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Should we have blind faith in bioinformatics software? Illustrations from the SNAP web-based tool
Sébastien Robiou-du-Pont1, Aihua Li1, Shanice Christie1
1Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada.
Plos One
|March 6, 2015
Summary
Bioinformatics tool validity is crucial. This study found the SNAP tool
Area of Science:
- Genetics and Bioinformatics
- Cardiovascular and Metabolic Research
- Population Cohort Studies
Background:
- Bioinformatics tools are widely used in biological research.
- The validity of these tools, particularly for genetic data analysis, is often not systematically assessed.
- Understanding tool accuracy is essential for reliable genetic association studies.
Purpose of the Study:
- To evaluate the accuracy of the SNAP bioinformatics tool in identifying single nucleotide polymorphisms (SNPs) within the Illumina Cardio-Metabochip.
- To assess the contribution of SNPs associated with cardio-metabolic traits in the FAMILY birth cohort.
- To determine the false-negative and false-positive rates of the SNAP tool compared to the official Illumina chip data.
Main Methods:
- Utilized 415 genome-wide significant SNPs for eight cardio-metabolic traits.
- Employed the SNAP web-based tool to check SNP availability in the Illumina Cardio-Metabochip.
- Compared SNAP outputs with the Illumina Cardio-Metabochip file using NCBI Human Genome Browser data and HapMap 3/1000 Genomes Project references.
- Calculated Cohen's Kappa coefficient to measure agreement between SNAP and Illumina data.
Main Results:
- SNAP reported 201 out of 415 SNPs as missing from the Cardio-Metabochip using the HapMap 3 reference.
- Further analysis revealed 152 of these were actually present, indicating a 36.6% false-negative rate.
- Using the 1000 Genomes Project reference, the false-negative rate decreased to 17.6%.
- No false-positive SNPs were identified by SNAP.
Conclusions:
- The SNAP tool demonstrates significant inaccuracies (invalid outputs) when assessing SNP content in the Illumina Cardio-Metabochip.
- The study highlights the critical need for independent validation of bioinformatics tools before their widespread implementation.
- Recommendations are proposed to enhance best practices for bioinformatics software development and usage.
