Contiguity Preserving Transposition

Abstract

Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.

1 .- 58 . (canceled) 
     
     
         59 . A composition comprising a plurality of solid supports,
 wherein each of the solid supports comprises a plurality of immobilized oligonucleotides; and   wherein each of the oligonucleotides on a given solid support comprises
 (a) a complementary capture sequence that is capable of hybridizing to at least a portion of an adaptor sequence on a transposon; 
 (b) a first barcode sequence, wherein the first barcode sequence from each solid support in the plurality of solid supports differs from the first barcode sequence from other solid supports in the plurality of solid supports; and 
 (c) a primer binding site, 
   wherein (a), (b) and (c) are the same for each of the oligonucleotides on the given solid support.   
     
     
         60 . The composition of  claim 59 , wherein the immobilized oligonucleotides further comprise
 (a) a second barcode sequence, or   (b) a second barcode sequence and a third barcode sequence.   
     
     
         61 . The composition of  claim 59 , wherein the solid support is a microsphere, bead, or particle. 
     
     
         62 . The composition of  claim 59 , wherein the primer binding site of each immobilized oligonucleotide is a P5 or P7 primer binding site or a complement thereof. 
     
     
         63 . The composition of  claim 59 , wherein an immobilized oligonucleotide on a given solid support comprises a partially double-stranded structure and a partially single-stranded structure. 
     
     
         64 . The composition of  claim 63 , wherein one strand of the double-stranded structure of the immobilized oligonucleotide is immobilized on the solid support and a second strand of the double-stranded structure is partially complementary to the strand immobilized on the solid support and comprises the complementary capture sequence. 
     
     
         65 . The composition of  claim 64 , wherein the complementary capture sequence is hybridized to the adaptor sequence of the transposon. 
     
     
         66 . The composition of  claim 65 , wherein the complementary capture sequence is ligated to the adaptor sequence of the transposon. 
     
     
         67 . The composition of  claim 65 , wherein the transposon comprises a transferred strand and a non-transferred strand and the adaptor sequence is on the transferred strand of the transposon. 
     
     
         68 . The composition of  claim 67 , further comprising a fragment of a target nucleic acid ligated to the 3′ end of the transferred strand of the transposon. 
     
     
         69 . The composition of  claim 67 , further comprising a transposase bound to the transposon that forms a transposome complex. 
     
     
         70 . The composition of  claim 69 , wherein the transposase is a Tn5 transposase. 
     
     
         71 . The composition of  claim 69 , wherein the transposome complex is bound to a target nucleic acid. 
     
     
         72 . The composition of  claim 71 , wherein the target nucleic acid comprises a plurality of fragments and the transposome complex is bound to at least one fragment of the target nucleic acid. 
     
     
         73 . The composition of  claim 72 , wherein the transferred strand is inserted into the 5′ end of at least one strand of the fragments while maintaining the contiguity of the target nucleic acid. 
     
     
         74 . The composition of  claim 63 , wherein an immobilized oligonucleotide on a given solid support within the plurality of solid supports comprises a single-stranded structure. 
     
     
         75 . The composition of  claim 74 , wherein the immobilized oligonucleotide is immobilized to the solid support via a linker at the 5′ end of the oligonucleotide and the complementary capture sequence is at the 3′ end of the immobilized oligonucleotide. 
     
     
         76 . The composition of  claim 74 , wherein the complementary capture sequence of the immobilized oligonucleotide on a given solid support is hybridized to the adaptor sequence of a transposon. 
     
     
         77 . The composition of  claim 76 , wherein the complementary capture sequence is ligated to the adaptor sequence of the transposon. 
     
     
         78 . The composition of  claim 76 , wherein the transposon comprises a transferred strand and a non-transferred strand and the adaptor sequence is on the non-transferred strand of the transposon. 
     
     
         79 . The composition of  claim 76 , wherein the transposon comprises a transferred strand and a non-transferred strand and the adaptor sequence is on the transferred strand of the transposon. 
     
     
         80 . The composition of any one of  claim 74 , further comprising a fragment of a target nucleic acid ligated to the 3′ end of the transferred strand of the transposon. 
     
     
         81 . The composition of  claim 76 , further comprising a transposase bound to the transposon to form a transposome complex. 
     
     
         82 . The composition of  claim 81 , wherein the transposase is Tn5 transposase. 
     
     
         83 . The composition of  claim 81 , wherein the transposome complex is bound to a target nucleic acid. 
     
     
         84 . The composition of  claim 83 , wherein the target nucleic acid comprises a plurality of fragments and the transposome complex is bound to at least one fragment of the target nucleic acid. 
     
     
         85 . The composition of  claim 84 , wherein the transposon comprises a transferred strand and a non-transferred strand, and wherein the transferred strand is inserted into the 5′ end of at least one strand of the at least one fragment while maintaining the contiguity of the target nucleic acid. 
     
     
         86 . The composition of  claim 59 , wherein the adaptor sequence of the transposon comprises a barcode sequence. 
     
     
         87 . The composition of  claim 59 , wherein the adaptor sequence of the transposon comprises a primer binding site. 
     
     
         88 . The composition  claim 87 , wherein the primer binding site of the transposon is a P5 or P7 primer binding site or a complement thereof.