AOAC SPADA Meeting

Ranking the assay signatures by in silico analyses

Oligo

Left Primer

Right Primer

Product Size Position Source

Rank Penalty Score

GCCCACCCTGCTTTATCTTCTTTTCG TGAGGTGGANCCCATGGATGA GCACTCTGACCACGTCGAAT 71 GCCCACCCTGCTTTATCTTCTTTTCG TTGAGGTGGANCCCATGGATGA GCACTCTGACCACGTCGAAT 71 GCCCACCCTGCTTTATCTTCTTTTCG TGAGGTGGANCCCATGGATG GCACTCTGACCACGTCGAAT 71 GCCCACCCTGCTTTATCTTCTTTTCG TGAGGTGGANCCCATGGATGA GCACTCTGACCACGTCGAA 71 CCCACCCTGCTTTATCTTCTTTTCGN GAGGTGGANCCCATGGATGAG GCACTCTGACCACGTCGAAT 71 AGGAAGACGAGGAGGCAGAGG TGGAGGAAGACAGTTTGGAGG GCGGTTGCTTCTTCCACCT 61 AGGAAGACGAGGAGGCAGAGG CTGGAGGAAGACAGTTTGGAGG GCGGTTGCTTCTTCCACCT 61 CCTTTCGAAGGCGGGCATAACC CAGCTGTTGGGGTAGGTATTC ACTGACAACCTGAGTGCAGA 63 AGGAAGACGAGGAGGCAGAGG GGAGGAAGACAGTTTGGAGG GCGGTTGCTTCTTCCACCT 61 AGGAAGACGAGGAGGCAGAGG CTGGAGGAAGACAGTTTGGAG GCGGTTGCTTCTTCCACCT 61 CTTTCGAAGGCGGGCATAACCT AGCTGTTGGGGTAGGTATTCC ACTGACAACCTGAGTGCAG 63 CTTTCGAAGGCGGGCATAACCT GCTGTTGGGGTAGGTATTCC ACTGACAACCTGAGTGCAG 63 CTTTCGAAGGCGGGCATAACCT CAGCTGTTGGGGTAGGTATTCC ACTGACAACCTGAGTGCAG 63 AGGAAGACGAGGAGGCAGAGG TGGAGGAAGACAGTTTGGAGG CGGTTGCTTCTTCCACCT 61 CCTTTCGAAGGCGGGCATAACCT CAGCTGTTGGGGTAGGTATTC ACTGACAACCTGAGTGCAG 63

21239 simian_adenovirus.tsv 1 2.035096245 21239 simian_adenovirus.tsv 2 2.433140669 21239 simian_adenovirus.tsv 3 2.555555725 21239 simian_adenovirus.tsv 4 2.654180891 21239 simian_adenovirus.tsv 5 2.704756485 26016 simian_adenovirus.tsv 6 3.30054983 26016 simian_adenovirus.tsv 7 3.890860561 5956 simian_adenovirus.tsv 8 4.042304313 26016 simian_adenovirus.tsv 9 4.082204992 26016 simian_adenovirus.tsv 10 4.651996715 5956 simian_adenovirus.tsv 11 5.53886043 5956 simian_adenovirus.tsv 12 6.03784778 5956 simian_adenovirus.tsv 13 6.115892516 26016 simian_adenovirus.tsv 14 6.500187891 5956 simian_adenovirus.tsv 15 6.613591098

2018_10_17_SPADA_Brief

UNCLASSIFIED

23

How do we change the paradigm? • All wet lab testing done just on one strain (live or inactivated or ‘rSurrogate’ or genomic material)

• Limit/eliminate Inclusivity and Exclusivity Panel organisms • Change the thinking from Inc/Exc to assay target identity

• Evaluate In Silico; target identity, assay performance with mismatches (software for predicting assay efficiency or PCR efficiency predictive models validated by wet lab testing- like the idea of crowd sourcing?) • Categorize genome sequences to TP, FP, TN, FN based on mismatches to target sequences (Standard based on consensus of the WG) • Testing done on only samples with potential issues • Attempt to get organisms • Alternatively, synthetic constructs • Matrix testing done on contrived samples or clinical samples again with one strain, or surrogates with different target sequences. • Potentially replace with synthetic data set spiked with target agent sequences to analyze in silico?

2018_10_17_SPADA_Brief

UNCLASSIFIED

24