Hardy-Weinberg Equilibrium Test Research Articles

Does PhenoAge acceleration impact adverse outcomes following major surgery (rehospitalization or death)? A genome-wide association study and mendelian randomisation

Abstract Background Biological aging reflects the state of an individual's cellular and molecular function, and is distinct from chronological age; which reflects the passage of time[1]. Validated measures of biological aging, such as Phenotypic aging (PhenoAge) estimated from nine routine clinical biomarkers, have been associated with increased risk of age-related diseases and mortality in cohort studies[2]. However, the potential causal relationship between them remains unclear. In this study, we aim to identify genetic variants associated with PhenoAge Acceleration (PhenoAgeAccl) and adverse outcome after surgery (rehospitalisation or death within 365-days] and assess the causal relationship between these two phenotypes using Mendelian Randomization framework. Objectives -Perform a genome-wide association study(GWAS) on adverse outcomes following major surgery. -Assess the potential causal relationship between PhenoAgeAccl and adverse outcomes following major surgery using Mendelian randomization analysis. Methods We conducted a GWAS via plink using participants from the UKBiobank (Application 77596) to generate summary statistics for 6509 participants who had undergone major surgery within 365 days of their baseline assessment date(3). For quality control, SNPs were excluded if they didn't meet the following criteria: (1) imputation information score <0.3 (2) minor allele frequency <1%, (3) Hardy–Weinberg equilibrium test p-value significant at the Bonferroni-corrected level. Summary statistics for PhenoAgeAccl was obtained from a previous GWAS of European descents[4]. Gene enrichment analysis was performed using Multi-marker Analysis of GenoMic Annotation (MAGMA) in Functional Mapping and Annotation (FUMA). Then, genetic instruments for PhenoAgeAccl and adverse outcomes following surgery were identified to conduct a summary-based Mendelian Randomisation [Assumptions are listed in Figure 1]. Results GWAS for adverse outcomes following major surgery identified 3 lead SNPs (rs1360618, rs11848297, rs7978) [Figure 2]. Gene-set analysis showed enrichment in the immune system, cell migration, fear response, and iron metabolism. For PhenoAge Acceleration, gene-set analysis showed enrichment in immune system, and cell signalling pathways. 17 SNPs were selected which were used for the Two-Sample MR. We found no causal relationship, as the beta coefficient for Inverse variance weighted was -0.308 [standard error - 0.075, p=0.68]. For every 5-year increase in PhenoAge compared to chronological age, the risk of emergency re-hospitalisation or death increased by 21% (HR 1.16 – 1.3, p < 0.001). Conclusion Gene-set analysis for adverse outcomes following major surgery showed enrichment in immune system, iron metabolism, and fear response which have all recently been associated with mortality post-surgery in cohort studies(4,5). No causal relationship between PhenoAgeAccel and mortality post-surgery was established.Mendelian Randomisation assumptionsManhattan plot adverse-outcomes post-sur

Interleukin-6 (-174G/C), Interleukin-1β (-511 C/T), and Apolipoprotein B-100 (2488 C/T) Gene Polymorphism in Pre-Eclampsia.

Background and objectives: Pre-eclampsia (PE) is a pregnancy-specific condition characterized by significant health risks for pregnant women worldwide due to its status as a multi-organ disorder. High blood pressure (hypertension) with or without proteinuria is usually considered an initial clinical sign of PE. The pathogenesis of pre-eclampsia is highly complex and likely involves multiple factors, including poorly developed uterine spiral arterioles, immunological issues, placental ischemia or infarction, and genetic abnormalities. Inflammatory cytokine production, regulated by cytokine gene polymorphisms, is one of the factors likely contributing to the development of PE. The present study aimed to assess IL-6, IL-1β, and Apo B-100 gene polymorphism and to evaluate the association of these polymorphisms with PE. Materials and Methods: This cross-sectional observational study involved 99 participants aged 16 to 45 years from Bahawal Victoria Hospital Bahawalpur, Punjab, Pakistan. The participants were divided into three groups: Group 1 (PE with severe hypertension), Group 2 (PE with hypertension), and Group 3 (control), each comprising 33 individuals. Maternal blood samples were collected, DNA was extracted, and molecular genetic analysis of the IL-6, IL-1β, and Apo B-100 genes was performed using the PCR-RFLP method. Allelic frequencies were compared, and statistical analysis was conducted using SPSS 25, applying the Hardy-Weinberg equation and chi-square test to evaluate the results. Results: There are differences in the distribution of allelic frequencies for IL-6 -174G/C (CC, GC, GG), IL-1β-511C/T (CC, CT, TT), and Apo B-100 2488 C/T (CC, CT, TT) between pre-eclamptic patients and the control group. The analysis using the Hardy-Weinberg equilibrium and chi-square test showed an association between the IL-6-174 G/C polymorphism and the severity of pre-eclampsia. Conclusions: The polymorphisms of the IL-6, IL-1β, and Apo B-100 genes revealed different alleles. The IL-6 gene alone was found to be in disequilibrium according to the Hardy-Weinberg equation, indicating a potential link to the severity of pre-eclampsia in the population studied.

