Haplotype Frequencies Research Articles

Signal Transducer and Activator of Transcription 4 (STAT4) Association with Pituitary Adenoma

Background/Objectives: This study aims to investigate whether Signal Transducer and Activator of Transcription 4 (STAT4) influences the anti-tumor immune response and is possibly involved in the initiation or relapse of pituitary adenomas (PAs) by examining STAT4 polymorphisms and serum levels. This research seeks to uncover potential connections that could inform future therapeutic strategies and improve our understanding of PA pathogenesis. Materials and Methods: This study was conducted at the Laboratory of Ophthalmology, Lithuanian University of Health Sciences. DNA was extracted from peripheral venous blood samples, and the genotyping of four STAT4 SNPs (rs7574865, rs10181656, rs7601754, and rs10168266) was performed using real-time PCR with TaqMan® Genotyping assays. The serum STAT4 levels were measured via ELISA, and the optical density was read at 450 nm. Genotype frequencies, allele distributions, and serum STAT4 levels were statistically analyzed to assess associations with pituitary adenoma occurrence. Results: A binary logistic regression revealed that the STAT4 rs7574865 GT + GG genotypes vs. TT were associated with 1.7-fold increased odds of PA occurrence under the dominant genetic model (p = 0.012). The stratification by gender showed no significant associations in females; however, in males, the STAT4 rs10168266 CC + CT genotypes compared to TT were linked to 2.5-fold increased odds of PA under the dominant genetic model (p = 0.005). STAT4 rs10181656, rs7574865, rs7601754, and rs10168266 were analyzed to evaluate the associations with the pituitary adenoma size. We found that the STAT4 rs7574865 GG genotype was statistically significantly less frequent in the macro PA group compared to in the reference group (p = 0.012). For PA relapse, the rs7574865 G allele was less frequent in the PA group without relapse (p = 0.012), and the GT + GG genotypes were associated with a 1.8-fold increase in the PA group without relapse occurrence (p = 0.008). The serum STAT4 levels were higher in the PA patients compared to those of the reference group (p < 0.001). Elevated STAT4 serum levels were observed in PA patients with the STAT4 rs10181656 CC or CG genotypes (CC: p = 0.004; CG: p = 0.023), and with the rs7574865 GG or GT genotypes (GG: p = 0.003; GT: p = 0.021). The PA patients with the STAT4 rs7601754 AA genotype exhibited higher serum levels compared to those of the reference group (p < 0.001). Similarly, higher serum levels were found in the PA patients with the STAT4 rs10168266 CC or CT genotypes (CC: p = 0.004; CT: p = 0.027). A haplotype frequency analysis revealed no statistically significant results. Conclusions: The STAT4 genotypes were significantly associated with the PA occurrence, size, and relapse. Elevated serum STAT4 levels were observed in the PA patients, highlighting its potential role in PA pathogenesis.

CYP2C gene polymorphisms in North African populations.

Cytochrome P450 is a superfamily of genes generating hemoproteins that metabolize foreign chemicals as well as endogenous compounds, such as steroids. The human CYP2C genes (CYP2C8, CYP2C9, CYP2C18, CYP2C19) cluster on chromosome 10 and metabolize many clinically useful drugs. CYP2C19 and CYP2C9 have been the most studied while CYP2C8 has been studied less frequently. CYP2C18 has been relatively ignored until recently but its importance has begun to be recognized. We studied the genotypes of 7 pharmacogenetic markers in 3 CYP2C genes: CYP2C19 (rs12248560), CYP2C9 (rs4918758, rs1799853), and CYP2C8 (rs10509681, rs11572103, rs1058930, rs11572080), in one Libyan population and 7 Tunisian populations. Five of the 7 SNPs are in exons and have functional consequences while one intronic SNP is considered to be in close proximity to a regulatory region because of the many studies that report associations with metabolic effects. We carried out principal component analysis (PCA) on the North African populations and 83 other populations from the 1000 Genomes Project and Kidd Laboratory. The geographic clustering observed via PCA was more pronounced when considering multi-SNP haplotype frequencies. This studyreveals the intermediate position of North Africans between Europeans and Asians and the varied dissimilarities with other world regions. The genetic variation observed within and between geographic regions have implications for drug metabolism and adverse individual responses to medical treatments.

