Methods and compositions for nucleic acid analysis

Abstract

The present invention is directed to methods, compositions and systems for analyzing sequence information while retaining structural and molecular context of that sequence information.

1 . A method of analyzing nucleic acids while maintaining structural context, the method comprising:
 (a) providing a sample comprising nucleic acids, wherein the nucleic acids comprise three dimensional structures;   (b) separating portions of the sample into discrete partitions such that portions of the nucleic acid three dimensional structures are also separated into the discrete partitions;   (c) obtaining sequence information from the nucleic acids, thereby analyzing nucleic acids while maintaining structural context.   
     
     
         2 . The method of  claim 1 , wherein the sequence information from obtaining step (c) includes identification of nucleic acids that were in spatial proximity to each other in the sample. 
     
     
         3 . The method of  claim 1 , wherein the obtaining step (c) provides information on intrachromosomal and/or interchromosomal interactions between genomic loci. 
     
     
         4 . (canceled) 
     
     
         5 . The method of  claim 1 , wherein prior to separating step (b), at least some of the three dimensional structures are processed to link different portions of the nucleic acids that are in proximity to each other within the three dimensional structures. 
     
     
         6 . The method of  claim 1 , wherein the sample is a formalin-fixed paraffin sample. 
     
     
         7 . The method of  claim 1 , wherein the nucleic acids are not isolated from the sample prior to the separating step (b). 
     
     
         8 . The method of  claim 1 , wherein the discrete partitions comprise beads. 
     
     
         9 . The method of  claim 8 , wherein the beads are gel beads. 
     
     
         10 . The method of  claim 1 , wherein prior to the obtaining step (c), the nucleic acids within the discrete partitions are barcoded to form a plurality of barcoded fragments, wherein fragments within a given discrete partition each comprise a common barcode, such that the barcodes identify nucleic acids from a given partition. 
     
     
         11 .- 37 . (canceled) 
     
     
         38 . A method of analyzing nucleic acids from a sample while maintaining structural context of nucleic acids within the sample, the method comprising:
 (a) forming linked nucleic acids within the sample such that spatially adjacent nucleic acid segments are linked;   (b) depositing the linked nucleic acids into discrete partitions;   (c) processing the linked nucleic acids to produce a plurality of ligation products, wherein the ligation products contain portions of the spatially adjacent nucleic acid segments;   (d) barcoding the ligation products within the discrete partitions to form a plurality of barcoded fragments, wherein fragments within a given discrete partition each comprise a common barcode, thereby associating each fragment with the linked nucleic acid from which it is derived;   (e) obtaining sequence information from the plurality of barcoded fragments, thereby analyzing nucleic acids from the sample while maintaining structural context.   
     
     
         39 . (canceled) 
     
     
         40 . The method of  claim 38 , wherein the sample is a formalin-fixed paraffin sample. 
     
     
         41 . The method of  claim 38 , wherein the sample comprises a nuclear matrix. 
     
     
         42 . (canceled) 
     
     
         43 . The method of  claim 38 , wherein the nucleic acids are not isolated from the sample prior to step (a). 
     
     
         44 .- 46 . (canceled) 
     
     
         47 . The method of  claim 38 , wherein the sample comprises a tumor sample. 
     
     
         48 . The method of  claim 38 , wherein the sample comprises a mixture of tumor and normal cells. 
     
     
         49 . The method of  claim 38 , wherein the processing step (c) results in ligation products comprising nucleic acids that were originally in close spatial proximity in the sample. 
     
     
         50 . The method of  claim 38 , wherein the obtaining step (e) provides information on intrachromosomal and/or interchromosomal interactions between genomic loci. 
     
     
         51 . (canceled) 
     
     
         52 . (canceled) 
     
     
         53 . A method of analyzing nucleic acids from a sample while maintaining structural context of nucleic acids within the sample, the method comprising:
 (a) cross-linking nucleic acids within the sample to form cross-linked nucleic acids, wherein the cross-linking forms covalent links between spatially adjacent nucleic acid segments;   (b) depositing the cross-linked nucleic acids into discrete partitions;   (c) processing the cross-linked nucleic acids to produce a plurality of ligation products, wherein the ligation products contain portions of the spatially adjacent nucleic acid segments;   (d) obtaining sequence information from the plurality of ligation products, thereby analyzing nucleic acids from the sample while maintaining structural context.   
     
     
         54 . (canceled) 
     
     
         55 . The method of  claim 53 , wherein the sample is a formalin-fixed paraffin sample. 
     
     
         56 . (canceled) 
     
     
         57 . (canceled) 
     
     
         58 . The method of  claim 53 , wherein the nucleic acids are not isolated from the sample prior to the cross-linking step (a). 
     
     
         59 . (canceled) 
     
     
         60 . The method of  claim 53 , wherein prior to the obtaining step (d), the ligation products are associated with a barcode. 
     
     
         61 . The method of  claim 60 , wherein ligation products within the same partition receive common barcodes, such that the barcodes identify ligation products from a given partition. 
     
     
         62 .- 85 . (canceled)