Next-generation sequencing characterization of HLA in multi-generation families of Kuwaiti descent

Ameen, Reem; Shemmari, Salem Al; Askar, Medhat

doi:10.1016/j.humimm.2017.12.012

Cited by 8 publications

(6 citation statements)

References 22 publications

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“…HLA-A*26 ~ C*07 ~ B*08 ~ DRB1*03 ~ DQB1*02 was the most frequent 5-locus HLA haplotype (4.25%) in the studied Emirati sample and was also detected in Iraqi Kurdish (2.4%), Iranian (7.8%), and Indian (5.9%) populations [ 32 ]. It was the second most common five- locus haplotype in the Kuwaiti population, while A*02 ~ C*06 ~ B*50 ~ DRB1*07 ~ DQB1*02 was the most common haplotype [ 35 , 36 ]. These haplotype results are concordant with those obtained by allele frequency analysis.…”

Section: Discussionmentioning

confidence: 99%

Analysis of the Origin of Emiratis as Inferred from a Family Study Based on HLA-A, -C, -B, -DRB1, and -DQB1 Genes

Yafei

Hajjej²,

Alvares

et al. 2023

Genes

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In this study, we investigated HLA class I and class II allele and haplotype frequencies in Emiratis and compared them to those of Asian, Mediterranean, and Sub-Saharan African populations. Methods: Two-hundred unrelated Emirati parents of patients selected for bone marrow transplantation were genotyped for HLA class I (A, B, C) and class II (DRB1, DQB1) genes using reverse sequence specific oligonucleotide bead-based multiplexing. HLA haplotypes were assigned with certainty by segregation (pedigree) analysis, and haplotype frequencies were obtained by direct counting. HLA class I and class II frequencies in Emiratis were compared to data from other populations using standard genetic distances (SGD), Neighbor-Joining (NJ) phylogenetic dendrograms, and correspondence analysis. Results: The studied HLA loci were in Hardy–Weinberg Equilibrium. We identified 17 HLA-A, 28 HLA-B, 14 HLA-C, 13 HLA-DRB1, and 5 HLA-DQB1 alleles, of which HLA-A*02 (22.2%), -B*51 (19.5%), -C*07 (20.0%), -DRB1*03 (22.2%), and -DQB1*02 (32.8%) were the most frequent allele lineages. DRB1*03~DQB1*02 (21.2%), DRB1*16~DQB1*05 (17.3%), B*35~C*04 (11.7%), B*08~DRB1*03 (9.7%), A*02~B*51 (7.5%), and A*26~C*07~B*08~DRB1*03~DQB1*02 (4.2%) were the most frequent two- and five-locus HLA haplotypes. Correspondence analysis and dendrograms showed that Emiratis were clustered with the Arabian Peninsula populations (Saudis, Omanis and Kuwaitis), West Mediterranean populations (North Africans, Iberians) and Pakistanis, but were distant from East Mediterranean (Turks, Albanians, Greek), Levantine (Syrians, Palestinians, Lebanese), Iranian, Iraqi Kurdish, and Sub-Saharan populations. Conclusions: Emiratis were closely related to Arabian Peninsula populations, West Mediterranean populations and Pakistanis. However, the contribution of East Mediterranean, Levantine Arab, Iranian, and Sub-Saharan populations to the Emiratis’ gene pool appears to be minor.

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Section: Discussionmentioning

confidence: 99%

Analysis of the Origin of Emiratis as Inferred from a Family Study Based on HLA-A, -C, -B, -DRB1, and -DQB1 Genes

Yafei

Hajjej²,

Alvares

et al. 2023

Genes

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“…Variation and polymorphism of the HLA complex has played a crucial role in studying population migration [61] as well as being used to establish ethnic genetic database and linkage analysis [62]. The HLA proteins are responsible for mediating immune responses and therefore also play a very important role in organ transplantation [53,54] as they are unique for every unrelated individual [63].…”

Section: Human Leukocyte Antigenmentioning

confidence: 99%

“…The micro-array method has made it possible to analyse over 1000 HLA alleles on a single microarray slide [62] while using a small sample volume [65]. As of late, HLA alleles are being sequenced with high throughput MPS [61,[66][67][68] 4. Application of the human leukocyte antigen complex in the field of forensic science…”

Section: Human Leukocyte Antigenmentioning

confidence: 99%

“…Markers such as STRs, mtDNA and YSTR have already significantly increased their forensic value due to MPS [91]. While MPS of HLA is being routinely utilised in clinical laboratories in fields such as transplantation [92], pharmacology [93] or population studies [61], there have not been any studies testing its suitability for typical forensic samples. However a recent study by Wu et al [66] showed promising results of applying HLA-based typing to kinship analysis.…”

Section: Potential Of Massively Parallel Sequencing In Forensic Analysis Of the Human Leukocyte Antigen Complexmentioning

confidence: 99%

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Human Leukocyte Antigen alleles as an aid to STR in complex forensic DNA samples

2020

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Human biological samples with multiple contributors remain one of the most challenging aspects of DNA typing within a forensic science context. With the increasing sensitivity of commercially available kits allowing detection of low template DNA, complex mixtures are now a standard component of forensic DNA evidence. Over the years, various methods and techniques have been developed to try to resolve the issue of mixed profiles. However, forensic DNA analysis has relied on the same markers to generate DNA profiles for the past 30 years causing considerable challenges in the deconvolution of complex mixed samples. The future of resolving complicated DNA mixtures may rely on utilising markers that have been previously applied to gene typing of nonforensic relevance. With Massively Parallel Sequencing (MPS), techniques becoming more popular and accessible even epigenetic markers have become a source of interest for forensic scientists.The aim of this review is to consider the potential of alleles from the Human Leukocyte Antigen (HLA) complex as effective forensic markers. While Massively Parallel Sequencing of HLA is routinely used in clinical laboratories in fields such as transplantation, pharmacology or population studies, there have not been any studies testing its suitability for forensic casework samples.

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“…The HaploStats database contains information from the NMDP registry on HLA haplotype frequency for the following ethnic groups: Caucasian, African American, Asian, Hispanic and Native American. Based on the described haplotype frequency for each ethnic group, we defined the most likely ethnicity of each estimated haplotype as described elsewhere (Ameen et al, 2018); some haplotypes are described at high frequencies, defined as equal or greater than 1/1000 (Kollman et al, 2007), in all populations, and were defined as "common". In 17 cases (9%), family typing was available and family study agreed with HaploStats estimation in 100%.…”

Section: Alleles and Haplotype Estimationmentioning

confidence: 99%

Immunogenetics in sickle cell disease

Maio¹

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Next-generation sequencing characterization of HLA in multi-generation families of Kuwaiti descent

Cited by 8 publications

References 22 publications

Analysis of the Origin of Emiratis as Inferred from a Family Study Based on HLA-A, -C, -B, -DRB1, and -DQB1 Genes

Analysis of the Origin of Emiratis as Inferred from a Family Study Based on HLA-A, -C, -B, -DRB1, and -DQB1 Genes

Human Leukocyte Antigen alleles as an aid to STR in complex forensic DNA samples

Immunogenetics in sickle cell disease

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