Comparing single-nucleotide polymorphism marker-based and microsatellite marker-based linkage analyses

We compared linkage analysis results for an alcoholism trait, ALDX1 (DSM-III-R and Feigner criteria) using a nonparametric linkage analysis method, which takes into account allele sharing among several affected persons, for both microsatellite and single-nucleotide polymorphism (SNP) markers (Affymetrix and Illumina) in the Collaborative Study on the Genetics of Alcoholism (COGA) dataset provided to participants at the Genetic Analysis Workshop 14 (GAW14). The two sets of linkage results from the dense Affymetrix SNP markers and less densely spaced Illumina SNP markers are very similar. The linkage analysis results from microsatellite and SNP markers are generally similar, but the match is not perfect. Strong linkage peaks were found on chromosome 7 in three sets of linkage analyses using both SNP and microsatellite marker data. We also observed that for SNP markers, using the given genetic map and using the map by converting 1 megabase pair (1 Mb) to 1 centimorgan (cM), did not change the linkage results. We recommend the use of the 1 Mb-to-1 cM converted map in a first round of linkage analysis with SNP markers in which map integration is an issue

Diabetes and bacterial co-infection are two independent risk factors for respiratory syncytial virus disease severity

Diabetes mellitus (DM) is common among older adults hospitalized with lower respiratory tract infection, yet information on the impact of DM on disease severity is limited. This study retrospectively analyzed 46 Turkish patients infected with respiratory syncytial virus (RSV), with information on their comorbidities, co-infection status, and symptoms. Patients are grouped into four severity levels from mild to severe, according to lung parenchymal infiltration status and oxygen level. Similar to previously published studies, we found that comorbidities of diabetes, heart failure, hypertension, co-infection of any type, bacterial co-infection, and age are associated with the disease severity. Cough is the most common symptom (89%) followed by fever (26%) and myalgia, dyspnea, and weakness (around 20%). Using a second-order analysis (two-variable regression), we identified two independent risks for disease severity, the first is represented by diabetes, and the second is represented by bacterial co-infection. We observed two patients whose more severe symptoms were not associated with an older age, but associated with a combination of diabetes and bacterial co-infection. To confirm the true causality from the statistical correlation, further studies are needed

Correlation between quantitative traits and correlation between corresponding LOD scores: detection of pleiotropic effects

We address the question of whether statistical correlations among quantitative traits lead to correlation of linkage results of these traits. Five measured quantitative traits (total cholesterol, fasting glucose, HDL cholesterol, blood pressure, and triglycerides), and one derived quantitative trait (total cholesterol divided by the HDL cholesterol) are used for phenotype correlation studies. Four of them are used for linkage analysis. We show that although correlation among phenotypes partially reflects the correlation among linkage analysis results, the LOD-score correlations are on average low. The most significant peaks found by using different traits do not often overlap. Studying covariances at specific locations in LOD scores may provide clues for further bivariate linkage analyses

Survival Analyses of COVID-19 Patients in a Turkish Cohort: Comparison between Using Time to Death and Time to Release

Survival analyses of COVID-19 data has its own unique features, in particular, the existence of two distinct events: death and release from the hospital within a very short period of time. This multiple-event situation belongs to a type where the occurrence of the first event prevents the second event to happen, and vice versa. We carried out two cause-specific univariate Cox regression survival analyses, one for time-to-death and another for time-to-release. Each survival analysis is further split into one for onset of symptom to event time and another for hospitalization to event time. We have also carried out a case-control (death vs. release) analysis without considering the time to event information. We observed that risk factors can be detected by either case-control or survival analysis, even though the goal of the two is quite different. We also observed that the two survival analyses may not both reveal a factor being a risk factor, but only one of them does. We prefer this two rounds of Cox regressions over mixture cure model which is only focused on time-to-death events which usually are sample size limited. By utilizing time-to-release events may greatly increase the sample size needed for revealing risk factors for COVID-19.   Doi: 10.28991/SciMedJ-2021-03-SI-1 Full Text: PD

XRCC4 rs6869366 polymorphism is associated with susceptibility to both nicotine dependence and/or schizophrenia

