Battelle Memorial Institute

Daniel M Bornman

Brian A Young

Joseph J Regensburger

Esley M Heizer

Scott C Nelson

Jared M Schuetter

Angela T Minard-Smith

Aaron J Sander

Seth A Faith

Nancy McMillan

Mark E Hester

Boyu Yang

Gokhan Yavas

Jr Heizer Esley M

Nancy J McMillan

Nancy J Mcmillan

Jr Esley M Heizer

In at least one illustrative embodiment, a method may comprise selecting a first plurality of text strings that each represent a nucleotide sequence that was read by a massively parallel sequencing instrument, where the nucleotide sequences represented by the selected first plurality of text strings each correspond to a first target locus, comparing the selected first plurality of text strings to one another to determine an abundance count for each unique text string included in the selected first plurality of text strings, identifying a first number of unique text strings included in the selected first plurality of text strings as representing noise responses, and determining a method detection limit as a function of the abundance counts for the first number of unique text strings identified as representing noise responses.

Methods of analyzing massively parallel sequencing data

In one illustrative embodiment, an allelotyping method may include selecting a plurality of text strings that each represent a nucleotide sequence that was read by a massively parallel sequencing (MPS) instrument, where the nucleotide sequences represented by the selected plurality of text strings each correspond to a particular locus, comparing the selected plurality of text strings to one another to determine an abundance count for each unique text string included in the selected plurality of text strings, and determining one or more alleles for the particular locus by comparing the abundance count for each unique text string included in the selected plurality of text strings to an abundance threshold.

Allelotyping methods for massively parallel sequencing

Short Tandem Repeats are currently used by law enforcement and others, for example, for the identification of individuals by DNA matching. A method is described herein that uses WPD to classify and identify repeating sequences in nucleotide sequences from the position and frequency information contained within nucleotide sequences. This decomposition allows for the quick classification of nucleotide sequences (i.e., reads) into two different classes, including, for example, one class that contains sequencer reads that contain a repeat motif with non-repeat sequence on either flank, and another class that contains sequencer reads that do not contain any repeat sequence.

Methods and compositions for identifying repeating sequences in nucleic acids

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Powell, OH, United States of America

Daniel M Bornman