Frequent Allele Research Articles

Design of SARS-CoV-2 protein S peptides recognized by the most frequent HLA alleles in the Moroccan population using an immunoinformatics approach

Background The coronavirus disease 2019 (COVID-19) is an infectious disease, caused by the new coronavirus known as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), and exhibits diverse clinical outcomes and symptoms in infected individuals, emphasizing the need to investigate how human genetic diversity influences the virus’s impact. This study aims to employ in silico methods to identify epitopes capable of eliciting an immune response, focusing on the most prevalent HLA-I and HLA-II alleles in the Moroccan population. Methods Our research consisted in predicting peptide-binding affinities between the most prevalent HLA Class I and Class II alleles in the Moroccan population and SARS-CoV-2 spike glycoprotein (S protein) peptides of variants isolated from strains of Moroccan patients. We performed the same analyses for SARS-CoV-2 wild type S protein to assess the ability of these HLA alleles to interact with peptides in the presence or absence of SARS-CoV-2 mutations. Results In a broader sense, 12 distinct HLA Class I and Class II alleles in the Moroccan population have been identified as possibly interacting with 19 epitopes in the SARS-CoV-2 S protein. Findings of this study must be validated in both in vitro and in vivo models. Conclusions These data may help clarify the issue of host cell susceptibility and the outcome of SARS-CoV-2 infection, and may guide further research to uncover potential targets for the vaccination strategy.

First characterization of major histocompatibility complex class II DRB3 diversity in cattle breeds raised in Egypt

Genes encoding bovine leukocyte antigen (BoLA) enable the immune system to identify pathogens. Therefore, these genes have been used as genetic markers for infectious and autoimmune diseases as well as for immunological traits in cattle. Although BoLA polymorphisms have been reported in various cattle breeds worldwide, they have not been studied in cattle populations in Egypt. In this study, we characterized BoLA-DRB3 in two local Egyptian populations and one foreign population using polymerase chain reaction-sequence-based typing (PCR-SBT) method. Fifty-four previously reported BoLA-DRB3 alleles and eight new alleles (BoLA-DRB3*005:08, *015:07, *016:03, *017:04, *020:02:02, *021:03, *164:01, and *165:01) were identified. Alignment analysis of the eight new alleles revealed 90.7–98.9 %, and 83.1–97.8 % nucleotide and amino acid identities, respectively, with the BoLA-DRB3 cDNA clone NR-1. Interestingly, BoLA-DRB3 in Egyptian cattle showed a high degree of allelic diversity in native (na = 28, hE > 0.95), mixed (na = 61, hE > 0.96), and Holstein (na = 18, hE > 0.88) populations. BoLA-DRB3*002:01 (14.3 %), BoLA-DRB3*001:01 (8.5 %), and BoLA-DRB3*015:01 (20.2 %) were the most frequent alleles in native, mixed, and Holstein populations, respectively, indicating that the genetic profiles differed in each population. Based on the allele frequencies of BoLA-DRB3, genetic variation among Egyptian, Asian, African, and American breeds was examined using Nei’s distances and principal component analysis. The results suggested that native and mixed cattle populations were most closely associated with African breeds in terms of their gene pool, whereas Holstein cattle were more distinct from the other breeds and were closely related to Holstein cattle populations from other countries.

Investigating growth associated genomic short tandem repeats (STRs) in a resource population generated through molecular breeding of RIR chicken

