SNP Genotyping Research Articles

ACE2 and TMPRSS2 genetic polymorphisms as potential predictors of COVID−19 severity and outcome in females

IntroductionACE2 and TMPRSS2 represent the major gateways for SARS-CoV-2 cell entry. The presence of functional ACE2 and TMPRSS2 genetic polymorphisms that affect gene expression may affect the risk of severe form of COVID-19 and its fatal outcome.Material and patientsThis observational study enrolled 178 hospitalized patients diagnosed with SARS-CoV-2 infection at the University Clinical Centre of Kragujevac, Serbia. Demographic, clinical, and laboratory data were gathered at admission. Genotyping for single nucleotide polymorphisms of ACE2 (rs2106809 and rs2074192) and TMPRSS2 (rs2070788 and rs4818239) was performed using the Real-Time PCR method with TaqMan assays.ResultsControlling for other factors of influence, such as CCI, N/L ratio, LDH level, and pO2, we showed that females with TMPRSS2 rs2070788 A/A genotype were less likely to develop severe COVID-19 (odds ratio [OR] [95% confidence interval (95% CI)]: 0.030 [0.001; 0.862]). Additionally, the likelihood of dying of SARS-CoV-2 infection was lower in female carriers of at least one ACE2 rs2106809 C allele (OR [95% CI]: 0.004 [0.000; 0.981]).ConclusionOur findings indicate TMPRSS2 rs2070788 and ACE2 rs2106809 polymorphisms as independent predictors of severity and outcome of COVID-19 in females.

Development of a panel of SNP loci in the emblematic southern damselfly (Coenagrion mercuriale) using a hybrid method: pitfalls and recommendations for large-scale SNP genotyping in a non-model endangered species.

Genomic markers are essential tools for studying species of conservation concern, yet non-model species often lack a reference genome. Here we describe a methodology for identifying and genotyping thousands of SNP loci in the southern damselfly (Coenagrion mercuriale), a bioindicator of freshwater stream quality classified as near-threatened, with locally declining populations. We used a hybrid approach combining reduced representation sequencing and target enrichment. First, we identified putative SNP loci using ddRADseq and de novo assembly. Then, single primer enrichment technology targeted 6,000 of these SNPs across 1,920 individuals. Challenges encountered included sequence recapture failure, coverage depth discrepancies, and aberrant FIS values. We provide recommendations to address such issues. After multiple filtering steps, 2,092 SNPs were retained and used to analyse the genetic structure of 131 individuals belonging to 11 populations in France, comparing central and marginal populations. Genetic differentiation was lower among central populations, with no sign of inbreeding. As compared to microsatellite loci, SNPs exhibited greater resolution in detecting fine-scaled genetic structure, identifying putative hybrids in adjacent populations. In this study, we emphasise the difficulties of large-scale SNP genotyping in non-model species via a hybrid method that ultimately did not offer the expected cost and time saving compared to classical ddRAD approaches. However, SNPs showed greater power than previously available markers in identifying conservation units or admixture events, and the panel of reusable probes we describe here offers the potential to improve conservation efforts through future diachronic studies or finer estimations of key parameters like effective population size.

From early methods for DNA diagnostics to genomes and epigenomes at high resolution during four decades - a personal perspective.

In the 1980s, my research career begun with microbial DNA diagnostics at Orion Pharmaceutica in Helsinki, Finland, where I was part of an innovative team that developed novel methods based on the polymerase chain reaction (PCR) and the biotin-avidin interaction. One of our key achievements during this time was the invention of the solid-phase minisequencing method for genotyping single nucleotide polymorphisms (SNPs). In the 1990s, I shifted focus to human genetics, investigating mutations of the 'Finnish disease heritage'. During this period, I also developed quantitative methods using PCR and minisequencing of mitochondrial mutations and for forensic analyses. In the late 1990s and early 2000s, microarray-based SNP genotyping became a major topic for my research, first in Helsinki and later with my research group at Uppsala University in Sweden. By the mid-2000s, I began collaborating with leading clinicians on genetics of autoimmune disease, specifically systemic lupus erythematosus and later worked on the classification and clinical outcome of pediatric acute lymphoblastic leukemia, when large-scale genomics and epigenomics emerged. These collaborations, which focused on integrating genomics into clinical practice, lasted almost two decades until I retired from research in 2022. In parallel with my research activities, I led the SNP/DNA Technology Platform in the Wallenberg Consortium North program from 2001 to 2006. I continued as Director of the SNP&SEQ Technology Platform, which expanded rapidly during the 2010s, and became part of Science for Life Laboratory in 2013. Today (in 2024), the SNP&SEQ Technology Platform is one of the largest units of the Swedish National Genomics Infrastructure hosted by SciLifeLab. The present article provides a personal perspective on nearly four decades of research, highlighting projects and methods I found particularly exciting or important.