Hardy-Weinberg Equilibrium in Meta-Analysis Studies and Large-Scale Genomic Sequencing Era.

The Hardy-Weinberg Equilibrium (HWE) is a fundamental principle employed in the analysis of genetic data, encompassing studies of meta-analysis and genomic sequencing. It has been demonstrated that HWE possesses the property of transitivity, wherein a multi-allelic polymorphism in equilibrium will persist in its equilibrium state even when alleles are deleted or combined. Nonetheless, the practice of filtering loci that do not adhere to HWE has been observed to impact the inference of population genetics within RADseq datasets. In response to this concern, the Robust Unified Test for HWE (RUTH) has been devised to consider population structure and genotype uncertainty, thereby offering a more precise evaluation of the quality of genotype data. Furthermore, deviations from HWE, such as extreme heterozygote excess, can be effectively utilized to identify genotyping errors or to pinpoint the presence of rare recessive disease-causing variants. In summary, it is evident that HWE holds immense significance in the field of genetic analysis, and its application in meta-analysis studies and genomic sequencing can yield invaluable insights into the intricacies of population structure and the genetics of diseases.

Vascular endothelial growth factor I/D variant and postmenopausal osteoporosis risk in the Turkish population

Introduction Postmenopausal osteoporosis (PMOP) is a common metabolic bone disorder manifested by low bone mineral density and increased fracture risks in postmenopausal women. Vascular endothelial growth factor (VEGF) has been shown to play an important role in bone formation. In this study, we investigated the potential association between the VEGF insertion/deletion (I/D) variant (rs35569394) and PMOP in a cohort of postmenopausal Turkish women. Methods This study included 300 women, including 150 PMOP patients and 150 healthy postmenopausal women. A T score was used in the diagnosis of OP. DNA was extracted from all subjects. The VEGF I/D polymorphism was analyzed by the PCR method. The Hardy-Weinberg equilibrium (HWE) test and odds ratio (OR) were analyzed, considering CI 95% and p ≤ 0.05. Results The mean age of patients aged between 40 and 74 was 60.32 ± 8.65. The frequency of the I/I, I/D, and D/D genotypes was 7.34% versus 6.66%; 67.33% versus 65.34%; and 25.33% versus 28%, in patients and the control group, respectively. The allele frequencies were I: 41% (patients) and 39.4% (controls); D: 59% (patients) and 60.66% (controls). There was no statistically significant difference in the VEGF − 2549 I/D allele and genotype distribution between patients with PMOP and control subjects (p = 0.349, p = 0.864, respectively). Conclusion Our results showed that the VEGF I/D variant was not a significant factor in the development of PMOP in a Turkish population sample. These findings need confirmation in other ethnic populations.

THE POTENTIAL ROLE OF CYP2D6∗10(C.100 C>T) GENE POLYMORPHISM IN KIDNEY INJURY OF PATIENTS WITH HYPERTENSION COMPLICATED WITH NON-ELEVATED CYSTATIN C

Objective: This study aims to investigate the potential role of CYP2D6∗10 (c.100 c>t) gene polymorphism in renal function injury among hypertensive patients without elevated cystatin C. Design and method: A cohort of hypertensive patients without elevated cystatin C was recruited, and the CYP2D6∗10 genotype was analyzed. The objective was to evaluate the association between CYP2D6∗10 gene polymorphism and renal function injury by comparing patients with different genotypes. Genetic equilibrium was assessed using the Hardy-Weinberg equilibrium test. Polymorphic genotype frequencies between case and control groups were examined using the Chi-square test, with statistical significance set at p<0.05. Results: Among the hypertensive patients in the study, a significant correlation was observed between CYP2D6∗10 genotype and renal function injury (p<0.05) in codominant model and super-dominant model. Patients with the CYP2D6∗10 genotype exhibited more severe renal function damage. Conclusions: This study proposes CYP2D610 gene polymorphism as a potential predictor of renal function injury in hypertensive patients with normal cystatin C levels. Further research is crucial to validate this association and delve into the specific mechanisms through which the CYP2D610 genotype influences renal function injury in hypertensive individuals.