Neuropathological Heterogeneity of Dementia Due to Combined Pathology in Aged Patients: Clinicopathological Findings in the Vallecas Alzheimer’s Reina Sofía Cohort

Background/Objectives: Clinicopathological research in late-life dementia has focused recently on combined neurodegenerative and vascular conditions underlying the high phenotypic heterogeneity of patients. The Vallecas Alzheimer’s Reina Sofía (VARS) cohort (n > 550), and particularly the series of associated brain donations (VARSpath cohort) are presented here. The aim of this study is to contribute to research in dementia with a well-characterized cohort from a single center. Methods: A total of 167 patients with complete neuropathological work-ups were analyzed here. The cohort is characterized by a high female predominance (79%), advanced age at death (88 yrs.), and a high frequency of ApoE-e4 haplotype (43%). Results: The main neuropathological diagnosis was Alzheimer’s disease (79.6%), followed by vascular dementia (10.2%) and Lewy body dementia (6%). Overall, intermediate-to-high cerebrovascular disease was observed in 38.9%, Lewy body pathology in 57.5%, LATE (TDP-43 pathology) in 70.7%, ARTAG in 53%, and argyrophilic grain disease in 12% of the patients. More than one pathology with a clinically relevant burden of disease was present in 71.1% of the brains, and a selection of premortem neuropsychological and functional scores showed significant correlation with the number of co-pathologies identified in postmortem brains. Conclusions: The VARS cohort, with thorough clinical follow-up, regular blood sampling, 3-Tesla MR, and a high rate of postmortem brain donation, can provide essential multidisciplinary data in the rising age of modifying therapies and biomarkers for Alzheimer’s disease and related dementias.

Archaic introgression contributed to shape the adaptive modulation of angiogenesis and cardiovascular traits in human high-altitude populations from the Himalayas.

It is well established that several Homo sapiens populations experienced admixture with extinct human species during their evolutionary history. Sometimes, such a gene flow could have played a role in modulating their capability to cope with a variety of selective pressures, thus resulting in archaic adaptive introgression events. A paradigmatic example of this evolutionary mechanism is offered by the EPAS1 gene, whose most frequent haplotype in Himalayan highlanders was proved to reduce their susceptibility to chronic mountain sickness and to be introduced in the gene pool of their ancestors by admixture with Denisovans. In this study, we aimed at further expanding the investigation of the impact of archaic introgression on more complex adaptive responses to hypobaric hypoxia evolved by populations of Tibetan/Sherpa ancestry, which have been plausibly mediated by soft selective sweeps and/or polygenic adaptations rather than by hard selective sweeps. For this purpose, we used a combination of composite-likelihood and gene network-based methods to detect adaptive loci in introgressed chromosomal segments from Tibetan WGS data and to shortlist those presenting Denisovan-like derived alleles that participate to the same functional pathways and are absent in populations of African ancestry, which are supposed to do not have experienced Denisovan admixture. According to this approach, we identified multiple genes putatively involved in archaic introgression events and that, especially as regards TBC1D1, RASGRF2, PRKAG2, and KRAS, have plausibly contributed to shape the adaptive modulation of angiogenesis and of certain cardiovascular traits in high-altitude Himalayan peoples. These findings provided unprecedented evidence about the complexity of the adaptive phenotype evolved by these human groups to cope with challenges imposed by hypobaric hypoxia, offering new insights into the tangled interplay of genetic determinants that mediates the physiological adjustments crucial for human adaptation to the high-altitude environment.

Archaic introgression contributed to shape the adaptive modulation of angiogenesis and cardiovascular traits in human high-altitude populations from the Himalayas

