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This is the first study that characterizes the sequence-based allelic variations of 22 autosomal Short Tandem Repeat (aSTR) loci in a population dataset collected from Lebanon. Genomic DNA extracts from 195 unrelated Lebanese individuals were amplified with PowerSeq 46GY System Prototype. Targeted amplicons were subjected to DNA library preparation and sequenced on the Verogen MiSeq FGx Sequencing System. Raw FASTQ data files were processed by STRait Razor v3. Sequence strings were annotated according to the considerations of the DNA Commission of the International Society for Forensic Genetics (ISFG) and tabulated herein with their respective allelic frequencies and GeneBank accession and version numbers. The sequenced Lebanese dataset resulted in 429 distinct allelic sequences as compared to the 236 alleles identified by length only. The increase in the number of alleles was observed at 18 out of 22 aSTR loci and was attributed to the sequence variations residing in both the STR repeat motifs and flanking regions. The study uncovered 25 novel aSTR allelic sequences across 12 loci for which GenBank records did not previously exist in the STRSeq BioProject, PRJNA380127. For a concordance check, the length-based allelic calls derived from the full sequences were compared to those genotyped using capillary electrophoresis (CE) methods. Population genetic parameters relevant to the evaluation of forensic DNA evidence were assessed for the sequence-based data and compared to the parameters generated from the length-based information. Using the sequence-based data, Analysis of MOlecular VAriance (AMOVA), genetic distances, and population genetic structure were evaluated for 1231 individuals sampled from the Lebanese and four U.S. populations (African American, Asian, Caucasian, and Hispanic). The results were tabulated and visualized in a population tree, multidimensional scaling scatter plots, and bar plots. This newly established sequence-based database for the Lebanese population can be beneficial for extending NGS applicability to casework or paternity testing and assessing the strength of evidence for NGS-STR profiles. The described novel sequence variants at certain loci can further help in the effort to characterize the sequence diversity of STR markers from different populations around the world. • DNA extracts from 195 Lebanese individuals are sequenced. • Genetic distance and population structure of the Lebanese individuals in relation to four U.S. populations are investigated. • The full allelic sequences at 22 autosomal STR loci are described with their respective repeat and flanking polymorphisms. • Allelic frequencies for the sequence variants are calculated. • Forensic informativeness metrics of the allelic sequences are assessed. [ABSTRACT FROM AUTHOR]

Abstract: Apolipoprotein E (ApoE) has an important role in the metabolism of lipids through its major isoforms (ε2, ε3, ε4). In particular, ApoE ε4, has been considered as a major genetic risk factor for cardiovascular diseases (CVD). The aim of our study is to investigate the frequency of ApoE gene polymorphisms (rs 429358C>T, rs 7412C>T) and their relationship to lipid parameters in a group of Lebanese hypercholesterolemic subjects (22 males and 24 females, aged 25–80years). Lipid profile, apolipoproteins A-I and B were determined using fasting serum samples; and molecular analysis of ApoE polymorphisms using blood in EDTA tubes. The distribution of the four ApoE genotypes detected in this study was: ε3/ε3 (73.9%), ε3/ε4 (17.4%), ε2/ε3 (6.5%), and ε2/ε4 (2.2%) resulting in allelic frequencies for ε2, ε3 and ε4 of 4.3%, 85.9% and 9.8%, respectively. No association was determined among any of the lipid parameters, gender and ApoE genotypes. Lipid parameters were not statistically different among various ApoE genotypes (p>0.05). ApoE ε2 frequency was found to be lower than that previously reported for healthy Lebanese (7.2%). CVD is one of the major leading causes of mortality in Lebanon with a reported prevalence of 12.2% in males and 7.7% in females, which incidentally agrees with our finding regarding ε4 allelic frequency of 13.6% in males and 6.3% in females. Consequently, larger prospective studies are recommended to highlight the correlation of ApoE polymorphisms to other biochemical and environmental factors involved in CVD. [Copyright &y& Elsevier]

