Single Nucleotide Polymorphism Variants Research Articles

Identification of a gene causing yellow endocarp in Cucumis sativus through high-throughput sequencing

Cucumber (Cucumis sativus) is a globally valued and widely cultivated vegetable crop. However, most commercially available cucumbers contain white or green fruit flesh color, which has very low ß-carotene and other carotenoids. Conversely, orange or yellow-fleshed cucumbers are rich in carotenoids and offer significant dietary and nutritional benefits. To generate cucumber varieties with carotenoid-enriched fruit flesh, we conducted high-throughput sequencing of a yellow-fleshed cucumber PI200815 (CS-C) and white-fleshed cucumbers JEF, and KWSA, to identify the genomic region responsible for yellow-fleshed fruit. Building on the previous report by Lu et al. (2015), we identified seven unique DNA variations in five genes specific to the CS-C line using HiSeq2000 and genomic mapping to 'Chinese-Long v3′. Further, based on the Sanger gene sequencing, among the five candidate genes, we found the CsaV3_7G029170 (encodes for an ATP-binding cassette (ABC) transporter C family member 4 [CsaYf]) gene with a single nucleotide polymorphism (SNP) variation in the third exon resulted in a missense mutation caused an amino acid change from Aspartic acid (Asp) to Aspargine (Asn) in the CS-C line. Accordingly, the gene segregation analysis based on the SNP variation revealed that the CsaYf gene confers the yellow endocarp trait in the CS-C line through recessive Mendelian single-gene inheritance. Notably, we observed a negative correlation between the downregulation of CsaYf gene expression and the accumulation of ß-carotene in meso and endo carp tissues in the CS-C line, suggesting a further investigation into the underlying molecular mechanism. This finding provides a novel genetic basis for breeding cucumbers with enriched carotenoid content to enhance their nutritional value.

Gender Differences in Response to Statin Therapy in Ischemic Stroke Patients With SLCO1B1 388A>G Polymorphism: A Clinical Study

Background: Statins are widely used for the medical management of vascular conditions, including ischemic stroke. However, genetic factors and polymorphisms, including SLCO1B1 388A>G single-nucleotide polymorphism (SNP), have shown significant effects in response to statin therapy. To the best of our knowledge, gender-gene interaction in response to statin therapy, affected by the SLCO1B1 388 A>G SNP, has not been investigated yet. The current study describes the therapeutic outcomes of this variation in terms of clinical evaluations and laboratory parameters. Methods: Seventy patients diagnosed with acute ischemic stroke were recruited for this study. Blood samples were collected. The SLCO1B1 388A>G gene was genotyped using a polymerase chain reaction-restriction fragment length polymorphism method, and the three possible polymorphisms (388GG, 388GA, and 388AA) were detected accordingly. Statin treatment was prescribed at a dose of 40 mg of Atorvastatin or 20 mg of Rosuvastatin daily. Laboratory assessments, including a lipid profile, liver function tests, and lactate dehydrogenase, as well as clinical evaluations, including scores of stroke severity, were obtained at baseline and after a three-month follow-up. Results: Iranian ischemic stroke patients showed all three possible polymorphisms, including 30 patients with AA, 28 patients with AG, and 12 patients with GG. Significant SNP variations and gender-gene interactions for most measures of the lipid profile and some clinical trends were found in such a manner that the GG genotype was associated with relevant resistance to statin treatment, while the AA genotype, particularly in male patients, was associated with more response to statin treatment. Conclusion: This investigation adds influential gender differences to the previously reported SLCO1B1 388A>G SNP-induced variations of statin therapeutic response in stroke patients.

Abstract PO-032: Association of a polymorphic variant in JMJD1C with tumor recurrence after adjuvant chemoradiation therapy in head and neck squamous cell carcinoma

