Assay methods and compositions for detecting contamination of nucleic acid identifiers

Abstract

The present invention relates to nucleic acid samples for massively parallel sequencing. More particularly, the present invention relates to assay methods, compositions and kits for detecting contamination of nucleic acid identifiers such as sample barcodes.

We claim: 
     
         1 . A kit for an assay for a set of oligonucleotide samples, the kit comprising:
 a set of oligonucleotide samples comprising oligonucleotides, each oligonucleotide having a 5′ constant region, a sample identifier, and a 3′ constant region, wherein each sample identifier is unique within the set; and   a set of assay primers comprising a priming portion and an assay identifier, wherein the priming portion is the same as or complementary to one of the constant regions of the oligonucleotides, wherein each assay identifier is unique within the set.   
     
     
         2 . The kit of  claim 1 , wherein each of the oligonucleotide samples of the set is in a separate vessel, and each vessel comprises only one sample identifier unless one or more of the samples is contaminated. 
     
     
         3 . The kit of  claim 1 , wherein the set of oligonucleotide samples comprises at least 8 samples. 
     
     
         4 . The kit of  claim 3 , wherein the set of assay primers comprises at least 8 assay primers. 
     
     
         5 . The kit of  claim 1 , wherein the set of oligonucleotide samples comprises at least 32 samples. 
     
     
         6 . The kit of  claim 5 , wherein the set of assay primers comprises at least 32 assay primers. 
     
     
         7 . The kit of  claim 1 , wherein the set of oligonucleotide samples comprises at least 96 samples. 
     
     
         8 . The kit of  claim 7 , wherein the set of assay primers comprises at least 96 assay primers. 
     
     
         9 . The kit of  claim 1 , wherein the assay primers further comprise a 5′ constant region comprising a standard 5′ amplification region for a sequencing platform and a sequencing priming region. 
     
     
         10 . The kit of  claim 9 , wherein the standard 5′ amplification region comprises a P5 sequence or a P7 sequence. 
     
     
         11 . The kit of  claim 1 , wherein the 5′ constant region of the oligonucleotides comprises a sequencing priming region. 
     
     
         12 . The kit of  claim 1 , wherein the 3′ constant region of the oligonucleotides comprises a standard 3′ amplification region for a sequencing platform. 
     
     
         13 . The kit of  claim 1 , wherein the assay identifies contamination in the set of oligonucleotide samples. 
     
     
         14 . A kit for an assay for a set of set of oligonucleotide samples comprising oligonucleotides, each oligonucleotide having a 5′ constant region, a sample identifier, and a 3′ constant region, wherein each sample identifier is unique within the set, the kit comprising:
 an assay primer comprising a priming portion and an assay identifier, wherein the priming portion is the same as or complementary to one of the constant regions of the oligonucleotides, wherein: 
 each assay identifier is unique within the set, and 
 the set comprises at least 8 assay primers in separate vessels. 
 
     
     
         15 . The kit of  claim 14 , wherein the set of assay primers comprises at least 16 assay primers in separate vessels. 
     
     
         16 . The kit of  claim 14 , wherein the set of assay primers comprises at least 32 assay primers in separate vessels. 
     
     
         17 . The kit of  claim 14 , wherein the set of assay primers comprises at least 48 primers in separate vessels. 
     
     
         18 . The kit of  claim 14 , wherein the set of assay primers comprises at least 96 primers in separate vessels. 
     
     
         19 . The kit of  claim 14 , wherein the assay primers further comprise a 5′ constant region comprising a standard 5′ amplification region for a sequencing platform and a sequencing priming region. 
     
     
         20 . The kit of  claim 14 , wherein the assay identifies contamination in sets of oligonucleotides comprising sample identifiers.