster haplotypes as prognostic indicators of vital organ failure.

Identification of the beta s-gene-cluster haplotype and alpha-gene status provide a useful tool to improve the possibility for early detection in high-risk SS patients. The DNA polymorphisms of the beta s-gene-cluster modify the clinical course in sickle cell anemia especially as it involves the risk of end-stage organ failure of the kidney, lung, and brain. In both Africa and America, the CAR beta s haplotype increases the risk of developing irreversible complications at an early age. The degree of anemia, the Hb F concentration, and the preservation (or lack thereof) of G gamma Hb F is haplotype dependent and correlates with the overall clinical course of the patient. Further modulation of the clinical course by the coinheritance of alpha-thalassemia-2 tends to decrease the risk of soft tissue organ failure but increases the risk of osteonecrosis. A single individual can be expected to fit into the overall pattern. Some sickle related illness will eventually occur in all patients. In the presence of a Senegal haplotype, the patient's health is better, with the CAR haplotype it is always worse; severity is intermediate in the Benin. These genetic markers can be used to identify the endangered patient before the onset of irreversible major organ failure. The high risk SS patient with a CAR chromosome or one who is homozygous Ben without alpha-thalassemia-2 should be monitored closely for evidence of vasculopathy-induced microinfarction of the brain, kidneys, or lungs. Such a patient needs preventive therapy before suffering a major hemisphere stroke, losing kidney function, or developing cor pulmonale secondary to restrictive lung disease.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