Abstract: Hyperhomocysteinemia is associated with several vascular and teratogenic conditions. Determinants of total homocysteine concentrations include genetic and nutritional factors. This study assesses the relation between homocysteine concentrations and MTHFR gene polymorphisms at two common alleles (C677T (rs1801133) and A1298C (rs1801131)) as well as other predictors of homocysteine (folate, vitamin B12, body mass index (BMI), age, and gender) in a group of healthy Lebanese: 109 males and 124 females aged 17–55years. We used serum for the determination of homocysteine, folate and vitamin B12 levels and blood drawn in EDTA tubes for molecular analysis of MTHFR polymorphisms. Hyperhomocysteinemia was present in 59/233 (25.3%) of the subjects, with male/female ratio of 1.95. Multivariable regression analysis showed that homocysteine levels were negatively related to folate and vitamin B12 and positively related to male gender and C677T homozygosity; but not A1298C polymorphism, BMI or age. The prevalence of wild, heterozygous, and homozygous C677T genotypes was 45.0%, 43.3% and 11.6%, respectively; with a carrier frequency of 54.9% and allelic frequency of 33.3%. The A1298C genotypic prevalence was 39.5%, 30.9%, and 29.6% respectively; with a carrier frequency of 60.5% and allelic frequency of 45.1%. C677T/A1289C compound heterozygosity was present in 47/233 (20.2%) of volunteers. In this first pilot study, gender, folate, vitamin B12 and C677T mutational status could explain around 32% of homocysteine variations. Future larger studies are recommended to investigate other predictors of homocysteine variation and combine them with markers explored in this and other studies, in order to evaluate their impact on vascular and/or congenital diseases. [Copyright &y& Elsevier]

Venous thromboembolism (VTE), including deep venous thrombosis (DVT) and pulmonary embolism (PE), occurs secondary to a number of hereditary and acquired disorders of hemostasis. A recently recognized polymorphism in Factor V (FV) gene H1299R (also named HR2) has been reported to be a possible risk factor for the development of VTE. The aim of this study is to evaluate the role of HR2 polymorphism in VTE in a group of Lebanese patients. Seventy-three VTE patients and 125 healthy subjects were examined for HR2. The average ages for the patients and controls were 45.0 ± 19.1 years and 35.4 ± 18.6 years, respectively. Sixty patients (82.2%) had DVT, eight patients (11%) had PE, and five patients (6.8%) had both. There was significant association between FV Leiden and VTE ( p < 0.001). HR2 haplotype had a prevalence of 16.4% in patients. VTE patients with normal FV were 2.7 times more likely to have the HR2 haplotype as compared to controls with normal FV ( p = 0.036, 95% CI = 1.04–7.06). We conclude that the FV HR2 haplotype significantly affects the risk of VTE in subjects with normal FV. This finding entails that screening for the HR2 haplotype should be done in VTE patients with normal FV Leiden results. [ABSTRACT FROM AUTHOR]

Background Multiple sclerosis (MS) is an autoimmune demyelinating disease affecting mostly young adult females with multifactorial etiology. Recent studies suggested that adequate vitamin D levels may lower the risk of developing MS. Objectives Our aim was to explore the relationship between vitamin D receptor (VDR) polymorphism, HLA-DR locus genotype, and serum vitamins D and A levels in the Lebanese population. Methods Fifty MS patients were recruited for this study. The control group consisted of 48 healthy and 51 patients with other neurological disorders (non-MS). Biochemical analysis included serum 25 hydroxyvitamin D (25OHD) and vitamin A. Molecular analysis targeted VDR genotypes ( ApaI , TaqI and BsmI ) and low resolution HLA typing for DRB1 locus. Results Healthy and non-MS groups had comparable parameters and were combined into one control group. No significant differences were found between MS and control groups for VDR genotypes. The frequency of HLA-DRB1*15 was significantly higher in MS patients (22%) compared to controls (8%) (p = 0.018). Odds ratio for MS in the presence of DRB1*15 allele was 3.21 (p = 0.018). Cosegregation with A ( ApaI ) and b ( BsmI ) alleles did not influence the risk for MS. 25OHD levels were significantly higher in MS patients compared to controls (p = 0.002), due to more frequent oral supplementation (p = 0.005). Vitamin A levels were comparable between the two groups. When all parameters were included in a logistic regression model adjusted for supplementation, only HLA-DRB1*15 (OR = 3.42; p = 0.027) contributed significantly to MS risk. Conclusion There was no association between serum vitamin D or A or VDR genotypes and MS. HLA-DRB1*15 was the major factor imposing more than 3 folds greater risk for developing MS among Lebanese. [ABSTRACT FROM AUTHOR]

