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An analysis of identical single-nucleotide polymorphisms genotyped by two different platforms
Brian K Suarez1, Chelsea Taylor, Sarah Bertelsen
1Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA. bks@themfs.wustl.edu
BMC Genetics
|February 3, 2006
Summary
Comparing SNP genotyping platforms, Affymetrix shows higher no-call rates than Illumina. However, when calls are made, agreement is high, though discrepancies can be resolved by studying recombination patterns.
Area of Science:
- Genetics
- Genomics
- Bioinformatics
Background:
- High-throughput genotyping platforms are crucial for genetic studies.
- Comparing different platforms like Illumina and Affymetrix is essential for data accuracy.
- Understanding platform discrepancies aids in reliable genotype calling.
Purpose of the Study:
- To assess the discrepancy rate between Illumina and Affymetrix SNP genotyping platforms.
- To investigate methods for resolving disputed genotypes without resorting to sequencing.
- To identify factors contributing to genotyping discrepancies.
Main Methods:
- Comparative analysis of 94 overlapping single-nucleotide polymorphisms (SNPs) between Illumina and Affymetrix linkage panels.
- Calculation of no-call rates and genotype agreement percentages.
- Recombination analysis in discrepant SNP regions, focusing on rs958883 and tsc02060848.
- Investigation of SNP clustering and potential causes, including secondary SNPs affecting restriction sites.
Main Results:
- Affymetrix platform exhibited an 8.6-fold higher no-call rate than Illumina.
- Despite differences, genotype agreement reached 99.85% when both platforms made a call.
- Recombination analysis indicated substantially more inferred recombinants with Affymetrix genotypes.
- A subset of discrepancies clustered within families, potentially due to secondary SNPs impacting amplification.
Conclusions:
- Illumina and Affymetrix platforms show high concordance but differ in no-call rates and discrepancy patterns.
- Recombination analysis can help resolve disputed genotypes, reducing the need for sequencing.
- Secondary SNPs and assay design (e.g., restriction site obliteration) can contribute to genotyping errors.