Blood Samples For DNA Extraction Research Articles

The Association between the rs3747406 Polymorphism in the Glucocorticoid-Induced Leucine Zipper Gene and Sepsis Survivals Depends on the SOFA Score.

The variability in mortality in sepsis could be a consequence of genetic variability. The glucocorticoid system and the intermediate TSC22D3 gene product-glucocorticoid-induced leucine zipper-are clinically relevant in sepsis, which is why this study aimed to clarify whether TSC22D3 gene polymorphisms contribute to the variance in sepsis mortality. Blood samples for DNA extraction were obtained from 455 patients with a sepsis diagnosis according to the Sepsis-III criteria and from 73 control subjects. A SNP TaqMan assay was used to detect single-nucleotide polymorphisms (SNPs) in the TSC22D3 gene. Statistical and graphical analyses were performed using the SPSS Statistics and GraphPad Prism software. C-allele carriers of rs3747406 have a 2.07-fold higher mortality rate when the sequential organ failure assessment (SOFA) score is higher than eight. In a multivariate COX regression model, the SNP rs3747406 with a SOFA score ≥ 8 was found to be an independent risk factor for 30-day survival in sepsis. The HR was calculated to be 2.12, with a p-value of 0.011. The wild-type allele was present in four out of six SNPs in our cohort. The promoter of TSC22D3 was found to be highly conserved. However, we discovered that the C-allele of rs3747406 poses a risk for sepsis mortality for SOFA Scores higher than 6.

Native American Ancestry Is Associated with Successful Immune Tolerance Induction in Admixed Brazilians with Hemophilia a

Immune tolerance induction (ITI) is the treatment of choice for eradicating neutralizing antibodies (inhibitors) against factor VIII (FVIII) in patients with hemophilia A (PwHA). Previous studies have investigated the association of ethnicity with inhibitor development with conflicting results. However, to our concern, studies targeting the role of ethnicity on ITI outcomes are still missing. Since unfavorable ITI response occurs in 30%-40% of these patients, establishing predictors of ITI response is needed. To evaluate genetic determinants of ITI outcome beyond FVIII genotype, we investigated the association of genomic ancestry and ITI response by analyzing the exomes of PwHA from the Brazilian Immune Tolerance Study (Camelo et al. 2021). PwHA were enrolled in 15 hemophilia treatment centers from all Brazilian regions. We collected clinical data and blood samples for DNA extraction. ITI was carried out using a single protocol, regardless of selection based on “good” or “bad” risk of ITI outcome. Inclusion criteria comprised patients with severe and moderately-severe (FVIII<2%) HA with high-responding inhibitors who completed a first course of ITI. Since the characteristics of PwHA who responded with partial and complete success yielded similar results, these groups were analyzed together. Exomes were obtained with high quality using the xGen Exome Research Panel v2 (Illumina). Quality control filters evaluated average coverage and deep coverage, phred score, genomic position, sex, heterozygosity, and duplicated SNPs. In a multiple regression analysis, we used geographic location, inhibitor levels, presence or absence of null mutations (i.e., frameshift, deletions, nonsense, and inversions; Oldenburg et al., 2002), and kinship coefficients as explanatory variables. Inhibitor levels were evaluated as historical inhibitor peak, titer immediately before the start of ITI, and inhibitor peak during ITI. We included 150 PwHA, of whom 136 (91%) had severe (FVIII<1%) HA, median age 0.9 years [IQR, 0.5,1.4] at diagnosis of HA. A total of 44 (29%) PwHA had ITI failure, 60 (40%) had partial success, and 46 (31%) had complete ITI success. Functional annotation showed that most SNPs were intronic (48%) and exonic (29%). We identified 808,706 variants, of which 90,075 were not reported in the dbSNP. Average ancestries of European, African, and Native American were 79.4% [IQR:75.4,83.4], 17.3% [IQR:17.0,17.6), and 3.3% [IQR:2.6,4.0], respectively (Table 1). There was an association between a higher Native American ancestry in patients with successful ITI (2% [IQR:1.95,2.05] ancestry mean) when compared with patients who failed ITI (1% [IQR:0.97,1.03] ancestry mean). A 1% increase in the Native American ancestry proportion was associated with a rise of ~10% in the probability of successful ITI ( odds ratio [OR], 10.43 [95% CI,7.45,13.41], p = 0.040 (Table 2). Neither European nor African ancestry was associated with ITI outcome. In conclusion, Native American ancestry was associated with successful ITI. To our concern, this is the first study to evaluate genomic ancestry as a predictor of ITI response and the first to enroll an admixed population of HA. Identifying ancestry as a predictor of ITI outcome may elicit different therapeutic approaches for inhibitor eradication. However, our findings may not apply to other populations due to a particular characteristic of admixture of the Brazilian population. REFERENCES Camelo, R.M. et al. (2021) ‘Predictors of the outcome of immune tolerance induction in patients with haemophilia A and inhibitors: The Brazilian Immune Tolerance (BRAZIT) study protocol’, PLOS ONE, 16(8). doi:10.1371/journal.pone.0256265. Oldenburg, J., El-Maarri, O. and Schwaab, R. (2002) ‘Inhibitor development in correlation to factor VIII genotypes’, Haemophilia, 8(s2), pp. 23-29. doi:10.1046/j.1351-8216.2001.00134.x.