The long-term selection based on phenotypes causes loss of variation in performance traits and slows down the genetic progress per generation in the population; genomic selection could restore the variability along with faster genetic progress. Genomic short tandem repeats (STRs) in a resource population of RIR chicken were explored investigating randomly selected 114 pedigreed chicks. Alleles separated through 3.4% MetaPhor agarose gel electrophoresis at ten STR loci, and data recorded on growth traits were analyzed. Twenty-six alleles were resolved with frequencies of 0.1140–0.7632 and > 38.60% for the most frequent alleles at ten STR loci. The most frequent genotypes appeared with frequency >21.93% at different loci. Polymorphic information contents ranged from 0.2961 (LEI0079) to 0.6716 (LEI0071). Effective number of alleles ranged from 1.5662 (LEI0079) to 3.5836 (LEI0071). Mean FIS statistics revealed overall 21.78% heterozygosity deficit. Average heterozygosity ranged from 0.3630 (LEI0079) to 0.7241 (LEI0071). Chi-square and G-square test showed the population in Hardy-Weinberg disequilibrium at nine loci. Chick weight was significantly influenced by the factor of sire, and body weight traits by sex and hatch factors of the birds coded with STR-genotypes. ADL0328-BB genotype had the highest chick weight. LEI0068-BC and LEI0071-CC genotypes showed maximum 28-weeks body weight. MCW0010-AA genotype had the potential bearing of the highest body weight records at 16, 32, 36 and 40 weeks of age. MCW0058-CC genotype revealed the same at 24 and 28 weeks of age. The study impacts on marker assisted selection program for genetic improvement of growth traits in poultry.

Association between rs1799724 of TNF- α gene and early onset preeclampsia in Chinese: A pilot study

ObjectiveTo investigate the association between polymorphisms of TNF- α (rs1799724, rs1800629), VEGF (rs3025039) and VEGFR1 (rs 722503) and early onset preeclampsia (EOPE) in Chinese. MethodsA total of 132 EOPE patients from January 2016 to December 2018 at the Second Hospital of Tianjin Medical University were selected as the EOPE group, and 156 normal pregnant patients as the Control group. In both groups, 5 ml of peripheral venous blood was obtained after admission. The characteristics of genotype and allele distribution at the four SNPs in the study subjects were examined by matrix-assisted laser desorption ionization time-of-flight mass spectrometric genotyping. ResultsThe genotype frequency distribution and allele frequency distribution of rs1799724 were significantly different between the EOPE group and the Control group (P = 0.002，P = 0.003). The T allele was statistically associated with the development of EOPE under a dominant genetic model (P = 0.001). The genotype and allele frequency distributions of rs1800629, rs3025039, and rs 722503 did not differ significantly between the EOPE group and the Control group (P > 0.05). There was no linkage disequilibrium among rs1799724, rs1800629 and rs3025039 loci, the corresponding haploid cannot be formed. ConclusionsThe rs1799724 of TNF- α gene is a genetic susceptibility locus for EOPE and may be a potential predictors of preeclampsia.

Detection of Blastocystis sp. and Dientamoeba fragilis using conventional and molecular methods in patients with celiac disease

Blastocystis sp. and Dientamoeba fragilis are intestinal protists, which are common worldwide, but the pathogenic role of these organisms in gastrointestinal diseases is still controversial. This study aimed to investigate the frequency of Blastocystis sp. and D. fragilis in stool samples from adult patients with celiac disease (CD) by using conventional and molecular methods. A total of 75 patients with CD and 75 healthy individuals were included in this study. Fresh stool specimens collected from each individual were analyzed by conventional and molecular methods. The overall prevalence of Blastocystis sp. and D. fragilis was 41.3% (31/75) and 24% (18/75) in patients with CD, and 46.7% (35/75) and 13.3% (10/75) in healthy controls, respectively. There was no statistically significant difference in the prevalence of Blastocystis sp. and D. fragilis between CD patients and healthy individuals. Blastocystis sp. subtypes were identified in 20 CD and 16 control patients and the overall subtype distribution was observed as ST1 13.9%, ST2 30.6%, and ST3 55.6%. The prevalence of Blastocystis sp. and D. fragilis in adults with CD is similar to the prevalence of protozoa in healthy adults. In this study, the most prevalent Blastocystis subtype was ST3 and the most frequent allele was a34 in both CD patients and healthy individuals. No significant difference was found between the two groups in terms of the detection rates of Blastocystis sp. and D. fragilis, and it is thought that both protists may be colonisers of the intestinal microbiome.

Frequency distribution of HLA class I and II alleles in Greek population and their significance in orchestrating the National Donor Registry Program.