Single Nucleotide Polymorphism of IL-18 (Rs 1946519) in Recurrent Aborted Iraqi Women and Its Association with Toxoplasmosis

Background: We aimed to shed light on the risks of elevated levels of IL-18 in aborted women with toxoplasmosis by evaluating the risk or protective function of alleles or genotypes for single nucleotide polymorphism (SNP) of IL-18 (rs 1946519), which might be related to the susceptibility to toxoplasmosis. Methods: IL-18 levels in patient and control blood samples were determined using ELISA, and the SNP IL-18 (ra 1946519) was subjected to the high-resolution method. Results: Compared to healthy pregnant women (HP), the IL-18 serum levels of recurrent abortion with toxoplasmosis (RAWT), recurrent abortion without toxoplasmosis (RAWOT), and healthy non-pregnant (HNP) women decreased with significant differences. Additionally, a strong association between patients and controls was found in the SNP IL-18 data. RAWT and RAWOT with the genotypes AA and AC had significantly lower IL-18 serum levels than women HP, according to the distribution of IL-18 serum levels by SNP. Conclusion: The serum level of IL-18 varied by genotype in patients with substantial differences compared to controls, while the SNP of IL-18 has been linked as a risk factor in toxoplasmosis-infected recurrent abortion women.

The Evolution and Role of Molecular Tools in Measuring Diversity and Genomic Selection in Livestock Populations (Traditional and Up-to-Date Insights): A Comprehensive Exploration

Distinctive molecular approaches and tools, particularly high-throughput SNP genotyping, have been applied to determine and discover SNPs, potential genes of interest, indicators of evolutionary selection, genetic abnormalities, molecular indicators, and loci associated with quantitative traits (QTLs) in various livestock species. These methods have also been used to obtain whole-genome sequencing (WGS) data, enabling the implementation of genomic selection. Genomic selection allows for selection decisions based on genomic-estimated breeding values (GEBV). The estimation of GEBV relies on the calculation of SNP effects using prediction equations derived from a subset of individuals in the reference population who possess both SNP genotypes and phenotypes for target traits. Compared to traditional methods, modern genomic selection methods offer advantages for sex-limited traits, low heritability traits, late-measured traits, and the potential to increase genetic gain by reducing generation intervals. The current availability of high-density genotyping and next-generation sequencing data allow for genome-wide scans for selection. This investigation provides an overview of the essential role of advanced molecular tools in studying genetic diversity and implementing genomic selection. It also highlights the significance of adaptive selection in light of new high-throughput genomic technologies and the establishment of selective comparisons between different genomes. Moreover, this investigation presents candidate genes and QTLs associated with various traits in different livestock species, such as body conformation, meat production and quality, carcass characteristics and composition, milk yield and composition, fertility, fiber production and characteristics, and disease resistance.

Association of genetic variations of interleukin-6 polymorphism (rs1800795) with susceptibility to Hashimoto’s thyroiditis in West Algerian population

Aim: Hashimoto’s thyroiditis is a polygenic auto-immune disease with a complex etiopathogenesis. It is more common in females. An imbalance between pro-inflammatory and anti-inflammatory cytokines may play an important role in the disease pathogenesis. Numerous studies have been conducted to find an association between genetic polymorphisms and the development of Hashimoto’s thyroiditis. In this context, we proposed to study the impact of the interleukin-6 (IL-6) gene polymorphism (rs1800795) on the genetic susceptibility to Hashimoto’s thyroiditis. Methods: Polymorphism in IL-6 gene (rs1800795) was assessed in a case-control study involving a population of Western Algeria with 81 Hashimoto’s thyroiditis patients and 211 unrelated healthy subjects, matched in age and sex. The DNA was extracted by a magnetic bead-based technique. The genetic study was performed by molecular biology: real-time PCR using TaqMan single nucleotide polymorphism (SNP) genotyping assay with Applied Biosystems 7500 device. Results: Results showed that the GG and GC genotypic distribution is similar between patient and control groups with a higher frequency of the GG genotype (80.25% in patients and 78.67% in controls vs. 19.75% of patients and 20.38% of controls with the GC genotype). The CC genotype is absent in patients and present in only 02/211 healthy subjects. The frequency of the polymorphic G allele was similar in the two groups, with 90.1% and 88.8% in patients and controls respectively (P > 0.05). Conclusions: This study reports no significant difference in IL-6 (-174 G/C) gene polymorphism at the allelic or the genotypic level between Hashimoto’s patients and the control group (P > 0.05). No association between the SNP IL-6 rs1800795 and susceptibility to Hashimoto’s thyroiditis in Western Algerian population.