Collection of genetic data in ethnic‐based studies across Aymaras, Quechuas and Mestizos: the challenges of the Genetics of Alzheimer’s in Peruvian Population (GAPP) study

AbstractBackgroundThe Genetics of Alzheimer’s Disease in Peruvian Population (GAPP) study aims to investigate genetic and environmental risk factors for Alzheimer’s Disease (AD) in Peru. The project is led by Columbia University (CU, New York, US) and the Instituto Peruano de Neurociencias (IPN, Lima, Peru). For the past year and a half, despite the ongoing COVID‐19 pandemic, the study has collected data on cognitive function, health, diet and numerous clinical and biological risk factors for AD. In addition, we collected blood samples for DNA extraction as well as serum and plasma to look at core AD biomarkers.MethodRecruitment prioritized populations from south Peru, the Quechuas and Aymaras, because of their high proportion of Native American ancestry (or, in other words, low admixture with European ancestry) as well as Mestizo (mixed Native‐European ancestry). Three recruitment sites were established in Lima, Puno and Arequipa. Interviewers were trained to clinically and cognitively assessed the participants and collect and ship blood samples to the main site (IPN). DNA samples were then sent to CU for processing. Serum and plasma samples were processed in Lima and stored at ‐80C for batch shipping to CU. DNA samples were sent to CD Genomics and Children’s Hospital of Philadelphia for APOE genotyping and GWAS, respectively.ResultA database with 350 participants has been created. Blood samples from all participants were collected; 268 successfully underwent GWAS and APOE genotyping. An additional 82 samples are pending QC and genotyping. No samples were dropped at extraction, and only 0.7% failed DNA quality standards for genotyping.ConclusionSample collections for genetic studies in South American indigenous populations such as Peru represent important logistic challenges. The use of blood as a main source of DNA provides an effective and reliable source for genetic data analysis. Plasma and serum biomarkers will provide additional insights into the disease manifestations and validation of the clinical diagnosis in these underrepresented populations. Ongoing recruitment will augment the analytical power of the cohort by collecting blood, serum and plasma samples from additional GAPP participants.

Single nucleotide polymorphisms in 5-HT receptors in the etiology of premature ejaculation

Introduction and objectivesPremature ejaculation (PE) is characterized by shorter intravaginal ejaculation latency time than it is acceptable for the patient or partner. It is thought that lifelong PE is a neurobiological dysfunction associated with genetic predisposition and with central serotonin neurotransmission dysfunction in receptors. To contribute to the understanding the genetic etiology of lifelong PE, it was planned to compare the 5-HT2C receptor gene rs3813929, rs518147, 5-HT1A receptor gene rs6295, 5-HT1B receptor gene rs11568817 of lifelong PE patients to healthy controls. Materials and methodsFor this purpose, 100 patients with premature ejaculation and 100 healthy controls were included in the study. Blood samples for DNA extraction were obtained. Appropriate procedures were applied to the probes (rs3813929, rs518147, rs6295, rs11568817) suitable for the DNA studied. ResultsA statistically significant relationship was found between the rs11568817 polymorphism (p=0.019) in the 5-HT1B receptor gene and the rs518147 polymorphism (p=0.016) in the 5-HT2C receptor gene. Also, no statistically significant relationship was found between 5-HT1A receptor gene rs6295 polymorphism and 5-HT2C receptor gene rs3813929 polymorphism and lifelong PE. ConclusionsThe relationship between rs3813929 and rs11568817 polymorphisms with lifelong PE was confirmed. Repeating the study in larger sample groups could be useful in determining the genetic etiology of PE.

