HostSeq: a Canadian whole genome sequencing and clinical data resource.

HostSeq was launched in April 2020 as a national initiative to integrate whole genome sequencing data from 10,000 Canadians infected with SARS-CoV-2 with clinical information related to their disease experience. The mandate of HostSeq is to support the Canadian and international research communities in their efforts to understand the risk factors for disease and associated health outcomes and support the development of interventions such as vaccines and therapeutics. HostSeq is a collaboration among 13 independent epidemiological studies of SARS-CoV-2 across five provinces in Canada. Aggregated data collected by HostSeq are made available to the public through two data portals: a phenotype portal showing summaries of major variables and their distributions, and a variant search portal enabling queries in a genomic region. Individual-level data is available to the global research community for health research through a Data Access Agreement and Data Access Compliance Office approval. Here we provide an overview of the collective project design along with summary level information for HostSeq. We highlight several statistical considerations for researchers using the HostSeq platform regarding data aggregation, sampling mechanism, covariate adjustment, and X chromosome analysis. In addition to serving as a rich data source, the diversity of study designs, sample sizes, and research objectives among the participating studies provides unique opportunities for the research community.

Immunohistochemical expression of the ERG gene in prostatic adenocarcinoma and its relationship with clinicopathological parameters.

INTRODUCTION: This study aimed to determine the immunohistochemical expression of the ERG gene in prostatic adenocarcinoma and to evaluate the relationships between ERG expression and clinicopathological parameters. DESIGN: Cross-sectional study. SETTING: Pathology department of a tertiary hospital. MATERIALS AND METHODS: The prostatectomy materials of 122 patients diagnosed with prostate adenocarcinoma between 2004 and 2017 in Zonguldak Bülent Ecevit University Faculty of Medicine, Department of Pathology were included in the study. MAIN OUTCOME MEASURES: Clinical data were obtained from patient files and macroscopic data were obtained from surgery and pathology reports. ERG expression, age, prostate-specific antigen levels, Gleason pattern and score, Gleason grade, and pathological stage were recorded. RESULTS: The mean age of the patients was 62.66 ± 5.81 years and overall preoperative PSA was 10.40 ± 8.88 ng/ml. ERG was positive in 52.46% of the patients. PSA levels were similar in ERG positive and negative samples (p = 0.935). There was no significant relationship between Gleason score and ERG positivity (p = 0.197). ERG expression did not change with regard to age groups (p = 0.441) or tumour stage (p = 0.371). CONCLUSION: This study shows that the frequency of ERG positivity was high in our patients and that ERG positivity was not associated with clinical and pathological features, such as PSA levels, Gleason score, age and pathological stage.

Modeling of recombinant yeast cells: reduction of phase space.

The mechanism of starch fermentation by recombinant Saccharomyces cerevisiae in batch reactor is studied. Experiments were carried in the presence and absence of oxygen, with different initial starch concentrations. A variety of data concerning biotic and abiotic phases are collected. Nonlinear data analysis techniques are used to determine the block diagram of the system under study. Data analysis and processing reported here, are believed to form a basis in further work in structured modeling of biological systems, recombinant yeast cultures in particular.