Genetics of rearing success in four pure laying hen lines during the first 17 weeks of age.

This study aimed to investigate the genetics of rearing success (RS) in laying hens. Four rearing traits: clutch size (CS), first week mortality (FWM), rearing abnormalities (RA), and natural death (ND), were included as factors determining RS. Pedigree, genotypic, and phenotypic records of 4 purebred genetic lines of White Leghorn layers were available for 23,000 rearing batches obtained between 2010 and 2020. FWM and ND showed little or no variation amongst the 4 genetic lines over the years 2010-2020, whereas an increase was observed for CS and a decrease for RA. To determine whether these traits were heritable, genetic parameters for each trait were estimated, using a Linear Mixed Model. Heritabilities within lines were low (0.05-0.19 for CS, 0.01-0.04 for FWM, 0.02-0.06 for RA, 0.02-0.04 for ND, and 0.01-0.07 for RS). Additionally, genome wide association study was done to scan the genomes of the breeders to reveal single nucleotide polymorphisms (SNPs) associated with these traits. Manhattan plots indicated the existence of 12 different SNPs having a significant effect on RS. Thus, the identified SNPs will increase the understanding of the genetics of RS in laying hens.

Predicting hatchability of layer breeders and identifying effects of animal related and environmental factors.

In this study, a data driven approach was used by applying linear regression and machine learning methods to understand animal related and environmental factors affecting hatchability. Data was obtained from a parent stock and grand-parent stock hatchery, including 1,737 batches of eggs incubated in the years 2010-2018. Animal related factors taken into consideration were strain (white vs. brown strain), breeder age, and egg weight uniformity at the start of incubation, whereas environmental factors considered were length of egg storage before incubation, egg weight loss during incubation and season. Effects of these factors on hatchability were analyzed with 3 different models: a linear regression (LR) model, a random forest (RF) model and a gradient boosting machine (GBM) model. In part one of the study, hatchability was predicted and the performance of the models in terms of coefficient of determination (R2) and root mean square error (RMSE) was compared. The ensemble machine learning models (RF: R2 = 0.35, RMSE = 8.41; GBM: R2 = 0.31, RMSE = 8.67) appeared to be superior than the LR model (R2 = 0.27, RMSE = 8.92) as indicated by the higher R2 and lower RMSE. In part 2 of the study, effects of these factors on hatchability were investigated more into detail. Hatchability was affected by strain, breeder age, egg weight uniformity, length of egg storage and season, but egg weight loss didn't have a significant effect on hatchability. Additionally, four 2-way interactions (breeder age × egg weight uniformity, breeder age × length of egg storage, breeder age × strain, season × strain) were significant on hatchability. It can be concluded that hatchability of parent stock and grand-parent stock layer breeders is affected by several animal related and environmental factors, but the size of the predicted effects varies between the methods used. In this study, 3 models were used to predict hatchability and to analyze effects of animal related and environmental factors on hatchability. This opens new horizons for future studies on hatchery data by taking the advantage of applying machine learning methods, that can fit complex datasets better than LR and applying statistical analysis.

A Genetic Biomarker of Oxidative Stress, the Paraoxonase-1 Q192R Gene Variant, Associates with Cardiomyopathy in CKD: A Longitudinal Study.

Background. Oxidative stress is a hallmark of CKD and this alteration is strongly implicated in LV hypertrophy and in LV dysfunction. Methods and Patients. We resorted to the strongest genetic biomarker of paraoxonase-1 (PON1) activity, the Q192R variant in the PON1 gene, to unbiasedly assess (Mendelian randomization) the cross-sectional and longitudinal association of this gene-variant with LV mass and function in 206 CKD patients with a 3-year follow-up. Results. The R allele of Q192R polymorphism associated with oxidative stress as assessed by plasma 8-isoPGF2α (P = 0.03) and was dose-dependently related in a direct fashion to LVMI (QQ: 131.4 ± 42.6 g/m(2); RQ: 147.7 ± 51.1 g/m(2); RR: 167.3 ± 41.9 g/m(2); P = 0.001) and in an inverse fashion to systolic function (LV Ejection Fraction) (QQ: 79 ± 12%; RQ: 69 ± 9%; RR: 65 ± 10% P = 0.002). On longitudinal observation, this gene variant associated with the evolution of the same echocardiographic indicators [LVMI: 13.40 g/m(2) per risk allele, P = 0.005; LVEF: -2.96% per risk allele, P = 0.001]. Multivariate analyses did not modify these associations. Conclusion. In CKD patients, the R allele of the Q192R variant in the PON1 gene is dose-dependently related to the severity of LVH and LV dysfunction and associates with the longitudinal evolution of these cardiac alterations. These results are compatible with the hypothesis that oxidative stress is implicated in cardiomyopathy in CKD patients.

