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PROF. MARK ADAMS | Genome-based targeted sequencing

27.09.2022

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Current sequencing-based methods for profiling microbial communities rely on marker gene (eg. 16S rRNA) or metagenome shotgun sequencing (mWGS) analysis. Mark will present an approach based on a single-primer extension reaction, using a highly multiplexed oligonucleotide probe pool based on Allegro Targeted Genotyping. This approach – termed MA GenTA (Microbial Abundances from Genome Tagged Analysis) – enables quantitative, straightforward, cost-effective microbiome analysis. The use of multiple probes per target genome, and rigorous probe design criteria, enabled robust determination of relative abundance. Probes were designed for 830 genome sequences representing bacteria present in mouse stool specimens. Comparison of the MA-GenTA data with mWGS data demonstrated excellent correlation down to 0.01 % relative abundance. Despite the incompleteness of the reference database, NMDS clustering of experimental sample groups was consistent between MA-GenTA, mWGS and 16S rRNA datasets. MA-GenTA represents a potentially useful new method for microbiome community profiling based on reference genomes. The Jackson Laboratory for Genomic Medicine, USA