Lekárska genetika a diagnostika 2/2024

Key factors influencing variant identification from whole-exome sequencing

The implementation of massively parallel sequencing methods into routine clinical practice has brought a great shift in the diagnosis of many genetically determined diseases. The speed with which these methods were incorporated into practice is the reflection of the incalculable benefit they bring both to the patient and to family members. The continuous improvement of massively parallel sequencing technologies, which adapts to a new knowledge in the field of genomics, brings the need for systematic innovation of bioinformatics software designed for data analysis. On the other hand, however, with the advent of new technologies and procedures, new challenges appear that must be overcome, so to speak, on the fly, so that the resulting diagnostic yield reaches the highest possible level. The accurate display of variants in individual positions of the human genome from the obtained sequencing data is a critical step, which is followed by further analyzes and interpretations, which also face many challenges. The aim of the review article is to point out the key factors influencing the identification of variants that may prevent the establishment of a final diagnosis.

Keywords: reference genome, sequencing coverage, pseudogenes, minor allele frequency, variant interpretation