Early prenatal diagnosis by celocentesis.

BACKGROUND: Celocentesis is the ultrasound-guided aspiration of fluid from the extra-amniotic cavity at 7-8 weeks of gestation. This paper reports on the clinical application of celocentesis for early prenatal diagnosis. METHODS: Celocentesis was successfully performed in nine pregnancies and 1-2 mL of fluid were obtained after one needle insertion. The indications were prenatal diagnosis of beta-thalassemia or sickle cell disease (n = 6), Marfan syndrome (n = 1) and paternity testing (n = 2). Molecular biological techniques were used to analyze the celomic fluid and this was successfully carried out in all cases. RESULTS: In two cases pregnancy termination was performed at the request of the mother because in one case the fetus was found to have sickle cell anemia and in the second case paternity testing demonstrated that the father was not the woman's husband. In both cases the results were confirmed using the placental samples collected after pregnancy termination. In six of the seven pregnancies with desirable results, amniocentesis was performed at 16 weeks and the results were concordant with those obtained from celocentesis. All pregnancies were uneventful and resulted in the delivery of healthy and appropriately grown babies. CONCLUSION: Celocentesis may be a viable alternative to the currently used tests of chorionic villus sampling and amniocentesis.

Distribution and frequency of beta-thalassemia mutations in northwestern and central Greece.

OBJECTIVES: Beta-Thalassemia is a common autosomal recessive disorder resulting from over 200 different mutations of the beta-globin genes. The spectrum of beta-thalassemia mutations in Greece has been previously described in the population of the capital city of Athens, or in beta-thalassemia patients having transfusion therapy. The aim of the present study was to identify the distribution of the most common beta-thalassemia mutations in the population of northwestern and central Greece. METHODS: The data for this study were derived from a total of 1,130 unrelated subjects including 46 beta-thalassemia major, three beta -thalassemia intermedia and 1,081 carriers identified in our antenatal screening program. beta-Thalassemia mutations were identified by ARMS, DGGE and Reverse Dot Blot. RESULTS: The most common mutation, IVS-I-110, is followed, in order of frequency, by the mutations Cd-39, IVS-I-1, IVS-II-1, Cd-6, IVS-I-6, IVS-I-5, IVS-II-745, Cd-5 and 44 bp del. IVS-I-110 and Cd-39 frequencies are similar with those found in other Balkan countries. Significant differences in regional distribution were observed. The results showed a clear drift of the distribution of the most frequent IVS-I-110 mutation in the south-north (29.4, 40.0, 44.6 and 61.7%) and the east-west axis (31.8 and 44.6%). CONCLUSIONS: Population screening and prenatal diagnosis are significantly facilitated by these data. Furthermore, the detailed distribution tables of beta-thalassemia mutations are essential for counseling and extraction of genetic diversity estimates for population genetic studies in other inherited disorders.

Association of oestrogen receptor alpha polymorphisms and androgen receptor CAG trinucleotide repeats with male infertility: a study in 109 Greek infertile men.

This study was performed to examine the contribution of genetic polymorphism of oestrogen and androgen receptor (AR) genes in male infertility. We have studied in total 173 Greek men, 109 infertile patients and 64 controls (group A). Patients were divided in to three subgroups: group B (n=29) with idiopathic moderate oligospermia, group C (n=42) with azoospermia or idiopathic severe oligospermia and group D (n=38) with azoospermia or oligospermia of various known aetiologies. All patients and controls were genotyped for two polymorphisms of the oestrogen receptor alpha (ERalpha) gene and also for the (CAG)n repeat length polymorphism of the X-linked androgen receptor (AR)gene. The control group had statistically significant difference from group C regarding the XbaI polymorphism of ERalpha gene. Despite the fact that we did not observe any statistically significant differences in the mean and range of the CAG repeat number, the frequency of the higher repeats of the nucleotide repeat sequence (CAG)n of the AR gene was 2-4 times higher in groups B and C compared with the control group A. Our results indicate that both ERalpha and AR gene play significant role in male fertility. It is possible that a synergy may exist between unfavourable genotypes of these two genes in male infertility.

Novel PKD1 deletions and missense variants in a cohort of Hellenic polycystic kidney disease families.