Aim: Study KIR expression of NK cells in CLL patients and in healthy controls, to check for any association between KIR genotypes and CLL. Methods: KIR genotype was analysed for 120 healthy Lebanese patients and 56 CLL patients. using the KIR Genotyping SSP kit. Results: KIR genotypic profile distribution among the 56 Lebanese patients with CLL is shown in Table 1 .[figure1] Table 2 shows the distribution of different KIR genotypes among the 120 healthy Lebanese controls. The content of KIR genes ranged from 6 to 15 and, as per Table 4, the AA, AB, and BB genotypes frequencies were, respectively, 42.5%, 50%, and 7.5% with an A:B ratio of 2.08:1. Table 3 shows the distribution of different KIR genes among the 120 controls and the 56 CLL patients.[figure2]KIR 2DL4, KIR 3DL2, and KIR 3DL3 were present in all individuals. KIR 2DS4∗001/002 and KIR 2DS5 were found to be significantly (with a p-value of 0.02 and 0.04, respectively) more prevalent among CLL patients as compared to controls. Conclusions: The interesting observation of the significant presence of KIR 2DS4 and KIR 2DS5 genes more among Chronic Lymphocytic Leukemia than controls is worth further clinical and translational research in the future as well as correlation with outcome of bone marrow transplantation in these cases. [Copyright &y& Elsevier]

The aim of this study is to analyze polymorphisms in genes involved in 6-mercaptopurine detoxification (TPMT); methotrexate (MTX) metabolism including ABCB1 (or MDR1), ABCC2, SLC19A1 (or RFC1), and SLCO1B1; and the MTX effect mainly MTHFR and TYMS, and to assess whether these polymorphisms are predictors of treatment toxicity and/or MTX clearance.This study included 127 Lebanese acute lymphoblastic leukemia patients, of whom 117 were treated following the St Jude’s Children Research Hospital protocol. Genotyping was performed using real-time PCR or restriction fragment length polymorphism. MTX levels were measured using a polarization fluorescence assay from Roche. MTX clearance was estimated on the basis of all available MTX levels measured after high-dose MTX treatment during the consolidation phase.Five variants in four genes (MTHFR, ABCB1, ABCC2, and TYMS) were shown to be associated with toxicity, but neither was associated with MTX pharmacokinetic parameters. For instance, during the consolidation phase, a statistically significant association was found between MTHFR rs1801133 variant allele carriers and a decrease in hemoglobin levels [odds ratio (OR)=3.057; 95% confidence interval (CI): 1.217; 7.680]. In addition, a statistically significant association was found among neutropenia (absolute neutrophil count<500) and variant allele carriers of ABCB1 rs1045642 (OR=5.174; 95% CI: 1.674; 15.989) and ABCB1 rs1128503 (OR=3.364; 95% CI: 1.257; 9.004), respectively. ABCC2 rs717620 variant allele carriers needed significantly more time to reach a MTX level below 0.1 µmol/l (β=5.122; 95% CI: 1.412; 8.831). During the continuation phase, a statistically significant association was found between ABCC2 rs717620 and TYMS 28-bp tandem repeats carriers with the need to decrease weekly MTX doses (β=-4.905; 95% CI: -9; -0.809 and β=-5.770; 95% CI: -10.138; -1.403), respectively.Genotyping for MTHFR, ABCB1, ABCC2, and TYMS polymorphisms may be useful in identifying patients at risk of increased MTX toxicity and the need for dose optimization before treatment initiation. [ABSTRACT FROM AUTHOR]

