Methods for nucleic acid detection

Abstract

The present disclosure provides methods and systems for sequencing nucleic acid molecules in a manner that enables higher sequencing accuracy. Methods and systems provided herein may enable sequences that may have low-accuracy reads, such as homopolymer sequences or other repeating sequences, to be determined at a higher accuracy and efficiency.

1 - 132 . (canceled) 
     
     
         133 . A method for nucleic acid sequencing, comprising:
 (a) subjecting a first nucleic acid sample of a subject to a first assay to generate a first data set, wherein the first data set comprises a nucleic acid sequence of a target nucleic acid molecule from the first nucleic acid sample;   (b) subjecting a second nucleic acid sample of the subject to a second assay to generate a second data set, wherein the second data set comprises a homopolymer sequence of the target nucleic acid molecule, wherein the first assay and the second assay are of different types; and   (c) using a programmed computer to combine the first data set and the second data set to generate a combined data set, wherein the combined data set comprises the nucleic acid sequence and the homopolymer sequence, wherein the homopolymer sequence is determined at an accuracy of at least 90%.   
     
     
         134 . The method of  claim 133 , wherein (a) is performed subsequent to (b). 
     
     
         135 . The method of  claim 133 , wherein (b) is performed subsequent to (a). 
     
     
         136 . The method of  claim 133 , wherein (b) comprises using an oligonucleotide probe to hybridize with the target nucleic acid molecule or clonal copies thereof. 
     
     
         137 . The method of  claim 136 , wherein the oligonucleotide probe further comprises a random sequence region. 
     
     
         138 . The method of  claim 137 , wherein the random sequence region comprises at least one nucleotide. 
     
     
         139 . The method of  claim 138 , wherein the random sequence region comprises from 1 nucleotide to 10 nucleotides in length. 
     
     
         140 . The method of  claim 133 , wherein the combined data set is a consensus sequence. 
     
     
         141 . A method for determining a sequence of a target nucleic acid molecule, comprising:
 (a) subjecting the target nucleic acid molecule to sequencing-by-synthesis to yield sequence data comprising a first sequence of the target nucleic acid molecule, which sequencing-by-synthesis generates a nucleic acid molecule that is complementary to the target nucleic acid molecule;   (b) hybridizing a homopolymer probe to a homopolymer region of the target nucleic acid molecule or a copy of the target nucleic acid molecule, wherein the homopolymer probe yields an observable signal that is indicative of a presence of the homopolymer region, and detecting the observable signal to identify a homopolymer sequence of the homopolymer region; and   (c) combining the sequence data from (a) with the homopolymer sequence identified in (b) to generate a second sequence of the target nucleic acid molecule, which second sequence comprises the first sequence and the homopolymer sequence.   
     
     
         142 . The method of  claim 141 , wherein (a) is performed subsequent to (b). 
     
     
         143 . The method of  claim 141 , wherein (b) is performed subsequent to (a). 
     
     
         144 . The method of  claim 141 , wherein the homopolymer probe further comprises a random sequence region. 
     
     
         145 . The method of  claim 144 , wherein the random sequence region is located at the 5′ end of the homopolymer probe. 
     
     
         146 . The method of  claim 145 , wherein the random sequence region comprises at least one nucleotide. 
     
     
         147 . The method of  claim 146 , wherein the random sequence region comprises from 1 nucleotide to 10 nucleotides in length. 
     
     
         148 . A method for determining a sequence of a nucleic acid sample, comprising:
 (a) using a massively parallel sequencer to identify a first nucleic acid sequence of the nucleic acid sample;   (b) using a targeted probe to identify a second nucleic acid sequence of the nucleic acid sample, wherein (b) is performed separately from (a); and   (c) using a programmed computer to generate a consensus sequence from the first nucleic acid sequence and the second nucleic acid sequence at an accuracy of at least 95%.   
     
     
         149 . The method of  claim 148 , wherein the targeted probe is targeted to an array, and wherein (b) comprises array hybridization. 
     
     
         150 . The method of  claim 148 , wherein the targeted probe is configured to identify a repeated sequence, and the second nucleic acid sequence comprises the repeated sequence. 
     
     
         151 . The method of  claim 150 , wherein the repeated sequence is a homopolymer sequence. 
     
     
         152 . The method of  claim 150 , wherein the repeated sequence is a dinucleotide repeated sequence or a trinucleotide repeated sequence.