DNA recovery from used malaria RDT to detect Plasmodium species and to assess Plasmodium falciparum genetic diversity: a pilot study in Madagascar

BackgroundRapid diagnostic tests (RDT) are widely used for malaria diagnosis in Madagascar, where Plasmodium falciparum is the predominant species. Molecular diagnosis is essential for malaria surveillance, but requires additional blood samples for DNA extraction. Used RDTs is an attractive alternative that can be used as a source of DNA. Plasmodium falciparum genetic diversity and multiplicity of infection, usually determined by the genotyping of polymorphic regions of merozoite surface proteins 1 and 2 genes (msp1, msp2), and the repeated region RII of the glutamate-rich protein gene (glurp) have been associated with malaria transmission levels and subsequently with the impact of the deployed control strategies.Thus, the study aims to use RDT as DNA source to detect Plasmodium species, to characterize Plasmodium falciparum genetic diversity and determine the multiplicity of infection.MethodsA pilot study was conducted in two sites with different epidemiological patterns: Ankazomborona (low transmission area) and Matanga (high transmission area). On May 2018, used RDT (SD BIOLINE Malaria Ag P.f/Pan, 05FK63) were collected as DNA source. Plasmodium DNA was extracted by simple elution with nuclease free water. Nested-PCR were performed to confirm Plasmodium species and to analyse P. falciparum msp1, msp2 and glurp genes polymorphisms.ResultsAmongst the 170 obtained samples (N = 74 from Ankazomborona and N = 96 from Matanga), Plasmodium positivity rate was 23.5% (40/170) [95% CI 17.5–30.8%] by nested-PCR with 92.2% (37/40) positive to P. falciparum, 5% (2/40) to Plasmodium vivax and 2.5% (1/40) to P. falciparum/P. vivax mixed infection. Results showed high polymorphisms in P. falciparum msp1, msp2 and glurp genes. Multiple infection rate was 28.6% [95% CI 12.2–52.3%]. The mean of MOI was 1.79 ± 0.74.ConclusionThis pilot study highlighted that malaria diagnosis and molecular analysis are possible by using used malaria RDT. A large-scale study needs to be conducted to assess more comprehensively malaria parasites transmission levels and provide new data for guiding the implementation of local strategies for malaria control and elimination.Trial registration Retrospectively registered

0031 Sleep Regularity is Associated with DNA Methylation in Cognitive, Cardiovascular and Mood-related Genes: A GWAS-informed Study in Adolescents

Abstract Introduction Adolescence is associated with a delay in the circadian timing of sleep. However, social factors prevent adolescents from adapting to a later sleep-wake pattern, leading to different forms of circadian misalignment that may increase the risk of cardiovascular and mental health disorders. Several GWAS have identified genes associated with sleep and circadian phenotypes, however, little is known regarding the epigenetic basis and significance of sleep timing and its regularity in adolescence. Methods We analyzed data from 230 adolescents from the Penn State Child Cohort follow-up study who provided a blood sample for DNA extraction and had complete at-home 7-night (at least 3) actigraphy (ACT) data. ACT-measured sleep midpoint was calculated as the intra-individual mean of the 7-night midpoint (zeroed to midnight) of the sleep period. ACT-measured sleep regularity was calculated as the intra-individual standard deviation of the 7-night sleep midpoint. Epigenome-wide single nucleotide resolution of DNA methylation in cytosine-phosphate-guanine (CpG) sites and surrounding regions were obtained from peripheral leukocytes. This study focuses on methylation sites in GWAS-informed genes previously associated with sleep and circadian phenotypes. Linear regression assessed the association between sleep midpoint and sleep regularity with site-specific methylation levels, adjusting for sex, age, race/ethnicity, body mass index, and psychotropic medication use. Using the Benjamini & Hochberg method to adjust for a false discovery rate. Adjusted p-values are reported as q-values. Results Sleep midpoint was not associated with a significant change in methylation at any of the measured intragenic sites. Sleep regularity was significantly associated with differential methylation at 238 intragenic sites in 147 genes with an adjusted p<0.05, of which, three sites were within GWAS-informed sleep/circadian-related genes. Higher sleep irregularity was associated with hypermethylation in MAD1L1 (q=2.4x10-2) and with hypomethylation in CALN1 (q=3.8 x 10-4) and ZNF618 (q=3.8 x 10-2). Conclusion Sleep irregularity is associated with altered DNA methylation in genes previously identified in GWAS of sleep/circadian phenotypes. Our data provides evidence for a potential epigenetic link between sleep irregularity and genes involved in neurocognitive functioning (CALN1), internalizing disorders (MAD1L1) and blood pressure (ZNF618). Support (If Any) National Institutes of Health (R01HL136587, R01MH118308, UL1TR000127)

