ICCFGG 2022
#29 AgriSeq™ solution to genotype structural variants Krishna Reddy Gujjula , Stephane Daly, Maite Lelievre, Srinivas Chadaram and Haktan Suren
krishnareddy.gujjula@thermofisher.com Thermo Fisher Scientific, Austin, TX, USA
AgriSeq™ targeted GBS is being used as a high throughput and cost-effective genotyping solution in various applications from animal and plant breeding studies to parentage testing and diagnos- tics. One of the many powers of this technology is supporting different type of markers including Single Nucleotide Polymorphisms (SNPs), Multiple Nucleotide Polymorphisms (MNPs), Insertions and Deletions (InDels), Long insertions and deletions (LongIndels) and other structural variants (SVs) (e.g. inversions, duplications). Structural variants are variants of size larger than 50bp and its primer design is slightly different than regular SNP design, having two amplicons per marker (one for wild-type and another for mutant). Because the current variant caller is incapable of making calls for such marker, we developed an analysis framework to genotype long indels and other structural variants. The robustness of this technology has been demonstrated across 96 samples using 13 canine long indel markers (insertion, deletion, and inversion). Overall, 97% marker call rate across samples and 100% concordance were observed (when compared to truth data). It has been also shown that primer design and down-stream analysis were not impacted by the indel size. High concordance across multiple samples with varying indel size indicates the reproducibility and flexibility of the method. Enhanced AgriSeq™ targeted GBS offers customers end to end solution for genotyping diverse marker types simultaneously using the analysis workflow. For Research Use Only. Not for use in diagnostic procedures #30 Clinical validation of a multi-cancer early detection blood-based “liquid biopsy” test in dogs using next-generation sequencing Kristina M Kruglyak , Andi Flory, John A Tynan, Lisa M McLennan, Jill M Rafalko, Daniel S Grosu, Katherine M Lytle, Lauren E. Holtvoigt, Angela L McCleary-Wheeler, Allison L O’Kell, Todd A Cohen, Susan C Hicks, Jason Chibuk, Ilya Chorny, and Dana WY Tsui kkruglyak@petdx.com PetDx, La Jolla, CA, USA Cancer is the leading cause of death in dogs; however, no established screening paradigms exist for early detection. Liquid biopsy methods that interrogate cancer-derived genomic alterations in cell-free DNA fragments in blood are being adopted for early cancer detection in human medicine and are now available for use in veterinary medicine. As demonstrated in human medicine, early detection of cancer in dogs may lead to improved outcomes. Blood samples from an all-comers cohort of 352 cancer-diagnosed dogs and 524 presumably cancer-free dogs were subjected to DNA extraction, proprietary library preparation, and next-gen- eration sequencing. Sequencing data were analyzed using an internally developed bioinformatics pipeline, previously established in an independent training cohort, to detect genomic alterations associated with the presence of cancer.
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