WHOLE GENOME SURVIVAL ANALYSIS OF 144,286 PEOPLE FROM UK BIOBANK IDENTIFIES NOVEL LOCI ASSOCIATED WITH BLOOD PRESSURE

Objective: Hypertension is a leading heritable cardiovascular risk factor worldwide associated with over 1000 common single nucleotide polymorphisms (SNPs). However, these SNPs only explain about half of its heritability, suggesting the presence of yet-to-be-identified genetic factors influencing this trait. This study used longitudinal UK Biobank data to discover novel genetic loci related to hypertension, addressing limitations in cross-sectional GWAS approaches. Design and method: The study sourced disease outcomes from diverse records (in-patient, self-reported, primary care, death registry, and time-to-event data) within the UK Biobank. It spanned from October 2010 (the last participant's enrolment) to the latest ’Essential hypertension’ diagnosis on October 2022, encompassing 12 years of follow-up. Utilizing whole genome sequence (WGS) data, our analysis employed the R package ‘SPACox’ for a genome-wide survival analysis, integrating Age, Age2, Sex, BMI, and 10 principal components as covariates. The WGS data underwent rigorous quality control (QC) measures, excluding SNPs with low call rates(<0.90), Hardy–Weinberg equilibrium test P-values<1×10-15, or minor allele frequencies less than 0.01. Results: The analysis included 21,248 hypertension cases and 123,038 controls, totalling 144,286 participants, with 58.0% women (average age - 55.3±0.0279 years). Post-genotype QC, 6,319,822 million SNPs underwent analysis, revealing 31 variants (P-value<5×10–08), including 29 new SNPs—15 in Fibrillin-2 (FBN2) and 2 in Junctophilin-2 (JPH2) genes. Subsequent Mendelian randomization studies, employing two identified SNPs (rs17677724 and rs1014754), revealed a genetically induced decrease in heart FBN2 expression and an increase in adrenal gland JPH2 expression was causally linked to increased blood pressure (P-Value =1.66×10-06, 3.19×10-06). Thereafter, FinnGen dataset PheWAS analysis reaffirmed rs17677724's (Beta = 0.492, P = 7.4×10-09) and rs1014754's (Beta = 0.0225, P = 4.8×10-05) positive association to hypertension, among 2,727 traits assessed in 377,277 individuals. Lastly, rs1014754 associated positively with kallistatin (Beta = 0.031, P = 0.0225) while rs17677724 negatively associated with Renin (Beta = -0.036, P = 0.0435), in the Fenland study (10,708 participants, 10.2 million variants, 4775 protein targets), suggesting a counter-regulatory response to high blood pressure. Conclusions: Our genome-wide time-to-event analysis unveils new genetic loci associated with hypertension, illuminating their role in hypertension via FBN2 and JPH2 expression.

Aquaculture Performance and Genetic Diversity of a New [(Crassostrea hongkongensis ♀ × C. gigas ♂) ♂ × C. hongkongensis ♀] Variety of the Oyster "South China No. 1" in Beibu Gulf, China.

Crassostrea hongkongensis is an economically important bivalve found in various parts of the South China Sea. A new interspecific backcross ([(Crassostrea hongkongensis ♀ × C. gigas ♂) ♂ × C. hongkongensis ♀]) variety was bred by the South China Sea Institute of Oceanology which named "South China No. 1". This study aims to explore the effects of stocking density on the growth performance of "South China No. 1", compared their growth performance and genetic diversity to C. hongkongensis, and found the best place breeding site for "South China No. 1" in Beibu Gulf. The results showed that stocking a density of 20 oysters/substrate can significantly increase the shell height, shell width, total weight, survival rate, daily shell height gain and daily body mass gain. It was found that the shell height and total weight of "South China No. 1" cultured in Fangchenggang were significantly higher than that of those in Beihai and Qinzhou from September 2018 to November 2018. Similarly, the shell width of oysters in Fangchenggang and Qinzhou was also significantly higher in September 2018, and the interaction between site and stocking density had significant effects on the shell width in March 2018 and November 2018. In addition, the shell height and shell width of "South China No. 1" were significantly higher than that of C. hongkongensis in all three sites. At all three sites, the phytoplankton community structure was mostly dominated by Bacillariophyta. In the Hardy-Weinberg equilibrium test, for the seven populations and ten microsatellites, in 10 of the 70 groups, the segregation distortion was significant. These results suggest that a stocking density of 20 oysters/substrate can promote the shell height, shell width and total weight of "South China No. 1" in Beibu Gulf, China. "South China No. 1" has better growth performance compared with C. hongkongensis. Fangchenggang is a suitable place to cultivate the "South China No. 1" breed according to the total weight and sum of all algal genus abundances. The results of this study can be used as a reference to further understand the stocking density and genetic diversity of the "South China No. 1" breed in Beibu Gulf, China.

