Reference Single Nucleotide Polymorphisms Research Articles

The association of ZIC5 gene rs965623242 polymorphism with neural tube defects

Objective: This study aims to evaluate the effects of the rs965623242 reference single nucleotide polymorphism (SNP) on the ZIC5 gene in patients with neural tube defect (NTD). Patients and Methods: One hundred sixty-eight controls and one hundred sixty-eight NTD patients were included in the study. Deoxyribonucleic acid (DNA) isolation from peripheral blood samples was carried out for all participants. rs965623242 polymorphic region was amplified by polymerase chain reaction (PCR) and then sequenced. Results: In the 5’ untranslated region (UTR) of the first exon, guanine (G) to adenine (A) base change was detected in the 38th base of NM_033132.5. G to A base change was determined as GG genotype in 117 (69.6%), AG genotype in 30 (17.86%), and AA genotype in 21 (12.5%) patients. In the control group, GG genotype in 107 (63.7%), AG genotype in 23 (13.7%) and AA genotype in 38 (22.7%) were observed. The statistically significant difference was observed between the NTD and the control groups in ZIC5 genotypes or allele frequencies [p=0.044, odds ratio (OR)=0.49 (0.27-0.88) and p=0.021, OR=0.65 (0.46-0.93), respectively]. Conclusion: ZIC5 rs965623242 polymorphism may have a protective role in the NTD development in the Eastern Anatolian population, in Turkey. Although, these findings demonstrate that the rs965623242 polymorphism is associated with NTD, we do not clarify how its expression is affected during the embryonic period and ongoing processes. We will need advanced ongoing genetic and clinical studies to obtain more detail.

A Multilayered Post-Genome-Wide Association Study Analysis Pipeline Defines Functional Variants and Target Genes for Systemic Lupus Erythematosus.

Systemic lupus erythematosus (SLE), an autoimmune disease with incompletely understood etiology, has a strong genetic component. Although genome-wide association studies (GWASs) have revealed multiple SLE susceptibility loci and associated single-nucleotide polymorphisms (SNPs), the precise causal variants, target genes, cell types, tissues, and mechanisms of action remain largely unknown. Here, we report a comprehensive post-GWAS analysis using extensive bioinformatics, molecular modeling, and integrative functional genomic and epigenomic analyses to optimize fine-mapping. We compile and cross-reference immune cell-specific expression quantitative trait loci (cis- and trans-expression quantitative trait loci) with promoter capture high-throughput capture chromatin conformation (PCHi-C), allele-specific chromatin accessibility, and massively parallel reporter assay data to define predisposing variants and target genes. We experimentally validate a predicted locus using CRISPR/Cas9 genome editing, quantitative polymerase chain reaction, and Western blot. Anchoring on 452 index SNPs, we selected 9,931 high linkage disequilibrium (r2 > 0.8) SNPs and defined 182 independent non-human leukocyte antigen (HLA) SLE loci. The 3,746 SNPs from 143 loci were identified as regulating 564 unique genes. Target genes are enriched in lupus-related tissues and associated with other autoimmune diseases. Of these, 329 SNPs (106 loci) showed significant allele-specific chromatin accessibility and/or enhancer activity, indicating regulatory potential. Using CRISPR/Cas9, we validated reference SNP identifier 57668933 (rs57668933) as a functional variant regulating multiple targets, including SLE-risk gene ELF1 in B cells. We demonstrate and validate post-GWAS strategies for using multidimensional data to prioritize likely causal variants with cognate gene targets underlying SLE pathogenesis. Our results provide a catalog of significantly SLE-associated SNPs and loci, target genes, and likely biochemical mechanisms to guide experimental characterization.

IKZF3 polymorphisms contribute to the increased risk of acute lymphoblastic leukemia in children.

