Illumina, Inc.
VARIANT PATHOGENICITY PREDICTION USING NEURAL NETWORK

Abstract:

The technology disclosed relates to constructing a computer-implemented method for variant classification. In particular, the method includes using a pathogenicity prediction neural network to process as input, (i) a reference protein sequence that has a first chain of amino acids with at least twenty amino acids, (ii) an alternative protein sequence aligned with the reference sequence, where the alternative protein sequence has a second chain of amino acids with at least twenty amino acids, and the first and second chains of amino acids differ by a variant amino acid caused by a nucleotide substitution, and (iii) a primate conservation profile generated using a primate cross-species multiple sequence alignment that aligns the reference protein sequence with other protein sequences from primate species. The method further includes based on the processing of the input by the neural network, generating as output a pathogenicity prediction for the nucleotide substitution.