Background: Oxidative stress induced DNA damage has been assumed to contribute to the etiopathogenesis of schizophrenia (Sch). Smoking prevalence was more common in patients with Sch. The X-ray repair cross-complementation group 4 (XRCC4) gene plays an important role in the repair of DNA double-strand breaks. Objective: The purpose of this study was to investigate whether XRCC4 rs6869366 polymorphism has a relationship both in nicotine dependence (ND) and Sch+ND risk. Methods: One hundred and four patients with Sch+ND, 133 subjects with ND only and 70 healthy controls were enrolled in the study. XRCC4 rs6869366 polymorphism was analyzed using PCR-RFLP assay. Results: The frequency of XRCC4 rs6869366 GG genotype was more common in the ND and Sch+ND group than controls (p = 0.001 and p = 0.001, respectively). XRCC4 rs6869366 TT genotype was lower in both ND and Sch+ND group compared to controls (p = 0.001 and p = 0.001, respectively). Also, XRCC4 rs6869366 G allele was higher in Sch+ND group than controls (p = 0.001) while XRCC4 rs6869366 T allele was lower in ND group than healthy controls (p=0.001). XRCC4 rs6869366 GT genotype was lower in ND group than control group (p = 0.003). Discussion: These results suggested that the XRCC4 rs6869366 polymorphism G related genotype/allele was associated with susceptibility to both ND and Sch+ND in a Turkish population

Relationship between Thyroid Hormone Levels and Crime Type: A Controlled Study in Prisoners

Various factors cause aggression, which can be related to imbalance of T3 and T4 hormones, which can act as neurotransmitters and are reported to be elevated during aggression. This indicates changes in the hypothalamic-pituitary-thyroid axis that cause long-term changes in aggressive behaviour, especially in criminals. Moreover, mental and behavioural disorders possibly occur in individuals with impairment in thyroid hormone balance. The main rationale for this study was to asses if high T3, high T4, and low TSH hormones may have an effect on aggression-related crime tendency. Furthermore, the study aimed to measure levels of thyroid hormones in prisoners and to examine relationships of the hormone levels with crime rates. Our study was conducted in Ankara Sincan Closed Prisons. The study group consisted of 208 male volunteers who were imprisoned and the control group included 82 male volunteers who were not imprisoned. Prisoners in the study group were divided into two groups: those who committed aggression-related crime (Group A, n = 96) and prisoners convicted of other crimes (Group B, n = 112). Pulse rates, T3, T4, and thyroid-stimulating hormone (TSH) levels, and theT3/T4 ratio were measured in these prisoners. Data were analysed using the Wilcoxon rank sum test and chi-square Fisher’s exact test to test for any statistically significant differences. Results showed that toxic goitre rates, T3 and T4 values, and pulse rates were significantly higher in Group A than in the control group. Significant increase in T3 and T4 levels and the presence of toxic goitre were associated with aggression-related crime. These examinations should be performed on prisoners in general, especially those convicted of violent crimes. Additional rehabilitation and research programs should also be developed for such patients

Solid lines correspond to multipoint analysis and dots correspond to single-point analysis

<p><b>Copyright information:</b></p><p>Taken from "Comparing single-nucleotide polymorphism marker-based and microsatellite marker-based linkage analyses"</p><p></p><p>BMC Genetics 2005;6(Suppl 1):S13-S13.</p><p>Published online 30 Dec 2005</p><p>PMCID:PMC1866807.</p><p></p

Three linkage analysis results are included: microsatellite multipoint, one run for Illumina data (1 Mb-to-1 cM rule), and one run for Affymetrix data (1 Mb-to-1 cM rule)

<p><b>Copyright information:</b></p><p>Taken from "Comparing single-nucleotide polymorphism marker-based and microsatellite marker-based linkage analyses"</p><p></p><p>BMC Genetics 2005;6(Suppl 1):S13-S13.</p><p>Published online 30 Dec 2005</p><p>PMCID:PMC1866807.</p><p></p

Three sets of results are included: one using the genetic map given by Affymetrix (G

<p><b>Copyright information:</b></p><p>Taken from "Comparing single-nucleotide polymorphism marker-based and microsatellite marker-based linkage analyses"</p><p></p><p>BMC Genetics 2005;6(Suppl 1):S13-S13.</p><p>Published online 30 Dec 2005</p><p>PMCID:PMC1866807.</p><p></p> Kennedy, personal communication), one using the map derived from the 1 Mb-to-1 cM rule, and another using the genetic map given by GAW14