Characteristics of Intron 17 and Exon 18 of Leptin Receptor Gene in Nigerian Locally Adapted and Exotic Turkeys

Leptin Receptor gene (LEPR) gene has been implicated as the activator of the JAK-STAT signaling pathway and plays an important role in regulating body energy storage and metabolism. Identification of Single nucleotide polymorphisms (SNPs) were carried out in intron 17 and exon 18 of LEPR gene in 200 turkeys comprising 100 each of Nigerian locally adapted and exotic (Nicholas White) turkeys. Blood samples for DNA extraction were collected at 20 weeks. DNA extraction was carried out using whole blood collected with Quick- DNA Miniprep Plus extraction kits by strictly followed the manufacturer’s protocol. The sequence data obtained were analyzed using GeneScan and Sequencing software (Applied Biosystems). The single nucleotide polymorphisms (SNPs) present in LEPR gene of the two turkey genotypes were identified using DnaSP 6 software. The allele frequency of each SNP, Heterozygosity (He) and Polymorphic information content (PIC) of the SNPs were calculated. Out of six SNPs identified in intron 17 of the turkey LEPR gene, four were found in local turkeys while all the six were found in exotic turkey. The major allele frequency of the SNPs ranged from 0.86 to 0.96. The SNP 28C>G in exotic turkey had the highest HE while SNPs 7T>G, 67A>T and 85G>C in local turkey had the least. The PIC ranged from 0.077 in local turkey to 0.211 in exotic turkey. In addition, ten SNPs were identified in exon 18 of the turkey LEPR gene, out of which eight were detected in local turkeys while seven were detected in exotic turkeys. The major allele frequency of the SNPs identified in exon 18 ranged from 0.54 in 602A>C in local turkey to 1.00 in 60T>G, 267A>G, 274A>G alleles that are fixed in both local and exotic turkeys. Also, SNP 602A>C in local turkey had the highest HE while incidentally SNPs 130G>C, 166G>A and 789G>A also in local turkey had the least heterozygosity. PIC discovered in exon 18 of LEPR gene ranged from 0.077 to 0.377 in local turkey. Intron 17 and exon 18 of LEPR gene is polymorphic in both Nigerian locally adapted and exotic turkeys and therefore could be used for further analysis to form a basis for genetic variation in growth in the two genotypes

Genome-wide family-based study in torus palatinus affected individuals

ObjectiveTori or exostoses are bony growths that appear in different oral regions. Torus palatinus, more specifically, develop in the palate midline and can impair proper word pronunciation and hinder the fabrication and use of dentures. Even though a multifactorial inheritance model has been suggested for torus palatinus appearance, precise genetic factors involved in its etiology remain unclear. Hence, in this study we aimed to identify variants across the genome of individuals from 46 Filipino families that associate with torus palatinus. DesignAll families were composed of fishermen or landless rural dwellers who provided blood samples for DNA extraction and genotyping. A total of 3519 single nucleotide polymorphisms (SNPs) were analyzed through a transmission disequilibrium test in individuals affected by torus palatinus and their unaffected family members. ResultsFourteen SNPs showed trends for associations to the level of p < .005 threshold and several others were nominally (p < .05) associated with torus palatinus. We highlight SNP rs6582285, which is located in the CAPS2 gene, being the C allele less transmitted than the T allele in our sample. The C allele of CAPS2 rs6582285 protects from having torus palatinus whereas the other associations found were linked to an increased risk of developing the condition. ConclusionsTrends for associations were identified for several markers across the genome, supporting the hypothesis that torus palatinus has a multifactorial mode of inheritance. We hope that our study contributes to a better understanding of torus palatinus etiology and helps guide future research in examining genes for this often-overlooked condition in different populations.

