FAILURE IN GENERATING DATA FILE DURING AXIOMTM MICROARRAY GENOTYPING: IDENTIFICATION OF CAUSES AND PROBABLE SOLUTIONS

Tejas Gohil; A. Sudhakar; Bhumika Parmar; Rutvi Rajpara; Hardik Poojara

doi:10.56093/ijvasr.v54i6.173061

Authors

Tejas Gohil Officer, Sabarmati Ashram Gaushala's Genomics Lab, D-Lab, National Dairy Development Board, Anand, Gujarat - 388 001
A. Sudhakar Manager, National Dairy Development Board, Anand, Gujarat - 388 001
Bhumika Parmar Technician, Sabarmati Ashram Gaushala's Genomics Lab, D-Lab, National Dairy Development Board, Anand, Gujarat - 388 001
Rutvi Rajpara Junior Analyst, National Dairy Development Board, Anand, Gujarat - 388 001
Hardik Poojara Technician, National Dairy Development Board, Anand, Gujarat - 388 001

https://doi.org/10.56093/ijvasr.v54i6.173061

Keywords:

AxiomTM analysis suite, CEL file, error, Gene TitanTM multichannel instrument, SNP microarray genotyping

Abstract

Genotyping of various biological samples using AxiomTM microarray genotyping technology (Thermo Fisher Scientific) generates five types of data files (.CEL, .ARR, .DAT, .JPG, and .AUDIT), among which the .CEL files are essential for further downstream data analysis. In our study, involving 63 microarray genotyping plates, we observed that the number of output data files occasionally did not match the number of samples processed, in either the 96F or 384F workflows. Although such discrepancies were rare, but its identification was crucial, considering the limited availability of sample quantities. A clear understanding of the types of output data files generated and the purpose for their generation was pivotal, which helped us in recognizing the underlying cause for failure in data file generation with .CEL extension, specifically. Broadly, the errors were categorized in to 4 types. Type one error was due to peg scan failure in Gene TitanTM multi-channel instrument’s scanner, whereas second type was due to unknowingly dispensing the hyb-ready DNA or staining reagents into incorrect wells in a reagent tray. The third type of error arose due to improper clamping of the array plate with the hybridization plate. The fourth type resulted because the ligation enzyme was not included during the ligation master mix preparation. Although the majority errors may be categorized as human factors, intensive practice, rigorous training, meticulous observations and process monitoring can substantially reduce their occurrence in high- throughput genotyping laboratories.

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