An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Performance of a computable phenotype for identification of patients with diabetes within PCORnet: The Patient-Centered Clinical Research Network

Purpose: PCORnet, the National Patient-Centered Clinical Research Network, represents an innovative system for the conduct of observational and pragmatic studies. We describe the identification and validation of a retrospective cohort of patients with type 2 diabetes (T2DM) from four PCORnet sites. Methods: We adapted existing computable phenotypes (CP) for the identification of patients with T2DM and evaluated their performance across four PCORnet sites (2012-2016). Patients entered the cohort on the earliest date they met one of three CP categories: (CP1) coded T2DM diagnosis (ICD-9/ICD-10) and an antidiabetic prescription, (CP2) diagnosis and glycosylated hemoglobin (HbA1c) ≥6.5%, or (CP3) an antidiabetic prescription and HbA1c ≥6.5%. We required evidence of health care utilization in each of the 2 prior years for each patient, as we also developed an incident T2DM CP to identify the subset of patients without documentation of T2DM in the 365 days before t 0 . Among a systematic sample of patients, we calculated the positive predictive value (PPV) for the T2DM CP and incident-T2DM CP using electronic health record (EHR) review as reference. Results: The CP identified 50 657 patients with T2DM. The PPV of patients randomly selected for validation was 96.2% (n = 1572; CI:95.1-97.0) and was consistently high across sites. The PPV for the incident-T2DM CP was 5.8% (CI:4.5-7.5). Conclusions: The T2DM CP accurately and efficiently identified patients with T2DM across multiple sites that participate in PCORnet, although the incident T2DM CP requires further study. PCORnet is a valuable data source for future epidemiological and comparative effectiveness research among patients with T2DM

Development of corn seedlings after a period of exposition to various water potential

Fungicide treated and untreated corn seeds were sets to germinate under varying water availability conditions (0 to -12atm water potential). The seedlings obtained on each individual treatment were subsequently grown under ideal available water conditions. The results permitted to conclude that the occurrence of a water deficit during the on set of the germination process results in reductions on the length of the embryonic structures, particularly the epicotil. This effect attenuates with times due to the increase in growth velocity in environments where water potential is lower. Fungicid treated seeds, did not appear to be consistently vantageous in environments with water stress.Submetendo sementes de milho com e sem tratamento fungicida, a ambientes de germinação variáveis quanto à disponibilidade de água (0 a -12atm), o presente trabalho avaliou o desenvolvimento posterior das plântulas postas em ambientes sem limitações hídricas. Os resultados obtidos permitiram concluir que a ocorrência de déficit hídrico, durante o início do processo de germinação, promove reduções posteriores no comprimento das estruturas embrionárias e, de forma mais acentuada, do epicótilo; apesar disso, esse efeito se atenua com o passar do tempo pela elevação progressiva na velocidade de crescimento em ambientes que oferecem menores potenciais hídricos. Paralelamente, o tratamento fungicida das sementes pode não trazer vantagens em ambientes hidricamente deficientes; esta afirmação, contudo, considera o papel toalha como meio fornecedor de água o que, em contrapartida, exige cautela na sua extrapolação para as condições proporcionadas pelo solo