Association of BCAT2 and BCKDH polymorphisms with clinical, anthropometric and biochemical parameters in young adults

Background and aimCirculating amino acids are modified by sex, body mass index (BMI) and insulin resistance (IR). However, whether the presence of genetic variants in branched-chain amino acid (BCAA) catabolic enzymes modifies circulating amino acids is still unknown. Thus, we determined the frequency of two genetic variants, one in the branched-chain aminotransferase 2 (BCAT2) gene (rs11548193), and one in the branched-chain ketoacid dehydrogenase (BCKDH) gene (rs45500792), and elucidated their impact on circulating amino acid levels together with clinical, anthropometric and biochemical parameters. Methods and resultsWe performed a cross-sectional comparative study in which we recruited 1612 young adults (749 women and 863 men) aged 19.7 ± 2.1 years and with a BMI of 24.9 ± 4.7 kg/m2. Participants underwent clinical evaluation and provided blood samples for DNA extraction and biochemical analysis. The single nucleotide polymorphisms (SNPs) were determined by allelic discrimination using real-time polymerase chain reaction (PCR).The frequencies of the less common alleles were 15.2 % for BCAT2 and 9.83 % for BCKDH. The subjects with either the BCAT2 or BCKDH SNPs displayed no differences in the evaluated parameters compared with subjects homozygotes for the most common allele at each SNP. However, subjects with both SNPs had higher body weight, BMI, blood pressure, glucose, and circulating levels of aspartate, isoleucine, methionine, and proline than the subjects homozygotes for the most common allele (P < 0.05, One-way ANOVA). ConclusionOur findings suggest that the joint presence of both the BCAT2 rs11548193 and BCKDH rs45500792 SNPs induces metabolic alterations that are not observed in subjects without either SNP.

COMT rs4680 single nucleotide polymorphism, ethnicity, and age are associated with fibromyalgia in women

To investigate the influence of the catechol-O-methyltransferase enzyme (COMT) single nucleotide polymorphism (SNP) rs4680 (G/A) on fibromyalgia in women. In this observational study of case-control type 29 women with a diagnosis of FM (cases) and 31 healthy non-fibromyalgia women (controls). Sociodemographic and anthropometric data were collected, as well as data relating to Symptom Severity Scale and Generalized Pain Index and peripheral blood samples for DNA extraction; genotypic analyzes were performed by PCR-SSP. We observed that rs4680 AA genotype was more frequently observed in fibromyalgia than controls (p=0.02). The A allele was also more often present in the fibromyalgia participants than in their control peers (p = 0.03). There was a statistically significant association between race and FM sufferers, showing that those of white ethnicity had a 2.05 times greater chance of developing the syndrome than non-white individuals (p=0.03; CI 95% 0.93 – 4.53). A statistically significant correlation between age and FM was observed (rS=0.812, p=0.01). This study demonstrates that white women above the age of 45, who have the AA genotype or A-allele, presents a higher risk of developing FM, showing that this polymorphism of the COMT gene may be one of the risk factors for the fibromyalgia.

Molecular Assay Proves the Presence of Theileria annulata Infection in Camels in Al-Diwaniyah Province, Iraq.

Background:Theileria camelensis and T. dromedarii are parasitic protozoans reported by several studies as specific species that infect the one-humped camel (Camelus dromedarius). However, other findings casted significant doubts on the true identity of the causative species of theileriosis in camels. Therefore, the present study was conducted to investigate of T. camelensis and T. dromedarii in one humped camels in Iraq during Apr-Oct 2017.Methods:Blood samples for DNA extraction were obtained from 181 slaughtered camels. Molecular investigation was performed following the amplification of 18S rRNA gene by conventional PCR technique. DNA sequencing was then utilized only for the positive samples to confirm the infection with the Theileria species.Results:Nine (4.97%) out of 181 examined samples showed a positive result to infection with Theileria spp., and all these appeared as a T. annulata when subjected to DNA amplification and sequencing techniques. There was a complete absence of any new sequence outside the known species.Conclusion:Most of Theileria infection in camels in the study area is caused by T. annulata and no other causative agents like T. camelensis or T. dromedarii.

Genetic Predisposition Related To Overuse Injuries In Athletes: Genome-wide Association Study In Estonian Elite Athletes.