Mapping genetic susceptibility to spontaneous preterm birth: Analysis of Utah pedigrees to find inherited genetic factors.

Spontaneous preterm birth (SPTB) is the leading cause of neonatal morbidity and mortality. It is a final common pathway for multiple etiologies, some of which are well known while others likely remain to be identified. Despite recent advancements in identifying genetic risk factors, the mechanisms of many SPTBs remain poorly understood due to the phenotypic heterogeneity and complexity. Large family-based studies decrease heterogeneity and improve power to identify genetic causes of SPTB. To identify inherited genetic factors in SPTB etiology using large families. Using the Utah Population Database, which links a 4.5 million-person genealogy to state birth certificate and fetal death records, we identified large pedigrees containing multiple women with early SPTB (<34 weeks' gestation) and any SPTB (<37 weeks' gestation). We reviewed birth certificate data to exclude those with maternal and fetal diagnoses associated with iatrogenic preterm birth, resulting in 74 large multiplex pedigrees for early SPTB. Enrolled women with SPTB underwent comprehensive clinical phenotyping with review of primary medical records. Seven pedigrees, each containing at least 3 sampled women with SPTB, were the focus of this genetic study. High-density single-nucleotide polymorphism genotyping was conducted in maternal peripheral blood samples from women in the seven pedigrees. Shared genomic segments analysis was performed to identify genome-wide significant chromosomal regions shared in excess by women with SPTB. We identified two genome-wide significant chromosomal regions. In single-pedigree SGS analysis, a 1.75 Mega base region in chromosome 8 (8q24.23) was shared by 5 out of 6 women with SPTB in a single large pedigree (false positive rate=0.028). In duo-pedigree analysis, a 1.05 Mega base region in the same 8q24.23 locus was identified in a second pedigree (false-positive rate [duo]= 0.0019). The intersecting region at the 8q24.23 locus contains FAM135B (family with sequence similarity 135 member B) and KHDRBS3 (KH RNA binding domain containing, signal transduction associated 3) genes, which have previously been implicated in oncogenesis and ovarian cancer, respectively. Duo-pedigree SPTB analysis also identified a second genome-wide significant 67 kilo base locus in chromosome 12 (12q21.1-q21.2) that was shared by all women with SPTB in two independent pedigrees (false-positive rate [duo] =0.01). The intersecting region at the 12q21.1-q21.2 locus contains CAPS2 (calcyphosine 2) and KCNC2 (potassium voltage-gated channel subfamily C member 2) genes, both implicated in vascular-related complications of pregnancy and preterm labor. Using large SPTB families, we identified shared chromosomal regions (8q24.23 and 12q21.1-q21.2), providing evidence for inherited (segregating) risk loci in SPTB etiology. Further investigation into genes in SPTB etiology, including functional validation may provide avenues for novel therapeutic development and guide efforts for SPTB prevention to prolong pregnancy and improve outcomes.

Integrative Genomic and Transcriptomic Analysis in Acute Interstitial Pneumonia.

Acute Interstitial Pneumonia (AIP) represents a severe form of diffuse lung injury within the idiopathic interstitial pneumonia spectrum. Given the limited understanding of its molecular basis, this study aims to elucidate AIP's genomic and transcriptomic profiles to uncover its pathophysiological underpinnings and identify potential therapeutic targets. We conducted a comprehensive analysis of genomic and transcriptomic data from lung tissues of 15 AIP patients. This included assessing differentially expressed genes (DEGs) and identifying mutations in exonic coding variants, as well as analysing expression quantitative trait loci (eQTL) profiles to link non-coding SNP genotypes with gene expression levels. Transcriptomic analysis revealed a significant upregulation of genes linked to the Type I interferon receptor and keratin filament, and a downregulation of genes related to focal adhesion and endothelial integrity, compared to healthy individuals. These patterns were distinct from those observed in idiopathic pulmonary fibrosis (IPF) and non-IPF interstitial lung diseases (ILDs). Genomic analysis highlighted mutations in genes associated with keratin and the extracellular matrix. Additionally, eQTL profiling provided insights into the genetic regulation of gene expression in AIP. Our findings reveals AIP's unique molecular landscape, differentiating it from other ILDs and laying the groundwork for future diagnostic and therapeutic research.

