HLA-A, -B, -C, -DRB1 and -DQB1 allele and haplotype frequencies and phylogenetic analysis of Bahraini population

AbstractTo date, there are very limited genetic studies conducted on the Kingdom of Bahrain and this is one of the first studies conducted to evaluate the 12 X-STRs included in the Investigator X-12 QS kit. Bahrain is a small archipelago located in the Arabian Gulf. X-STRs are very informative in population genetics studies, human identification and complex kinship analysis. One hundred and fifty-six (156) buccal swabs were collected using cotton from non-relatives’ Bahraini males from four different regions of Bahrain. DNA was processed using QIAsymphony SP instrument following quantification with Investigator Quantiplex HYres Kit in the 7500 Real-Time PCR System and detected in ABI 3500xl Genetic Analyzer. Analysis was done using different statistical softwares to obtain allele frequencies and haplotype frequencies-based upon the available four clusters of Linkage Groups (LGs)- and the forensic parameters.. Results indicated the diversity of the Bahraini population in terms of high Power of Discrimination (PD) and Probability of Match (PM) values obtained. The combined values of each forensic parameter such as cPDM, Mean exclusion chance (CMEC) Krüger, CMEC Kishida, and CMEC Desmarais as well as CMEC Desmarais Duo, were 0.9999983, 9999979, 0.9999939, 0.9999996 and 0.9999514 respectively based on the allele and haplotype frequencies. No shared profiles were observed. Number of non-standard alleles and null samples were obtained with more profoundly in locus DXS10148. We have conducted phylogenetic tree as well as multidimensional scale to analyze the Interpopulation diversity between Bahraini population and nine other populations and found out they reflect the geographical and social background of the region. Overall, the results confirm the importance of X-STRs in discriminating between individuals among Bahraini population and in establishing DNA databases for forensic and kinship studies.

Download Full-text

HLA-A, -B, -C, -DRB1 and -DQB1 allele and haplotype frequencies of 1463 umbilical cord blood units typed in high resolution from Bogotá, Colombia

Human Immunology ◽

10.1016/j.humimm.2019.03.006 ◽

2019 ◽

Vol 80 (7) ◽

pp. 425-426 ◽

Cited By ~ 1

Author(s):

Iván Aurelio Páez-Gutiérrez ◽

David Guillermo Hernández-Mejía ◽

Diana Vanegas ◽

Bernardo Camacho-Rodríguez ◽

Ana María Perdomo-Arciniegas

Keyword(s):

High Resolution ◽

Cord Blood ◽

Umbilical Cord ◽

Umbilical Cord Blood ◽

Haplotype Frequencies ◽

Dqb1 Allele

Download Full-text

HLA-A, -B, -C, -DRB1, and -DQB1 Allele Lineages and Haplotype Frequencies among Saudis

Immunology and Immunogenetics Insights ◽

10.4137/iii.s16769 ◽

2014 ◽

Vol 6 ◽

pp. III.S16769

Author(s):

Awad E. Osman ◽

Faviel F. Gonzalez-Galarza ◽

Mohamed Mubasher ◽

Hanan Al-Harthi ◽

Nezar Eltayeb Elsheikh ◽

...

Keyword(s):

Principal Component ◽

Human Leukocyte ◽

Marrow Transplant ◽

Genetic Distances ◽

Specific Oligonucleotide Probe ◽

Haplotype Frequencies ◽

Medical City ◽

Reported Data ◽

Sequence Specific Oligonucleotide Probe ◽

Dqb1 Allele

There are few reported studies on Saudi population for human leukocyte antigens (HLA) genes. We investigated allele lineages (two-digit) and haplotype frequencies of HLA-A, -B, -C, -DRB1, and -DQB1 loci in 499 healthy unrelated individuals, selected from potential bone marrow transplant (BMT) families’ donors at King Fahad Medical City (KFMC), Saudi Arabia (SA). Genotyping was performed by Sequence Specific Oligonucleotide Probe (SSOP) utilizing a Luminex-based method. Allele lineages and haplotype frequencies were evaluated along with principal component analysis (PCA) to compare findings with previously reported data on Arab related populations. A total of 18 allele lineages for HLA-A, 28 for -B, 14 for -C, 13 for -DRB1, and 5 for -DQB1 were detected. High values for linkage disequilibrium indicators were found for B:C ( D’ = 0.86599) and DRB1:DQB1 ( D’ = 0.89468) loci. Additionally, PCA results confirmed previous findings on this population, but also indicated some genetic distances from other Arab related populations. The present study helps in further investigations of this population in anthropological analysis and HLA-associated disease studies.

Download Full-text

HLA-A, -B, -C, -DRB1 and -DQB1 allele and haplotype frequencies in Saudis using next generation sequencing technique

Tissue Antigens ◽

10.1111/tan.12200 ◽

2013 ◽

Vol 82 (4) ◽

pp. 252-258 ◽

Cited By ~ 17

Author(s):

A. H. Hajeer ◽

M. A. Al Balwi ◽

F. Aytül Uyar ◽

Y. AlHaidan ◽

A. AlAbdulrahman ◽

...

Keyword(s):

Next Generation Sequencing ◽

Next Generation ◽

Haplotype Frequencies ◽

Sequencing Technique ◽

Dqb1 Allele ◽

Generation Sequencing

Download Full-text

Human Leukocyte Antigen-A, B, C, DRB1, and DQB1 Allele and Haplotype Frequencies in a Subset of 237 Donors in the South African Bone Marrow Registry

Journal of Immunology Research ◽

10.1155/2018/2031571 ◽

2018 ◽

Vol 2018 ◽

pp. 1-8

Author(s):

Mqondisi Tshabalala ◽

Charlotte Ingram ◽

Terry Schlaphoff ◽

Veronica Borrill ◽

Alan Christoffels ◽

...

Keyword(s):

Bone Marrow ◽

Human Leukocyte Antigen ◽

South African ◽

Association Studies ◽

Human Leukocyte ◽

The South ◽

Multiple Allele ◽

Leukocyte Antigen ◽

Haplotype Frequencies ◽

Dqb1 Allele

Human leukocyte antigen- (HLA-) A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 allele and haplotype frequencies were studied in a subset of 237 volunteer bone marrow donors registered at the South African Bone Marrow Registry (SABMR). Hapl-o-Mat software was used to compute allele and haplotype frequencies from individuals typed at various resolutions, with some alleles in multiple allele code (MAC) format. Four hundred and thirty-eight HLA-A, 235 HLA-B, 234 HLA-DRB1, 41 HLA-DQB1, and 29 HLA-C alleles are reported. The most frequent alleles were A∗02:02g (0.096), B∗07:02g (0.082), C∗07:02g (0.180), DQB1∗06:02 (0.157), and DRB1∗15:01 (0.072). The most common haplotype was A∗03:01g~B∗07:02g~C∗07:02g~DQB1∗06:02~DRB1∗15:01 (0.067), which has also been reported in other populations. Deviations from Hardy-Weinberg equilibrium were observed in A, B, and DRB1 loci, with C~DQB1 being the only locus pair in linkage disequilibrium. This study describes allele and haplotype frequencies from a subset of donors registered at SABMR, the only active bone marrow donor registry in Africa. Although the sample size was small, our results form a key resource for future population studies, disease association studies, and donor recruitment strategies.

Download Full-text