Abstract Background: Adjuvant chemoradiation therapy (CRT) is the standard treatment for locally advanced head and neck squamous cell carcinomas (HNSCCs). Over 50% of HNSCC cases are diagnosed at the locally advanced stage, with in-field persistence and recurrence major causes of morbidity and poor survival outcome. Apart from human papillomavirus (HPV) status, there are no predictive biomarkers for CRT outcomes. CRT lethality arises from unrepaired double strand breaks (DSBs) in DNA. Recent work has suggested that dynamic changes in lysine modification of chromatin regulate DSB repair. This study investigated the association of germline single nucleotide polymorphisms (SNPs) in lysine-modifying genes with DSB repair and CRT outcomes in HNSCC. Methods: Blood specimens and associated retrospective clinical data from HNSCC patients (n=90; age range=41-89, median age 64; males=69, females=21) were obtained under IRB# 21-9921. The patients had HPV-negative tumors in the larynx or oral cavity, and had received radiation, with some receiving concurrent chemotherapy. Patients receiving concurrent chemotherapy were: 40% in disease-free group, 21% in recurrence disease group, and 38% in never disease-free group. The patients were segregated into 3 groups: disease-free (n=30), recurrent disease (n=28), and never-disease free (n=32). DNA from blood was genotyped for specific germline SNPs in lysine-modifying genes. Isogenic HNSCC lines (Cal-27, SCC9) carrying either the wild type (WT) or homozygous SNP were generated using CRISPR/Cas9 technology, and bulk RNA sequencing and immunofluorescence (IF)-based studies were performed to assess cellular pathways affected. Results: A homozygous variant SNP in the coding region of JMJD1C was significantly enriched in the disease-free group (n=21/30) versus the recurrent disease (n=3/28) and never disease-free (n=2/32) groups (p=0.0003, OR=0, Fisher’s Exact test). Analysis of SNP frequency in large population datasets found that while it was abundant in European Americans (EAs), it is relatively rare in African Americans (AAs) (EA= 0.3139 vs. AA=0.072; gnomAD population). Cal-27 JMJD1C SNP cells were significantly enriched for altered mRNA levels of genes associated with DNA repair, replication, cell cycle, oxidative phosphorylation, and histone kinase activity versus CAL-27 with WT JMJD1C (q-value<0.05). The SCC9 JMJD1C SNP cells were significantly enriched in extracellular matrix organization, cytokine-cytokine receptor interaction, and humoral immune response versus SCC9 with WT JMJD1C (q-value<0.05). On irradiation, the JMJD1C SNP cells had robust activation of the DSB repair pathway (BRCA1- mediated repair foci) versus the WT cell lines. Conclusion and future work: This work provides novel insight into a germline SNP in a lysine-modifying gene effecting DSB repair and associating with CRT outcomes in HNSCC. It may serve as a predictive biomarker for recurrence. Future research will explore racial disparities in tumor recurrence and confirm results in larger HNSCC datasets. Citation Format: Adria Hasan, Elena V. Demidova, Shreya M. Shah, Philip Czyzewicz, Karthik Devarajan, Thomas Galloway, Barbara Burtness, Erica A. Golemis, Joshua E. Meyer, Sanjeevani Arwesd. Association of a polymorphic variant in JMJD1C with tumor recurrence after adjuvant chemoradiation therapy in head and neck squamous cell carcinoma [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Innovating through Basic, Clinical, and Translational Research; 2023 Jul 7-8; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2023;29(18_Suppl):Abstract nr PO-032.

ВАРИАБЕЛЬНОСТЬ ГЕНОВ НАТРИЙУРЕТИЧЕСКИХ ПЕПТИДОВ И АНТИОКСИДАНТНОЙ ЗАЩИТЫ У ПАЦИЕНТОВ С ИНФАРКТОМ МИОКАРДА

Introduction. Cardiovascular diseases (CVD) continue to be the subject of scientific research in relation to molecular genetic predictors of their development. It has been proven that diseases of the cardiovascular continuum have a multifactorial nature with a significant genetic component, including the hereditary risk of myocardial infarction (MI). CVDs are characterized by a complex genetic structure with diverse combinations of single nucleotide polymorphic variants (SNVs). A promising task is to study the relationship of SNV adaptogenesis genes: inflammatory response, myocardial and endothelial dysfunction with developed MI in the Siberian population. Purpose: to reveal the relationship between SNV genes of natriuretic peptides and the antioxidant defense system with the development of myocardial infarction. Materials and methods. The material for the study was genomic DNA isolated from the peripheral blood of patients (n=146, 38 women and 108 men) admitted for treatment at the Kuzbass Clinical Cardiological Dispensary, Kemerovo, with a diagnosis of MI. The control group is represented by a population sample of residents of the city of Kemerovo (n=300, 190 women and 110 men). 20 polymorphic variants of 7 natriuritic peptide genes (NPPA, NPPA-AS1, NPPB, NPPC, NPR1, NPR2, NPR3) and 5 genes of the antioxidant defense system (SOD2, NCF4, CBR1, CBR3, CAT) were selected for the study. Genotyping of selected polymorphic variants was performed by real-time PCR using TaqMan technology. Statistical data analysis was carried out using GraphPad Prism 8 and SNPstats software. Results. Protective associations of allelic variants of the CBR1 rs9024 genes (OR=0.21 (95% CI 0.13-0.34); p=0.0001) and CBR3 (OR=0.44 (95% CI 0.28-0) .69); p=0.001) regardless of gender according to the dominant model of inheritance. When separating patients by gender, it was found that in men, the rs9024 CBR1 allele A (OR=0.20 (95% CI 0.11-0.36); p<0.0001) and the rs1056892 CBR3 allele A (OR=0, 51 (95% CI 0.28-0.91); p=0.022) have a protective effect in the development of MI according to the dominant model of inheritance. Allele T rs2236289 (OR=1.93 (95% CI 1.04-3.58); p=0.035) and allele A rs7034957 (OR=1.88 (95% CI 1.03-3.45); p =0.038) of the NPR2 gene are associated with a risk effect on the development of myocardial infarction in men according to the dominant model of inheritance. In women, rare alleles of the polymorphic loci rs13288085 (OR=0.25 (95% CI 0.08-0.73); p=0.0034) and rs7034957 (OR=0.30 (95% CI 0.11-0, 79); p=0.007) of the NPR2 gene, rs9024 (OR=0.21 (95% CI 0.09-0.47); p=0.00001) of CBR1, as well as rs1056892 (OR=0.31 (95% CI 0.15-0.64); p=0.0014) CBR3 are characterized by a protective effect on the development of MI according to the dominant model of inheritance. Conclusion. It has been shown that polymorphism of genes for natriuretic peptides and antioxidant protection may have a risky and protective effect in relation to predisposition to the development of MI. The obtained preliminary results indicate the need for further studies of the identified SNV genes of adaptogenesis in relation to the severity of MI and the risk of recurrent cardiovascular events in the long-term period after MI.