Injuries in sports are the most common causes where athletes are forced to change their training plans temporarily, or more, to interrupt trainings and competitions for a certain time. Several genome-wide association studies have concluded that variations in DNA sequence interacting with non-genetic risk factors may play an important role in the etiology of injuries, including overuse injuries. PURPOSE: To identify potential loci (chromosomal regions) that are associated with the tendinopathy of Achilles and patellar tendons. METHODS: Study group consisted of 121 elite athletes (21 females and 100 males), current and former Estonian national team members, in the age range 27.5±5.1 years, involved in 16 different sports. The case group (n=42) consisted of athletes with patellar and Achilles tendinopathies, and the control group (n=79) was formed by athletes without these injuries. The electronic health record system was used to find clinical diagnoses of the respective injuries of the athletes participating in this study. Peripheral venous blood samples for DNA extraction and genotyping for known SNPs (SNP arrays) from all study subjects were collected. The comparison of allelic frequencies of these SNPs was made between cases and controls. For statistical analysis, we used the software PLINK. To estimate the magnitude of the effectiveness OR was used to estimate the magnitude of the effectiveness, and p-values for the significance of ORs were calculated using the χ2 - test. The p value of 10-8 was set as a threshold for genome-wide statistical significance. To display significant SNPs, the Manhattan plot was used. RESULTS: Association analysis revealed 2 genes that could be important as risk factors for investigated injuries, the PAPPA2 (chr 1: rs1158045, OR 13.8, p= 1.64·10-5) and the GNG12 (chr 1: rs28435277 OR 13.8, p=1.64·10- 5) with the p-value remaining at the level of "suggestive significance" (p=5·10-5). CONCLUSIONS: Our study results identified suggestive significance in allelic differences of PAPPA2 and GNG12 between case and control groups. It is important to continue with further research of genetic risk profile to understand the biological processes associated with injury risk.

Increased risk for uterine cancer among first-degree relatives to Swedish gastric cancer patients

PurposeIn order to further understand genetically predisposing factors of gastric cancer, a retrospective study on 107 patients with gastric cancer was conducted. The family history of cancer cases was registered, in search of associations between gastric cancer and other cancer types.Materials and methodsWithin Stockholm County in Sweden, all patients previously diagnosed with gastric cancer and still alive were invited to participate in the study. Patients were asked to complete a questionnaire about their gastric cancer diagnosis and if any cancers had occurred in their family. A blood sample for DNA extraction was collected. The proportions of different cancer types in the relatives of the patients were compared to the general Swedish population in 1970 and 2010.ResultsAmong first- and second-degree relatives to the index patients with gastric cancer, the frequency of uterine cancer as well as gastric cancer was significantly overrepresented compared to the general population in Sweden. The frequency of breast cancer was significantly lower.ConclusionsThere seems to be an increased risk of both gastric cancer and uterine cancer in the families of gastric cancer survivors, indicating a possible hereditary connection between these two cancer types.

Study of Interleukin 23 Gene Polymorphism in Egyptian Patients with Allergic Rhinitis

Objective: Polymorphism of the interleukin-23 receptor gene corresponds with susceptibility to several immune-related diseases. For the terminal differentiation of IL-17-producing effector T-helper cells in vivo, the interleukin-23 receptor gene is of vital importance. As shown recently, Th17 cells probably have a great influence on the pathogenesis of allergic airway diseases. Our intention was to establish an association between polymorphisms in the IL-23R gene and allergic rhinitis (AR) in Egyptians. Methods: we included 100 AR patients and 75 control Egyptian subjects in a case-control study. The study involved obtaining blood samples for DNA extraction, genotyping and determination of a selected single-nucleotide polymorphisms in IL-23R by performing TaqMan assay PCR. Results: A substantially growing prevalence of the homozygous rs7517847 GG genotype and G allele appeared in the AR patients unlike that observed in the control individuals (p 0.001). Conclusions: To the best of our knowledge, this is the first study to demonstrate an important association between polymorphisms in IL-23R and AR in the Egyptian population. A strong association between rs7517847 in a SNP of IL-23R, and AR was identified.

Associations between IGF1, IGFBP2 and TGFß3 Genes Polymorphisms and Growth Performance of Broiler Chicken Lines.