Acute lymphoblastic leukemia (ALL) is the most common cancer in children. IKZF3 (IKAROS family zinc finger 3) is a hematopoietic-specific transcription factor, and it has been validated that it is involved in leukemia. However, the role of IKZF3 single-nucleotide polymorphisms (SNPs) remains unclear. In this case-control study, the authors investigated the association of IKZF3 SNPs with ALL in children. Six IKZF3 reference SNPs (rs9635726, rs2060941, rs907092, rs12946510, rs1453559, and rs62066988) were genotyped in 692 patients who had ALL (cases) and in 926 controls. The associations between IKZF3 polymorphisms and ALL risk were determined using odds ratios (ORs) and 95% confidence intervals (CIs). The associations of rs9635726 and rs2060941 with the risk of ALL were further estimated by using false-positive report probability (FPRP) analysis. Functional analysis in silico was performed to evaluate the probability that rs9635726 and rs2060941 might influence the regulation of IKZF3. The authors observed that rs9635726C>T (adjusted OR, 1.49; 95% CI, 1.06-2.11; p=.023) and rs2060941G>T (adjusted OR, 1.51; 95% CI, 1.24-1.84; p=.001) were related to and increased risk of ALL in the recessive and dominant models, respectively. Furthermore, the associations of both rs9635726 (FPRP=.177) and rs2060941 (FPRP<.001) with ALL were noteworthy in the FPRP analysis. Functional analysis indicated that rs9635726 and rs2060941 might repress the transcription of IKZF3 by disrupting its binding to MLLT1, TAF1, POLR2A, and/or RAD21. This study revealed that IKZF3 polymorphisms were associated with increased ALL susceptibility in children and might influence the expression of IKZF3 by disrupting its binding to MLLT1, TAF1, POLR2A, and/or RAD21. IKZF3 polymorphisms were suggested as a biomarker for childhood ALL.

Combined reference-free and multi-reference based GWAS uncover cryptic variation underlying rapid adaptation in a fungal plant pathogen.

Microbial pathogens often harbor substantial functional diversity driven by structural genetic variation. Rapid adaptation from such standing variation threatens global food security and human health. Genome-wide association studies (GWAS) provide a powerful approach to identify genetic variants underlying recent pathogen adaptation. However, the reliance on single reference genomes and single nucleotide polymorphisms (SNPs) obscures the true extent of adaptive genetic variation. Here, we show quantitatively how a combination of multiple reference genomes and reference-free approaches captures substantially more relevant genetic variation compared to single reference mapping. We performed reference-genome based association mapping across 19 reference-quality genomes covering the diversity of the species. We contrasted the results with a reference-free (i.e., k-mer) approach using raw whole-genome sequencing data in a panel of 145 strains collected across the global distribution range of the fungal wheat pathogen Zymoseptoria tritici. We mapped the genetic architecture of 49 life history traits including virulence, reproduction and growth in multiple stressful environments. The inclusion of additional reference genome SNP datasets provides a nearly linear increase in additional loci mapped through GWAS. Variants detected through the k-mer approach explained a higher proportion of phenotypic variation than a reference genome-based approach and revealed functionally confirmed loci that classic GWAS approaches failed to map. The power of GWAS in microbial pathogens can be significantly enhanced by comprehensively capturing structural genetic variation. Our approach is generalizable to a large number of species and will uncover novel mechanisms driving rapid adaptation of pathogens.

Genetic Control of GCF Exudation: Innate Immunity Genes and Periodontitis Susceptibility.

Chronic periodontitis is a bacterial infection associated with dentally adherent biofilm (plaque) accumulation and age-related comorbidities. The disease begins as an inflammatory exudate from gingival margins, gingival crevicular fluid (GCF) in response to biofilm lysine. After a week of experimental gingivitis (no oral hygiene), biofilm lysine concentration was linearly related to biofilm accumulation (plaque index) but to GCF as an arch-shaped double curve which separated 9 strong from 6 weak GCF responders (hosts). Host DNA was examined for single nucleotide polymorphisms (SNPs) of alleles reported in 7 periodontitis-associated genes. Across all 15 hosts, an adenine SNP (A) at IL1B-511 (rs16944), was significant for strong GCF (Fisher's exact test, p < 0.05), and a thymidine SNP (T) at IL1B+3954 (rs1143634) for weak GCF provided 2 hosts possessing IL6-1363(T), rs2069827, were included. The phenotype of IL1B+3954(T) was converted from weak to strong in one host, and of the non-T allele from strong to weak in the other (specific epistasis, Fisher's exact test, p < 0.01). Together with homozygous alternate or reference SNPs at IL10-1082 or CD14-260 in 4 hosts, all hosts were identified as strong or weak GCF responders. The GCF response is therefore a strong or weak genetic trait that indicates strong or weak innate immunity in EG and controllable or uncontrollable periodontal disease, dental implant survival and late-life comorbidities.