Identification, expression and DNA variation analysis of high affinity nitrate transporter NRT2/3 gene family in Sorghum bicolor

Nitrate is the main form of inorganic nitrogen that crop absorbs, and nitrate transporter 2 (NRT2) is a high affinity transporter using nitrate as a specific substrate. When the available nitrate is limited, the high affinity transport systems are activated and play an important role in the process of nitrate absorption and transport. Most NRT2 cannot transport nitrates alone and require the assistance of a helper protein belonging to nitrate assimilation related family (NAR2) to complete the absorption or transport of nitrates. Crop nitrogen utilization efficiency is affected by environmental conditions, and there are differences between varieties, so it is of great significance to develop varieties with high nitrogen utilization efficiency. Sorghum bicolor has high stress tolerance and is more efficient in soil nitrogen uptake and utilization. The S. bicolor genome database was scanned to systematically analyze the gene structure, chromosomal localization, physicochemical properties, secondary structure and transmembrane domain, signal peptide and subcellular localization, promoter region cis-acting elements, phylogenetic evolution, single nucleotide polymorphism (SNP) recognition and annotation, and selection pressure of the gene family members. Through bioinformatics analysis, 5 NRT2 gene members (designated as SbNRT2-1a, SbNRT2-1b, SbNRT2-2, SbNRT2-3, and SbNRT2-4) and 2 NAR2 gene members (designated as SbNRT3-1 and SbNRT3-2) were identified, the number of which was less than that of foxtail millet. SbNRT2/3 were distributed on 3 chromosomes, and could be divided into four subfamilies. The genetic structure of the same subfamilies was highly similar. The average value of SbNRT2/3 hydrophilicity was positive, indicating that they were all hydrophobic proteins, whereas α-helix and random coil accounted for more than 70% of the total secondary structure. Subcellular localization occurred on plasma membrane, where SbNRT2 proteins did not contain signal peptides, but SbNRT3 proteins contained signal peptides. Further analysis revealed that the number of transmembrane domains of the SbNRT2s family members was greater than 10, while that of the SbNRT3s were 2. There was a close collinearity between NRT2/3s of S. bicolor and Zea mays. Protein domains analysis showed the presence of MFS_1 and NAR2 protein domains, which supported executing high affinity nitrate transport. Phylogenetic tree analysis showed that SbNRT2/3 were more closely related to those of Z. mays and Setaria italic. Analysis of gene promoter cis-acting elements indicated that the promoter region of SbNRT2/3 had several plant hormones and stress response elements, which might respond to growth and environmental cues. Gene expression heat map showed that SbNRT2-3 and SbNRT3-1 were induced by nitrate in the root and stem, respectively, and SbNRT2-4 and SbNRT2-3 were induced by low nitrogen in the root and stem. Non-synonymous SNP variants were found in SbNRT2-4 and SbNRT2-1a. Selection pressure analysis showed that the SbNRT2/3 were subject to purification and selection during evolution. The expression of SbNRT2/3 gene and the effect of aphid infection were consistent with the expression analysis results of genes in different tissues, and SbNRT2-1b and SbNRT3-1 were significantly expressed in the roots of aphid lines 5-27sug, and the expression levels of SbNRT2-3, SbNRT2-4 and SbNRT3-2 were significantly reduced in sorghum aphid infested leaves. Overall, genome-wide identification, expression and DNA variation analysis of NRT2/3 gene family of Sorghum bicolor provided a basis for elucidating the high efficiency of sorghum in nitrogen utilization.

