The present invention relates to the detection and analysis of by-products, such as short RNA transcripts, in a process of RNA in vitro transcription by HPLC. It further relates to the use of this method for the quality control of RNA produced by in vitro transcription or for identifying suitable RNA purification conditions.

Techniques are provided for locating and validating single-nucleotide polymorphism (SNP) islands by scanning a reference genome. A system scans a reference genome to locate a high-variance region containing at least a minimum number of known impactful SNP locations in less than a maximum length, wherein the high-variance region is flanked by low-variance regions of at least minimum length and each having fewer than a maximum number of known relevant SNP locations. The system allows for tuning maximum and minimum region lengths, maximum and minimum SNP-location quantities, and rate-of-occurrence thresholds that define relevant and/or impactful SNP locations. Primers are designed for portions of the low-variance regions that are unique within the reference genome, wherein the primers amplify for the high-variance region. The primers are used to amplify genetic material samples in order to perform analyses to distinguish sample identity and/or to determine whether a sample corresponds to single or multiple contributors.