Human leukocyte antigens (HLA) represent one of the most polymorphic systems in humans, responsible for the identification of foreign antigens and the presentation of immune responses. Therefore, HLA is considered to play a major role in human disorders, donor-recipient matching and transplantation outcomes. This study aimed to determine the HLA class I and II alleles and haplotypes in the Greek population. Moreover, a comparative analysis of HLA alleles and haplotype frequencies found in Greek and pooled European populations was also performed to acquire a better knowledge about the HLA alleles distribution. A total number of 1896 healthy individuals were typed for their HLA alleles in the National Tissue Typing Center of Greece. High-resolution HLA typing for the HLA-A, -B, -C and -DR, -DQ, -DP with the use of the next-generation sequencing analysis was performed, followed by data analysis for establishing the HLA allele and haplotype differences. The results of this study showed that the most frequent alleles for the HLA-A were the A*02:01:01 (27.1%), *24:02:01 (14.4%), *01:01:01 (9.3%), for the HLA-B were the B*51:01:01 (15.3%), *18:01:01 (9.7%), *35:01:01 (6.8%) and for the HLA-C were the C*04:01:01 (15.4%), *07:01:01 (13.1%), *12:03:01 (9.6%). For the HLA class II, the most frequent alleles for the HLA-DRB1 were the DRB1*11:04:01 (16.4%), *16:01:01 (11.3%), *11:01:01 (9.5%), for the HLA-DQB1 were the DQB1*03:01:01 (30.5%), *05:02:01 (15.1%), *05:01:01 (10.6%) and for the HLA-DPB1 were the DPB1*04:01:01 (34.8%), *02:01:01 (11.6%), *04:02:01 (7.3%). Additionally, the most frequent haplotypes were the A*02:01:01∼C*07:01:01-B*18:01:01∼DRB1*11:04:01 (2.3%), followed by the A*01:01:01∼C*07:01:01∼B*08:01:01∼DRB1*03:01:01 (2.2%), A*24:02:01∼C*04:01:01∼B*35:02:01∼DRB1*11:04:01 (1.4%) and A*02:01:01∼C*04:01:01∼B*35:01:01-DRB1*14:01:01 (1.2%). The results herein were comparable to those obtained from the pooled European populations. Moreover, these results can be used for the improvement of the donor-recipient matching procedure and to understand better the disease association in Greece.

Frequencies of HLA-B alleles in Indonesian Malay Ethnic

BackgroundThe HLA-B alleles have been used as a marker to predict drug-induced adverse reactions and as a major contributor to hypersensitivity reactions. We examined the feasibility of HLA-B alleles as pharmacogenomic markers of drug-induced hypersensitivity in an Indonesian Malay Ethnic. MethodsFifty-eight Indonesian individuals of Malay ethnicity were enrolled in this study. HLA-B alleles were determined using reverse sequence-specific oligonucleotide probe coupled with xMAP technology. ResultsHLA-B*15:02 (15.52%), HLA-B*35:05 (9.48%), and HLA-B*07:05 (7.76%) were frequent alleles in the Indonesian Malay ethnic populations. We discovered at least eight pharmacogenomics markers of drug-induced hypersensitivity: HLA-B*15:02, HLA-B*15:21, HLA-B*13:01, HLA-B*35:05, HLA-B*38:02, HLA-B*51:01, HLA-B*57:01, and HLA-B*58:01. HLA-B*15:02 was in the same serotype group with HLA-B*15:21, which is a B-75 serotype associated with genetic predisposition for carbamazepine-induced Stevens–Johnson syndrome and toxic epidermal necrolysis. The Indonesian population, represented by Malay, Javanese, and Sundanese ethnicities, was similar to South East Asian, Han Chinese, and Taiwanese populations based on HLA-B*15:02 frequency as the most common allele found in Malay ethnics. ConclusionWe provided valuable information on the frequency of drug hypersensitivity-associated HLA-B alleles in Indonesian Malay ethnic population, which can improve treatment safety.

Recognition of HLA-DPB1 alleles and their associated HLA haplotypes in 55 randomized unrelated Taiwanese individuals.

