A tale of two genotypes: consistency between two high-throughput genotyping centers

Area of Science:

• Genetics
• Ophthalmology
• Bioinformatics

Background:

• Genome-wide scans are crucial for complex genetic conditions.
• Comparing and combining data from multiple scans necessitates understanding genotyping errors and data discrepancies.

Purpose of the Study:

• To assess the agreement between two genome-wide scans for age-related maculopathy conducted by different laboratories (Center for Inherited Disease Research and Mammalian Genotyping Service).
• To evaluate potential challenges in merging genetic data from distinct genotyping centers.

Main Methods:

• Conducted two genome-wide scans for age-related maculopathy.
• Utilized data from the Center for Inherited Disease Research (CIDR) and the Mammalian Genotyping Service (MGS).
• Typed 30 individuals in common across both labs, analyzing 8914 genotypes over 321 shared markers.

Main Results:

• Demonstrated excellent agreement between the CIDR and MGS laboratories, with low internal error rates.
• Observed good alignment of alleles between the two centers, with less than 0.65% of aligned alleles showing significant size differences.
• Highlighted that integer allele labels may not reflect true sizes, requiring careful preparation for data merging.

Conclusions:

• Data from different genotyping laboratories can show excellent agreement, facilitating comparative genetic studies.
• Direct merging of data from different laboratories may require careful pre-alignment strategies beyond minimal controls.
• Linkage analysis can be performed effectively using laboratory-specific allele labels and frequencies, circumventing data merging issues.