It is well established that several Homo sapiens populations experienced admixture with extinct human species during their evolutionary history. Sometimes, such a gene flow could have played a role in modulating their capability to cope with a variety of selective pressures, thus resulting in archaic adaptive introgression events. A paradigmatic example of this evolutionary mechanism is offered by the EPAS1 gene, whose most frequent haplotype in Himalayan highlanders was proved to reduce their susceptibility to chronic mountain sickness and to be introduced in the gene pool of their ancestors by admixture with Denisovans. In this study, we aimed at further expanding the investigation of the impact of archaic introgression on more complex adaptive responses to hypobaric hypoxia evolved by populations of Tibetan/Sherpa ancestry, which have been plausibly mediated by soft selective sweeps and/or polygenic adaptations rather than by hard selective sweeps. For this purpose, we used a combination of composite-likelihood and gene network-based methods to detect adaptive loci in introgressed chromosomal segments from Tibetan WGS data and to shortlist those presenting Denisovan-like derived alleles that participate to the same functional pathways and are absent in populations of African ancestry, which are supposed to do not have experienced Denisovan admixture. According to this approach, we identified multiple genes putatively involved in archaic introgression events and that, especially as regards TBC1D1, RASGRF2, PRKAG2, and KRAS, have plausibly contributed to shape the adaptive modulation of angiogenesis and of certain cardiovascular traits in high-altitude Himalayan peoples. These findings provided unprecedented evidence about the complexity of the adaptive phenotype evolved by these human groups to cope with challenges imposed by hypobaric hypoxia, offering new insights into the tangled interplay of genetic determinants that mediates the physiological adjustments crucial for human adaptation to the high-altitude environment.

Genetics of Latin American Diversity Project: Insights into population genetics and association studies in admixed groups in the Americas

Latin Americans are underrepresented in genetic studies, increasing disparities in personalized genomic medicine. Despite available genetic data from thousands of Latin Americans, accessing and navigating the bureaucratic hurdles for consent or access remains challenging. To address this, we introduce the Genetics of Latin American Diversity (GLAD) Project, compiling genome-wide information from 53,738 Latin Americans across 39 studies representing 46 geographical regions. Through GLAD, we identified heterogeneous ancestry composition and recent gene flow across the Americas. Additionally, we developed GLAD-match, a simulated annealing-based algorithm, to match the genetic background of external samples to our database, sharing summary statistics (i.e., allele and haplotype frequencies) without transferring individual-level genotypes. Finally, we demonstrate the potential of GLAD as a critical resource for evaluating statistical genetic software in the presence of admixture. By providing this resource, we promote genomic research in Latin Americans and contribute to the promises of personalized medicine to more people.

How have breeders adapted rice flowering to the growing region?

Flowering time is a crucial rice trait that influences its adaptation to various environments, cropping schedules, and agronomic characteristics. Rice breeders have exploited spontaneous mutations in heading date genes to regulate the flowering time. In the present study, we investigated how breeders in Fukui Prefecture regulated days to heading while developing promising rice varieties. Genome-wide association studies (GWAS) identified Hd1, Hd16, and Hd18 as the major genes controlling days to heading in the population. However, we suspected that this highly bred population might exhibit genomic stratification, which could lead to spurious or false correlations in the GWAS. Thus, we also conducted correlation and partial correlation analyses, which uncovered another key heading date gene, Hd17, that GWAS failed to detect because of its linkage disequilibrium with the major effect gene Hd16. Examination of haplotype frequencies across different breeding periods revealed that the early-heading Hd16 (Hd16(E)) and late-heading Hd17 (Hd17(L)) were increasingly co-selected in the Hd1 functional population. Varieties carrying this Hd16(E)/Hd17(L) combination exhibited days to heading in the range of 70-80, which corresponds to the peak temperature and sunshine period and is also optimal for grain quality and yield components in the Fukui environment. The present study highlights that it is imperative to remain vigilant for Type I (false positives) and Type II (false negatives) errors when performing GWAS on highly bred populations and to implement appropriate countermeasures by accounting for gene-by-gene interactions established through the breeding process. We also discuss the effectiveness of Hd16(E), which is not used outside Japan for subtle days to heading control but is widely used in Japan at certain latitudes.

Roles of NR1I3 and NR1H4 polymorphisms in the susceptibility to antituberculosis drug-induced liver injury in China: a case‒control study.