Here, we report the distribution of HLA-DPB1 alleles studied in a cohort of 55 randomly collected blood samples from unrelated Taiwanese individuals and the deduced most likely HLA haplotypes associated with the defined DPB1 alleles in the cohort. Our aim is to reveal the unprecedented data on the distribution of HLA-DPB1 alleles in the Taiwanese population and to find out the most probable HLA haplotypes associated with the HLA-DPB1 alleles detected. The material for this study was blood samples, preserved in K2EDTA and/or acid citrate dextrose anticoagulants. The blood donors were voluntary individuals of Tzu Chi Bone Marrow Donor Registry, Tzu Chi Stem Cells Center, Hualien Tzu Chi Hospital. Sequence-based typing of the Sanger's sequencing method was performed for the HLA allelic typing. To discern the HLA-DPB1 alleles, exons 2 and 3 of the HLA-DPB1 locus were sequenced. Target exon sequence amplifications were achieved by polymerase chain reaction, and the resulting amplicons were sequenced by BigDye Terminator Cycle Sequencing Ready Reaction Kit according to the manufacturer's protocols. In the total number of 55 randomized unrelated Taiwanese individuals studied, we detected 11 different HLA-DPB1 alleles. DPB1*05:01 (44.54%) was the allele with the highest frequency observed and the next highest frequency allele found was DPB1*02:01 (17.27%), while DPB1*38:01 (0.90%) and DPB1*700:01N (0.90%) ranked the least observed DPB1 alleles. Our findings in this study may be useful in researches reinforcing the comprehensive understanding on the distribution of DPB1 alleles and their associated HLA haplotypes and their clinical applications in Taiwanese.

Influence of HLA-A, [sbnd]B, and -DRB1 genes and panel-reactive antibodies on the waitlist time for kidney transplantation in the state of Sao Paulo-Brazil

BackgroundBrazil ranks second in the absolute number of transplants. However, the supply remains insufficient to meet the demands, resulting in a lengthy waitlist. This study aimed to analyze whether the frequency of human leukocyte antigen (HLA) and the value of calculated panel reactive antibody (cPRA) would influence the waiting time for kidney transplantation. MethodsThe HLA-A, B, and -DRB1 frequencies and the cPRA value were analyzed in 11,186 kidney transplant candidates included in the waitlist from 2006 to 2016. ResultsThe most frequent alleles were HLA-A*02, HLA-B*35, and HLA-DRB1*13. The overall mean length of stay on the list was 986 ± 1001 days. The mean waiting time for the three most frequent alleles of the HLA-A and B loci showed no significant difference when compared with the least frequent alleles; however, for the HLA-DRB1 locus, the most frequent alleles showed a shorter waiting time. In the association between HLA and PRA, the average length of stay on the list increased according to the candidate's degree of sensitization, regardless of the analyzed HLA frequency. ConclusionThe length of stay on the waitlist is influenced by the frequency of the HLA alleles of the DRB1 locus and the degree of sensitization.

Allele and Phenotype Frequencies of CYP2D6 In The Turkish Population

Aim: Cytochrome P450 is a hepatic enzyme system responsible for drug metabolism comprising different iso-enzymes. CYP2D6 enzyme, which composes 2-4% of all cytochrome enzymes, is responsible for 25% of the metabolisms of the drugs used in clinics. The genetic polymorphisms of this enzyme can change the efficiency and toxicity of the drugs used. In this study, the retrospective evaluation of CYP2D6 gene polymorphisms that influence enzyme activity in the Turkish population is targeted. Materials and Methods: From the 192 patients sent from psychiatry, medical genetics and neurology polyclinics to our laboratory, by the methods of Multiplex Polymerase Chain Reaction (PCR) and Multiplex Allele Specific Primer Extension (ASPE), CYP2D6 enzyme gene polymorphisms were determined. Results: Of all the cases, 82,29% were determined as extensive, 12,5% as intermediate, 2,08% as poor and 3,13% as ultra-rapid metabolizers. In our population, the most frequent alleles were *1 (37,63%), *2 (24,75%), *41 (15,15%), *4 (9,85%) and *10 (4,29%), respectively. Conclusion: In the current examined population, compared to the previous studies conducted on Turkish society, it was determined that the percentage of extensive metabolizers was higher while the percentages of poor metabolizers and ultra-rapid metabolizers were lower. In addition, *41 allele that follows the decrease in enzyme function was detected as the most frequent allele in this study. The fact that the percentage of the cases in which changes were observed was 17,1% will help determine the CYP2D6 gene mutations in the pre-treatment cases.

