An exploration of linkage fine-mapping on sequences from case-control studies

Linkage analysis maps genetic loci for a heritable trait by identifying genomic regions with excess relatedness among individuals with similar trait values. Analysis may be conducted on related individuals from families, or on samples of unrelated individuals from a population. For allelically heterogeneous traits, population-based linkage analysis can be more powerful than genotypic-association analysis. Here, we focus on linkage analysis in a population sample, but use sequences rather than individuals as our unit of observation. Earlier investigations of sequence-based linkage mapping relied on known sequence relatedness, whereas we infer relatedness from the sequence data. We propose two ways to associate similarity in relatedness of sequences with similarity in their trait values and compare the resulting linkage methods to two genotypic- association methods. We also introduce a procedure to label case sequences as potential carriers or non-carriers of causal variants after an association has been found. This post-hoc labeling of case sequences is based on inferred relatedness to other case sequences. Our simulation results indicate that methods based on sequence-relatedness improve localization and perform as well as genotypic-association methods for detecting rare causal variants. Sequence-based linkage analysis therefore has potential to fine-map allelically heterogeneous disease traits.

Multidrug Resistant Acinetobacter baumannii Biofilms: Evaluation of Phenotypic–Genotypic Association and Susceptibility to Cinnamic and Gallic Acids

Acinetobacter baumannii armed with multidrug resistance (MDR) and biofilm-forming ability is increasingly recognized as an alarming pathogen. A deeper comprehension of the correlation between these two armories is required in circumventing its infections. This study examined the biofilm-forming ability of the isolates by crystal violet staining and the antibiotic susceptibility by broth microdilution method. The genetic basis of the MDR and biofilm-forming phenotypes was screened by polymerase chain reaction. The antimicrobial activities of cinnamic and gallic acids against planktonic cells and biofilms of A. baumannii were investigated, and the findings were confirmed with scanning electron microscopy (SEM). Among 90 A. baumannii isolates, 69 (76.6%) were MDR, and all were biofilm formers; they were classified into weak (12.2%), moderate (53.3%), and strong (34.5%) biofilm formers. Our results underlined a significant association between MDR and enhanced biofilm formation. Genotypically, the presence of blaVIM and blaOXA–23 genes along with biofilm-related genes (ompA, bap, and csuE) was statistically associated with the biofilm-forming abilities. Impressively, both gallic and cinnamic acids could significantly reduce the MDR A. baumannii biofilms with variable degrees dependent on the phenotype–genotype characteristics of the tested isolates. The current findings may possess future therapeutic impact through augmenting antimicrobial arsenal against life-threatening infections with MDR A. baumannii biofilms.

Genotype association of IP6K3 gene with Hashimoto’s thyroiditis in Algerian population (Aures region)

Background Hashimoto’s thyroiditis (HT) is a chronic autoimmune disease of the thyroid gland and is also the main cause of hypothyroidism. A recent genome-wide association study (GWAS) suggested an association of three novel genetic variants with HT in a population of Caucasian origin (Croatian). A case-control study was performed to investigate the association of these three newly suggested genetic variants with HT in a non-Caucasian ethnic group, an Arab-Berber from Algeria. Three variants (rs12944194 located 206 kb from SDK2, rs791903 inside IP6K3, and rs75201096 inside GNA14) were genotyped using real-time PCR. Results There were no significant differences in allele frequencies of the three genetic variants between HT cases and controls. However, the present study showed nominal significance in the genotype distribution of rs791903 (IP6K3 gene) between HT patients and the control group (P = 0.024); we observed a decrease in the frequency of rs791903 recessive homozygotes (CC) in HT cases versus controls (OR = 0.476, P = 0.025). Conclusion This is the first study that showed the genotypic association of IP6K3 intronic variant with decreased risk for HT in non-Caucasian, Algerian, population, whereas we did not confirm the association of SDK2 and GNA14 genetic variants with HT. The IP6K3 gene (inositol hexaphosphate kinase 3), located near major histocompatibility complex (MHC), has previously been associated with other common autoimmune diseases beside HT, such as Graves’s disease and rheumatoid arthritis, which is providing more evidence of a good candidacy for the genetic contribution to the development of HT and autoimmunity.