The pathogenesis of antituberculosis drug-induced liver injury (AT-DILI) remains largely unknown. The current investigation aimed to determine the genetic contribution of the nuclear receptor subfamily 1 Group I member 3 (NR1I3) and nuclear receptor subfamily 1 Group H member 4 (NR1H4) genes to the risk of AT-DILI in the Chinese population. A 1:4 matched case‒control study was conducted, and five single nucleotide polymorphisms (SNPs) in the NR1I3 and NR1H4 genes were detected and assessed. Utilizing a multivariate conditional logistic regression model, the effects of haplotype and genotype on the risk of AT-DILI were examined. Extended subgroup analysis was carried out based on sex. The distribution of the peak value of serum liver enzymes also compared among different genotypes. 224 AT-DILI cases and 896 controls were included in this study. No significant difference was observed in genotypes or haplotypes frequencies between AT-DILI cases and controls. However, comparisons of liver function indicators revealed significant differences in the peak values of alanine aminotransferase (ALT), aspartate aminotransferase (AST) and total bilirubin (TBil) among patients with different genotypes of NR1H4 rs56163822 (GG vs. GT vs. TT, 27.1 U/L vs. 26.0 U/L vs. 23.0 U/L, p = 0.020; 34.0 U/L vs. 31.0 U/L vs. 30.6 U/L, p = 0.008; 15.5μmol/L vs. 15.0μmol/L vs. 13.7μmol/L, p = 0.029, respectively), as well as in the peak values of ALT and AST among male patients with different genotypes of NR1H4 rs56163822 (29.0 U/L vs. 26.9 U/L vs. 22.6 U/L, p = 0.002; 34.0 U/L vs. 32.0 U/L vs. 30.5 U/L, p = 0.019, respectively). Based on this 1:4 individual-matched case‒control study, the SNP rs56163822 in the NR1H4 gene may be linked to the susceptibility to AT-DILI in Chinese patients receiving anti-TB treatment. Further studies in larger varied populations are needed to validate our findings.

Genetic variability and discriminatory power of RM Y-STRs in gilgit men: a population study

AbstractShort Tandem Repeats (STRs) found on the Y chromosome have multiple applications, such as in forensic investigations, male identification for legal reasons, as well as population genetics. However, commercially accessible Y-STR tests are limited in their capability to distinguish closely linked male individuals in forensic genetics. Recent studies have revealed that Rapidly Mutating Y-STRs (RM Y-STRs) offer significantly greater haplotype diversity around the worldwide populations associated to conventional Y-STRs, though some RM Y-STR loci are not contained, current commercial kits. The objective of this research is to create a database of RM Y-STR haplotype frequencies for the Gilgit population in Pakistan and evaluate the effectiveness of these genetic markers in distinguishing individuals with genetic variations. The research involved examining several RM Y-STRs in 56 unrelated Gilgit men. The statistical analysis determined that the majority of the loci-maintained haplotype values, as specific varied in certain cases. The results presented that the RM Y-STRs were very effective in distinguishing genetic changes among the Gilgit population, through a GD value of 0 for DYD403S1 and GD values greater than 0.7 for all other loci, with maximum value of 0.9920 for the RM Y-STR DYS612.

ONT sequencing identifies a high prevalence of crt sensitive, triple mutant dhfr and single mutant dhps parasites within an ANC population in Nigeria.

Malaria in pregnancy is a major public health issue, particularly among vulnerable populations in malaria-endemic sub-Saharan African countries. To mitigate its risks, WHO recommends sulphadoxine-pyrimethamine (SP) for chemoprevention and artemisinin-based combination therapy (ACT) to treat uncomplicated Plasmodium falciparum malaria. These interventions have helped to alleviate the risk associated with malaria in pregnancy; however, in the context of the emergence of SP- and ACT-resistant P. falciparum, maintained efficacy is under threat. Molecular surveillance is a reliable tool to monitor the emergence of resistance where molecular markers are known. Thus, the objective of the study was to use a multiplexed amplicon Oxford Nanopore sequencing approach to assess the molecular markers for antimalarial resistance among pregnant women in Nigeria. Dried blood spots (DBS) were collected from pregnant women who received IPTp-SP at the enrollment and follow-up visits. P. falciparum genomic DNA was extracted by the Chelex® method and Pf18S qPCR was used to detect parasite DNA in each sample. With nested PCR assays, fragments of Pfdhps, Pfdhfr, Pfmdr1, Pfcrt, Pfk13 and Pfama1 genes were amplified and multiplexed amplicon-based sequencing was conducted on the minION Oxford Nanopore Technology. In total, 251 pregnant women were enrolled in the study and 457 DBS samples were collected. P. falciparum genomic DNA was detected in 12% (56/457) of the samples, 31 at baseline and the remaining during the follow-up visits. Pfama1, pfk13, Pfdhps, Pfdhfr, Pfmdr1 and Pfcrt were successfully sequenced in a single run. Notably, k13 artemisinin resistance mutations were absent, the frequencies of Pfdhfr and Pfdhps SP resistance haplotypes, IRN for pyrimethamine resistance and ISGKA/IAGKA associated with sulphadoxine resistance were 82% (36/44) and 64% (27/42), respectively, and the Pfcrt CVIET resistant haplotype was at approximately 22% (7/32). Here a multiplexed amplicon-based ONT assay established that triple mutant Pfdfhr-IRN, double mutant Pfdhps-SG haplotypes and the chloroquine sensitive strain were prevalent among pregnant women in Nigeria.