Effects of DNA degradation and genotype imputation on high-density SNP microarray in pairwise kinship analysis

High-density single nucleotide polymorphisms (SNPs) can detect distant relatives even in the context of pairwise kinship analysis. Although DNA microarrays conveniently generate genome-wide SNP data, they require large quantities of high-quality DNA. Genotyping data obtained from low-quantity and low-quality samples are likely unreliable owing to the incidence of no-called or mistyped SNPs. In this study, we examined the effects of insufficient sample densities and sample degradation on the efficacy of kinship analysis. While low DNA amounts had a minor effect, DNA degradation led to a significant increase in no-call rates and error rates. Posterior probabilities of kinship determination, calculated using the index of chromosomal sharing, were markedly lower in proportion to the no-call rates and error rates. We also investigated the effect of genotype imputation to complement the no-called genome data utilizing SNPs reference panels. We found that the posterior probability of the relative-assumed person increased with genotype complementation in case of mild degradation, even with mistyped genotypes. Therefore, DNA microarray with imputation is a promising method for analyzing forensic DNA samples taken from situations where DNA quantity and quality may be compromised, such as disaster victim identification using pairwise kinship analysis.

PSIII-A-4 Analysis of Galectin Gene Variants from Diverse Sheep and Goat Populations Genotyped with the Illumina Beadchip

Abstract Galectins are a highly conserved family of β-galactoside binding lectins encoded by lectin, galactosidebinding soluble genes (LGALS). They are found on a variety of cells and tissues of vertebrates and invertebrates. Understanding the roles of galectins in host–pathogen interaction and activation of host innate, and adaptive immunity has become an important research question. Galectins are known to play a role in parasitic infection in small ruminants. However, little is known about LGALS variants in sheep and goat breeds across the world. In this study, we investigated galectin single nucleotide polymorphism (SNP) variants on five distinct sheep breeds from different geographical regions of Ethiopia. A total of 88 sheep (Arsi-Bale=12, Horro=24, Menz=18, Wolayita=18 and Blackhead Somali=16) were genotyped with Ovine Infinium HD SNP BeadChip (600K). An In Silico approach with Ensembl database (https://useast.ensembl.org/index.html) and SNP BeadChip (perfect matched reference SNP along with their genomic position) identified a total of nineteen SNPs from LGALS-1, -2, -3, -4, -7, -8, -9, -11 and -12 with a consequence of upstream, downstream, and missense gene variant. For all these variants, a highly variable minor allele frequency (MAF) was observed across five sheep populations. We also investigated a total of 308 Chinese goat (Qinggeli=48, Nanjiang=48, Luoping=48, Liaoning=116, and Guangfeng=48) genotyped with Illumina Goat 50K BeadChip. The goat chip only contained a SNP from LGal-4 (rs268252010) which was also found at variable MAF level across the said populations. These results have implications for animal health and production and warrant further investigation using targeted sequencing of galectin genes across different local and international sheep and goat breeds.

No association between dopamine D2 receptor (DRD2) alleles and crack/cocaine dependence in Brazilians

Introduction: The causal mechanisms behind crack/cocaine use are still unknown, but genetic influences are suggested. Objective: To investigate the relationship between the genetic polymorphism TaqI (rs1800497) in the dopamine D2 receptor (DRD2) gene and susceptibility to crack/cocaine dependence in a group of addicts to crack/cocaine and a non-addicted group. Methods: The case group (n=515) was composed of crack/cocaine-dependent men and the control group (n=106) comprised men who were considered not dependent on crack/cocaine. The oral hygiene habits, decayed, missing, and filled teeth index, gingival index, and plaque index were evaluated. The reference single nucleotide polymorphism (rs1800497 C/T) of the DRD2 gene was genotyped by a real-time polymerase chain reaction technique. Student’s t-tests for independent samples or the non-parametric Mann-Whitney test were used to compare groups regarding quantitative variables. Results: The case group showed a mean time of 9.91±7.03 years of crack use, and 61.06±92.96 stones/week. The socio-demographic profile of the sample was White, single men, with basic education, blue-collar worker, smoker, and reporting alcohol use. There was a high frequency of gingival inflammation, plaque accumulation, and caries experience. For all genetic models tested, there was no significant difference in the genotypic frequency in rs1800497 of the DRD2 gene, between case and control groups (p&gt;0.05). Conclusion: The genetic variant in the DRD2 did not increase the vulnerability to develop crack/cocaine dependence. The complex genetic nature of crack/cocaine dependence and a large variation of DRD2 allele frequencies, depending on the population group sampled, could be one explanation for the no association.