The clinical and genetic landscape of early-onset thrombophilia in Japan.

To determine the optimal management for early-onset thrombophilia (EOT), the genetic and clinical features of protein C (PC)-, protein S (PS)-, or antithrombin (AT)-deficient patients of ≤20years of age were studied in Japan. Clinical and genetic information of all genetically diagnosed cases was collected through the prospective, retrospective study, and literature review. One-hundred-one patients had PC (n=55), PS (n=29), or AT deficiency (n=18). One overlapping case had PC- and PS-monoallelic variant. Fifty-five PC-deficient patients (54%) had 26 monoallelic or 29 biallelic variant(s), and 29 (29%) PS-deficient patients had 20 monoallelic or nine biallelic variant(s). None of the patients had AT-biallelic variants. The frequent low-risk allele p.K193del (PC-Tottori) was found in five patients with monoallelic (19%) but not 29 with biallelic variant(s). The most common low-risk allele p.K196E (PS-Tokushima) was found in five with monoallelic (25%) and six with biallelic variant(s) (67%). One exceptional de novo PC variant was found in 32 families with EOT. Only five parents had a history of thromboembolism. Thrombosis concurrently developed in three mother-newborn pairs (two PC deficiency and one AT deficiency). The prospective cohort revealed the outcomes of 35 patients: three deaths with PC deficiency and 20 complication-free survivors. Neurological complications were more frequently found in patients with PC-biallelic variants than those with PC-, PS-, or AT-monoallelic variants (73% vs. 24%, p=.019). We demonstrate the need for elective screening for EOT targeting PC deficiency in Japan. Early prenatal diagnosis of PC deficiency in mother-infant pairs may prevent perinatal thrombosis in them.

Prevalence and molecular basis of null blood group phenotypes in the Korean population: Analysis using a public database.

Null phenotypes are characterized by complete absence of all antigens within a blood group system and caused by null variants (e.g., nonsense, frameshift, initiation codon, and canonical splice site variants) in the genes encoding the antigens. Knowing the prevalence and molecular basis of null phenotypes is essential to establish a rare donor program, and the aim of this study was to reveal the prevalence and molecular basis of null phenotypes using the Korean Reference Genome Database (KRGDB) containing whole-genome sequences of 1722 Korean individuals. Population allele frequencies of null alleles in 39 blood group systems except ABO, MNS, Rh, Lewis, and FORS were obtained from the KRGDB. The prevalence of null phenotypes was calculated using Hardy-Weinberg equation. The prevalence of null phenotypes were estimated to be less than 0.001% in all blood group systems except JR and SID. The prevalence of the Jr(a-) and Sd(a-) phenotypes were estimated to be 0.0453% and 0.2323%, respectively. The most frequent null allele of the JR system was ABCG2*01N.01, accounting for approximately 85% of null alleles. Our approach using a public database allowed us to investigate the prevalence and molecular basis of null phenotypes in the Korean population, which will serve as a guide for establishing a rare donor program in Korea. Considering the clinical significance, Jr(a-) is an important null phenotype that should be typed in the Korean population, and molecular assays targeting the most frequent allele ABCG2*01N.01 may be useful in detecting this phenotype.

Evaluation of the Allelic Variations in Vernalisation (VRN1) and Photoperiod (PPD1) Genes and Genetic Diversity in a Spanish Spelt Wheat Collection.

