Method for preparing a counter-tagged population of nucleic acid molecules
First Claim
1. A method of sequencing, comprising:
- a) amplifying a population of distinct initial target DNA molecules from a tagged genomic sample thereby producing a population of amplified target DNA molecules, wherein the distinct initial target DNA molecules that comprise a polymorphic target sequence are tagged with;
(i) different degenerate base region (DBR) sequences, wherein said DBR sequences comprise at least one nucleotide base selected from;
R, Y, S, W, K, M, B, D, H, V, N and modified versions thereof and (ii) a unique multiplex identifier (MID) sequence that identifies a source for each of the initial target DNA molecules to which it is associated, and wherein each of a plurality of the amplified target DNA molecules comprises said polymorphic target sequence, an associated DBR sequence of said different DBR sequences and said unique MID sequence; and
b) sequencing the plurality of the amplified target DNA molecules, thereby producing a plurality of sequence reads, wherein the sequencing step provides, for each of the amplified target DNA molecules that are sequenced;
the nucleotide sequence of;
(i) at least a portion of the polymorphic target sequence;
(ii) an associated DBR sequence of said DBR sequences; and
(iii) said unique MID sequence.
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Abstract
Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications.
299 Citations
25 Claims
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1. A method of sequencing, comprising:
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a) amplifying a population of distinct initial target DNA molecules from a tagged genomic sample thereby producing a population of amplified target DNA molecules, wherein the distinct initial target DNA molecules that comprise a polymorphic target sequence are tagged with;
(i) different degenerate base region (DBR) sequences, wherein said DBR sequences comprise at least one nucleotide base selected from;
R, Y, S, W, K, M, B, D, H, V, N and modified versions thereof and (ii) a unique multiplex identifier (MID) sequence that identifies a source for each of the initial target DNA molecules to which it is associated, and wherein each of a plurality of the amplified target DNA molecules comprises said polymorphic target sequence, an associated DBR sequence of said different DBR sequences and said unique MID sequence; andb) sequencing the plurality of the amplified target DNA molecules, thereby producing a plurality of sequence reads, wherein the sequencing step provides, for each of the amplified target DNA molecules that are sequenced;
the nucleotide sequence of;
(i) at least a portion of the polymorphic target sequence;
(ii) an associated DBR sequence of said DBR sequences; and
(iii) said unique MID sequence. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25)
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Specification