Genetic Determinants of Type 2 Diabetes Mellitus in Adults of African Ancestry: Identification of the Associated Factors

ObjectivesH1: ADCYAP1R1, BDNF, CD36, HDAC4, NOS3, PON1, TCF7L2, TGFB1 were predominant in adults of African ancestry with or without T2DM. H2: There is a relationship between HBA1C, TG, LDL, FG, FI and genetic associations among adults of African ancestry and the following: H2a: ACGT risk alleles H2b: Chromosomal regions 2, 7, 10, 11, 19 H2c: Sequence variant impacts: intergenic, intron, missense, and synonymous H2d: Minor allele frequencies < .05 H2e: Lead reference SNPs H2f: Variant coordinates H3: ALDH1A1, B3GALT2, C8orf37, CASP16, CCSAP, CDKN2B, CHRNA5, CRNN, CYP7B1, FAT4, FOXP1, GPC6, GRM4, LMCD1, MMP19, MYOM2, NOL11, PHF8, RP11-180C1.1, SLC45A1, SLC9A8, TLE1, ZPLD1 were predominant in adults of African ancestry with peripheral vascular disease in T2DM.MethodsQuantitative assessment of secondary data in the Type 2 Diabetes Knowledge Portal comprising nutritional phenotypic traits (peripheral vascular disease, hemoglobin A1C, triglycerides, low-density lipoprotein, fasting glucose, fasting insulin) and genetic associations risk allele, minor allele frequencies, reference single nucleotide polymorphisms, candidate genes, chromosomal regions, variant coordinates, and sequence variation impacts) related to Type 2 Diabetes Mellitus (T2DM) among adults of African ancestry with or without Type 2 Diabetes Mellitus to understand T2DM hereditary disease risk.ResultsH1 Results: χ2 (126, n = 5,877) = 1228.713, p < .001 H2a Results: χ2 (20, n = 62) = 43.052, p = .002 H2b Results: χ2 (20, n = 62) = 106.969, p < .001 H2c Results: χ2 (15, n = 62) = 60.470, p < .001 H2d Results: χ2 (228, n = 60) = 210.000, p = .798 H2e Results: χ2 (240, n = 61) = 269.118, p = .095 H2f Results: χ2 (245, n = 62) = 273.529, p = .102 H3 Results: χ2 (264, n = 23) = 276.000, p = .293ConclusionsHereditary disease risks for Type 2 Diabetes nutritional phenotypes and genetic associations are distinct in adults of African ancestry with or without Type 2 Diabetes Mellitus diagnosis.Funding SourcesHoward University.

Occurrence of Cystic Fibrosis Transmembrane Conductance Regulator Gene Mutations in Patients with Allergic Bronchopulmonary Aspergillosis Complicating Asthma.

Whether cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations contribute to the high prevalence of allergic bronchopulmonary aspergillosis (ABPA) in India remains unknown. We aimed to evaluate the occurrence of CFTR mutations in subjects with ABPA complicating asthma. We sequenced the CFTR gene using genomic DNA from blood on the Illumina NextSeq500 platform. Before undertaking zygosity analysis by genome analysis toolkit, the known or novel single nucleotide polymorphisms (SNPs) and indels were called. For rigorous analysis, we included only high-quality SNPs (scores > 500) and coverage ranging from 30 × 150x. We included 18, 12, and eight adult participants of ABPA, asthma, and healthy controls, respectively. The frequency of SNPs was higher in asthmatic subjects than ABPA or healthy controls, albeit not statistically significant (9/12 [75%] vs. 11/18 [61.1%] vs. 3/8 [37.5%], p = 0.24). Of the 38 subjects, 23 yielded 50 variants (healthy controls [n = 5], ABPA [n = 22], asthma [n = 23]) corresponding to six SNPs not previously linked with ABPA. Of these, four SNPs (rs213950, rs200735475, rs1800113, and rs1800136) were catalogued in the NCBI database. We identified two novel SNPs (chr7:117250703, chr7:117282655) in four (ABPA [n = 1], asthma [n = 3]) subjects without corresponding reference SNP. Most SNPs (85.5%) were heterozygous. The frequency of SNPs was higher in ABPA subjects with high-attenuation mucus (52.2%) and bronchiectasis (39.1%) than serological ABPA (8.7%). Our study suggests the role of CFTR mutations in the pathogenesis of ABPA. The SNPs in the CFTR gene may contribute to disease severity in ABPA. Larger studies are required to confirm our findings.