Simple SummaryThe main goal of breeding programs for broiler chickens is to increase growth rate and breast and thigh muscles weight. The candidate gene approach is a powerful technique for genetically improving performance traits in chickens. We studied the associations of the single nucleotide polymorphisms of three genes involved in protein synthesis, glucose metabolism and cell proliferation (IGF1, IGFBP2, TGFβ3) with performance traits in the Hubbard F15 and Cobb E chicken lines. Based on our results, it can be concluded that the TGFβ3 gene could be used as a candidate gene marker for chicken growth traits.Marker-assisted selection based on fast and accurate molecular analysis of individual genes is considered an acceptable tool in the speed-up of the genetic improvement of production performance in chickens. The objective of this study was to detect the single nucleotide polymorphisms (SNPs) in the IGF1, IGFBP2 and TGFß3 genes, and to investigate their associations with growth performance (body weight (BW) and average daily gain (ADG) at 14, 21, 28, 35 and 42 days of age) and carcass traits in broilers. Performance (carcass) data (weight before slaughter; weights of the trunk, giblets, abdominal fat, breast muscle and thigh muscle; slaughter value and slaughter percentage), as well as blood samples for DNA extraction and SNP analysis, were obtained from 97 chickens belonging to two different lines (Hubbard F15 and Cobb E) equally divided between the two sexes. The genotypes were detected using polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) methods with specific primers and restrictase for each gene. The statistical analysis discovered significant associations (p < 0.05) between the TGFβ3 SNP and the following parameters: BW at 21, 28 and 35 days, trunk weight and slaughter value. Association analysis of BWs (at 21, 28 and 35 days) and SNPs was always significant for codominant, dominant and overdominant genetic models, showing a possible path for genomic selection in these chicken lines. Slaughter value was significant for codominant, recessive and overdominant patterns, whereas other carcass traits were not influenced by SNPs. Based on the results of this study, we suggested that the TGFβ3 gene could be used as a candidate gene marker for chicken growth traits in the Hubbard F15 and Cobb E population selection programs, whereas for carcass traits further investigation is needed.

Health-related motivational and behavioral processes associated with DNA methylation of the TNF gene.

Epigenetics has been described as one of the most exciting areas of contemporary biology, and research has begun to explore whether epigenetic modifications are influenced by psychological processes. The present research explored the associations of health-related motivation and behavior with the DNA methylation of tumor necrosis factor (TNF) gene. Participants (N = 88) completed questionnaires examining engagement with health-related behavior (i.e., physical activity, diet, and smoking) and health-related motivation from the perspective of self-determination theory. They also provided a capillary blood sample for DNA extraction and analysis of four CpG sites via bisulfite conversion within Exon 1 of TNF. Health-related autonomous motivation was weakly but positively associated with TNF methylation (β = .18, p = .08). Indirect effects were identified in a subsequent step; autonomous motivation was positively associated with fruit consumption (β = .29, p = .004), negatively associated with smoking (β = -.22, p = .03), but not associated with physical activity (β = .10, p = .34). Moreover, TNF methylation was positively associated with lifetime physical activity (β = .18, p = .08) and negatively associated with smoking (β = -.23, p = .03). Direct effects of autonomous motivation on DNA methylation did not persist when these indirect effects were included (β = .09, p = .43). Results support the idea that autonomous motivation is associated with DNA methylation, albeit indirectly through tobacco consumption. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

Lower limb muscle strength and serotonin receptor gene polymorphism as factors associated in women with fibromyalgia

BackgroundFibromyalgia (FM) is a chronic pain syndrome characterized by generalized skeletal muscle chronic pain. Its etiology is not well defined, because there are several factors that may trigger it such as physical and/or emotional stresses, or a genetic susceptibility, involving serotonergic, dopaminergic and catecholaminergic paths. The objective of this study was to investigate the association between the strength of the lower limb, genetic polymorphism of the serotonin receptor gene HTR2A in women with fibromyalgia.MethodsIn this observational study of case-control type 48 women were evaluated who belonged to the group with FM (52 ± 12 years) and 100 women in the control group (58 ± 11 years). Socio demographic and anthropometric data were collected and peripheral blood samples for DNA extraction; genotypic analyzes were performed by means of PCR in real time by TaqMan® system. The lower limb muscle strength was assessed through the test of sitting down and standing up for 30 s. The chi-square test or Fischer Exact was used for possible associations among the variables; the t-test for independent samples was used to compare the averages among the groups; the value of significance adopted was 5%.ResultsThere was an association between the polymorphism of the HTR2A gene with FM, demonstrating that carriers of the genotype GG have 24.39 times more likely to develop the syndrome (IC95% 5.15–115.47; p = 0.01). It was observed an association between FM and the test to sit and stand up demonstrating that women with fibromyalgia have lower limb muscle strength (p = 0.01). The study showed that the white race has 3.84 times more likely to develop FM (p = 0.01).ConclusionThe results of this study suggest that women of Caucasian ethnicity with GG genotype or G allele presented greater risk of developing fibromyalgia and that these patients have lower limb muscle strength compared to the control group.

The UroLife study: protocol for a Dutch prospective cohort on lifestyle habits in relation to non-muscle-invasive bladder cancer prognosis and health-related quality of life

IntroductionPatients with non-muscle-invasive bladder cancer (NMIBC) have a good survival but are at high risk for tumour recurrence and disease progression. It is important to identify lifestyle habits that may...