Analysis of ABCB1 Gene Polymorphisms and Their Impact on Tacrolimus Blood Levels in Kidney Transplant Recipients.

Tacrolimus (Tc) is an immunosuppressant used in transplant patients, but its therapeutic range is narrow, making precise dosing essential. This study investigates the association of three single nucleotide polymorphisms (SNPs) (ABCB1 3435C>T, 1236C>T, 2677G>T/A) with Tc levels over time to gain better insights into their role in personalized medicine. We conducted the study over four distinct periods: 1-14 days, 15-30 days, 31-60 days, and beyond 60 days post-transplantation. The analysis included allele, genotype, haplotype, and diplotype frequencies of the three SNPs concerning Tc blood levels. Statistical significance was determined, and false discovery rate (PFDR) correction was applied where appropriate. Significant associations were found between the C (ABCB1 C1236T), A alleles (ABCB1 G2677T/A), the CAC haplotype and lower Tc levels. The CAC-TGT and TGT-TGT diplotypes significantly influence how patients metabolize the drug. The TGT haplotype and the AA genotype (ABCB1 G2677T/A) were associated with higher Tc levels, suggesting a long-term genetic influence. Genetic factors, specifically certain SNPs and diplotypes, significantly impact Tc blood levels, with their influence varying over time.

Investigation of genetic polymorphisms in genes encoding growth factors and dental pulp calcification in orthodontic patients

Background and objectivesPulp calcification is associated with many factors and triggers, including individual genetic predisposition and orthodontic forces. This study aimed to investigate whether genetic polymorphisms in epidermal growth factor (EGF), epidermal growth factor receptor (EGFR1), transforming growth factor-beta 1 (TGFβ1), and transforming growth factor-beta receptor 2 (TGFβR2) are associated with a risk of dental pulp calcifications in orthodontic patients. Materials and methodsDigital orthopantomography (OPG) and genomic DNA from 132 patients were analyzed in this cross-sectional study. Pulp calcification was observed in the maxillary and mandibular first molars. Genomic DNA extracted from saliva cells was used to genotype eight genetic polymorphisms using real-time polymerase chain reaction: EGF (rs2237051 and rs4444903), EGFR (rs2227983 and rs763317), TGFβ1 (rs1800469 and rs4803455), and TGFβR2 (rs3087465 and rs764522). The association between pulp calcification and genetic polymorphisms was analyzed using allelic and genotypic distributions, and haplotype frequencies (P < 0.05). ResultsThe prevalence of pulp calcification was 42.4 % in 490 molars. Genotypic analysis and allelic distribution showed no statistically significant association between the evaluated growth factors and molar calcification (P > 0.05). No haplotype combinations showed a statistically significant difference (P > 0.05). ConclusionThe genetic polymorphisms investigated were not associated with dental pulp calcification in orthodontic patients. Further studies should investigate other polymorphisms in genes encoding growth factors.

Distributions of MICA and MICB Alleles Typed by Amplicon-Based Next-Generation Sequencing in South Koreans.