Allelic variation within genes controlling the vernalisation requirement (VRN1) and photoperiod response (PPD1) determines the adaptation of wheat to different environmental growing conditions as well as influences other traits related to grain yield. This study aimed to screen a Spanish spelt wheat collection using gene-specific molecular markers for VRN-A1, VRN-B1, VRN-D1, and PPD-D1 loci and to phenotype for heading date (HD) in both field and greenhouse experiments under a long photoperiod and without vernalisation. Fifty-five spelt genotypes (91.7%) exhibited a spring growth habit, and all of them carried at least one dominant VRN1 allele, whereas five (8.3%) genotypes had a winter growth habit, and they carried the triple recessive allele combination. The Vrn-D1s was the most frequent allele in the studied set of spelt accessions, and it was found in combination with both the dominant Vrn-A1b and/or Vrn-B1a alleles in 88.3% of the spelt accessions tested. All spelt accessions carried the photoperiod-sensitive Ppd-D1b allele, which may explain the late heading of spelt germplasm compared to the commercial spring bread wheat Setenil used as a control. The least significant difference test showed significant differences between allelic combinations, the earliest accessions being those carrying two or three dominant alleles, followed by the one-gene combinations. In addition, the genetic diversity was evaluated through capillary electrophoresis using 15 wheat simple sequence repeat (SSR) markers. Most markers had high levels of polymorphism, producing 95 different alleles which ranged between 53 and 279 bp in size. Based on the polymorphic information content values obtained (from 0.51 to 0.97), 12 out of the 15 SSRs were catalogued as informative markers (values > 0.5). According to the dendrogram generated, the spelt accessions clustered as a separate group from the commercial bread wheat Setenil. Knowledge of VRN1 and PPD1 alleles, heading time, and genetic variability using SSR markers is valuable for spelt wheat breeding programs.

Mathematical bounds on Shannon entropy given the abundance of the ith most abundant taxon

The measurement of diversity is a central component of studies in ecology and evolution, with broad uses spanning multiple biological scales. Studies of diversity conducted in population genetics and ecology make use of analogous concepts and even employ equivalent mathematical formulas. For the Shannon entropy statistic, recent developments in the mathematics of diversity in population genetics have produced mathematical constraints on the statistic in relation to the frequency of the most frequent allele. These results have characterized the ways in which standard measures depend on the highest-frequency class in a discrete probability distribution. Here, we extend mathematical constraints on the Shannon entropy in relation to entries in specific positions in a vector of species abundances, listed in decreasing order. We illustrate the new mathematical results using abundance data from examples involving coral reefs and sponge microbiomes. The new results update the understanding of the relationship of a standard measure to the abundance vectors from which it is calculated, potentially contributing to improved interpretation of numerical measurements of biodiversity.

Evolution and spread of Plasmodium falciparum mutations associated with resistance to sulfadoxine–pyrimethamine in central Africa: a cross-sectional study

Efficacy of sulfadoxine-pyrimethamine, the malaria chemoprophylaxis used in pregnant women, and in children when combined with amodiaquine, is threatened by the accumulation of mutations in the Plasmodium falciparum dihydropteroate synthase (pfdhps) and dihydrofolate reductase (pfdhfr) genes. Data on the prevalence of resistant alleles in central Africa and the new pfdhps I431V mutation, particularly associated with other mutations to form the pfdhps vagKgs allele, are scarce. We explored the frequency and geographical distribution of pfdhps and pfdhfr mutations in central Africa in 2014-18, and assessed the evolutionary origin of the vagKgs allele. Samples were collected at 18 health-care centres in seven countries (Angola, Cameroon, Central African Republic, Democratic Republic of the Congo, Gabon, Nigeria, and Republic of the Congo) from patients who showed possible symptoms of malaria between March 1, 2014, and Oct 31, 2018. Samples that were positive for P falciparum were transported to a laboratory in Toulouse, France, and genotyped. The frequency of pfdhfr and pfdhps mutations was studied in 1749 samples. Microsatellites in pfdhps flanking regions and whole-genome analysis compared with parasite genomes from the data-sharing network MalariaGEN were performed on samples carrying the vagKgs allele. Mapping of the prevalence of single nucleotide polymorphisms and corresponding alleles of pfdhfr and pfdhps showed a substantial spread of alleles associated with sulfadoxine-pyrimethamine resistance in central Africa during the 2014-18 period, especially an increase going west to east in pfdhps alleles carrying the K540E and A581G mutations. A high prevalence of the pfdhps I431V mutation was observed in Cameroon (exceeding 50% in the northern region) and Nigeria. Genomic analysis showed a recent African emergence and a clonal expansion of the most frequent pfdhps vagKgs allele. Reduced sulfadoxine-pyrimethamine efficacy due to increased resistance is a worrying situation, especially because the malaria transmission level is high in central Africa. Although the resistance phenotype remains to be confirmed, the emergence and spread of the vagKgs allele in west and central Africa could challenge the use of sulfadoxine-pyrimethamine. Toulouse Institute for Infectious and Inflammatory Diseases.