Current status and relevance of single nucleotide polymorphisms in IL-6-/IL-12-type cytokine receptors.

Cytokines control immune related events and are critically involved in a plethora of patho-physiological processes including autoimmunity and cancer development. In rare cases, single nucleotide polymorphisms (SNPs) or single nucleotide variations (SNVs) in cytokine receptors eventually cause detrimental ligand-independent, constitutive activation of signal transduction. Most SNPs have, however, no or only marginal influences on gene expression, protein stability, localization and function and thereby only slightly affecting pathogenesis probability. The SNP database (dbSNP) is an archive for a broad collection of polymorphisms in which SNPs are categorized and marked with a locus accession number "reference SNP" (rs). Here, we engineered an algorithm to directly align dbSNP information to DNA and protein sequence information to clearly illustrate a genetic SNP landscape exemplified for all tall cytokine receptors of the IL-6/IL-12 family, including IL-23R, IL-12Rβ1, IL-12Rβ2, gp130, LIFR, OSMR and WSX-1. This information was complemented by a comprehensive literature summary and structural insights of relevant disease-causing SNPs in cytokine/cytokine receptor interfaces. In summary, we present a general strategy with potential to apply to other cytokine receptor networks.

Ancestral Spectrum Analysis With Population-Specific Variants.

With the advance of sequencing technology, an increasing number of populations have been sequenced to study the histories of worldwide populations, including their divergence, admixtures, migration, and effective sizes. The variants detected in sequencing studies are largely rare and mostly population specific. Population-specific variants are often recent mutations and are informative for revealing substructures and admixtures in populations; however, computational methods and tools to analyze them are still lacking. In this work, we propose using reference populations and single nucleotide polymorphisms (SNPs) specific to the reference populations. Ancestral information, the best linear unbiased estimator (BLUE) of the ancestral proportion, is proposed, which can be used to infer ancestral proportions in recently admixed target populations and measure the extent to which reference populations serve as good proxies for the admixing sources. Based on the same panel of SNPs, the ancestral information is comparable across samples from different studies and is not affected by genetic outliers, related samples, or the sample sizes of the admixed target populations. In addition, ancestral spectrum is useful for detecting genetic outliers or exploring co-ancestry between study samples and the reference populations. The methods are implemented in a program, Ancestral Spectrum Analyzer (ASA), and are applied in analyzing high-coverage sequencing data from the 1000 Genomes Project and the Human Genome Diversity Project (HGDP). In the analyses of American populations from the 1000 Genomes Project, we demonstrate that recent admixtures can be dissected from ancient admixtures by comparing ancestral spectra with and without indigenous Americans being included in the reference populations.

Effect of SLCO1B1 T521C on Statin-Related Myotoxicity With Use of Lovastatin and Atorvastatin.

The association between the c.521T>C variant allele in SLCO1B1 (reference single nucleotide polymorphism (rs)4149056) and simvastatin-induced myotoxicity was discovered over a decade ago; however, whether this relationship represents a class effect is still not fully known. The aim of this study was to investigate the relationship between rs4149056 genotype and statin-induced myotoxicity in patients taking atorvastatin and lovastatin. Study participants were from the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort. A total of 233 statin-induced myopathy + rhabdomyolysis cases met the criteria for inclusion and were matched to 2,342 controls. To validate the drug response phenotype, we replicated the previously established association between rs4149056 genotype and simvastatin-induced myotoxicity. In particular, compared with homozygous T allele carriers, there was a significantly increased risk of simvastatin-induced myopathy+rhabdomyolysis in homozygous carriers of the C allele (CC vs. TT, odds ratio [OR] 4.62, 95% confidence interval [CI] 1.58-11.90, P=0.003). For lovastatin users, homozygous carriers of the C allele were also at increased risk of statin-induced myopathy+rhabdomyolysis (CC vs. TT, OR 4.49, 95% CI 1.68-10.80, P=0.001). In atorvastatin users, homozygous carriers of the C allele were twice as likely to experience statin-induced myopathy, though this association did not achieve statistical significance (CC vs. TT, OR 2.00, 95% CI 0.44-6.59, P=0.30). In summary, our findings suggest that the association of rs4149056 with simvastatin-related myotoxicity may also extend to lovastatin. More data is needed to determine the extent of the association in atorvastatin users. Altogether, these data expand the evidence base for informing guidelines of pharmacogenetic-based statin prescribing practices.