Genetic Diversity in Katchaikatty Sheep based on Microsatellites Polymorphism

Background: Sheep is one of the important species of livestock in India contributing to meat production. India has 44 distinct breeds of sheep, out of which 10 are found in Tamil Nadu. The present study describes the molecular characterization of recently registered breed of sheep - Katchaikatty sheep, genetic variability and genetic structure of the population by microsatellite marker analyses. Methods: DNA from 50 unrelated Katchaikatty sheep was amplified with 25 FAO recommended fluorescent tagged ovine-specific microsatellite markers and genotyped on an automated Genetic Analyzer. In each locus, observed (no) and effective number of microsatellite alleles (ne), allele frequencies, observed (Ho) and expected (He) heterozygosity and heterozygosity deficit estimate (FIS), polymorphism information content (PIC) and Chi-square (χ2) test for Hardy-Weinberg equilibrium (HWE) were assessed. Mode-shift analyses were performed. Result: The study revealed a total of 144 alleles across all the loci. The number of alleles at each locus varied from one to 10 with a mean of 5.76 alleles. The PIC values in the microsatellite loci ranged from 0.34 (OarAE129) to 0.83 (OarFCB48) with an average of 0.59, which showed a high genetic polymorphism. Six out of 25 microsatellite loci studied were in Hardy-Weinberg equilibrium and 19/25 loci showed positive FIS values. The overall mean observed and expected heterozygosity were 0.50 and 0.65 respectively and the estimates elucidated a substantial genetic variability in Katchaikatty sheep population. Mode shift analysis revealed a normal L-shaped curve, describing that the Katchaikatty population had not experienced any genetic bottleneck and remained in mutation-drift equilibrium.

Forensic autosomal and gonosomal short tandem repeat marker reference database for populations in Burkina Faso

Tandem repeat genetic profiles used in forensic applications varies between populations. Despite the diversity and security issues in the Sahel that require the identification of victims (soldiers and civilians), Burkina Faso (BF) remains understudied. To fill this information gap, 396 unrelated individuals from BF were genotyped using a MICROREADER 21 ID System kit. All 20 short tandem repeat (STR) loci tested passed the Hardy–Weinberg equilibrium (HWE) test. The combined powers of exclusion for duos (CPE duos) and trios (CPE trios) for the 20 tested loci were 0.9999998 and 0.9999307, respectively. The probability that two individuals would share the same DNA profiles among the BF population was 9.80898 × 10–26. For the X-chromosome STR analysis, 292 individuals were included in this study using a MICROREADER 19X Direct ID System kit. Among the 19 loci, no significant deviations from HWE test were observed in female samples after Bonferroni correction (p < 0.05/19 = 0.0026), except for loci GATA165B12 and DXS7423. The results showed that the combined power of exclusion (CPE) and the combined power of discrimination in females (CPDF) and males (CPDM) were 0.999999760893, 0.999999999992, and 1, respectively. Comparison with other African sub-populations showed that geographical proximity is a reliable indicator of genetic relatedness.

Investigation of cosmopolitan and local Italian beef cattle breeds uncover common patterns of heterozygosity

The analysis of livestock heterozygosity is less common compared to the study of homozygous patterns. Heterozygous-Rich Regions (HRRs) may harbor significant loci for functional traits such as immune response, survival rate, and fertility. For this reason, this study was conducted to investigate and characterize the heterozygosity patterns of four beef cattle breeds, which included two cosmopolitan breeds (Limousine and Charolaise) and two local breeds (Sarda and Sardo Bruna). Our analysis identified regions with a high degree of heterozygosity using a consecutive runs approach, the Tajima D test, nucleotide diversity estimation, and Hardy Weinberg equilibrium test. These regions exhibited recurrent heterozygosity peaks and were consistently found on specific chromosomes across all breeds, specifically autosomes 15, 16, 20, and 23. The cosmopolitan and Sardo Bruna breeds also displayed peaks on autosomes 2 and 21, respectively. Thirty-five top runs shared by more than 25% of the populations were identified. These genomic fragments encompassed 18 genes, two of which are directly linked to male fertility, while four are associated with lactation. Two other genes play roles in survival and immune response. Our study also detected a region related to growth and carcass traits in Limousine breed. Our analysis of heterozygosity-rich regions revealed particular segments of the cattle genome linked to various functional traits. It appears that balancing selection is occurring in specific regions within the four examined breeds, and unexpectedly, they are common across cosmopolitan and local breeds. The genes identified hold potential for applications in breeding programs and conservation studies to investigate the phenotypes associated with these heterozygous genotypes. In addition, Tajima D test, Nucleotide diversity, and Hardy Weinberg equilibrium test confirmed the presence of heterozygous fragments found with Heterozygous-Rich Regions analysis.

Implications of the Codominance Model for Hardy-Weinberg Testing in Genetic Association Studies

Introduction: The standard way of using tests for compatibility of genetic markers with the Hardy-Weinberg equilibrium (HWE) assumption as a means of quality control in genetic association studies (GAS) is to carry out this step of preliminary data analysis with the sample of non-diseased individuals only. We show that this strategy has no rational basis whenever the genotype-phenotype relation for a marker under consideration satisfies the assumption of codominance. Methods: The justification of this statement is obtained through rigorous analytical arguments. Results: The key result of the paper is that there holds the following proposition: under the codominance model, the genotype distribution of a diallelic marker is in HWE among the controls if and only if the same is true for the cases. Conclusion: The major practical consequence of that theoretical result is that under the codominance model, testing for HWE should be done both for cases and controls aiming to establish the combined (intersection) hypothesis of compatibility of both underlying genotype distributions with the HWE assumption. A particularly useful procedure serving this purpose is obtained through applying the confidence-interval inclusion rule derived by Wellek, Goddard, and Ziegler (Biom J. 2010; 52:253–270) to both samples separately and combining these two tests by means of the intersection-union principle.