879P - Germline sequencing of advanced prostate cancer patients in the BARCODE2 trial

BackgroundThe BARCODE2 trial is investigating the response to platinum chemotherapy in men with advanced prostate cancer (PrCa) and a germline mutation in a DNA repair gene. We present the germline DNA sequencing results for 94 men who underwent genetic screening. MethodsEligible men with advanced PrCa consented to trial entry and provided a blood sample for DNA extraction and sequencing. All patients were known to have metastatic castration resistant PrCa (mCRPC) and had been treated with one or both of: Docetaxel chemotherapy and an androgen receptor targeted agent. Next generation sequencing (NGS) using a customised 115 gene panel (Agilent Technologies) was carried out on a MiSeq machine. Protein truncating variants (PTVs) in DNA repair genes by NGS were validated by Sanger sequencing. Patients found to carry a PTV were eligible to receive carboplatin upon disease progression. Results94 patients have undergone genetic testing. The median age of patients entering the trial was 67 (range 46-84). 21 patients (22%) carried one or more PTVs in a DNA repair gene: 3 carriers of a BRCA2 variant and 3 carriers of a variant in ALKBH3, 2 carriers of an ATM variant and 2 carriers of a PALB2 variant. One of the ATM variant carries also carried a PTV in POLQ and 2 further carriers of the same POLQ variant were identified. One carrier was identified to carry a variant in each of the following genes: MRE11A, PARP2, BLM, CHEK2, EXO1, LIG4, FANCD2, MSH5 and PMS1. Of the 20 identified PTVs, 11 are classified as pathogenic or likely pathogenic in ClinVar. There was no significant difference in the age at PrCa diagnosis between carriers and non-carriers (mean age 59 years vs 60; p=0.34). There was also no difference in the presence of a family history of cancer. ConclusionsThe initial NGS results in the BARCODE2 trial demonstrate a higher frequency of germline mutations in mCRPC patients compared with previously published data. This study is ongoing and aims to sequence 450 patients. If the frequency of germline mutations in men with advanced PrCa is confirmed to be 20% or higher, this would support the roll-out of routine genetic testing in the oncology setting to identify men who may benefit from targeted treatments such as platinum chemotherapy and PARP inhibitors. Clinical trial identificationNCT02955082. Legal entity responsible for the studyInstitute of Cancer Research. FundingEuropean Research Council. DisclosureAll authors have declared no conflicts of interest.

A National Population-Based E-cohort of People with Psychosis (PsyCymru) Linkage of Phenotypical and Genetic Data to Routinely Collected Records

IntroductionPsyCymru was established to investigate the feasibility of linking a prospectively ascertained, well characterised (linked clinical cohort) of people with psychosis in Wales, UK with large amounts of anonymised routinely collected health record data. We are now additionally linking genetic data.&#x0D; Objectives and ApproachPsyCymru aimed to create a research platform for psychosis research in Wales by establishing two cohorts. The first was a well-characterised clinically assessed cohort with genetic data. Consented individuals underwent structured interviews using well-validated questionnaires and gave blood sample for DNA extraction, sequencing, and candidate gene identification. This data was then linked to routinely collected health and social datasets with identity encryption. The second is a larger e-cohort of prevalent psychosis cases created using a validated algorithm applied to anonymised routine data. Both cohorts were tracked prospectively and retrospectively in the Secure Anonymised Information Linkage (SAIL) databank.&#x0D; ResultsIn total, data from 958 individuals for the clinical cohort were imported to SAIL. Among these individuals, genetic data for 740 were analysed. The genetic data included robust loci for schizophrenia, pathogenic copy-number variations (CNVs) for various conditions (e.g., autism, intellectual disability, congenital malformations), polygenic risks scores for schizophrenia, as well as pathogenic/non-pathogenic duplications or deletions of chromosome spanning more than 500kb or 1Mb. For the e-cohort, 29,797 individuals were found having a psychosis diagnosis from primary and secondary care between 2004 to 2013. Social demographic data for both cohorts were also analysed based on sex, age, area deprivation, urbanicity, and employment status.&#x0D; Conclusion/ImplicationsThis unique platform pooled data together from multiple sources; linking clinical, psychological, biological, genetic, and health care factors to address assorted research questions. This resource will continue to expand over the coming years in size, breadth and depth of data, with continued recruitment and additional measures planned.