Lipoprotein Lipase/Apolipoprotein Cll Gene Polymorphism in Kurdish Patients With Severe Hypertriglyceridemia.

Background Polymorphisms in thelipoprotein lipase(LPL) and apolipoprotein CII (APO CII)genes have been linked to severe hypertriglyceridemia in several populations. This study investigated the frequency ofLPL-Hind lllandAPO Cll-Ava ll polymorphism among Kurdishpatientswith severe hypertriglyceridemia. Methodology We investigated LPL-Hind llland APO Cll-Ava ll gene polymorphism in a sample of Kurdish patients receiving treatment at Azadi Teaching Hospital in Duhok, Kurdistan Region, Iraq. We included a total of 100 subjects in this study, of which 64 had severe hypertriglyceridemia, and 36 had normotriglyceridemia. There were 56 males and 44 females. We used the polymerase chain reaction-restriction fragment length polymorphism technique to determine the polymorphism of the LPL-Hind lll and APO Cll-Ava ll genes. Results In those with severe hypertriglyceridemia, the most frequent alleles were H+H+LPL-Hind lll polymorphism (42, 65.6%) followed by A1A1APO Cll-Ava ll polymorphism (30, 46.9%), whereas these frequencies were 16 (44.4%) and 6 (16.7%) in those with normotriglyceridemia, respectively. The H+H+ genotype group had considerably higher triglyceride levels and lower high-density lipoprotein cholesterol levels compared with the H-H- genotype group. A similar pattern was observed when comparing the A1A1 and A2A2 genotype groups, with both patterns being statistically significant. Conclusions Our results showed a high frequency of H+H+LPL-Hind III polymorphism in those with hypertriglyceridemia, which may be a hereditary indicator of vulnerability to this condition in the Kurdish population.

Allelic variation in TUSC1 gene: rs1462218557 is associated with male infertility and azoospermia

BackgroundMale infertility is rapidly growing, and single nucleotide polymorphism (SNP) association studies are of critical importance. Tumor suppressor candidate 1 (TUSC1) gene is associated with azoospermia. We investigated association between rs1462218557 in TUSC1 with azoospermia.MethodsWe performed tetra-ARMS PCR analysis and sequencing on healthy and infertile individuals.ResultsTetra-ARMS PCR results revealed that the allele frequency of the SNP for T alleles was 0.66, while the same value for C allele was 0.36. It was different from the previous reports of the other countries because they reported the allele C as the frequent allele and it was considered an ancestral allele. The genotype frequencies obtained showed that 67% of the samples were heterozygotes (T/C), while 33% were homozygotes (TT). SNP-STAT analysis showed a significant association (p = 0.04) with the studied SNP and azoospermia in Iranian samples.ConclusionsThe present study reports a new allele frequency of rs1462218557 in TUSC1 gene, which may be associated with azoospermia in Iranian people. Moreover, no association was observed between neighboring sequences/SNPs with male infertility.

Assessing the genetic risk of nodular melanoma using a candidate gene approach.

Nodular melanoma (NM) is a challenge to diagnose early due to its rapid growth and more atypical clinical presentation, making it the largest contributor to melanoma mortality. Our study aim was to perform a rare-variant allele (RVA) analysis of whole-exome sequencing of patients with NM and non-NM (minor allele frequency ≤ 1% non-Finnish European) for a set of 500 candidate genes potentially implicated in melanoma. This study recruited 131 participants with NM and 194 with non-NM from South-east Queensland and patients with NM from Victoria to perform a comparative analysis of possible genetic differences or similarities between the two melanoma cohorts. Phenotypic analysis revealed that a majority of patients diagnosed with NM were older males with a higher frequency of fair skin and red hair than is seen in the general population. The distribution of common melanoma polygenic risk scores was similar in patients with NM and non-NM, with over 28% in the highest quantile of scores. There was also a similar frequency of carriage of familial/high-penetrant melanoma gene and loss-of-function variants. We identified 39 genes by filtering 500 candidate genes based on the greatest frequency in NM compared with non-NM cases. The genes with RVAs of greatest frequency in NM included PTCH1, ARID2 and GHR. Rare variants in the SMO gene, which interacts with PTCH1 as ligand and receptor, were also identified, providing evidence that the Hedgehog pathway may contribute to NM risk. There was a cumulative effect in carrying multiple rare variants in the NM-associated genes. A 14.8-fold increased ratio for NM compared with non-NM was seen when two RVAs of the 39 genes were carried by a patient. This study highlights the importance of considering frequency of RVA to identify those at risk of NM in addition to known high penetrance genes.