The autosomal dominant form of polycystic kidney disease is a very frequent genetically heterogeneous inherited condition affecting approximately 1 : 1000 individuals of the Caucasian population. The main symptom is the formation of fluid-filled cysts in the kidneys, which grow progressively in size and number with age, and leading to end-stage renal failure in approximately 50% of patients by age 60. About 85% of cases are caused by mutations in the PKD1 gene on chromosome 16p13.3, which encodes for polycystin-1, a membranous glycoprotein with 4302 amino acids and multiple domains. Mutation detection is still a challenge owing to various sequence characteristics that prevent easy PCR amplification and sequencing. Here we attempted a systematic screening of part of the duplicated region of the gene in a large cohort of 53 Hellenic families with the use of single-strand conformation polymorphism analysis of exons 16-34. Our analysis revealed eight most probably disease causing mutations, five deletions and three single amino acid substitutions, in the REJ domain of the protein. In one family, a 3-bp and an 8-bp deletion in exons 20 and 21 respectively, were co-inherited on the same PKD1 chromosome, causing disease in the mother and three sons. Interestingly we did not find any termination codon defects, so common in the unique part of the PKD1 gene. In the same cohort we identified 11 polymorphic sequence variants, four of which resulted in amino acid variations. This supports the notion that the PKD1 gene may be prone to mutagenesis, justifying the relatively high prevalence of polycystic kidney disease.

Glutathione S-transferase null genotypes in transitional cell bladder cancer: a case-control study.

OBJECTIVES: This study was conducted (1) to examine whether the GSTM1 and GSTT1 null genotypes are risk factors for bladder cancer, and (2) to study a possible association of these genotypes with disease severity. METHODS: This case-control study was undertaken over a 21-month period and included 89 newly diagnosed transitional cell bladder cancer patients and 147 controls; both patients and controls originated from a defined population (residents of the loannina region, Northwestern Greece) and were similar with regard to mean age, male to female ratio and smoking habits. The GSTM1 and GSTT1 genotypes were identified by multiplex polymerase chain reaction on peripheral blood DNA samples. Genotype frequencies among patients and controls were assessed and the association of the genotypes with tumor grade and stage at presentation were statistically evaluated by the chi(2) test. RESULTS: The GSTM1 null genotype was strongly associated with bladder cancer. The odds ratio, attributable and population attributable risks were estimated at 2.76, 0.64 and 0.40, respectively. The correlation between the GSTM1 null genotype with stage, although not statistically significant, was estimated at an odds ratio of 2.6 for invasive disease. The correlation of GSTM1 null genotype with tumor grade did not yield a statistically significant result. The GSTT1 null genotype was not statistically associated with bladder cancer. CONCLUSION: According to our study, individuals with the GSTM1 null genotype carry a substantially higher risk for bladder carcinogenesis. The GSTM1 null genotype is not associated with more aggressive disease in terms of tumor grade, although there is a correlation between this genotype and stage of the disease.

Association of estrogen receptor gene polymorphisms with endometriosis.

OBJECTIVE: To explore the association of the estrogen receptor two-allele (point) polymorphism and multiallele (microsatellite) polymorphism with endometriosis. DESIGN: Case-control study. SETTING: Genetics and Endoscopy Unit, Department of Obstetrics and Gynecology, Ioannina University HOSPITAL, Ioannina, Greece. PATIENT(S): Fifty-seven women with surgically and histologically diagnosed endometriosis of stages I-IV. INTERVENTION(S): Diagnostic laparoscopy. MAIN OUTCOME MEASURE(S): Frequency and distribution of the estrogen receptor gene polymorphisms. RESULT(S): There was a statistically significant difference between the patients and the controls in the frequency of the two-allele Pvu II polymorphism (0.72 vs. 0.49) and in the median repeats of the (TA)n multiallele polymorphism (15 vs. 20 repeats). In both groups, linkage was found between the fewer (TA)n repeats (range, 12-19) and the positive Pvu II polymorphism. CONCLUSION(S): The variability of the estrogen receptor gene likely contributes to the pathogenesis of endometriosis.

Fragile X premutations and (TA)n estrogen receptor polymorphism in women with ovarian dysfunction.

We studied five groups of women with ovarian dysfunction for the CGG expansion in FMR1 and a (TA)n polymorphism in the estrogen receptor gene: a) poor responders to ovarian stimulation as part of in vitro fertilization (n = 13); b) women with familial premature ovarian failure (POF) (n = 7); c) sporadic cases with POF (n = 16); d) FRAXA premutation carriers with POF (n = 7); and e) FRAXA premutation carriers without POF (n = 9). FRAXA premutation was found in one woman with familial POF. A significant association of familial POF and FRAXA premutation carriers with POF having low copy of the (TA)n polymorphism as compared to controls was observed. Our preliminary data suggest a potential role of the estrogen receptor in POF, and it may influence the variable age of menopause of the FRAXA premutation carriers.