Polymorphism of the Forkhead box-O3 (FOXO3) Longevity Gene rs2802292 and senescence-associated secretory phenotype (SASP) in Indonesian Elderly Population

BACKGROUND: Forkhead box O3 (FOXO3) is a transcription factor that regulates stress resistance, metabolism, cell cycle, and apoptosis. Several studies exhibited the association of the FOXO3 polymorphism rs2802292 with human longevity and protects individuals from degenerative diseases. The emergence of degenerative diseases in the elderly is associated with the accumulation of senescent cells that secrete a secretome known as a senescence-associated secretory phenotype (SASP) consists of several cytokines, chemokines, growth factors, proteases. OBJECTIVE: The aim of this research was to analysis polymorphism of FOXO3 gene rs2802292 G-allele and its impact to the SASP by measuring IL-1α, IL-6, IL-8, and IL-10 in Indonesian elderly populations. METHODS: This study was conducted on 92 elderly subjects living at Jakarta. DNA was isolated from the whole blood then continued with PCR and sequencing for FOXO3 rs2802292 analysis. SASP was analyzed from the plasma using Luminex. Statistical analysis was performed using ANOVA and Kruskal Wallis. RESULTS: The results showed that FOXO3 rs2802292 was detected in Indonesian elderly population as follows GG, GT, TT genotype frequencies were 17.4 %, 42.4 % and 40.2 % respectively. Meanwhile, G and T allele frequencies based on the Hardy-Weinberg equilibrium test were 0.385 and 0.615 respectively. GG genotype was significantly found in subjects with longevity. Nevertheless, SASP analysis was found no significant differences both among GG, GT, TT genotypes. CONCLUSION: The frequency of FOXO3 rs2802292 G-allele in Indonesian elderly population was 0.385 and significantly detected in subjects with longevity. However, the FOXO3 rs2802292 polymorphism did not affect cytokines level as the component of SASP.

Towards pharmacogenomics-guided tuberculosis (TB) therapy: N-acetyltransferase-2 genotypes among TB-infected Kenyans of mixed ethnicity

BackgroundThough persons of African descent have one of the widest genetic variability, genetic polymorphisms of drug-metabolising enzymes such as N-Acetyltransferase-2 (NAT2) are understudied. This study aimed to identify prevalent NAT2 single nucleotide polymorphisms (SNPs) and infer their potential effects on enzyme function among Kenyan volunteers with tuberculosis (TB) infection. Genotypic distribution at each SNP and non-random association of alleles were evaluated by testing for Hardy-Weinberg Equilibrium (HWE) and Linkage Disequilibrium (LD).MethodsWe isolated genomic DNA from cryopreserved Peripheral Blood Mononuclear Cells of 79 volunteers. We amplified the protein-coding region of the NAT2 gene by polymerase chain reaction (PCR) and sequenced PCR products using the Sanger sequencing method. Sequencing reads were mapped and aligned to the NAT2 reference using the Geneious software (Auckland, New Zealand). Statistical analyses were performed using RStudio version 4.3.2 (2023.09.1 + 494).ResultsThe most frequent haplotype was the wild type NAT2*4 (37%). Five genetic variants: 282C > T (NAT2*13), 341 T > C (NAT2*5), 803A > G (NAT2*12), 590G > A (NAT2*6) and 481C > T (NAT2*11) were observed with allele frequencies of 29%, 18%, 6%, 6%, and 4% respectively. According to the bimodal distribution of acetylation activity, the predicted phenotype was 76% rapid (mainly consisting of the wildtype NAT2*4 and the NAT2*13A variant). A higher proportion of rapid acetylators were female, 72% vs 28% male (p = 0.022, odds ratio [OR] 3.48, 95% confidence interval [CI] 1.21 to 10.48). All variants were in HWE. NAT2 341 T > C was in strong complete LD with the 590G > A variant (D′ = 1.0, r2 = − 0.39) but not complete LD with the 282C > T variant (D′ = 0.94, r2 = − 0.54).ConclusionThe rapid acetylation haplotypes predominated. Despite the LD observed, none of the SNPs could be termed tag SNP. This study adds to the genetic characterisation data of African populations at NAT2, which may be useful for developing relevant pharmacogenomic tools for TB therapy. To support optimised, pharmacogenomics-guided TB therapy, we recommend genotype-phenotype studies, including studies designed to explore gender-associated differences.

Application of a 24-SNP Multiplex Genotyping Assay System for Phenotypic Identification of Fujian Han Population.