Functional analyses of single nucleotide polymorphic variants of the DNA glycosylase NEIL1 in sub-Saharan African populations

Nei-like glycosylase 1 (NEIL1) is a DNA repair enzyme that initiates the base excision repair (BER) pathway to cleanse the human genome of damage. The substrate specificity of NEIL1 includes several common base modifications formed under oxidative stress conditions, as well as the imidazole ring open adducts that are induced by alkylating agents following initial modification at N7 guanine. An example of the latter is the persistent and mutagenic 8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxyaflatoxin B1 (AFB1-FapyGua) adduct, resulting from the alkylating agent aflatoxin B1 (AFB1) exo-8–9-epoxide. Naturally occurring single nucleotide polymorphic (SNP) variants of NEIL1 are hypothesized to be associated with an increased risk for development of early-onset hepatocellular carcinoma (HCC), especially in environments with high exposures to aflatoxins and chronic inflammation from viral infections and alcohol consumption. Given that AFB1 exposures and hepatitis B viral (HBV) infections represent a major problem in the developing countries of sub-Saharan Africa, it is pertinent to study SNP NEIL1 variants that are present in this geographic region. In this investigation, we characterized the three most common NEIL1 variants found in this region: P321A, R323G, and I182M. Biochemical analyses were conducted to determine the proficiencies of these variants in initiating the repair of DNA lesions. Our data show that damage recognition and excision activities of P321A and R323G were near that of wild-type (WT) NEIL1 for both thymine glycol (ThyGly) and AFB1-FapyGua. The substrate specificities of these variants with respect to various oxidatively-induced base lesions were also similar to that of WT. In contrast, the I182M variant was unstable, such that it precipitated under a variety of conditions and underwent rapid inactivation at a biologically relevant temperature, with partial stabilization being observed in the presence of undamaged DNA. This study provides insight regarding the potential increased risk for early-onset HCC in human populations carrying the NEIL1 I182M variant.

Sequence analysis of TLR4 gene in river buffalo (Egyptian breed) and SNPs association with Mastitis

BackgroundMastitis is a major cause of economic loss for dairy farmers and industry. River buffalo plays an economically significant role in Egypt. Buffaloes with mastitis have reduced milk yield and change in milk composition. Genetic variations in the Toll-like receptor4 (TLR4) gene have been related to several diseases in farm animals and humans including mastitis. The present investigation aims to find the genotypic variations in the TLR4 gene and their relation to mastitis in the river buffalo, Egyptian breed.ResultsDNA from 30 buffaloes' blood samples (15 healthy and 15 with mastitis) were extracted and the TLR4 gene was sequenced. Twenty-one Single nucleotide polymorphisms (SNPs) were found from which four SNPs were associated with mastitis: one in 5'UTR (c.1-g27) and 3 SNPs in the coding region at c.87, c.575, and c.576. The nucleotide variations in SNPs c.1-g27(C > A) and c.87 (C > A) were only present in buffalo with mastitis, while buffaloes with genotype CC at both locations were healthy. The AA genotype at c.87 (P.29) results in a stop codon leading to an abnormally shortened protein. The nonsynonymous SNPs c.575 A > G and c.576 T > G shared amino acid 192 resulting in three amino acids (His192Arg/Gln). The dominant genotypes AA at c.575 and TT at c.576 were associated with mastitis resistance (OR < 1.00), while recessive genotype GG at c.575 was associated with mastitis susceptibility (OR > 1.00). These two SNPs may affect their role in ligand recognition since they were in the LRR4 domain (p.174–p.197) which is part of coreceptor binding region 1.ConclusionsThe present study confirms the relation between TLR4 genotypes and mastitis resistance or mastitis susceptibility in Egyptian dairy buffalo. The study suggested four SNPs (c1-g27C > A, c.87 C > A, c.575A > G, and c.576 T > G) have the potential to be markers for assisted buffalo selection to improve milk production.

Single Nucleotide Polymorphisms of FAM13A Gene in Chronic Obstructive Pulmonary Disease-A Case Control Study in Vietnam.

