Comparison of SNP Genotyping Platforms
Author Information
Author(s): Brian K Suarez, Chelsea Taylor, Sarah Bertelsen, Laura J Bierut, Gerald Dunn, Carol H Jin, John S Kauwe, Andrew D Paterson, Anthony L Hinrichs
Primary Institution: Washington University School of Medicine
Hypothesis
Can discrepancies in SNP genotyping between Illumina and Affymetrix platforms be resolved without sequencing?
Conclusion
The study found a high agreement of 99.85% between the two platforms, but a significantly higher no-call rate for Affymetrix.
Supporting Evidence
- The no-call rate for the Affymetrix platform is approximately 8.6 times greater than for the Illumina platform.
- For 116,457 occurrences where both platforms made a genotype call, only 180 (0.15%) were discrepant.
- The discrepancies were primarily due to one platform calling a genotype homozygous while the other called it heterozygous.
Takeaway
This study looked at how two different methods of reading genes agreed with each other, and found they mostly did, but one method often missed calls.
Methodology
The study compared SNP calls from Illumina and Affymetrix platforms using data from the Collaborative Study on the Genetics of Alcoholism.
Potential Biases
Potential bias due to the specific populations and SNPs selected for analysis.
Limitations
The study's findings may not be generalizable beyond the specific SNPs and populations analyzed.
Participant Demographics
245 unrelated Whites from the Collaborative Study on the Genetics of Alcoholism.
Statistical Information
P-Value
p < 0.0001
Statistical Significance
p < 0.0001
Digital Object Identifier (DOI)
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