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Where in the genome are we? A cautionary tale of database use in genomics research.

ABSTRACT: With the advent of high throughput data genomic technologies the volume of available data is now staggering. In addition databases that provide resources to annotate, translate, and connect biological data have grown exponentially in content and use. The availability of such data emphasizes the importance of bioinformatics and computational biology in genomics research and has led to the development of thousands of tools to integrate and utilize these resources. When utilizing such resources, the principles of reproducible research are often overlooked. In this manuscript we provide selected case studies illustrating issues that may arise while working with genes and genetic polymorphisms. These case studies illustrate potential sources of error which can be introduced if the practices of reproducible research are not employed and non-concurrent databases are used. We also show examples of a lack of transparency when these databases are concerned when using popular bioinformatics tools. These examples highlight that resources are constantly evolving, and in order to provide reproducible results, research should be aware of and connected to the correct release of the data, particularly when implementing computational tools.

SUBMITTER: Vaughan LK

PROVIDER: S-EPMC3604632 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Where in the genome are we? A cautionary tale of database use in genomics research.

Vaughan Laura K LK Srinivasasainagendra Vinodh V

Frontiers in genetics 20130321

With the advent of high throughput data genomic technologies the volume of available data is now staggering. In addition databases that provide resources to annotate, translate, and connect biological data have grown exponentially in content and use. The availability of such data emphasizes the importance of bioinformatics and computational biology in genomics research and has led to the development of thousands of tools to integrate and utilize these resources. When utilizing such resources, th ...[more]

PMID: 23519237

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Project description:BACKGROUND: The National Health and Nutrition Examination Survey (NHANES) is one example of cross-sectional datasets that have been used to draw causal inferences regarding environmental chemical exposures and adverse health outcomes. Our objectives were to analyze four NHANES datasets using consistent a priori selected methods to address the following questions: Is there a consistent association between urinary bisphenol A (BPA) measures and diabetes, coronary heart disease (CHD), and/or heart attack across surveys? Is NHANES an appropriate dataset for investigating associations between chemicals with short physiologic half-lives such as BPA and chronic diseases with multi-factorial etiologies? Data on urinary BPA and health outcomes from 2003-2004, 2005-2006, 2007-2008, and 2009-2010 were available. METHODOLOGY AND FINDINGS: Regression models were adjusted for creatinine, age, gender, race/ethnicity, education, income, smoking, heavy drinking, BMI, waist circumference, calorie intake, family history of heart attack, hypertension, sedentary time, and total cholesterol. Urinary BPA was not significantly associated with adverse health outcomes for any of the NHANES surveys, with ORs (95% CIs) ranging from 0.996 (0.951-1.04) to 1.03 (0.978-1.09) for CHD, 0.987 (0.941-1.04) to 1.04 (0.996-1.09) for heart attack, and 0.957 (0.899-1.02) to 1.01 (0.980-1.05) for diabetes. CONCLUSIONS: Using scientifically and clinically supportable exclusion criteria and outcome definitions, we consistently found no associations between urinary BPA and heart disease or diabetes. These results do not support associations and causal inferences reported in previous studies that used different criteria and definitions. We are not drawing conclusions regarding whether BPA is a risk factor for these diseases. We are stating the opposite--that using cross-sectional datasets like NHANES to draw such conclusions about short-lived environmental chemicals and chronic complex diseases is inappropriate. We need to expend resources on appropriately designed epidemiologic studies and toxicological explorations to understand whether these types of chemicals play a causal role in chronic diseases.

Project description:FURIN is a pro-protein convertase previously shown to be important for placental syncytialisation (Zhou et al. [1]), a process of cell fusion whereby placental cytotrophoblast cells fuse to form a multinucleated syncytium. This finding has been broadly accepted however, we have evidence suggesting the contrary. Spontaneously syncytialising term primary human trophoblast cells and BeWo choriocarcinoma cells were treated with either FURIN siRNA or negative control siRNA or the protease inhibitor, DEC-RVKR-CMK, or vehicle. Cells were then left to either spontaneously syncytialise (primary trophoblasts) or were induced to syncytialise with forskolin (BeWo). Effects on syncytialisation were measured by determining human chorionic gonadotrophin secretion and E-cadherin protein levels. We showed that FURIN is not important for syncytialisation in either cell type. However, in primary trophoblasts another protease also inhibited by DEC-RVKR-CMK, may be involved. Our results directly contrast with those published by Zhou et al. Zhou et al. however, used first trimester villous explants to study syncytialisation, and we used term primary trophoblasts. Therefore, we suggest that FURIN may be involved in syncytialisation of first trimester trophoblasts, but not term trophoblasts. What is more concerning is that our results using BeWo cells do not agree with their results, even though for the most part, we used the same experimental design. It is unclear why these experiments yielded different results, however we wanted to draw attention to simple differences in measuring syncytialisation or flaws in method reporting (including omission of cell line source and passage numbers, siRNA concentration and protein molecular weights) and choice of immunoblot loading controls, that could impact on experimental outcomes. Our study shows that careful reporting of methods by authors and thorough scrutiny by referees are vital. Furthermore, a universal benchmark for measuring syncytialisation is required so that various studies of syncytialisation can be validated.

Dataset Information

Where in the genome are we? A cautionary tale of database use in genomics research.

Publications

Where in the genome are we? A cautionary tale of database use in genomics research.

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