Polymorphic Variants of BH4 Pathway Genes and Isolated Hypospadias Risk

Background: Hypospadias (HS) is one of the most common congenital malformations. Complications of corrective surgery in HS correlate with patients’ opinions on their voiding ability and sexual life as adults. Etiology of HS involves both genetic and environmental factors. GCH1, which belongs to recently identified urothelial genes influencing voiding behavior, encodes rate-limiting enzyme catalyzing the production of tetrahydrobiopterin (BH4). A requirement for BH4, a metabolite structurally related to folic acid and riboflavin, in embryonic development was reported. Objectives: The aim of the present study was to investigate the association of selected polymorphic variants of BH4 pathway genes with hypospadias. Methods: We performed an analysis of 6 SNPs of GCH1, PAH and AGMO-DGKB loci in a group of 166 boys with isolated hypospadias and a properly matched control group. Results: There was no evidence for either allelic or genotypic association with the risk of HS for the tested nucleotide variants (rs12425434, rs7485331, rs17128050, rs8004018, rs17128077, rs2191349). The lack of association with single SNPs was confirmed at the haplotype level. The exhaustive multifactor dimensionality reduction (MDR) analysis revealed no significant interactive effect of polymorphic variants of BH4 pathway genes on HS susceptibility. Conclusions: The presented results did not support an association between SNPs of GCH1 and PAH and the risk of HS.

Prevalence of Staphylococcal Superantigens and their association among bacteremic and Infective Endocarditis patients in Egypt

AimInfective endocarditis (IE) is a major complication of Staphylococcus (S.) aureus infection in humans particularly those with bacteremia. Although Staphylococcus species are commensal on or in different parts of the human body, it is also known to be a serious pathogen causing bacteremia and sepsis that could lead to IE. Therefore, our aim was to assess the prevalence as well as phenotypic and genotypic association of the Staphylococcal superantigens (SAgs) among bacteremic and IE patients.MethodsThis study was conducted on Staphylococcus isolates recovered from bacteremic and IE patients. The isolates were screened phenotypically for the detection of SAgs including Staphylococcal enterotoxins (SEs) and toxic shock syndrome toxin-1 (TSST-1). Molecular detection and analysis of sea, seb, sec, sed, see and tsst-1, the major SAgs coding genes were performed using PCR and agarose gel electrophoresis, respectively. The obtained findings were statistically analyzed using standard methods.ResultsDetection of SAgs using ELISA revealed that 12 (46%) isolates were positive for enterotoxin production. However, the PCR revealed that 19 (73%) isolates were positive for enterotoxin genes with the highest prevalence of the sea gene (79%), followed by the seb (63%), tsst-1 (21%). The least frequent gene was the sed (5.3%). Accordingly, phenotypic and genotypic screening for prevalence of SAgs among Staphylococcal isolates showed significant difference (P value =0.046703), however, no significant correlation could be observed among the coagulase negative Staphylococci (CoNS) isolates (P value =0.248213). Statistical correlations between bacteremic and IE isolates with respect to prevalence of SAgs, showed no significant difference (P-value = 0.139, Effect size = 0.572) indicating no specific association between any of the detected SAgs and IE.Conclusionno significant difference has been found between Staphylococcal IE and bacteremia isolates regarding both phenotypic and genotypic detection of the most commonly SAgs. Therefore, all Staphylococcal bacteremic patients are suspected for IE. Also, future work should be conducted for analysis of SAgs gene expression.

Association of regulatory variants of dopamine β-hydroxylase with cognition and tardive dyskinesia in schizophrenia subjects

Background: Dopamine-β-hydroxylase (DBH, EC 1.14.17.1), which converts dopamine to norepinephrine, is a candidate gene in neuropsychiatric diseases. Aim: To assess the effect of regulatory variants in DBH on schizophrenia and its endophenotypes –cognition and tardive dyskinesia. Methods: We tested association of functional variants 19bp Ins/Del, rs1989787 and rs1611115 in DBH with i) schizophrenia (1236 cases, 1136 controls), ii) tardive dyskinesia (83 positive, 162 negative) and iii) performance functions of cognition (357 cases, 306 controls) estimated by the Penn Computerized Neurocognitive Battery. Results: A modest haplotypic ( Ins-C; 19bp Ins/Del – rs1989787 C>T; p=0.04) association was observed with schizophrenia. We observed ~39% reduction in activity of 19bp Del allele on luciferase assay. Analysis of covariance revealed interactions of tardive dyskinesia status and: i) 19bp Ins/Del (genotypic, p=0.04) and ii) rs1989787 and rs1611115 (combined genotypic, p=0.004) on Abnormal Involuntary Movement Scale total score. Association of rs1611115 with positive and negative syndrome scale (PANSS) total score ( p=0.05) and allelic/genotypic association with lower positive ( p=0.03/0.04), general psychopathology ( p=0.01/0.01) PANSS scales in tardive dyskinesia-positive; and allelic/genotypic ( p=0.02/0.05) with higher score of depressive factors in tardive dyskinesia-negative subgroups were observed. Analysis of covariance with continuous variable of cognition showed interaction of health status with: i) rs1989787 on accuracy and efficiency ( p=0.03) of abstraction and mental flexibility; ii) rs1611115 on accuracy of working memory and emotion ( p=0.05); iii) 19bp Ins/Del on processing speed of emotion ( p=0.03). Allelic/genotypic association of rs1989787 with spatial ability ( p=0.02–0.05) among healthy controls; association of rs1611115 with Global Assessment Scale scores in the past month ( p=0.05) among schizophrenia subjects of cognition cohort was also observed. Conclusions: With modest genotype–phenotype correlations available for DBH variants, personalized treatment regimens based on DBH activity for ameliorating tardive dyskinesia and cognitive symptoms may be plausible.

