Study of the HLA system in the Haitian population

Liau, S. W.; Mickey, Ray; Romano, Paula J.; Lee, T. D.

doi:10.1111/j.1399-0039.1984.tb00050.x

Cited by 15 publications

(8 citation statements)

References 4 publications

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“…Linkage disequilibrium (LD) between HLA-G alleles and the polymorphic sites within the 3’UTR were evaluated using the likelihood ratio test as described by (Lewontin, 1964). The statistical significance of the LD between each of the SNP pairs was evaluated by the approximate chi-square described by (Liau et al, 1984). For associations of MTCT risk, comparisons of HLA-G allele and genotype frequencies were analyzed between NT and TR maternal groups, as well as EU and HIV-1 infected infants using the online Fisher exact test, VassarStats (http://www.vassarstats.net/odds2x2.html) which was also used to estimate the odds ratio (OR) and its 95% confidence interval (95%CI).…”

Section: Methodsmentioning

confidence: 99%

Maternal human leukocyte antigen-G (HLA-G) genetic variants associate with in utero mother-to-child transmission of HIV-1 in Black South Africans

Hong

Paximadis

Gray

et al. 2015

Infection, Genetics and Evolution

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A 14-bp insertion/deletion (indel) within the 3' untranslated region (3’UTR) that affects HLA-G expression has been associated with HIV-1 mother-to-child transmission (MTCT). However, other 3’UTR single nucleotide polymorphisms (SNPs) that influence HLA-G mRNA stability have been described but not analyzed in the context of MTCT, and little is known about the role of HLA-G alleles. We examined HLA-G alleles and 3’UTR SNPs, including the 14-bp indel, in 216 mother-infant pairs from Johannesburg, South Africa. Mother-infant pairs were classified as HIV-1 non-transmitting (NT, n=144) or HIV-1 transmitting (TR, n=72) with either intrapartum (IP, n=29) or in utero (IU, n=19) infected infants. We found HLA-G allele, G*01:01:02 (in strong linkage disequilibrium with the 14-bp insertion) and +3187G SNP were significantly over-represented in IU-TR mothers compared to NT mothers (P=0.036, OR=2.26; P=0.011, OR=2.96, respectively). These findings suggest that maternal HLA-G alleles and/or SNPs that might alter expression of HLA-G potentially influence IU HIV-1 MTCT.

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Section: Methodsmentioning

confidence: 99%

Maternal human leukocyte antigen-G (HLA-G) genetic variants associate with in utero mother-to-child transmission of HIV-1 in Black South Africans

Hong

Paximadis

Gray

et al. 2015

Infection, Genetics and Evolution

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“…D ′ values are defined in the range [−1, 1] with a value of ‘1’ representing perfect disequilibrium. The statistical significance of the linkage disequilibrium between each of the SNP pairs was evaluated by the approximate chi-square described by Liau et al (1984).…”

Section: Methodsmentioning

confidence: 99%

Genetic variation within the gene encoding the HIV-1 CCR5 coreceptor in two South African populations

Picton

Paximadis²,

Tiemessen

2010

Infection, Genetics and Evolution

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Polymorphisms within the open reading frame as well as the promoter and regulatory regions can influence the amount of CCR5 expressed on the cell surface and hence an individual's susceptibility to HIV-1. In this study we characterize CCR5 genes within the South African African (SAA) and Caucasian (SAC) populations by sequencing a 9.2 kb continuous region encompassing the CCR5 open reading frame (ORF), its two promoters and the 3′ untranslated region. Full length CCR5 sequences were obtained for 70 individuals (35 SAA and 35 SAC) and sequences were analyzed for the presence of single-nucleotide polymorphisms (SNPs), indels and intragenic haplotypes. A novel SNP (+258G/C) within the ORF leading to a non-synonomous amino acid (Trp → Cys) change was detected in one Caucasian individual. Results demonstrate a high degree of genetic variation: 68 SNP positions, four indels, as well as the Δ32 deletion mutant, were detected. Seven complex putative haplotypes spanning the length of the sequenced region have been identified. These haplotypes appear to be extensions of haplotypes previously described within CCR5. Two haplotypes, SAA-HHE and SAC-HHE were found in high frequency in the SAA and SAC population groups studied (20.0% and 18.6%, respectively) and share four SNP positions suggesting an evolutionary link between the two haplotypes. Only one of the identified haplotypes, SAA/C–HHC, is common to both study populations but the haplotype frequency differs markedly between the two groups (8.6% in SAA and 52.9% in SAC). The two population groups show differences in both haplotype arrangement as well as SNP profile.

