Genotyping Polymorphic Bands of Microsatellite DNA with Automatic Object Segmentation and Translated Absolute Size

Abstract

Automatic image data analysis (Aida) on the genotyping polymorphic bands of microsatellite DNA requires routinely automatic image segmentation and especially translated absolute data. Computerized automatic analysis is crucial in reproducibility and artifact-proof despite of the available commercial software which is highly interactive and hence gravely time-consuming. Albeit, the genotyping data of microsatellite DNA fragment that is represented as relative mobility sizes with floating points based on selected DNA size standards may lead to great loss in data integration. The implemented Aida system with general-Aida-modules (GAM) of object segmentation and specific-Aida-modules (SAM) of data translation intends to provide efficient solutions in its semi-automatic format. In an experiment of twenty images, the Aida system demonstrated 85~95% accuracy in automatic band segmentation. Moreover, the Aida system along with in-house DNA size standards of MarkQoff (Marker-Quarter-Off) successfully translated absolute size data of DNA fragments with zero standard deviation while analyzing triplicate genotyping images of three running distances. In contrast to Aida system’s superior performance, the results of commercial software based on fifteen DNA size standards in triplicate genotyping images delivered the DNA fragment size data up to 2.19 base pair of standard deviation along with the discrepancies of data floating points and missing bands.