Patent ID: 8481292
Filing Date: 2013-07-09
Classification: C12N,C12Q,G16B

Abstract:
1. A method for enhancing a determination of the presence of alleles in a genomic sample, said method comprising: a) attaching a set of oligonucleotides that comprises a degenerate base region (DBR) comprising at least one nucleotide base selected from: R, Y, S, W, K, M, B, D, H, V, N and modified versions thereof to the nucleic acid molecules of a genomic sample that contains a polymorphic target region, thereby producing a population of adapter-attached polynucleotides in which each of said adaptor-attached polynucleotides that comprises said polymorphic target region is attached to a DBR sequence of an oligonucleotide of said set of oligonucleotides, wherein said oligonucleotides further comprise a unique multiplex identifier (MID) sequence that identifies a source for each of the nucleic acid molecules to which it is attached; b) amplifying the adapter-attached polynucleotides, thereby producing amplified adapter-attached polynucleotides that contain the polymorphic target region; c) sequencing some of the amplified adapter-attached polynucleotides that contain the polymorphic target region, thereby producing a plurality of sequences, wherein the sequencing step provides, for each of the amplified adaptor-attached polynucleotides that contain the polymorphic target region and are sequenced: (i) the nucleotide sequence of at least a portion of said polymorphic target region and (ii) the DBR sequence of the oligonucleotide to which said polymorphic target region is attached; d) determining, for one allele of the polymorphic target region, the number of different DBR sequences in the oligonucleotides that are associated with said allele; and e) repeating step d) for additional alleles of said polymorphic target region, thereby enhancing said determination of the presence of said alleles in said genomic sample based on the numbers of different DBR sequences in the oligonucleotides that are associated with said allele and said additional alleles.