Lekárska genetika a diagnostika 2/2024

Rapid whole-genome sequencing and comprehensive analysis using AI Emedgene

Purpose: Protocol optimization of the rapid whole-genome sequencing providing highquality data with subsequent annotation of priority variants using the AI software tool Emedgene. Materials and methods: Genomic DNA was isolated using the EZ1&2 DNA Blood 350 μl Kit from venous blood from 3 participants (family trio: mother, father and proband daughter); proband diagnosed with Mayer-Rokitansky-Küster-Hauser syndrome. Whole-genome libraries were prepared using the TruSeq DNA PCR-Free High Throughput Library Prep Kit. Sequencing was performed on a NovaSeq 6000 using S1 flowcell sequencing chemistry. Dynamic Read Analysis for GENomics (DRAGEN) On Premise Server v4.1 (Illumina) with hg38 Alignment and Variant Calling and DRAGEN v4.0 Cloud System and AI software tool Emedgene (Illumina) were used for subsequent secondary analysis. Results: High-quality genomic DNA was successfully isolated from the venous blood of all 3 study participants. Whole-genome libraries were successfully sequenced with a generated volume of data: 464.92 Gb, with 92.57% of reads covered more than 35× and 94.66% of reads with a Phred quality score above 30 (Q30). All whole-genome libraries met the required criterion of 800 million of pair-end reads. Secondary analysis using the DRAGEN v4.0 cloud system and artificial intelligence Emedgene identified 7 pathological variants of Mayer- Rokitansky-Küster-Hauser syndrome, which were evaluated by a laboratory diagnostician. Conclusion: The optimized protocol enables rapid preparation of high-quality indexed wholegenome sequencing libraries, sequencing and bioinformatic analysis in 39 hours and 54 minutes.

Keywords: genomic DNA, whole genome sequencing, Rapid WGS, NovaSeq6000, variants´ annotation, Emedgene artificial intelligence