Battelle Memorial Institute

Esley M Heizer

Mark E Hester

Craig Bartling

Daniel M Bornman

Brian A Young

Angela T Minard-Smith

Nancy McMillan

Boyu Yang

Gokhan Yavas

Illustrative embodiments of systems and methods for the identification of traits associated with DNA samples using epigenetic-based patterns detected via massively parallel sequencing (MPS) are disclosed. Illustrative embodiments may involve digesting a DNA sample with a methylation-dependent endonuclease, amplifying loci of the digested DNA sample (including a positive control locus that does not contain a restriction site for the methylation-dependent endonuclease) using a multiplex PCR to produce amplicons, sequencing the amplicons using an MPS instrument to generate sequence reads, determining a sequence count for each of the loci by comparing each of the sequence reads to reference sequences, normalizing the sequence count for each of the loci to the sequence count of the positive control locus, and identifying a trait associated with the DNA sample by applying a classification algorithm to the normalized sequence counts.

Identification of traits associated with DNA samples using epigenetic-based patterns detected via massively parallel sequencing

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

Growing community of inventors

Galloway, OH, United States of America

Esley M Heizer