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“…The linkage disequilibrium coefficient ( D ), standardized linkage disequilibrium coefficient ( D′ ), and square of the correlation coefficient between allele frequencies ( r 2 ) were also calculated using this software. The significance test between linkage disequilibrium coefficient ( D ) and 0 was estimated by calculating chi square with the Mickey formula (10), where χ 2 > 3.84 ( P < 0.05) implies significant linkage disequilibrium, while χ 2 > 10.83 ( P < 0.001) implies a strong linkage. The standard error (σs) of the two‐locus haplotype was calculated according to the…”

Section: Methodsmentioning

confidence: 99%

Determination of TAP1 and TAP2 polymorphism in the Chinese Han population by real‐time TaqMan polymerase chain reaction

Feng¹,

Yin²,

Shen³

et al. 2008

Tissue Antigens

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The heterodimeric transporter associated with antigen processing (TAP) complex plays a key role in immune surveillance. TAP1 and TAP2 typing was usually performed by polymerase chain reaction (PCR)-restriction fragment length polymorphism and PCR-sequence-specific oligonucleotide probe. As an alternative to these methods, we have established TaqMan assays to determine the frequencies of the TAP1 and TAP2 alleles. We have used these new TaqMan assays to genotype the polymorphisms in 339 unrelated Chinese Hans residing in North and South China. We detected five TAP1 and four TAP2 alleles. All the loci conform to the Hardy-Weinberg expectations. The most frequent alleles in Chinese Hans were TAP1*0101 (79.79%) and TAP2*0101 (82.74%). The two-locus haplotype analysis showed highly significant positive linkage disequilibrium for one TAP1-TAP2 haplotype (TAP1*020101-TAP2*0102), three TAP1-DRB1 haplotypes (TAP1*020101-DRB1*03, TAP1*020102-DRB1*13, and TAP1*0301-DRB1*16), and three TAP2-DRB1 haplotypes (TAP2*0102-DRB1*09, TAP2*0103-DRB1*04, and TAP2*0201-DRB1*01). The three-locus haplotype analysis showed highly significant positive linkage disequilibrium for TAP1*0101-TAP2*0101-DRB1*07, TAP1*0101-TAP2*0103-DRB1*04, TAP1*020101-TAP2*0101-DRB1*03, and TAP1*020101-TAP2*0102-DRB1*13. Comparison of the allele frequencies with those of other populations showed that the TAP1 allele distribution was very similar in all the groups, except for the Guarani, Kaingang, and Anatolian populations, but TAP2 distribution was significantly different from that of the other populations. The new TaqMan method provides relatively accurate, high-resolution, simple, and fast assays for TAP genotyping.

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Study of the HLA system in the Haitian population

Cited by 15 publications

References 4 publications

Maternal human leukocyte antigen-G (HLA-G) genetic variants associate with in utero mother-to-child transmission of HIV-1 in Black South Africans

Maternal human leukocyte antigen-G (HLA-G) genetic variants associate with in utero mother-to-child transmission of HIV-1 in Black South Africans

Genetic variation within the gene encoding the HIV-1 CCR5 coreceptor in two South African populations

Determination of TAP1 and TAP2 polymorphism in the Chinese Han population by real‐time TaqMan polymerase chain reaction

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