Secure and optimized detection of PNPLA3 rs738409 genotype by an improved PCR-restriction fragment length polymorphismmethod.

The PNPLA3reference single-nucleotide polymorphism rs738409 has been identified as a predisposing factor for nonalcoholic fatty liver disease. A simple method based on PCRandrestriction fragment length polymorphism (RFLP) analysis had been published to detect the nonpathogenic allelePNPLA3 rs738409variant. The presence of the pathogenic variant was deduced by the indigestibility of the corresponding PCR product with BtsCI recognizing the nonpathogenic allele. However, one cannot exclude that an enzymatic reaction does not occur for other, more trivial, reasons. For safe and secure detection of the pathogenic PNPLA3 rs738409, we have further developed the PCR-restriction fragment length polymorphism methodby adding a second restriction enzyme digest, clearly identifying the correct PNPLA3 alleles and in particular the pathogenic variant.

Association between interleukin 28B polymorphism and sustained virological response to sofosbuvir plus daclatasvir in chronic hepatitis C genotype 4 Egyptian patients

Sofosbuvir has been approved as the first nonstructural protein 5Bpolymerase inhibitor with pan-genotypic activity against the hepatitis C (HCV) virus. Daclatasvir is a first-in-class hepatitis C virus nonstructural protein 5A replication complex inhibitor. We aimed to evaluate the usefulness of the reference single nucleotide polymorphism (rs12979860) interleukin 28B (CC genotype) for predicting sustained virological response to sofosbuvir plus daclatasvir in Egyptian patients infected with HCV-4. Samples were collected at week zero. One hundred and thirty-one patients who reached the end of treatment (at week 12) were divided into three groups, according to their interleukin 28B genotype: Group A included 31 patients (CC genotype), group B included 79 patients (CT genotype) and group C had 21 patients (TT genotype). All patients received treatment for 3months in the form of sofosbuvir plus daclatasvir with ribavirin (in case of cirrhotic patients) or without ribavirin (in case of non-cirrhotic patients). Sustained virological response rate was significantly higher in patients with IL28B (CC genotype) vs. (non-CC genotype) (100 vs.88%) (p<0.0001).These patients also showed lower rates of post-treatment relapse and non-response, compared with the CT and TT patients (0% vs. (7.59% and 28.5%, respectively) (p<0.0001). Also, patients with CC genotype showed higher sustained virological response than non-CC genotypes on both cirrhotic (100% vs. 68.75%) and non-cirrhotic patients (100% vs. 91.66%) (p≤0.0001). Our results suggest that IL28B genotype contributes to the prediction of response to sofosbuvir plus daclatasvir.

Inference of Ancestries and Heterozygosity Proportion and Genotype Imputation in West African Cattle Populations.