In 2018, GOLD addressed the issues of genotypes associated with risk factors for COPD. The genome-wide association study (GWAS) demonstrated an association between COPD and several genetic variants of single nucleotide polymorphisms (SNPs) of the FAM13A gene with the risk of COPD. To study the single nucleotide polymorphisms rs2869967 and rs17014601 of the FAM13A gene in chronic obstructive pulmonary disease. Subjects and research methods: 80 subjects diagnosed with COPD and 80 subjects determined not to have COPD according to GOLD 2020 criteria; the subjects were clinically examined, interviewed, and identified as possessing single nucleotide polymorphisms using the sanger sequencing method on whole blood samples. The male/female ratio of the patient group and the control group was 79/1 and 39/1, respectively. The percentages of C and T alleles of rs2869967 in COPD patients were 50.6% and 49.4%, respectively. The percentages of C and T alleles of rs17014601 in COPD patients were 31.9% and 68.1%, respectively. At rs17014601, the ratio values of alleles T and C in the disease group and the control group were markedly different, making them statistically reliable (p = 0.031). The rate of CT genotype in the group of patients was considerably higher than that of the control group. The TT homozygous genotype had a lower risk of COPD compared with the other genotypes in the dominant model (ORTT/(CC + CT) = 0.441; CI95% = 0.233-0.833); this difference was statistically significant (p = 0.012). With rs17014601, it is characteristic that the frequency of the T allele appears more than the C allele, and the CT heterozygous phenotype accounts for the highest proportion in rs17014601 and rs2869967 recorded in COPD patients. There is an association between the genetic variant of the SNP FAM13A-rs17014601 and the risk of COPD.

Genome-Wide Association Analysis for Resistance to Coniothyrium glycines Causing Red Leaf Blotch Disease in Soybean.

Soybean is a high oil and protein-rich legume with several production constraints. Globally, several fungi, viruses, nematodes, and bacteria cause significant yield losses in soybean. Coniothyrium glycines (CG), the causal pathogen for red leaf blotch disease, is the least researched and causes severe damage to soybean. The identification of resistant soybean genotypes and mapping of genomic regions associated with resistance to CG is critical for developing improved cultivars for sustainable soybean production. This study used single nucleotide polymorphism (SNP) markers generated from a Diversity Arrays Technology (DArT) platform to conduct a genome-wide association (GWAS) analysis of resistance to CG using 279 soybean genotypes grown in three environments. A total of 6395 SNPs was used to perform the GWAS applying a multilocus model Fixed and random model Circulating Probability Unification (FarmCPU) with correction of the population structure and a statistical test p-value threshold of 5%. A total of 19 significant marker-trait associations for resistance to CG were identified on chromosomes 1, 5, 6, 9, 10, 12, 13, 15, 16, 17, 19, and 20. Approximately 113 putative genes associated with significant markers for resistance to red leaf blotch disease were identified across soybean genome. Positional candidate genes associated with significant SNP loci-encoding proteins involved in plant defense responses and that could be associated with soybean defenses against CG infection were identified. The results of this study provide valuable insight for further dissection of the genetic architecture of resistance to CG in soybean. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving resistance traits in soybean.

Genome-Wide Association Study Identifies the Crucial Candidate Genes for Teat Number in Crossbred Commercial Pigs.

The number of teats is a crucial reproductive trait with significant economic implications on maternal capacity and litter size. Consequently, improving this trait is essential to facilitate genetic selection for increased litter size. In this study, we performed a genome-wide association study (GWAS) of the number of teats in a three-way crossbred commercial Duroc × (Landrace × Yorkshire) (DLY) pig population comprising 1518 animals genotyped with the 50K BeadChip. Our analysis identified crucial quantitative trait loci (QTL) for the number of teats, containing the ABCD4 and VRTN genes on porcine chromosome 7. Our results establish SNP variants of ABCD4 and VRTN as new molecular markers for improving the number of teats in DLY pigs. Furthermore, the most significant noteworthy single nucleotide polymorphism (SNP) (7_97568284) was identified within the ABCD4 gene, exhibiting a significant association with the total teat number traits. This SNP accounted for a substantial proportion of the genetic variance, explaining 6.64% of the observed variation. These findings reveal a novel gene on SSC7 for the number of teats and provide a deeper understanding of the genetic mechanisms underlying reproductive traits.

High‐throughput genotyping in estimating genetic resources and detecting pathogens in aquaculture

High‐throughput genotyping in estimating genetic resources and detecting pathogens in aquaculture

Genetic Preference for Sweet Taste in Mothers Associates with Mother-Child Preference and Intake.

