Targeted neoepitope vectors and methods therefor
A new epitope and carrier technology, applied in the field of recombinant nucleic acid therapeutics, can solve the problems of prohibitive production time limit and poor effect, etc.
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[0132] Exemplary sequence alignment
[0133] Neo-epitope sequences were determined by in silico by position-guided simultaneous alignment of tumor and normal samples using BAM files and BAM servers, as disclosed eg in US 2012 / 0059670 and US 2012 / 0066001. Specifically, tumors for DNA analysis were from the B16-F10 mouse melanoma line, and matched normal controls were blood from C57b1 / 6 parental mouse DNA. These results were filtered for expression by RNA sequencing of the tumor cell line. The neo-epitopes found to be expressed were further analyzed for binding affinity towards murine MHC-I (here Kb) and MHC-II (here I-Ab). After an additional step of dbSNP filtering, selected binders (with affinities equal to or less than 200 nM) were further analyzed to generate representative A score for the likelihood of the presence and / or strength of a hydrophobic sequence or signal peptide is present. The best scoring alignment (lowest likelihood of hydrophobic sequence or signal pepti...
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