Several studies have evaluated computational methods that infer the haplotypes from population genotype data in European cattle populations. However, little is known about how well they perform in African indigenous and crossbred populations. This study investigates: (1) global and local ancestry inference; (2) heterozygosity proportion estimation; and (3) genotype imputation in West African indigenous and crossbred cattle populations. Principal component analysis (PCA), ADMIXTURE, and LAMP-LD were used to analyse a medium-density single nucleotide polymorphism (SNP) dataset from Senegalese crossbred cattle. Reference SNP data of East and West African indigenous and crossbred cattle populations were used to investigate the accuracy of imputation from low to medium-density and from medium to high-density SNP datasets using Minimac v3. The first two principal components differentiated Bos indicus from European Bos taurus and African Bos taurus from other breeds. Irrespective of assuming two or three ancestral breeds for the Senegalese crossbreds, breed proportion estimates from ADMIXTURE and LAMP-LD showed a high correlation (r ≥ 0.981). The observed ancestral origin heterozygosity proportion in putative F1 crosses was close to the expected value of 1.0, and clearly differentiated F1 from all other crosses. The imputation accuracies (estimated as correlation) between imputed and the real data in crossbred animals ranged from 0.142 to 0.717 when imputing from low to medium-density, and from 0.478 to 0.899 for imputation from medium to high-density. The imputation accuracy was generally higher when the reference data came from the same geographical region as the target population, and when crossbred reference data was used to impute crossbred genotypes. The lowest imputation accuracies were observed for indigenous breed genotypes. This study shows that ancestral origin heterozygosity can be estimated with high accuracy and will be far superior to the use of observed individual heterozygosity for estimating heterosis in African crossbred populations. It was not possible to achieve high imputation accuracy in West African crossbred or indigenous populations based on reference data sets from East Africa, and population-specific genotyping with high-density SNP assays is required to improve imputation.

The Plasma Levels and Polymorphisms of Vitronectin Predict Radiation Pneumonitis in Patients With Lung Cancer Receiving Thoracic Radiation Therapy

Our previous findings have identified vitronectin (VTN) as a potential biomarker for radiation pneumonitis (RP) through proteomics and molecular mechanism studies. In a recent study, we further explored associations of plasma level and single nucleotide polymorphisms of VTN with the risk of RP in patients with lung cancer receiving radiation therapy. A total of 165 patients with lung cancer were prospectively enrolled with detection of VTN concentration before radiation therapy. VTN reference single nucleotide polymorphisms, rs704 and rs2227721, were genotyped by Taqman probe method. Cox proportional hazard models were performed to identify clinical variables and genotypes associated with the risk of RP on univariate and multivariate analyses, and t tests and analysis of variance were conducted to evaluate the expression level of VTN. The baseline secretion level of VTN in patients with grade ≥3 RP was significantly higher than that in grade <3 RP patients (P < .0001), and elevated levels were observed in patients having the AA genotype compared with GA/GG genotypes of rs704. The VTN rs704 GA/GG and rs2227721 AA/AC genotypes had a significantly lower risk of RP (hazard ratio [HR], 0.448, P = .005; HR, 0.419, P = .008, respectively). In addition, combining cut-off values of mean lung dose (MLD) and VTN plasma level, grade ≥3 RP risk groupings were as follows: high risk: MLD ≥12 Gy and VTN level ≥132 μg/mL (RP rate, 10 of 16 patients, 62.5%); intermediate risk: MLD ≥12 Gy and VTN level <132 μg/mL or MLD <12 Gy and VTN level ≥132 μg/mL (8 of 70 patients, 11.4%); and low risk: MLD <12 Gy and VTN level <132 μg/mL (1 of 79 patients, 1.3%) (P < .0001). Among patients receiving radiation therapy, relatively high plasma levels of VTN before radiation therapy were associated with the higher incidence of RP, and VTN rs704 and rs2227721 each had a significant effect on predicting RP risk. Combining VTN concentration with MLD appeared to facilitate stratification of patients with lung cancer who received radiation therapy into low-, intermediate-, and high-risk RP groups. This study indicated that VTN may serve as a blood biomarker for susceptibility to RP in patients with lung cancer.

HLA-Cw6 and other HLA-C alleles, as well as MICB-DT, DDX58, and TYK2 genetic variants associate with optimal response to anti-IL-17A treatment in patients with psoriasis