GBA1 variants in Brazilian Gaucher disease patients

Gaucher disease (GD) is an autosomal recessive lysosomal disorder caused by pathogenic variants in GBA1 which result in the deficient activity of glucocerebrosidase (GCase). There are few data on the genetic characterization of Brazilian GD patients. This study aimed at characterizing the genotype of 72 unrelated Brazilian GD patients (type I = 63, type II = 4, type III = 5; male = 31). Forty patients were from South Brazil (SB), and 32 were from other regions of Brazil (Others). The exons and exon/intron junctions of GBA1 were analyzed by Sanger sequencing in 8 patients, or by massive parallel sequencing followed by Sanger of exons 9 and 10 in 64 patients. In total, 31 pathogenic variants were identified. The most frequent allele found was N370S (p.(Asn409Ser)) (41.0%), and the most frequent genotype was N370S/RecNciI p.[Asn409Ser];[Leu483Pro;Ala495Pro;Val499=](23.6%). Three variants (N370S – in exon 9, and RecNciI and L444P (p.(Leu483Pro), in exon 10) correspond to 76.3% of total alleles in SB and 59.4% in Others. Two novel variants were described: c.326del(p.(Gln109Argfs*9)) and c.690G>A (p.(?)). Although sequencing all the exons of GBA1 is the gold-standard method for the genetic analysis of GD patients, a step analysis can be proposed for Brazilian patients, starting with analysis of exons 9 and 10. The N370S allele is the most frequently associated with GD in Brazil.

Evaluation of GenDx Protocol for HLA NGS Genotyping Using the Ion Torrent Sequencing Platform

Abstract Background: The Human Major Histocompatibility Complex (HLA) is the most polymorphic region of the human genome and encodes molecules with a central role in antigen-specific immune responses. Class I and class II HLA genes have an important role in bone marrow and solid organ transplantations. HLA typing by Next Generation Sequencing (NGS) provides unambiguous second field or allelic level resolution and, therefore, better matching of donor and recipient and a higher chance of survival for transplanted patients. The aim of this study was to validate GenDx NGS HLA typing protocol for 6 HLA loci (HLA-A, -B, -C, DRB1, -DQB1 and DPB1). Materials and methods: 240 samples of both bone marrow healthy donors from the Bulgarian Bone Marrow Donors Registry (BBMDR) and bone marrow recipients were sequenced on the Ion Torrent System using the GenDx NGS HLA typing kit, compared to 65 samples from the BBMDR analyzed by Holotype HLA kit (Omixon) and sequenced on the Illumina platform MiniSeq. A number of metrics including allele balance, read length, mappability, coverage and ambiguity were assessed in order to evaluate the GenDx NGS HLA typing protocol. We also investigated haplotype and allele frequencies of class I (HLA-A, -B, -C) and class II (HLA-DRB1, -DQB1 and -DPB1) alleles. Results: The results demonstrate the accuracy of this protocol, eliminating almost all ambiguities, providing a reasonable read length of 180, 76% mappability and 1267 depth of coverage on average for all 6 HLA loci. We found that the most frequent alleles for class I are HLA-A*02:01:01 (27,5%), B*51:01:01 (16,5%), C*07:01:01 (16,5%) and class II – DRB1*11:04:01 (14,5%), DQB1*03:01:01 (26,9%) and DPB1*04:01:01 (33,2%) which corresponds with other investigations of the research team on HLA diversity in the Bulgarian population. Conclusion: The main advantages of GenDx NGS HLA typing protocol are the shorter time for DNA library preparation and the shorter sequencing time. Phasing ambiguities are also liminated, which is a significant advantage in the clinical environment. The presented data show the suitability of this NGS protocol for clinical practice, especially in HLA typing of donors from Bone Marrow Donors registries.