Methods, systems, computer readable media, and kits for sample identification

Abstract

A method for sequencing a polynucleotide sample having a barcode sequence, includes: introducing a series of nucleotides to the polynucleotide sample according to a predetermined flow ordering; obtaining a series of signals resulting from the introducing of nucleotides to the polynucleotide sample; and resolving the series of signals over the barcode sequence to render a flowspace string, wherein the flowspace string is a codeword of an error-tolerant code capable of distinguishing the barcode sequence from other barcode sequences in the presence of one or more errors.

What is claimed is: 
     
         1 . A method for sequencing a polynucleotide sample having a barcode sequence, comprising:
 introducing a series of nucleotides to the polynucleotide sample according to a predetermined flow ordering;   obtaining a series of signals resulting from the introducing of nucleotides to the polynucleotide sample; and   resolving the series of signals over the barcode sequence to render a flowspace string, wherein the flowspace string is a codeword of an error-tolerant code capable of distinguishing the barcode sequence from other barcode sequences in the presence of one or more errors.   
     
     
         2 . The method of  claim 1 , wherein the error-tolerant code is an error-correcting code. 
     
     
         3 . The method of  claim 2 , wherein the error-correcting code is a ternary code using a three character alphabet. 
     
     
         4 . The method of  claim 3 , wherein a first character of the alphabet represents a 0-mer signal, a second character in the alphabet represents a 1-mer signal, and a third character in the alphabet represents a 2-mer signal. 
     
     
         5 . The method of  claim 3 , wherein the ternary code is a ternary Hamming code. 
     
     
         6 . The method of  claim 3 , wherein the ternary code is a ternary Golay code. 
     
     
         7 . The method of  claim 1 , wherein the codeword has a length of 15 or fewer characters. 
     
     
         8 . The method of  claim 2 , wherein the error-correcting code is capable of correcting up to two errors in the flowspace string. 
     
     
         9 . The method of  claim 2 , wherein the error-correcting code is capable of correcting one error in the flowspace string. 
     
     
         10 . The method of  claim 1 , wherein the barcode sequence has a length in the range of 5-15 bases. 
     
     
         11 . The method of  claim 1 , further comprising determining whether the flowspace string contains an error. 
     
     
         12 . The method of  claim 11 , further comprising correcting the flowspace string if an error is detected. 
     
     
         13 . The method of  claim 12 , further comprising translating the flowspace string into a base sequence to obtain the sequence of the barcode sequence. 
     
     
         14 . The method of  claim 1 , further comprising:
 decoding the flowspace string to the correct flowspace codeword; and   translating the flowspace codeword into a base sequence to obtain the sequence of the barcode sequence.   
     
     
         15 . The method of  claim 2 , further comprising providing multiple different polynucleotide samples for multiplex sequencing by the series of flowed nucleotides, each different polynucleotide sample comprising a different barcode sequence that gives a different flowspace string, each different flowspace string being a different codeword of the error-correcting code. 
     
     
         16 . The method of  claim 15 , wherein any two flowspace codewords of the error-correcting code have a Hamming distance of at least 3. 
     
     
         17 . The method of  claim 15 , wherein any two flowspace codewords of the error-correcting code have a Hamming distance of at least 5. 
     
     
         18 . The method of  claim 1 , further comprising one or both of:
 (i) detecting hydrogen ions released by the incorporation of nucleotides into the polynucleotide sample, wherein the amplitude of the signals is related to the amount of hydrogen ions detected, and   (ii) detecting inorganic pyrophosphate released by the incorporation of nucleotides into the polynucleotide sample, wherein the amplitude of the signals is related to the amount of inorganic pyrophosphate detected.   
     
     
         19 . A system, including:
 a machine-readable memory; and   a processor configured to execute machine-readable instructions, which, when executed by the processor, cause the system to perform a method for sequencing a polynucleotide sample having a barcode sequence, comprising:
 introducing a series of nucleotides to the polynucleotide sample according to a predetermined flow ordering; 
 obtaining a series of signals resulting from the introducing of nucleotides to the polynucleotide sample; and 
 resolving the series of signals over the barcode sequence to render a flowspace string, wherein the flowspace string is a codeword of an error-tolerant code capable of distinguishing the barcode sequence from other barcode sequences in the presence of one or more errors. 
   
     
     
         20 . A set of barcodes for nucleic acid sequencing, comprising: a plurality of nucleic acid base sequences, each nucleic acid base sequence being a base space representation of a flowspace representation of a codeword of an error-tolerant sample discrimination code.