ABSTRACT Objective: Our pharmacogenomic study evaluated the influence of the presence/absence of genetic variants of psoriasis-risk loci on the clinical response to secukinumab. Differences in the single-nucleotide polymorphism (SNP) pattern characterizing HLA-Cw6+ or HLA-Cw6− patient subpopulations, showing high or low responses to secukinumab, were also analyzed. Methods: 417 SNPs were analyzed by Next-Generation Sequencing technology, in a cohort of 62 psoriatic patients and undergone secukinumab treatment. Univariate regression analysis was employed to examine the association between SNP and clinical response to secukinumab. Multivariate analysis was also performed to assess multivariate differences in SNP pattern of HLA-Cw6+ or HLA-Cw6− patients showing high or low responses to secukinumab. Results: Eight SNPs in HLA-C and upstream region (rs13207315, rs6900444, rs12189871, rs12191877, rs4406273, and rs10484554), including HLA-Cw6 classical allele (rs1131118), and three in MICB-DT (rs9267325), DDX58 (rs34085293) and TYK2 (rs2304255) genes, associating with excellent response to secukinumab were identified. Importantly, rs34085293 or rs2304255 SNP status defined a subgroup of super-responder patients. We also found that HLA-Cw6+ and HLA-Cw6− patients carried out specific patterns of SNPs associating with different responses to secukinumab. Conclusion: Assessment of HLA-Cw6, together with other allelic variants of genes, could be helpful to define patients which better benefit from anti-IL-17 therapy. Abbreviations: PASI: Psoriasis Area and Severity Index; SNP: Single-Nucleotide Polymorphism Rs: Reference SNP; PASI75: 75% reduction in Psoriasis Area and Severity Index; PASI90: 90% reduction in Psoriasis Area and Severity Index; PASI100: 100% reduction in Psoriasis Area and Severity Index; NGS: Next-Generation Sequencing; OR: Odds Ratio; CAP: Canonical Analysis of Principal coordinates; BMI: Body Mass Index; LD: Linkage Disequilibrium

Decoding the Genetic Alterations in Genes of DNMT Family (DNA Methyl-Transferase) and their Association with Head and Neck Squamous Cell Carcinoma.

Objective:Epigenetic modifications are gaining focus due to their indirect association with tumorigenesis. DNA methylation plays a prime role in regulation of gene expression. Any aberrations in this gene family may lead to chromosomal instability and increased magnitude of tumour progression. In line with the above fact, the present study has been designed to identify genetic alterations in the genes of the DNMT (DNA methyl-transferase) family among head and neck squamous cell carcinoma patients (HNSCC). Methods:The present study follows an observational design employing computational tools for analysis. The TCGA-Firehose Legacy data was assessed using the cBioportal database. The dataset comprised of 530 samples from HNSCC patients which were assessed for genetic alterations in the DNMT family. Furthermore, the protein stability analysis and pathogenicity of the mutations were assessed using I-Mutant Suite and PROVEAN tools. Results:Almost all genes of the DNMT family harboured gene amplification. The TRDMT1 and DNMT3L genes showed deep deletions. Apart from these several non-synonymous, truncating and splice-site mutations were also documented. Protein stability and pathogenicity analysis revealed that majority of the mutations were found to decrease the stability and impose pathogenicity. Upon probing for reported mutations using gnomAD database, around six reference single nucleotide polymorphisms were identified which were found to exhibit a minor allele frequency less than 0.01. Conclusions:Screening of an exhaustive collection of patient’s samples could provide immense knowledge about the disease pathogenesis and identification of therapeutic leads. The variants identified in the present study could be used as diagnostic markers. However, further experimental analysis through genotyping assay is warranted to validate the present findings.

Identification of Genetic Variants Associated With Myocardial Infarction in Saudi Arabia.

The genetic variants associated with various genetic disorders have not been identified decisively in Saudi Arabia. Among these variants, six known for their association with coronary artery disease or myocardial infarction (MI) were studied on Saudi patients. Reference single nucleotide polymorphisms (SNPs) of these variants are rs5174, rs11591147, rs2259816, rs111245230, rs3782886 and rs2259820, referring to genes LRP8, PCSK9, HNF1A, SVEP1, BRAP and HNF1A, respectively. The analysis employed polymerase chain reaction panel coupled with mini-sequencing (SNapShot multiplex system) in order to identify these variants. A total of 100 MI patients and 103 healthy control individuals participated in this study. The six variants (SNPs) were evaluated for the risk of developing MI in the Saudi patients. Analysis of allele frequencies indicated that A allele of rs11591147 variant can be a protective allele, thus, is associated with the decreased risk of MI in Saudi individuals. Rare allele of rs111245230 variant (e.g., C allele) was extremely reduced, while rare allele of rs3782886 variant (e.g., G allele) does not exist in the ethnic signature of the Saudi population. This study elucidates the possible prediction of risk factors associated with severe diseases in Saudi population utilizing SNapShot multiplex system.