Association of Single-Nucleotide Polymorphisms With Chronic Rhinosinusitis in a Southwestern Han Chinese Population: A Replication Study

Background Chronic rhinosinusitis (CRS) is a multifactorial inflammatory disease. The role of genetic variations of related genes in the development of CRS and severity of symptoms is unknown in Southwestern Chinese populations. Objective We selected candidate CRS-related genetic polymorphisms and evaluated the associations that were different according to the presence of nasal polyp, asthma, and allergic rhinitis (AR) in a Southwestern Chinese population. Detailed phenotypes were compared among different genotypes. Methods In 452 CRS patients and 591 healthy controls, clinico-epidemiological information was collected and 23 previously reported CRS-related single-nucleotide polymorphisms (SNPs) were genotyped. Genotypes were determined using a Sequenom MassARRAY SNP genotyping system. Clinical disease measures including the sinonasal outcome test, visual analogue scale (VAS), and symptom severity VAS were evaluated for each patient. The association between CRS, genotypes, asthma, AR, and symptoms was analyzed. The effect of sex, age, body mass index, and status of smoking was considered. Results Statistically significant genotypic association with CRS was observed with an IL1RL1 genetic polymorphism (rs13431828; odds ratio [OR] = 1.45; 95% confidence interval [CI], 1.06–1.99; P = .02). Similar association was observed with rs13431828 in subgroups of CRS with nasal polyps (OR = 1.53; 95% CI, 1.03–2.29; P = .04), asthma (OR = 2.08; 95% CI, 1.14–3.79; P = .02), and AR (OR = 1.59; 95% CI, 1.06–2.39; P = .02). No significant association with other SNPs was observed. The evaluated genetic polymorphisms were not associated with clinical symptom scores. Conclusion This study replicated rs13431828 as being associated with CRS in Southwestern Chinese. rs13431828 was also significantly associated with CRS patients who have concurrent allergic nasal diseases.

Coding Region Mutation Screening in Optineurin in Chinese Normal-Tension Glaucoma Patients

Purpose. To study the roles of sequence alterations in the optineurin (OPTN) gene-coding region in normal-tension glaucoma (NTG) among Chinese patients. Methods. Genomic DNA was extracted from 190 NTG patients and 201 control subjects. The thirteen exons of OPTN were amplified by polymerase chain reaction and analyzed by direct sequencing. Detected sequence changes were compared between NTG patients and control subjects. Results. Seven sequence changes in OPTN were identified in both NTG patients and control subjects. Among them, c.464G>A (T34 T), c.509C>T (T49T), c.806G>A (V148V), and c.959T>C (P199P) were synonymous codon changes, whilst c.655T>A (M98K), c.1996G>A (R545Q), and c.1582T>C (I407T) were missense changes. Two previously reported heterozygous mutations, c.458G>A (E50K) in exon 4 and c.691_692insAG in exon 6, were not found in this study. Out of these seven OPTN sequence variants, c.464G>A (T34T) was significantly associated with NTG in both the allelic and genotypic association analyses (allelic association: p=0.0001, OR=2.20, 95% CI: 1.46-3.31; genotypic association: p=0.0001), whereas the association of other variants with NTG did not reach statistical significance (p>0.05). Variants c.1582 T>C (I407T) and c.806G>A (V148V) were identified in one and two NTG patients, respectively, but not in the control subjects. Conclusions. This study confirmed the association of the OPTN T34T variant with NTG, suggesting that OPTN is a susceptibility gene for NTG in Chinese. Moreover, a variant with amino acid change (I407T) was identified in NTG but not in controls. Further studies are warranted to assess whether this variant is a causative mutation for NTG.