Investigation of polymorphism and expression of the tyrosinase (TYR) gene as a gene controlling coat color in Bali cattle

Cattle coat color is governed by numerous genes, notably the tyrosinase gene (TYR). This study analyzed coat color anomalies like albinism and white spotting in Bali cattle. It aims to discern the TYR gene's diversity, expression patterns, and correlation with coat color abnormalities. The research encompassed 189 cattle, including those with standard coat color (n=53), white-spotted (n=11), and albino (n=17) Bali cattle, as well as Simmental (n=37), Limousin (n=14), Madura (n=21), and Peran-akan Ongole (PO) cattle (n=36). Total DNA was extracted and the TYR gene in exon 1 was amplified using forward and reverse primers with a target amplicon length of 994 bp. Direct sequencing unveiled TYR gene diversity, analyzed using BioEdit and MEGA6 software to identify SNPs. PCR-RFLP was used for SNP genotyping, while qPCR analyzed TYR gene expression. Two mutations (SNP g. 939A&gt;G and SNP g. 887C&gt;T) were discovered in Bali cattle TYR exon 1. SNP g. 939A&gt;G exhibited polymorphism, with the highest GG genotype frequency in standard Bali cattle, indicating a high G allele frequency. Conversely, Madura, Simmental, Limousin, and PO cattle had the lowest allele fre-quency. Chi-square (χ² test) results showed non-significance across all cattle types. TYR gene expres-sion differed significantly between standard Bali cattle and albinos (p&lt;0.05).

Higher relapse and worse overall survival in recipients with CTLA-4 AA genotype of rs231775 following single-unit cord blood transplantation in adults

We retrospectively investigated the impact of CTLA-4 polymorphism on outcomes for adult patients who received single-unit cord blood transplantation (CBT) at our institution. CTLA-4 genotyping was performed using real-time polymerase chain reaction with the TaqMan® SNP genotyping assay for rs231775. This study included 143 recipient–donor pairs. The multivariate analysis showed that recipient rs231775 AA was associated with worse overall survival (OS) (hazard ratio [HR], 2.92; p = 0.008) and a higher relapse rate (HR, 4.79; p = 0.002), but donor rs231775 was not. The rs231775 polymorphism in recipients and donors did not affect non-relapse mortality, hematopoietic recovery, or acute and chronic graft-versus-host disease. The beneficial effects of rs231775 GG+GA recipients on OS and relapse were notable in subgroups of patients with high-risk disease status and those with myeloid diseases. The polymorphism of CTLA-4 rs231775in recipients might be associated with the clinical outcomes of single-unit CBT.

Association of MicroRNA-146a-5p Polymorphism with Cognitive Impairment in Adolescents with Depressive Disorder

Introduction: The incidence of depression in adolescents is increasing and is associated with severe cognitive impairment. This paper aimed to investigate the relationship between polymorphisms in microRNA-146a-5p (miR-146a-5p) and cognitive impairment in adolescent depression patients. Methods: Quantitative real-time polymerase chain reaction was used to quantify miR-146a-5p in serum. Detection of miR-146a-5p gene polymorphism was performed by TaqMan SNP Genotyping Assay. Odds ratios and 95% confidence intervals (CIs) were calculated by chi-square test (χ2) and logistic regression analysis. Results: Genotyping of miR-146a rs2910164 showed that CC (OR = 0.443, 95% CI, 0.264–0.741, p = 0.002) and GC (OR = 0.445, 95% CI, 0.279–0.712, p = 0.001) genotype reduced the risk of cognitive impairment in adolescent depression. The C allele (OR = 0.794, 95% CI, 0.694–0.741, p = 0.001) was a protective factor for cognitive impairment in adolescent depression compared to the rs2910164 G allele. Rs2910164 (OR = 0.425, 95% CI = 0.273–0.662, p = 0.000) showed a negative correlation with adolescents with cognitive impairment in depression by logistic regression analysis. The level of miR-146a-5p was decreased in carriers of the CC and CG genotypes. Conclusion: Rs2910164 C allele carriers have a low risk of cognitive impairment in adolescent depression and could reduce miR-146a-5p level.