Major histocompatibility complex class I chain-related genes A and B (MICA and MICB) play a role as ligands in activating the NKG2D receptor expressed in natural killer cells, γδ T-cells and αβ CD8 T-cells and have been defined in human diseases and haematopoietic stem cell transplantation (HSCT). MICA and MICB alleles were genotyped at the three-field level by amplicon-based next-generation sequencing (NGS) using a MiSeqDx system and compared with the results from previous studies in healthy South Korean donors. Exons 2-5 of MICA and exons 2-4 of MICB were amplified using a multiplex polymerase chain reaction (PCR). Sequence reads of ≥ 51 depth counts were consistently obtained for each sample exon, and target exons were determined to match reference sequences contained in the IPD-IMGT/HLA database. MICA and MICB alleles were tested using exon combinations. The program was designed to recognise specific sequences and discriminate between the MICA*008:01:01/*027 alleles. A total of 22 alleles were found in MICA and MICB. We observed 1 HLA-C ~ HLA-B ~ MICA ~ MICB ~ HLA-DRB1 haplotype with significant linkage disequilibrium between alleles at all neighbouring HLA loci. These results are consistent with previous microarray results. Genotyping of MICA and MICB was possible using 11-loci HLA genes. We updated the distribution of MICA and MICB based on three-field allele and haplotype frequencies containing linkage disequilibrium in South Koreans using amplicon-based NGS. These data suggest that high-resolution MICA and MICB typing data obtained using NGS may aid in performing HSCT and disease association studies.

Assessing the performance of multi-InDel panels for human identification among admixed Brazilians

Insertion/deletion polymorphisms, or InDels, are widely present in the human genome. They have been considered as potential markers for forensic analysis because they can be genotyped using the CE platform and compatible typing techniques used in forensic laboratories. Additionally, InDels have lower mutation rates and often short amplicon sizes, making them ideal for detecting degraded samples. However, most InDels are bi-allelic; therefore, their discrimination power is relatively low. A new set of genetic marker called multi-InDels was reported to improve InDel's informativeness. Multi-InDel markers are generally designated as microhaplotypes encompassing two or more InDels within a short distance, usually less than 200bp. In this study, we evaluated the applicability of three previously proposed panels of multi-InDel markers, designed for Asian populations, for human identification in Brazil. We assessed all the multi-InDel markers using high-coverage whole-genome sequencing data from a census-based cohort of 1,171 Brazilians residing in São Paulo, the largest Brazilian capital. The results showed that most markers are informative for Brazilian individuals since they present more than three frequent haplotypes with different sizes. However, most markers are prone to amplification/sequencing errors due to repetitive or low-complexity regions. Among the tested panels, the one from Huang et al. (2014) is the most promising for forensic use in Brazil, with a combined match probability and cumulative power of exclusion of 4.92 ×10-14 and 0.9991, respectively. Nevertheless, these values are low compared to the ones obtained with CODIS STRs (short tandem repeats) and larger SNP (single nucleotide polymorphisms) panels. Therefore, new attempts to scan the human genome for highly polymorphic multi-InDel markers are still necessary to obtain a suitable panel of multi-InDels for worldwide populations.

Investigation of the relationships between eNOS T786C, G894T, intron 4 VNTR (4a/b) gene variations and prostate cancer development and progression

