OBJECTIVEWe evaluated the accuracy and efficiency of computational inference methods for haplotype on estimate HLA-A-B-C haplotype frequencies by compared with the haplotypes manually defined in a family-base dataset.

METHODS558 individuals with pedigree information were selected, and their haplotyps were compared with the data obtained by the following three method: the Expectation-Maximization (EM) and Excoffier-Laval-Balding (ELB)algorithms using the AELEQUIN software, and the SAS/Genetics PROC HAPLOTYPE method.

RESULTSAfter performing the SAS/Genetics method, and the Expectation-Maximization (EM) and Excoffier-Laval-Balding (ELB) algorithms using the AELEQUIN software, 248, 247, and 238 different haplotypes were obtained respectively. The accuracy rates of these three methods were 88.5%, 89.1%, and 90.3% respectively. There are no significant different in the accuracy and estimated haplotype frequency comparisons among any two of these computational inference methods.

CONCLUSIONHigh accuracy haplotype frequency estimate rates could be obtained by these three computational inference methods, and there are no significant difference in the comparison of haplotypes estimated by SAS/Genetics, the EM and ELB algorithms using the AELEQUIN software. However, ELB algorithm shows better performance than EM algorithm and SAS/Genetics PROC HAPLOTYPE method for haplotype frequencies estimation in general.

Adult ; Algorithms ; Computational Biology ; methods ; Computer Simulation ; Databases, Genetic ; Female ; Haplotypes ; Histocompatibility Antigens Class I ; genetics ; Humans ; Male ; Middle Aged ; Nose Neoplasms ; diagnosis ; genetics ; Pedigree ; Software ; Young Adult

PURPOSE: Surgical resection for gastric adenocarcinoma is associated with significant post-operative morbidity and mortality. The aim of this study was to assess the prognostic significance of sarcopenia in patients undergoing resection for gastric adenocarcinoma with respect to post-operative morbidity and survival. MATERIALS AND METHODS: A retrospective analysis was conducted on a cohort of consecutive patients who underwent surgical resection for gastric adenocarcinoma between 2008 and 2014. Patient demographics, radiological parameters, and pathological data were collected. OsiriX software (Pixmeo) was used to measure skeletal muscle area, which was normalized for height to calculate skeletal muscle index. RESULTS: A total of 56 patients (41 male, 15 female; mean age, 68.4 ± 11.9 years) met the inclusion criteria. Of these, 36% (20 of 56) of the patients were sarcopenic pre-operatively. Both sarcopenic and non-sarcopenic patient groups were equally matched with the exception of weight and body mass index (P=0.036 and 0.001, respectively). Sarcopenia was associated with a decreased overall survival (log-rank P=0.003) and was an adverse prognostic predictor of overall survival in multivariate analysis (hazard ratio, 10.915; P=0.001). Sarcopenia was a predictor of serious in-hospital complications in multivariate analysis (odds ratio, 3.508; P=0.042). CONCLUSIONS: In patients undergoing curative resection for gastric cancer, there was a statistically significant association between sarcopenia and both decreased overall survival and serious post-operative complications. The measurement and reporting of skeletal muscle index on pre-operative computed tomography should be considered.
Adenocarcinoma ; Body Mass Index ; Cohort Studies ; Demography ; Female ; Humans ; Male ; Mortality* ; Multivariate Analysis ; Muscle, Skeletal ; Prognosis ; Retrospective Studies ; Sarcopenia* ; Stomach Neoplasms* ; Tomography, X-Ray Computed

There is evidence that a substantial part of genetic predisposition to prostate cancer (PCa) may be due to lower penetrance genes which are found by genome-wide association studies. We have recently conducted such a study and seven new regions of the genome linked to PCa risk have been identified. Three of these loci contain candidate susceptibility genes: MSMB, LMTK2 and KLK2/3. The MSMB and KLK2/3 genes may be useful for PCa screening, and the LMTK2 gene might provide a potential therapeutic target. Together with results from other groups, there are now 23 germline genetic variants which have been reported. These results have the potential to be developed into a genetic test. However, we consider that marketing of tests to the public is premature, as PCa risk can not be evaluated fully at this stage and the appropriate screening protocols need to be developed. Follow-up validation studies, as well as studies to explore the psychological implications of genetic profile testing, will be vital prior to roll out into healthcare.
Genetic Predisposition to Disease ; genetics ; Genetic Testing ; Humans ; Kallikreins ; genetics ; Male ; Membrane Proteins ; genetics ; Prostatic Neoplasms ; diagnosis ; genetics ; Prostatic Secretory Proteins ; genetics ; Protein-Serine-Threonine Kinases ; genetics ; Risk Factors