Molecular Analysis of Genes CEBPA, NPM1, IDH1, and RUNX1 Polymorphisms as Biomarker Potential in Leukemia Patients.

Leukemia is found in approximately 2.3 million people worldwide and causes many deaths all over the world. This research study was conducted to figure out the link of single nucleotide polymorphisms of genes CEBPA (rs34529039), NPM1 (rs753788683), IDH1 (of rs11554137) and RUNX1 (rs13051066) polymorphisms as biomarker potential in leukemia patients. A total of 600 subjects were included in the study which included 300 patients and 300 healthy controls with age and gender matched. After DNA extraction, PCR was carried out to analyze polymorphisms of selected genes. A significant association with increased risk of leukemia by almost twofolds is observed in homozygous mutant (AA) of rs34529039 SNP of gene CEBPA (odds ratio [OR] = 1.71; 95% confidence interval [CI] = 1.04-2.82; p = 0.03) while highly significant association but with decrease risk of leukemia is observed in heterozygote genotype (CA) of same SNP (OR = 0.36; 95% CI = 0.22-0.59; p = 0.0001). A highly significant association with increased risk of leukemia up to twofolds is observed in heterozygote genotype (AG) of rs753788683 of gene NPM1 (OR 2.10: 95% CI 1.32-3.36 p = 0.0017) while increasing risk by two-fold and show significant association in homozygous mutant (AA) (OR = 1.75; 95% Cl = 1.09-2.79; p = 0.01). Leukemia risk increases by twofold and shows significant association in the homozygous mutant (AA) of rs11554137 (OR = 1.75; 95%Cl = 1.09-2.79; p = 0.01). Leukemia risk increases by twofold and shows significant association in the homozygous mutant (AA) of rs13051066 of gene RUNX1 (OR = 0.63; 95%Cl = 0.39-1.63; p = 0.06).

History and genetic diversity of African sheep: Contrasting phenotypic and genomic diversity.

Domesticated sheep have adapted to contrasting and extreme environments and continue to play important roles in local community-based economies throughout Africa. Here we review the Neolithic migrations of thin-tailed sheep and the later introductions of fat-tailed sheep into eastern Africa. According to contemporary pictorial evidence, the latter occurred in Egypt not before the Ptolemaic period (305-25 BCE). We further describe the more recent history of sheep in Egypt, the Maghreb, west and central Africa, central-east Africa, and southern Africa. We also present a comprehensive molecular survey based on the analysis of 50 K SNP genotypes for 59 African breeds contributed by several laboratories. We propose that gene flow and import of fat-tailed sheep have partially overwritten the diversity profile created by the initial migration. We found a genetic contrast between sheep north and south of the Sahara and a west-east contrast of thin- and fat-tailed sheep. There is no close relationship between African and central and east Asian fat-tailed breeds, whereas we observe within Africa only a modest effect of tail types on breed relationships.

Relationships between growth characteristics and GDF9 gene polymorphisms in Awassi sheep

ABSTRACT The Awassi sheep, a breed with a distinctive fat tail, is bred specifically in the south-eastern region in Turkey. It has proven its adaptability to the hot environment of this region, especially in the provinces of Şanlıurfa, Hatay and Gaziantep, which are close to the Syrian border. The aim of this study was to investigate the SNP polymorphisms in the GDF9 gene/exon2 using DNA sequencing. In addition, the study investigated the relationships between SNP genotypes and growth traits, in particular birth weight (BW), weaning weight (WW) and weight at the end of the grazing season (GSW), in Awassi sheep. Four different flocks with a total of 131 Awassi lambs were used. PCR was used to amplify exon2 of the GDF9 gene region, which has a length of 815 base pairs (bp), from the genomic DNA of the Awassi sheep. Thus, four new single nucleotide polymorphisms (SNPs) were identified. The results showed that although the effects of SNP2 and SNP4 on body weight (BW) were statistically significant, only SNP4 had a significant effect on weaning weight (WW) (P < 0.05). In addition, SNP1 and SNP3 were found to have no significant effect on any developmental trait in the dataset.