Aim: Study KIR expression of NK cells in MM patients and in healthy controls, to check for any association between KIR genotypes and MM. Methods: KIR genotype was analysed for 120 healthy Lebanese patients and 34 MM patients. using the KIR Genotyping SSP kit. Results: The content of KIR genes ranged from 7 to 15 and as per Table 4, the AA, AB, and BB genotypes frequencies were, respectively, 38.24%, 47.06% and 14.71% with an A:B ratio of 1.62:1. [figure1] Table 2 shows the distribution of different KIR genotypes among the 120 healthy Lebanese controls. The content of KIR genes ranged from 6 to 15 and, as per Table 4, the AA, AB, and BB genotypes frequencies were, respectively, 42.5%, 50%, and 7.5% with an A:B ratio of 2.08:1.[figure2]Fig. 2 shows the distribution of different KIR genes among the 120 controls and the 34 MM patients. KIR 3DL2 KIR 3DL3, and KIR 3DP1∗003 were present in all individuals. KIR 2DS4∗001/002 and KIR 2DS5 were found to be significantly (with a p-value of 0.04 and 0.007, respectively) more prevalent among MM patients as compared to controls. Conclusions: The interesting observation of the significant presence of KIR 2DS4 and KIR 2DS5 genes more among Multiple Myeloma than controls is worth further clinical and translational research in the future as well as correlation with outcome of bone marrow transplantation in these cases. [Copyright &y& Elsevier]

Abstract: The highly polymorphic Human Leukocyte Antigen system encompasses different loci that have been studied in transplantation as well as diseases and population associated research. This study is the first and largest of its kind to describe the distribution of HLA-A, -B and -C alleles in Lebanon. Respectively, 1994, 1309 and 1163 Lebanese individuals referred for HLA typing and possible bone marrow/kidney donation were tested for HLA-A, HLA-B and HLA-C alleles using the polymerase chain reaction/Sequence specific priming (PCR-SSP) method. Our data were compared to that of several populations with interesting and common findings shared with the Moroccan, Jordanian, Tunisian, Omani, Korean, Chinese, Japanese, Peruan, Bulgarian, Irish, Polish, Spanish, Swiss, American, African and Brazilian populations. The following data concerning the Lebanese population will help future investigators to study the relation of HLA-A, -B and -C alleles with common diseases in Lebanon and will add to the available international literature. This new data will serve as a major reference report in the region. [Copyright &y& Elsevier]

Abstract: Aims: Being one of the most polymorphic genetic systems , the Human Leukocyte Antigen system is divided into class I (HLA-A, HLA-B and HLA-C) and class II (HLA-DP, -DQ and -DR). This study is the first and largest of its kind to describe the distribution of HLA-DQB1 and HLA-DRB1 alleles in Lebanon and the region. Methods: Respectively, 560 and 563 Lebanese individuals referred for HLA typing and possible bone marrow/kidney donation were tested for HLA-DQB1 and HLA-DRB1 alleles using the polymerase chain reaction/sequence specific priming (PCR-SSP) method. Results: Our data were compared to that of several populations with interesting common findings between the Lebanese, Jordanian, Bahraini, Saudi, Kuwaiti, Tunisian, Korean, Japanese, Thai, Irish, Bulgarian and Polish populations. Conclusion: These data about the Lebanese population are going to aid future researchers to study the relation of HLA-DQB1 and HLA-DRB1 alleles with major and common diseases in the Lebanese population and will add to the available international literature associated with these loci. In addition it will serve as a reference for the future national bone marrow registry program in our country. We also reviewed the literature for the described association between HLA-DRB1 and -DQB1 loci and different disease entities. [Copyright &y& Elsevier]

Aim: The aim is to study NK KIR genotpyes in symptomatic patients infected with H. pylori and in H. pylori negative patients. Methods: KIR genotype was analysed for 101 Lebanese symptomatic patients (51 H. pylori-positive and 50 H. pylori-negative) using the KIR Genotyping SSP kit. Results: KIR genotypic profile distribution among the 51 Lebanese patients with Helicobacter pylori is shown in Table 1. The content of KIR genes ranged from 5 to 13 and as per Table 4, the AA, AB, and BB genotypes frequencies were, respectively, 43.14%, 41.18% and 15.68% with an A:B ratio of 1.76:1. Table 2 [figure1] shows the distribution of different KIR genotypes among the 50 Helicobacter pylori-negative Lebanese patients. The content of KIR genes ranged from 7 to 13 and, as per Table 4, the AA, AB, and BB genotypes frequencies were, respectively, 18%, 62%, and 20% with an A:B ratio of 0.96:1. [Table 1] Conclusions: Although there was no statistical significance in the difference between the KIR gene distributions among the two compared groups, we noticed a reduced distribution of A haplotype among the “H pylori negative” patients as compared to the “H. Pylori positive” group. This means that more activating genes (through a B haplotype) are present in the former group which may explain faster eradication of the organism. [Copyright &y& Elsevier]