Illumina, Inc.
METHODS AND COMPOSITIONS FOR ADDRESSING INEFFICIENCIES IN AMPLIFICATION REACTIONS

Abstract:

Methods and systems for decreasing amplification bias and primer-dimer formation in amplification reactions and for amplifying a plurality of target polynucleotides from a sample in a single reaction and for sequencing the target polynucleotides where samples can include forensic samples and where target polynucleotides can include identity- or ancestry-informative markers, short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs). Methods of determining a nucleotide spacer sequence for disrupting primer dimer formation can include: receiving a set of primer sequences; determining a plurality of candidate spacers between an adapter sequence and a gene-specific portion of the primer sequence, the determined plurality of candidate spacers comprises sequences that disrupt stable interactions between sequences of the set of primer sequences; ranking candidate spacers that meet a predetermined threshold value of stable interactions in the extension sequences; and outputting a set of the ranked spacers that meet the predetermined threshold.