This study aimed to evaluate the utility of 24 single nucleotide polymorphism (SNP) loci associated with iris color and hair color in phenotypic identification of the Han Chinese population in Fujian Province. The selected SNPs, known for their strong correlation with specific human phenotypic features, provide valuable reference data for developing a molecular phenotypic identification system. A multiplex genotyping assay system was established with primers for the 24 SNPs linked to iris color and hair color synthesized based on existing literature. In total, 235 unrelated individuals of Han Chinese ethnicity in Fujian Province were included in this study. PowerStats v12 was employed to calculate forensic parameters associated with the 24 SNP loci, including gene frequencies, genotype frequencies, minor allele frequencies, discrimination power (DP), polymorphism information content (PIC), and observed heterozygosity (Ho). Hardy-Weinberg equilibrium tests were conducted for each locus. The SNP genotyping results were uploaded to the HIrisPlex model (https://HIrisPlex.erasmusmc.nl/) to predict iris and hair colors, and the inferred results were compared with manually assessed images. The accuracy of pigment phenotype inference was evaluated by using ROC curves in SPSS 26.0 software. The accuracy rates of inferring brown iris and black hair phenotypes were 99.6% and 99.5%. The area under the curve (AUC) values were 0.923 and 0.980, respectively. The 24 SNP loci demonstrated high accuracy in inferring iris color and hair color; it seems to be a useful tool for forensic phenotypic identification and anthropological or evolutionary applications. Establishment of suitable pigment classification criteria and optimized prediction models is based on revealing more phenotypic genetic markers.

DGAT1 Gene Polymorphism in Morkaraman and Tushin

This study aims to investigate the polymorphism of the Diacylglycerol acyltransferase1 (DGAT1) gene locus in 105 Morkaraman and 65 Tushin lambs to determine the distribution of genotype and allele frequencies of lambs in terms of related genes. DGAT1/Alu1 gene polymorphism was defined by using the PCR-RFLP method in the DNAs isolated from hair samples taken from Morkaraman and Tushin lambs used in this study. PCR- RFLP products were run in an electrophoresis medium and the results were visualized on an ultraviolet (UV) transluminator. When the population was examined in terms of allele frequencies, it was defined that the C allele and the T allele were 0.72% and 0.28% for the Morkaraman, and 0.71% and 0.29% for Tushin, respectively. The CC, CT, and TT genotype frequencies of the DGAT1 gene in the population were found to be 53.3%, 38.1%, and 8.6% for the Morkaraman and 50.8%, 40.0%, and 9.2% for the Tushin, respectively. In the Hardy-Weinberg genetic equilibrium test, it was observed that the distribution of genotype frequencies was in balance (P&gt;0.05) in the population. It has been defined that the genotype and allele frequencies determined in terms of DGAT1 gene polymorphism may be found to be sufficient to reveal the genotype diversity of the breeds. The genotype and allele frequencies determined in terms of DGAT1 gene polymorphism were sufficient to reveal the genotype diversity of the breed, the sheep with CC genotype are economically advantageous in the herd, and therefore DGAT1 gene can be used for marker-assisted selection (MAS).

PSXII-1 Genetic Regions Associated with Cryptorchidism in Related Wagyu Cattle

Abstract Wagyu cattle have gained popularity in recent years due to their increased amounts of intramuscular marbling and their calving ease in crossbred cattle. The small effective population size of Wagyu cattle outside of Japan has led to inbreeding and an increased presentation of autosomal recessive traits. Cryptorchidism, the absence of at least one testicle from the scrotum, is the most common genital defect in males and is seen more commonly in inbred populations suggesting an autosomal recessive inheritance. The objective of this study was to identify genetic regions associated with unilateral cryptorchidism in related Wagyu cattle. All individuals in the study shared a common cow ancestor in their pedigree. Fourteen individuals, three cases and eleven controls, were genotyped using the Illumina BovineHD BeadChip (San Diego, CA). There were 450,083 SNPs that remained for the haplotype analysis after SNPs were removed for quality control parameters of genotyping call rate (&amp;lt; 90%), minor allele frequency (&amp;lt; 1%) and failure to meet Hardy Weinberg equilibrium testing (P &amp;lt; 1 x 10-5). No animals were removed due to low call rate (&amp;lt; 90%). Haplotypes were detected within the SNP and Variation Suite v8.2 (Golden Helix, Bozeman, MT) for an association with cryptorchidism using a chi-square test (P &amp;lt; 0.05) and false discovery rate (FDR &amp;lt; 0.05). There were 107,439 different SNP haplotype combinations among 49,627 haplotypes identified in the Wagyu cattle. The average haplotype size was 21.7 kb in Wagyu cattle. Prior to multiple testing correction, 1,233 haplotypes were associated (P &amp;lt; 0.05), with 6 haplotypes on BTA7 (P = 0.001 to P = 0.002) being of particular interest as the SNPs for those haplotypes were identical and homozygous, whereas none of the controls were homozygous for the SNPs. The SNP haplotype pattern observed on BTA7 was consistent with an autosomal recessive trait. When applying multiple testing corrections (FDR &amp;lt; 0.05), none of the haplotypes were significant. Additional unilateral cryptorchid bulls that share the same common cow ancestor have been identified and will be tested to see if the haplotypes on BTA7 are segregating with the phenotype. Identifying genetic regions associated with cryptorchidism will allow the identification of carriers for this trait that can then be used for choosing mates that are not carrying this trait. Reducing the number of cryptorchid males in a breed with a small effective population size would allow breeders to utilize the genetics of carriers without increasing the frequency of cryptorchidism.