BackgroundThis study aimed to investigate the relationships between eNOS T786C, G894T, intron 4 VNTR (4a/b) gene variations and prostate cancer development and progression. Materials and methodsThis study included 88 patients diagnosed with prostate cancer and 91 healthy controls. Polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) methods were used to determine the genotype distributions of eNOS T786C, G894T, intron 4 VNTR (4a/b) gene variations. ResultsIn our study, the CC homozygous genotype of eNOS T786C gene variation was determined to be significantly higher in the prostate cancer patient group compared to the healthy control group (OR: 2.343, 95%Cl: 0.990–5.544, p = 0.026), while the CT heterozygous genotype was found to be significantly higher in the healthy control group compared to the prostate cancer patient group was found to be significantly higher (OR: 0.589, 95%Cl: 0.325–1.068, p = 0.041). In addition, while the TT homozygous genotype of the eNOS G894T gene variation was found to be significantly higher in the prostate cancer patient group compared to the healthy control group (OR: 9.068, 95%Cl: 4.396–18.777, p < 0.001), the GT heterozygous genotype was found to be significantly higher in the healthy control group compared to the prostate cancer patient group was determined significantly higher (OR: 0.227, 95%Cl: 0.121–0.427, p < 0.001). For eNOS (4VNTR (4a/b) - G894T) gene variations, aa-TT (p = 0.042) and bb-TT (p < 0.001) haplotype frequencies were significantly higher in the prostate cancer patient group, while aa-GT (p = 0.017), bb-GG (p = 0.049) and bb-GT (p < 0.001) haplotype frequencies were found to be significantly higher in the healthy control group. For eNOS (4VNTR (4a/b) - T786C) gene variations, the bb-CC haplotype frequency was determined to be significantly higher in the patient group (p = 0.049), while the bb-CT haplotype frequency was determined to be significantly higher in the control group (p = 0.008). For eNOS (T786C -G894T) gene variations, TT-TT (p < 0.001) and CC-TT (p = 0.025) haplotype frequencies were found to be significantly higher in the patient group. On the other hand, TT-GT (p = 0.002) and CT-GT (p < 0.001) haplotype frequencies were determined to be significantly higher in the control group. The aa genotype of the intron 4 VNTR (4a/b) gene variation was determined to be significantly higher at Gleason score ≥7 compared to Gleason score <7 (OR: 0.184, 95%Cl: 0.050–0.677, p = 0.005). PSA levels were determined significantly higher in patients with Gleason score 7 and above (p = 0.008). The risk of developing prostate cancer was found to be significantly higher in patients carrying the CC homozygous mutant genotype of the eNOS T786C gene variation (p = 0.024) and in patients carrying the TT homozygous genotype of the G894T gene variation (p = 0.021). ConclusionsIn our study, the CC homozygous genotype of the eNOS T786C gene variation was determined as a genetic risk factor for the development of prostate cancer, while the CT heterozygous genotype was determined as a protective factor against prostate cancer. For the eNOS G894T gene variation, the TT homozygous genotype was determined as a genetic risk factor for the development of prostate cancer, while the GT heterozygous genotype was determined as a protective factor against prostate cancer. Additionally, for eNOS (4VNTR (4a/b) - G894T) gene variations, aa-TT and bb-TT haplotypes have been identified as genetic risk factors for the development of prostate cancer, while aa-GT, bb-GG and bb-GT haplotypes have been identified as protective factors against the disease has been determined. For eNOS (4VNTR (4a/b) - T786C) gene variations, the bb-CC haplotype was determined as a genetic risk factor in the development of prostate cancer, while the bb-CT haplotype was determined as a protective factor against the disease. TT-TT and CC-TT haplotypes for eNOS (T786C -G894T) gene variations have been identified as genetic risk factors for the development of prostate cancer. In contrast, TT-GT and CT-GT haplotypes were found to be protective factors against the disease. The aa genotype of the intron 4 VNTR (4a/b) gene variation has also been identified as an important genetic risk factor in prostate cancer progression. Significantly increased PSA levels in patients with Gleason score 7 and above, and significantly increased PSA levels in patients carrying the CC and TT homozygous mutant genotype for T786C and G894T gene variations were determined as important risk factors. It is thought that the genetic biomarkers in our study may play a role as personalized therapeutic agents in slowing down the development of prostate cancer, increasing the effectiveness of treatment in prostate cancer, affecting the responses to drugs that regulate NO signaling, predetermining genetic predisposition to prostate cancer, and risk assessment in patients with prostate cancer.

The battle of the sexes in humans is highly polygenic

Sex-differential selection (SDS), which occurs when the fitness effects of alleles differ between males and females, can have profound impacts on the maintenance of genetic variation, disease risk, and other key aspects of natural populations. Because the sexes mix their autosomal genomes each generation, quantifying SDS is not possible using conventional population genetic approaches. Here, we introduce a method that exploits subtle sex differences in haplotype frequencies resulting from SDS acting in the current generation. Using data from 300K individuals in the UK Biobank, we estimate the strength of SDS throughout the genome. While only a handful of loci under SDS are individually significant, we uncover highly polygenic signals of genome-wide SDS for both viability and fecundity. Selection coefficients of [Formula: see text] may be typical. Despite its ubiquity, SDS may impose a mortality load of less than 1%. An interesting life-history tradeoff emerges: Alleles that increase viability more strongly in females than males tend to increase fecundity more strongly in males than in females. Finally, we find marginal evidence of SDS on fecundity acting on alleles affecting arm fat-free mass. Taken together, our findings connect the long-standing evidence of SDS acting on human phenotypes with its impact on the genome.