The development of two fast genotyping assays for the differentiation of hemp from marijuana

AbstractThe legalization of hemp cultivation in the United States has raised the need for reliable methods to distinguish between legal hemp and illegal marijuana. Genetic analysis has emerged as a powerful tool, surpassing traditional chemical methods in specific aspects, such as analyzing trace amounts, aged samples, and different parts of the sample. Genetic differences in cannabinoid synthase genes offer promise for precise crop type determination, particularly focusing on genes like tetrahydrocannabinolic acid synthase (THCAS), cannabidiolic acid synthase (CBDAS), and cannabichromenic acid synthase (CBCAS). However, previous research faced several challenges in developing discriminatory genetic markers, including limited sample sizes, high similarity between the synthase genes, and the presence of pseudo synthase genes. A comprehensive study using Next‐Generation Sequencing (NGS) introduced a differentiation flowchart based on THCAS, CBDAS, and THCAS pseudogenes. To bridge the gap between NGS and the practical requirements of crime laboratories, two rapid genotyping assays were developed: a CE‐based SNaPshot™ assay and a TaqMan™ real‐time PCR assay. While the SNaPshot™ assay effectively differentiated various hemp and marijuana types, differentiation was limited with marijuana samples containing THC% close to the 0.3% legal threshold (0.3%–1%). The TaqMan™ qPCR SNP genotyping assay provided quicker results, making it an efficient choice for crime laboratories. However, this method had the same limitations as the SNaPshot™ assay with addtional challenges in differentiating edible hemp seed samples, and it did not provide additional CBD information. The study also highlighted the influence of two variants of one THCAS pseudogene on chemotype determination, emphasizing the necessity for precise genetic analysis for accurate categorization of cannabis varieties.

Association between the rs1800624 and rs80096349 SNPs and diabetic retinopathy: a pilot study

ABSTRACT Background One of the conditions that might harm your eyesight is diabetic retinopathy (DR), DR may set in slowly but surely for those with long-term diabetes and poor glucose control. ‎ Objective To establish a connection between the various genotypes of the rs1800624 SNP and the rs80096349 SNP located in the AGER gene and DR patients. ‎ Methods The current case-control research examined one hundred thirty-four individuals diagnosed with type 2 diabetes and thirty-six healthy individuals who did not have DM. These samples were obtained from Amir Al-Muminin, a private hospital in Najaf, Iraq. The tetra primers ARMS-PCR method was utilized to determine the genotype of rs1800624 SNP of the AGER gene. Results A significant association was found between genotypes (AA, AG, and GG) and DR subgroups (NPDR & PDR) in patients (p = 0.001). The AG genotype of rs1800624 SNP is associated with a lowering the risk of developing NPDR (OR = 0.30; 95% CI = 0.12-0.74; p = 0.009 between controls and NPDR, OR = 0.36; 95% CI = 0.14-0.90; p = 0.029 between NDR and NPDR). HRM analysis verified the presence of only two genotypes in the samples: wild type (GG) and a heterozygous mutant (GA). However, a significant association between genotypes was observed when comparing DR status with controls and NDR (p = 0.031). Conclusion The rs1800624 SNP of the AGER gene is associated with the risk of NPDR and PDR in T2DM, and the polymorphism of the rs80096349 may be associated with retinopathy in the Iraqi population.

Gender-modulated influence of BDNF concentration and Val66Met polymorphism on cognitive outcomes in chronic limb ischemia patients.

While numerous studies have established associations between brain-derived neurotrophic factor (BDNF) and cognitive functioning, limited research has delved into the role of BDNF concerning cognitive outcomes in atherosclerosis-related conditions. This study aimed to investigate the correlations between cognitive performance, serum BDNF levels, and the BDNF Val66Met polymorphism in individuals diagnosed with chronic limb ischemia (CLI). The study encompassed 159 CLI patients (52 females, 107 males) aged 59-73 years. Genetic analysis involved assessing the BDNF Val66Met single-nucleotide polymorphism using a TaqMan SNP Genotyping Assay and the ViiA™ 7 Real-Time PCR System. Serum BDNF levels were quantified. Cognitive functioning was evaluated through a computerized battery of tests, including the simple reaction test (SRT) for speed and accuracy assessment, verbal memory test (VMT) for short and long-term memory evaluation, and the GoNoGo test for cognitive control and inhibition. Gender differences in cognitive performance were observed, with women excelling in VMT, while men demonstrated superior performance in SRT and the GoNoGo test. No statistically significant differences were noted between the Met/Met or Met/Val and Val/Val subgroups. However, notable differences emerged in female Met carriers, exhibiting superior VMT scores but more incorrect Go responses in the GoNoGo test. Conversely, female Val homozygotes showed significantly more incorrect NoGo responses compared to male Val homozygotes. In men carrying the Met allele, higher BDNF concentrations correlated with improved GoNoGo test results (r = 0.248, p = 0.01). Conversely, in women with the Val/Val variant, lower BDNF concentrations were associated with better VMT scores. This study underscores the sex-specific impact of BDNF serum levels and the BDNF polymorphism on cognitive processes among CLI patients. The findings highlight the nuanced influence of BDNF in shaping cognitive functioning, emphasizing the need for further research into these sex-dependent associations.

