Paiva's Adaptive Window Heuristic Applied to the PRNP Variant Scanner: Rapid Computational Screening of Pathogenic PRNP Variants by Rabin-Karp Algorithm with Polynomial Hash over a Prime Field.

Human prion diseases, particularly Creutzfeldt-Jakob Disease (CJD), are characterized by rapid progression and a narrow therapeutic window. A documented mean diagnostic delay of 7.8 months - exceeding the median survival of 4 to 6 months - compromises patient eligibility for active clinical trials requiring early-stage disease. This paper describes the development of a computational proof-of-concept tool termed PRNP Variant Scanner, which applies the Rabin-Karp rolling hash algorithm and Paiva's Adaptive Window Heuristic to perform simultaneous multi-pattern screening of 16 pathogenic or clinically relevant variants of the human prion protein gene (PRNP). The approach detects variants in under 1 ms on sequences up to 759 bp, with a mathematically zero false-positive rate, and delivers integrated clinical interpretation including codon 129 haplotype status and eligibility information for the PRISM (NCT07444580) and PrProfile (NCT06153966) clinical trials.