Taste perception is a well-documented driving force in food selection, with variations in, e.g., taste receptor encoding and glucose transporter genes conferring differences in taste sensitivity and food intake. We explored the impact of maternal innate driving forces on sweet taste preference and intake and assessed whether their children differed in their intake of sweet foods or traits related to sweet intake. A total of 133 single nucleotide polymorphisms (SNPs) in genes reported to associate with eating preferences were sequenced from saliva-DNA from 187 mother-and-child pairs. Preference and intake of sweet-, bitter-, sour-, and umami-tasting foods were estimated from questionnaires. A total of 32 SNP variants associated with a preference for sweet taste or intake at a p-value < 0.05 in additive, dominant major, or dominant minor allele models, with two passing corrections for multiple testing (q < 0.05). These were rs7513755 in the TAS1R2 gene and rs34162196 in the OR10G3 gene. Having the T allele of rs34162196 was associated with higher sweet intake in mothers and their children, along with a higher BMI in mothers. Having the G allele of rs7513755 was associated with a higher preference for sweets in the mothers. The rs34162196 might be a candidate for a genetic score for sweet intake to complement self-reported intakes.

EVALUATING THE ASSOCIATION BETWEEN APOLIPOPROTEIN A5 SINGLE NUCLEOTIDE POLYMORPHISMS (APOA5 SNPS) AND HYPERTRIGLYCERIDEMIA

The retrospective study was conducted at the Faisalabad Institute of Cardiology from January 2022 to January 2023 to evaluate the association between apolipoprotein A5 single nucleotide polymorphisms (APOA5 SNPS) and hypertriglyceridemia in the Pakistani population and assess the efficacy of fibrate therapy in hypertriglyceridemic patients. Blood samples of patients were collected for DNA extraction by the standard inorganic method. Extracted DNA was analyzed biochemically and genetically following the selection and genotyping of the APOA5 gene to know SNP variants with risk alleles. We analyzed lipid profiles, including TG (triglyceride), HDL (high-density lipoprotein), and LDL (low-density lipoprotein) levels of hypertriglyceridemic patients, then compared them to normal and fibrate-treated individuals. We compared APOA5 (rs662799) SNP (single nucleotide polymorphism) among 50 hypertriglyceridemic, 50 healthy controls, and among the same 50 hypertriglyceridemic patients who were given fibrate. Results showed that fibrate decreased TG level and LDL by about 30-45% and 20-25%, respectively; increased high-density lipoprotein by 10-15% and total cholesterol decreased by 6-8% in Pakistani. Hypertriglyceridemia risk was significantly increased by a minor allele of APOA5 rs662799 polymorphism. Minor allele carriers of rs662799 had an odd ratio of (95% CI) 1.5 (1.03-2.18) (P = 0.032). Risk allele frequency differed among hypertriglyceridemic patients, healthy controls, and fibrate-treated hypertriglyceridemic individuals. We analyzed that 87.5% of healthy controls exhibited no risk allele, while 78% did not show this risk allele among hypertriglyceridemic patients. It was concluded that APOA5 rs662799 polymorphism is a genetic determinant of hypertriglyceridemia. Fibrate caused a reduction in TG and LDL and caused an elevation of HDL-C among hypertriglyceridemic patients.

Molecular characterization and SNP identification using genotyping-by-sequencing in high-yielding mutants of proso millet.

Proso millet (Panicummiliaceum L.) is a short-duration C4 crop that is drought tolerant and nutritionally rich and can grow well in marginal lands. Though the crop has many climate-resilient traits like tolerance to drought and heat, its yield is lower than that of common cereals like rice, wheat, and maize. Being an underutilized crop, the molecular resources in the crop are limited. The main aim of the present study was to develop and characterize contrasting mutants for yield and generate functional genomic information for the trait in proso millet. Gamma irradiation-induced mutant population was screened to identify high-yielding mutants, which were evaluated up to M4 generation. One mutant with a dense panicle and high yield (ATL_hy) and one with a lax panicle and low yield (ATL_ly) along with the wild type were sequenced using the genotyping-by-sequencing approach. The variants detected as single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) were annotated against the reference genome of proso millet. Bioinformatic analyses using the National Center for Biotechnology Information (NCBI) and UniProt databases were performed to elucidate genetic information related to the SNP variations. A total of 25,901, 30,335, and 31,488 SNPs, respectively, were detected in the wild type, ATL_hy mutants, and ATL_ly mutants. The total number of functional SNPs identified in high-yielding and low-yielding mutants was 84 and 171, respectively. Two functional SNPs in the high-yielding mutant (ATL_hy) and one in the low-yielding mutant (ATL_ly) corresponded to the gene coding for "E3 ubiquitin-protein ligase UPL7". Pathway mapping of the functional SNPs identified that two SNPs in ATL_ly were involved in the starch biosynthetic pathway coding for the starch synthase enzyme. This information can be further used in identifying genes responsible for various metabolic processes in proso millet and in designing useful genetic markers.