Genetic Association Between ICAM-1 Gene Variants and Susceptibility to Ischemic Cardiomyopathy.

The current work was aimed at exploring the association between single nucleotide polymorphisms (SNPs) in the ICAM-1 gene, along with the identification of additional haplotypes and their potential role in the susceptibility to ischemic cardiomyopathy (ICM). The control group underwent a Hardy-Weinberg equilibrium test. The associations of genotypes and alleles with susceptibility to ICM were then analyzed using logistic regression analysis. Subsequently odds ratios (ORs) along with 95% confidence intervals (95% CI) were calculated. Interaction analysis was conducted between these SNPs. Furthermore, linkage disequilibrium analysis and haplotype analysis were performed on SNPs that showed interactions with each other. The incidence of ICM was significantly higher among individuals carrying the T allele of rs3093032 (OR = 2.032, 95% CI, 1.275-3.241, P = 0.003) relative to those with the C allele. In addition, CT genotype carriers had a higher susceptibility to ICM than CC genotype carriers (OR = 2.490, 95% CI, 1.445-4.29, P = 0.001). Furthermore, 3 SNPs (rs3093032, rs923366, rs3093030) exhibited a strong interaction with each other, whereas rs281437 showed no interaction with the other 3 SNPs. Individuals carrying the C rs3093032 -T rs923366 -C rs3093030 haplotype had an elevated risk of ICM compared with those carrying the C rs3093032 -C rs923366 -C rs3093030 haplotype (OR = 2.280, 95% CI, 1.568-3.315, P < 0.001). Moreover, individuals carrying the T rs3093032 -C rs923366 -C rs3093030 haplotype were more susceptible to ICM than those carrying the C rs3093032 -C rs923366 -C rs3093030 haplotype (OR = 2.388, 95% CI, 1.469-3.880, P < 0.001). Regarding rs3093032, the minor alleles and haplotypes are associated with an increased ICM risk: 3 SNPs (rs3093032, rs923366, rs3093030) in ICAM-1 have strong interaction with each other.

Genetic diversity and population structure of Mastacembelus armatus in the river systems of southern China revealed by microsatellites

The Zig-zag eel (Mastacembelus armatus) is an economically important species in southern China. Its natural resources have declined year by year due to overfishing. Understanding its genetic diversity and population structure is very important for resource conservations. Here, we first successfully developed 28 polymorphic microsatellite markers for zig-zag eels and ten of them were used to examine the genetic diversity and differentiation of 7 populations collected from the major river systems of south China. In total, 224 alleles were found with the 10 microsatellite loci in 7 populations, ranging from 4.6 (Nandujiang: NDJ) to 11.1 (Xijiang, XJ), with an average of 8.871 alleles. The average observed and expected heterozygosity ranged from 0.550 (NDJ) to 0.964 (Yuangjiang, YJ) and from 0.537 (NDJ) to 0.775 (Tanjiang, TJ), respectively. The average polymorphism-information content ranged from 0.472 (NDJ) to 0.757 (TJ). Hardy–Weinberg equilibrium test results revealed the loci showed differing deviation in different populations. In total, low level of genetic diversity was only found in HJ (Hanjiang) and NDJ populations. Besides, evidence of recent bottleneck was found in the HJ populations. Analysis of molecular variation showed that the percent variation within individuals (75.00%) was higher than that among populations (25%). In addition, population structure and the pairwise FST revealed that there was low differentiation among XJ, TJ and YJ populations. These data provide important genetic resources for understanding the population differentiation and facilitating genetic conservation and utilization of this species.

Potential role of glutathione S‑transferase M1 gene polymorphism in kidney calcium oxalate stone formation.

