This tool was created for use with Agena MassARRAY genotyping but may also be applicable to other genotyping assays. It rapidly compares SNP genotypes between two samples. The tool displays allele bases in Sanger sequencing colors (A: green, T: red, G: black, C: blue) and categorizes each SNP as follows:

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Homozygous Match:

If Sample 1 and Sample 2 are both homozygous and the same (e.g., "AA" vs. "AA"), the outcome is Homozygous Match.

Homozygous Mismatch:

If both samples are homozygous but differ (e.g., "AA" vs. "GG"), the outcome is Homozygous Mismatch.

Heterozygous Match:
The tool sorts the alleles in each genotype (so that "AG" and "GA" both become "AG") and compares them. If they match, the outcome is Heterozygous Match.
Heterozygous Mismatch:
If, after sorting, the heterozygous genotypes differ, the outcome is Heterozygous Mismatch.
Mixed Type (One Homozygous and One Heterozygous):
In this situation, regardless of the specific alleles, the outcome is classified as Heterozygous Mismatch.

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Total Match:
This is the sum of all Homozygous Matches and Heterozygous Matches.
Total Mismatch:
This is the sum of all Homozygous Mismatches and Heterozygous Mismatches.

This tool enables early detection of sample mix-ups, ensuring that only properly identified samples proceed to the costly process of  sequencing. This tool has not been validated and it is investigational use only.

Input: AA AG GG, ... delimited by space, tab or comma.

Sample1

Sample2

Output

Reference

1. Ho, C., et al. Using Genotyping-Based Mendelian Error Analysis to Identify and Minimize the Risk of Sample Misidentification in Trio Exome Sequencing Service. in JOURNAL OF MOLECULAR DIAGNOSTICS. 2023. ELSEVIER SCIENCE INC STE 800, 230 PARK AVE, NEW YORK, NY 10169 USA. https://www.jmdjournal.org/issue/S1525-1578(23)X0003-8

2. Demichelis, F., Greulich, H., Macoska, J. A., Beroukhim, R., Sellers, W. R., Garraway, L., & Rubin, M. A. (2008). SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines. Nucleic acids research, 36(7), 2446-2456. https://doi.org/10.1093/nar/gkn089

3. Sanchez, J. J., Phillips, C., Børsting, C., Balogh, K., Bogus, M., Fondevila, M., ... & Morling, N. (2006). A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis, 27(9), 1713-1724. https://doi.org/10.1002/elps.200500671