Whole-Genome Analysis of Bordetella pertussis MT27 Isolates from School-Associated Outbreaks: Single-Nucleotide Polymorphism Diversity and Threshold of the Outbreak Strains.

Bordetella pertussis, the causative agent of whooping cough, can cause pertussis outbreaks in humans, especially in school-aged children. Here, we performed whole-genome sequencing of 51 B. pertussis isolates (epidemic strain MT27) collected from patients infected during 6 school-associated outbreaks lasting less than 4 months. We compared their genetic diversity with that of 28 sporadic isolates (non-outbreak MT27 isolates) based on single-nucleotide polymorphisms (SNPs). Our temporal SNP diversity analysis revealed a mean SNP accumulation rate (time-weighted average) of 0.21 SNPs/genome/year during the outbreaks. The outbreak isolates showed a mean of 0.74 SNP differences (median, 0; range, 0 to 5) between 238 isolate pairs, whereas the sporadic isolates had a mean of 16.12 SNP differences (median, 17; range 0 to 36) between 378 isolate pairs. A low SNP diversity was observed in the outbreak isolates. Receiver operating characteristic analysis demonstrated that the optimal cutoff value to distinguish between the outbreak and sporadic isolates was 3 SNPs (Youden's index of 0.90 with a true-positive rate of 0.97 and a false-positive rate of 0.07). Based on these results, we propose an epidemiological threshold of ≤3 SNPs per genome as a reliable marker of B. pertussis strain identity during pertussis outbreaks that span less than 4 months. IMPORTANCE Bordetella pertussis is a highly infectious bacterium that easily causes pertussis outbreaks in humans, especially in school-aged children. In detection and investigation of outbreaks, excluding non-outbreak isolates is important for understanding the bacterial transmission routes. Currently, whole-genome sequencing is widely used for outbreak investigations, and the genetic relatedness of outbreak isolates is assessed based on differences in the number of single-nucleotide polymorphisms (SNPs) in the genomes of different isolates. The optimal SNP threshold defining strain identity has been proposed for many bacterial pathogens, but not for B. pertussis. In this study, we performed whole-genome sequencing of 51 B. pertussis outbreak isolates and identified a genetic threshold of ≤3 SNPs per genome as a marker defining the strain identity during pertussis outbreaks. This study provides a useful marker for identifying and analyzing pertussis outbreaks and can serve as a basis for future epidemiological studies on pertussis.

US Population Data for 94 Identity-Informative SNP Loci.

The US National Institute of Standards and Technology (NIST) analyzed a set of 1036 samples representing four major US population groups (African American, Asian American, Caucasian, and Hispanic) with 94 single nucleotide polymorphisms (SNPs) used for individual identification (iiSNPs). The compact size of iiSNP amplicons compared to short tandem repeat (STR) markers increases the likelihood of successful amplification with degraded DNA samples. Allele frequencies and relevant forensic statistics were calculated for each population group as well as the aggregate population sample. Examination of sequence data in the regions flanking the targeted SNPs identified additional variants, which can be combined with the target SNPs to form microhaplotypes (multiple phased SNPs within a short-read sequence). Comparison of iiSNP performance with and without flanking SNP variation identified four amplicons containing microhaplotypes with observed heterozygosity increases of greater than 15% over the targeted SNP alone. For this set of 1036 samples, comparison of average match probabilities from iiSNPs with the 20 CODIS core STR markers yielded an estimate of 1.7 × 10-38 for iiSNPs (assuming independence between all 94 SNPs), which was four orders of magnitude lower (more discriminating) than STRs where internal sequence variation was considered, and 10 orders of magnitude lower than STRs using established capillary electrophoresis length-based genotypes.

Genetic polymorphism between the Sorani and Hawrami kurdish populations and COVID-19 outcome.

Coronavirus Disease 2019 (COVID-19) is a global pandemic, and mortality and clinical consequences vary across countries. One of the factors influencing COVID-19 outcomes is genetic polymorphism. Two Kurdish populations, Sorani and Hawrami, live in the Sulaimani province of the Kurdistan Region of Iraq. It seems Hawrami had a milder COVID-19 outcome. According to previous research conducted on various ethnic groups across the globe, single nucleotide polymorphisms (SNPs) in the interferon-induced transmembrane protein 3 (IFITM3) and interluken-6 (IL6) genes were associated with the severity of COVID-19 in those populations. We hypothesized that Hawrami may have protective SNPs. So, in this study, we used DNA sequencing to genotype three IFITM3 SNPs and nine IL6 SNPs by DNA sequencing to investigate the association of Sorani and Hawrami population polymorphisms. Genotype AA for the rs12252 SNP in IFITM3 was insignificantly more common in the Sorani group (54% vs. 44%). The Hawrami population showed a higher percentage of the CC genotype of the rs34481144 SNP in the IFITM3 gene (62% vs. 44.3%) and a higher proportion of the non-risky GG genotype of the rs1800795 SNP in the IL6 gene (53.4 vs. 43.3); however, the SNPs were insignificantly associated between the two populations. IFITM3 and IL6 SNPs have no statistically significant association between the two Kurdish populations. The decreased proportion of non-risk alleles at rs34481144 and rs1800795 in the Hawrami population may partially support the research hypothesis. However, contrary to our hypothesis, the Sorani group had an insignificantly higher protective variant of the rs12252 SNP.

