Should we have blind faith in bioinformatics software? Illustrations from the SNAP web-based tool

PloS One
Sébastien Robiou-du-PontDavid Meyre

Abstract

Bioinformatics tools have gained popularity in biology but little is known about their validity. We aimed to assess the early contribution of 415 single nucleotide polymorphisms (SNPs) associated with eight cardio-metabolic traits at the genome-wide significance level in adults in the Family Atherosclerosis Monitoring In earLY Life (FAMILY) birth cohort. We used the popular web-based tool SNAP to assess the availability of the 415 SNPs in the Illumina Cardio-Metabochip genotyped in the FAMILY study participants. We then compared the SNAP output with the Cardio-Metabochip file provided by Illumina using chromosome and chromosomal positions of SNPs from NCBI Human Genome Browser (Genome Reference Consortium Human Build 37). With the HapMap 3 release 2 reference, 201 out of 415 SNPs were reported as missing in the Cardio-Metabochip by the SNAP output. However, the Cardio-Metabochip file revealed that 152 of these 201 SNPs were in fact present in the Cardio-Metabochip array (false negative rate of 36.6%). With the more recent 1000 Genomes Project release, we found a false-negative rate of 17.6% by comparing the outputs of SNAP and the Illumina product file. We did not find any 'false positive' SNPs (SNPs specified as available in t...Continue Reading

References

Nov 25, 2003·Bioinformatics·Christos A Ouzounis, Alfonso Valencia
Jul 21, 2005·Bioinformatics·Ted LiefeldJill P Mesirov
Nov 1, 2008·Bioinformatics·Andrew D JohnsonPaul I W de Bakker
Feb 6, 2009·PLoS Medicine·Julian LittleUNKNOWN STrengthening the REporting of Genetic Association Studies
Oct 15, 2010·Nature·Zeeya Merali
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Aug 2, 2011·Briefings in Bioinformatics·Kristian RotherJanusz M Bujnicki
Nov 2, 2011·Current Genomics·Hélène Choquet, David Meyre
Nov 7, 2012·Nature·UNKNOWN 1000 Genomes Project ConsortiumGil A McVean

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Citations

Jun 27, 2015·BMC Medical Genomics·Akram AlyassDavid Meyre
Apr 21, 2019·Allergy·Olga IvanovaAnke H Maitland-van der Zee

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Methods Mentioned

BETA
genotyping
chip
other
chips

Software Mentioned

Cardio
Metabochip
SNAP
HuGE

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