The purpose of this study was to look into the effects of glutathione S-transferase M1 (GSTM1) gene polymorphism on the formation of kidney calcium oxalate stones. A total of 159 patients with kidney calcium oxalate stones were included in this study as a case group. One hundred and three healthy individuals were included in the control group. The age, gender, and levels of calcium (Ca), uric acid (UA), creatinine (Cr), and urinary creatinine (Ucr) are tracked. Peripheral blood samples are used to perform a polymerase chain reaction to identify the glutathione S-transferase (GST) gene polymorphism (PCR). A commercial kit was used in this study to measure the levels of malondialdehyde (MDA), nitric oxide (NO), total antioxidant capacity (T-AOC), and 8-hydroxydeoxyguanosine (8-OHdG) in peripheral blood. There was no difference in age or gender distribution between the case and control groups (P > 0.05). The Cr, Ucr, Ca, UA, 8-OHdG, MDA, NO, and T-AOC in the case group were significantly higher than those in the control group (P < 0.001). The Hardy-Weinberg genetic equilibrium test showed no difference between the case group (P = 0.23) and the control group (P = 0.09). In the case group, the 8-OHdG and NO in GSTM1 null genotype were significantly higher than those in GSTM1 genotype(P < 0.05), but there was no significant difference in MDA and T-AOC (P > 0.05). Multivariate regression analysis showed that the GSTM1 null genotype was positively correlated with 8-OHdG (P < 0.001) and NO (P < 0.001). GSTM1 gene polymorphism might be a detecting risk factor for kidney calcium oxalate stone formation. ChiCTR2100051300.

Effect of vitamin D binding protein gene polymorphism on susceptibility and prognosis of severe acute pancreatitis

To investigate the effect of vitamin D binding protein (DBP) gene polymorphism on susceptibility and prognosis of severe acute pancreatitis (SAP). A prospective study was conducted. Eighty-three patients with SAP who were admitted to the department of general surgery of Tianjin Fifth Central Hospital from March 2018 to March 2021 were selected as the research objects, and 83 healthy people in the same period were selected as controls. Peripheral blood RNA was extracted and reverse transcribed into cDNA, and the genotype and allele frequency of DBP gene rs7041 locus were detected by fluorescence quantitative analyzer. Hardy-Weinberg equilibrium was used to test the genetic balance. On the day of admission, serum C-reactive protein (CRP) level was detected by scattering immunoturbidimetry, serum procalcitonin (PCT) level was detected by electrochemiluminescence, serum DBP level was detected by enzyme-linked immunosorbent assay (ELISA), and neutrophil to lymphocyte ratio (NLR) was calculated automatically by the instrument. The length of intensive care unit (ICU) stay, the length of hospital stay and prognosis during hospitalization of patients were statistically analyzed. Multivariate Logistic regression analysis was used to screen the influencing factors of SAP occurrence. The results of Hardy-Weinberg equilibrium test showed that the distribution of gene polymorphisms in the two groups of subjects conformed to the law of genetic equilibrium. The frequencies of TT genotype and T allele of DBP gene rs7041 locus in the patients of SAP group were significantly higher than those in the healthy control group [TT genotype: 34.94% (29/83) vs. 9.64% (8/83), T allele: 55.42% (92/166) vs. 38.55% (64/166), both P < 0.01], and the frequency of GT genotype was significantly lower than that in the healthy control group [40.96% (34/83) vs. 57.83% (48/83), P < 0.05]. There was no significant difference in the frequency of GG genotype between the healthy control group and SAP group [32.53% (27/83) vs. 24.10% (20/83), P > 0.05]. Further multivariate Logistic regression analysis showed that TT genotype [odds ratio (OR) = 2.831, 95% confidence interval (95%CI) was 1.582-5.067, P < 0.001] and T allele (OR = 2.533, 95%CI was 1.435-4.472, P < 0.001) of DBP gene rs7041 locus were independent risk factors for SAP in healthy people, while GT genotype was a protective factor for SAP (OR = 0.353, 95%CI was 0.143-0.868, P = 0.041). The levels of CRP, PCT, NLR and DBP in patients with TT genotype of DBP gene rs7041 locus were significantly higher than those in patients with GG/GT genotype on the day of admission in SAP group [CRP (mg/L): 43.25±13.25 vs. 31.86±12.83, PCT (μg/L): 1.53±0.24 vs. 1.21±0.20, NLR: 3.15±0.53 vs. 2.71±0.48, DBP (μg/L): 87.78±19.64 vs. 70.58±18.67, all P < 0.01]. The length of ICU stay in patients with TT genotype of DBP gene rs7041 locus in SAP group was significantly longer than that in patients with GG/GT genotype (days: 11.35±1.58 vs. 9.71±1.35, P < 0.01). The length of hospital stay of patients with TT genotype was longer than that of patients with GG/GT genotype (days: 23.41±3.64 vs. 23.17±3.57), and the in-hospital mortality was higher than that of patients with GG/GT genotype [34.48% (10/29) vs. 29.63% (16/54)], but the difference was not statistically significant (both P > 0.05). The risk of SAP was significantly increased in patients with TT genotype of rs7041 locus of DBP gene, and the mechanism may be related to the increase of DBP expression. And carrying the TT genotype will prolong the ICU hospitalization time of SAP patients, but the effect on prognosis is not obvious.