LSPR-Based Biosensing Enables the Detection of Antimicrobial Resistance Genes.

The development of rapid, simple, and accurate bioassays for the detection of nucleic acids has received increasing demand in recent years. Here, localized surface plasmon resonance (LSPR) spectroscopy for the detection of an antimicrobial resistance gene, sulfhydryl variable β-lactamase (blaSHV), which confers resistance against a broad spectrum of β-lactam antibiotics is used. By performing limit of detection experiments, a 23 nucleotide (nt) long deoxyribonucleic acid (DNA) sequence down to 25nm wasdetected, whereby the signal intensity is inversely correlated with sequence length (23, 43, 63, and 100nt). In addition to endpoint measurements of hybridization events, the setup also allowed to monitor the hybridization events in real-time, and consequently enabled to extract kinetic parameters of the studied binding reaction. Performing LSPR measurements using single nucleotide polymorphism (SNP) variants of blaSHV revealed that these sequences can be distinguished from the fully complementary sequence. The possibility to distinguish such sequences is of utmost importance in clinical environments, as it allows to identify mutations essential for enzyme function and thus, is crucial for the correct treatment with antibiotics. Taken together, this system provides a robust, label-free, and cost-efficient analytical tool for the detection of nucleic acids and will enable the surveillance of antimicrobial resistance determinants.

Identification of novel Carnobacterium maltaromaticum strains in bone marrow samples of patients with acute myeloid leukemia using a metagenomic binning approach.

The aim of this study aimed to examine the existence of a bacterial metagenome in the bone marrow of patients with acute myeloid leukemia (AML). We re-examined whole-genome sequencing data from the bone marrow samples of seven patients with AML, four of whom were remitted after treatment, for metagenomic analysis. After the removal of human reads, unmapped reads were used to profile the species-level composition. We used the metagenomic binning approach to confirm whether the identified taxon was a complete genome of known or novel strains. We observed a unique and novel microbial signature in which Carnobacterium maltaromaticum was the most abundant species in five patients with AML or remission. The complete genome of C. maltaromaticum "BMAML_KR01," which was observed in all samples, was 100% complete with 8.5% contamination and closely clustered with C. maltaromaticum strains DSM20730 and SF668 based on single nucleotide polymorphism variations. We identified five unique proteins that could contribute to cancer progression and 104 virulent factor proteins in the BMAML_KR01 genome. To our knowledge, this is the first report of a new strain of C. maltaromaticum in patients with AML. The presence of C. maltaromaticum and its new strain in patients indicates an urgent need to validate the existence of this bacterium and evaluate its pathophysiological role.

Risk Loci For Chronic Obstructive Disease Reside On Chromosome 14: A Case-Control Study On The Pakistani Population.

Chronic Obstructive Pulmonary Disease (COPD), the third leading cause of death worldwide, is characterized by airflow limitation that can be due to abnormalities in the airway and/or alveoli. Genetic diagnosis at an early stage can be a key factor in the provision of accurate and timely treatment. Single Nucleotide polymorphisms (SNPs) are an important tool to study genetic association/ predisposition of the disease and have great potential to be diagnostic markers for early diagnosis of disease. This case-control COPD association study was designed for the five SNPs residing on potential candidate genes (SERPINA1, SERPINA3, RIN3), to check whether these genes are involved in the genetic predisposition for COPD in the Pakistani population or not. The SNAPshot method was used to find out the risk alleles and haplotypes using ABI Genetic analyzer 3130. GeneMapper, Haploview and PLINK 1.9 software were used for analyzing the genotypes and haplotypes taking smoking exposure and gender as covariates. Two of the SNPs, rs4934 and rs17473 were found to be independently and significantly associated with COPD in our studied population whereas haplotype H1 for two SNPs, rs754388 and rs17473 (that are in high linkage disequilibrium), was found to be a significant risk factor for developing COPD symptoms. SNP variants of SERPINA1 and SERPINA3 are significantly and independently associated with COPD in the local population of Pakistan.