Rare copy number variant analysis in case–control studies using snp array data: a scalable and automated data analysis pipeline

BackgroundRare copy number variants (CNVs) significantly influence the human genome and may contribute to disease susceptibility. High-throughput SNP genotyping platforms provide data that can be used for CNV detection, but it requires the complex pipelining of bioinformatic tools. Here, we propose a flexible bioinformatic pipeline for rare CNV analysis from human SNP array data.ResultsThe pipeline consists of two major sub-pipelines: (1) Calling and quality control (QC) analysis, and (2) Rare CNV analysis. It is implemented in Snakemake following a rule-based structure that enables automation and scalability while maintaining flexibility.ConclusionsOur pipeline automates the detection and analysis of rare CNVs. It implements a rigorous CNV quality control, assesses the frequencies of these rare CNVs in patients versus controls, and evaluates the impact of CNVs on specific genes or pathways. We hence aim to provide an efficient yet flexible bioinformatic framework to investigate rare CNVs in biomedical research.

Genetic and epigenetic factors affecting carotid intima-media thickness in monozygotic twins

Background and aimsThe intima-media thickness (IMT) of the carotid artery, an indicator of subclinical atherosclerosis, varies in close association with various factors such as diabetes and immune response. The extent of changes in IMT varies among individuals owing to both genetic and epigenetic factors. In this study, we aimed to identify single nucleotide polymorphisms (SNPs) and DNA methylation patterns that affect carotid IMT in monozygotic (MZ) twins. MethodsWe measured the maximum IMT (IMT-Cmax) and the mean IMT in the common carotid artery wall using ultrasonography in 107 pairs of MZ twins recruited from the Osaka University Twin Registry. The genotyping of SNPs and the measurement of methylation levels were performed using a beads array, and the expression of each gene was determined by RNA sequencing. Linear regression analysis was performed on each of the two groups: one group consisted of twins randomly selected from each pair, and the other group consisted of co-twins. ResultsWe identified a CpG site (cg02432467) on HS3ST6 as a significant epigenetic factor in both IMT-Cmax and mean IMT analyses. The methylation level at another site (cg07927379) was negatively correlated with LINC01006 expression and IMT-Cmax. Furthermore, there were significant differences in AP2A2 expression and mean IMT among individuals with each genotype of the rs10902263 polymorphism. ConclusionsWe identified genetic and epigenetic factors associated with carotid IMT that may be useful for individualized assessments.

Optimization of Whole-Genome Resequencing Depth for High-Throughput SNP Genotyping in Litopenaeus vannamei.

The application of whole-genome resequencing in genetic research is rapidly expanding, yet the impact of sequencing depth on data quality and variant detection remains unclear, particularly in aquaculture species. This study re-sequenced 31 Litopenaeus vannamei (L. vannamei) samples at over 28× sequencing depth using the Illumina NovaSeq system and down-sampled the data to simulate depths from 0.5× to 20×. Results showed that when the sequencing depth was below 10×, the number of SNP identifications increased sharply with the rise in depth, with single nucleotide polymorphisms (SNPs) detected at 10× accounting for approximately 69.16% of those detected at 20×. The genotyping accuracy followed a similar trend to SNP detection results, being approximately 0.90 at 6×. Further analyses showed that the main cause of genotyping errors was the misidentification of heterozygous variants as homozygous variants. Therefore, considering both the quantity and quality of SNPs, a sequencing depth of 10× is recommended for whole-genome studies and genetic mapping, while a depth of 6× is more cost-effective for population structure analysis. This study underscores the importance of selecting optimal sequencing depth to ensure reliable variant detection and high data quality, providing valuable guidance for whole-genome resequencing in shrimp and other aquatic species.