AGBT 2023, Hollywood, FL. Oral presentation.
Avidity-based sequencing improves sensitivity and detection in metagenomic analysis
Shawn Levy1 , Brian Fanelli2 , Andrew Boddicker1 , Juan Moreno1 , William Light1 , Kelly Blease1 , Andrew Altomare1 , Dana Walsh2 , June Zhao1 and Manoj Dadlani2
1Element Biosciences, San Diego, CA USA
2CosmosID, Germantown, MD USA
The ability to decipher the complex populations present in metagenomic samples from a variety of sources is critical in infection surveillance, food safety, environmental safety, and the microbiome. Element’s AVITI™ platform and Avidity Sequencing™ can be effectively applied to complex metagenomic analysis and reveals enhanced sensitivity and specificity. The CosmosID-HUB Microbiome pipeline utilizes a high-performance data-mining k-mer algorithm that rapidly disambiguates millions of short sequence reads into the discrete genomes engendering the particular sequences. The genomes were assembled into metagenome-assembled genomes (MAGs) and parsed by completeness of the assembly. Sequencing quality of three library preparation methods and two sequencing platforms was assessed using MultiQC. Microbiome composition was compared by subsampling all samples to 6 million reads prior to transforming the data to relative abundance. Shannon alpha and Bray-Curtis beta diversity indices were calculated and individual taxa were compared using the Wilcoxon Rank-Sum test with multiple testing correction. Sequencing the same library on the Illumina NextSeq™ and the Element AVITI platform showed enhanced sensitivity on the AVITI platform with 4x the number of MAGs at 95% or more completeness with Element compared to Illumina. For genomes with 5% to 95% completeness, the advantage AVITI varied from 1.2 to 2.5x more assembled MAGs. When the same samples were prepared with the Element Elevate™ library preparation kit, the advantage for the Element platform increased with average N50 and longest contig increasing by 1.8 and 2.1-fold, respectively compared to Illumina. All other statistics showed higher sensitivity and better assemblies on the Element platform compared to Illumina. These assembly results show that alternate sequencing technologies such as the Element AVITI platform with higher Q scores can support more complete assembly and bring novel sensitivity to complex analysis such as microbiome and metagenomic assembly from short sequencing reads.