Population data for 12 X-STRs loci in Malaysian Malay and Chinese populations

The utilization of X-chromosome short tandem repeats (X-STRs) for human identification particularly in resolving complex kinship cases has been advocated. Since, forensic statistical parameters vary among different populations, and because the X-STRs population data representing the diverse population of Peninsular Malaysia remain unavailable, the specific attempt reported here for the Malays (n = 224) and Chinese (n = 201) populations appears forensically relevant to support the evidential value of the 12 X-STRs markers for human identification in Malaysia. Results derived from the Qiagen Investigator® Argus X-12 kit revealed that DXS10135 as the most polymorphic locus with high genetic diversity, polymorphic information content, heterozygosity as well as power of exclusion. Based on allele frequencies, the combined power of discrimination as well as the mean exclusion chance (MECKrüger, MECKishida, MECDesmarais and MECDesmaraisDuo) values for the Malays and Chinese were individually ≥0.999995532964908. As for the combined power of discrimination as well as the mean exclusion chance (MECKrüger, MECKishida, MECDesmarais and MECDesmaraisDuo) calculated based on haplotype frequencies, the values were ≥0.9999986410567 for the Malays and Chinese populations. In addition, results from the genetic distance, neighbor-joining phylogenetic tree and principal component analysis revealed close biogeographical distributions of the studied populations with other South East Asian populations. Hence, the utilization of the X-STRs data for identifying individuals among the Malays and Chinese populations in Peninsular Malaysia for forensic application appears as highly supported.

Associations between end stage renal disease and HLA polymorphisms in the Guangxi Zhuang population

To investigate the genetic relationship between end stage renal disease (ESRD) and human leukocyte antigen (HLA) alleles in the Guangxi Zhuang population. We performed polymerase chain reaction reversed sequence-specific oligonucleotide (PCR-rSSO) in 325 patients with ESRD and genotyped the HLA-A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 loci. The direct counting method was used to determine the frequencies of HLA alleles, and Arlequin software (version 3.5.2.2) was used for haplotypic frequency analyses to compare the included ESRD patients with 350 healthy donors from the Guangxi Zhuang population. In our study, 120 HLA alleles, 284 HLA-A-B-DRB1 haplotypes, and 332 HLA-A-C-B-DRB1-DQB1 haplotypes were detected. We found that only A*11:01-B*15:02-DRB1*12:02 had a positive association with ESRD (P = 0.001, Pc = 0.020, OR = 3.106, 95% CI = 1.497–6.446) after Bonferroni correction; thus, individuals with this haplotype may be susceptible to ESRD. A*11:01-B*15:02-DRB1*12:02 is a potentially valuable haplotype for evaluating the risk of ESRD in the Guangxi Zhuang population.

Calculated Panel Reactive Antibody for an Organ-Sharing Zone: Concept and Execution Based on Data from North Kerala

Background Calculated-PRA (CPRA) is derived by virtually matching a recipient’s antibody profile against HLA antigens of a representative donor pool of a geographical region. Materials and Methods An android application–based CPRA calculator was created from HLA typing data (A/B/DR loci) of 712 consecutive living donors spanning over last 10 years from an organ-sharing region in Kerala. Only an open-source software was used. Results Our HLA data, compared with the National Marrow Donor Program (NMDP) 2011 database, show that the most common haplotype frequencies show comparable positions in order of prevalence. Available online PRA calculators like OPTN and Canadian CPRA show significant differences in PRA estimation when used in our population. This calculator provides a more accurate and realistic estimate of sensitization against the representative donor pool. Conclusion This CPRA tool can be customized for any allocation region using portable open-source software. The donor pool can be updated continually by populating data from multiple regional centers.

Current Landscape of iPSC Haplobanks.

The use of allogeneic induced pluripotent stem cell (iPSC)-derived cell therapies for regenerative medicine offers an affordable and realistic alternative to producing individual iPSC lines for each patient in need. Human Leukocyte Antigens (HLA)-homozygous iPSCs matched in hemi-similarity could provide cell therapies with reduced immune rejection covering a wide range of the population with a few iPSC lines. Several banks of HLA-homozygous iPSCs (haplobanks) have been established worldwide or are underway, to provide clinical grade starting material for cell therapies covering the most frequent HLA haplotypes for certain populations. Harmonizing quality standards among haplobanks and creating a global registry could minimize the collective effort and provide a much wider access to HLA-compatible cell therapies for patients with less frequent haplotypes. In this review we present all the current haplobank initiatives and their potential benefits for the global population.