Dataset Information

Characterization of carotenoids in sorghum germplasm

ABSTRACT: Common SNPs for GBS data for global sorghum germplasm incluiding Sorghum association pannel, carotenoid panel, Haiti breeding program, NPGS collection for Sudan and Ethiopia, Niger germplasm and Nigeria germplasm

INSTRUMENT(S): -

ORGANISM(S): Sorghum Bicolor

SUBMITTER: Colorado State University

PROVIDER: PRJEB60406 | EVA | 2023-03-06

REPOSITORIES: EVA

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Dataset's files

Source:

			Action	DRS
	GS_all_countries_and_casap_imputed_refallele-fixed.accessioned.vcf.gz	Vcf
	GS_all_countries_and_casap_imputed_refallele-fixed.accessioned.vcf.gz.csi	Vcf
	GS_all_countries_and_casap_imputed_refallele-fixed.vcf.csi	Other
	GS_all_countries_and_casap_imputed_refallele-fixed.vcf.gz	Vcf

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Project description:Colorectal cancer (CRC) is the third most common type of cancer among men and the second among women in Brazil. Despite the high incidence and significance of CRC in Brazil, very little is known about its prevalence among the asymptomatic population. Recently, a CRC screening program was implemented at the Cancer Hospital of Barretos. Characterization of the clinical findings detected in the screening population and the prevalence of basal CRC might contribute to better organization of the program and define the best strategy for a future national screening program. We hypothesize that recruitment and the early outcomes of our screening program based on the fecal immunochemical test (FIT) will differ from the outcomes corresponding to other populations due to sociodemographic differences. Aims: i. To implement a data collection and storage system for follow-up of the screening program participants and to measure early outcomes (adenoma, advanced adenoma and cancer) and associate them with sociodemographic risk factors; ii. to quantify the risk of CRC in the Brazilian population and to develop algorithms for risk stratification of CRC screening; and iii. to compare the risk stratification to other countries with low, medium and high incomes. Methods: Individuals aged 50 to 65 years will be included in the HCB screening program from November 2017 to December 2018. The following data will be collected from all participants: sociodemographic and ethnic (skin color) characteristics; risk factors for CRC, such as smoking and drinking; comorbidities, including diabetes mellitus and arterial hypertension; and FIT, colonoscopy and histopathology examination results. Data collection will be performed using the REDCap data collection/database system. The risk score will be formulated using the Chi-square test (or Fisher’s exact test) and simple logistic regression, and the regression coefficients will be calculated. Then, the model identified for the training sample will be replicated with a validation sample. The resulting score will be used to calculate the sensitivity, specificity, positive predictive value, negative predictive value, accuracy, area under the receiver operating characteristic (ROC) curve and Kolmogorov D statistic.

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Characterization of carotenoids in sorghum germplasm

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