Preserving genomic connectivity information in fragmented genomic DNA samples

A method of sequencing a target nucleic acid polymer, comprising:

• (a) modifying a target nucleic acid polymer to produce a modified nucleic acid polymer, wherein the modified nucleic acid polymer comprises a plurality of sequence regions from the target nucleic acid polymer;
• (b) attaching the modified nucleic acid polymer to an area on a solid support surface;
• (c) producing fragments of the modified nucleic acid polymer that is attached to the solid support surface, wherein the fragments are attached to locations at the area on the solid support surface;
• (d) determining nucleotide sequences from the fragments by detecting the fragments at the locations;
• (e) determining relative physical distances between the fragments at the locations;
• and
• (f) producing a representation of the nucleotide sequence for the target nucleic acid polymers based on the nucleotide sequences from the fragments and the determined relative physical distances between the locations on the solid support surface, wherein the relative physical distances are indicative of distances between the sequence regions along a given strand of the target nucleic acid polymer.

A method of sequencing a target nucleic acid polymer, comprising:

• (a) adding inserts into a target nucleic acid polymer to form a modified nucleic acid polymer comprising a plurality of internal inserts;
• (b) producing fragments of the modified nucleic acid polymer in a fluid that is in contact with a solid support surface, thereby releasing fragments that each comprise at least a portion of the inserts having the priming sites;
• (c) capturing the fragments from the fluid randomly at locations on the solid support surface;
• (d) determining nucleotide sequences from the fragments by detecting the fragments at the locations;
• (e) determining relative physical distances between the fragments at the locations;
• and
• (f) producing a representation of the nucleotide sequence for the target nucleic acid polymer based on the nucleotide sequences from the fragments and the determined relative physical distances between the locations on the solid support surface, wherein the relative physical distances are indicative of distances between sequence regions along a given strand of the target nucleic acid polymer.

A method of sequencing a target nucleic acid polymer, comprising:

• (a) adding inserts into a target nucleic acid polymer to form a modified nucleic acid polymer comprising a plurality of internal inserts, wherein the inserts have priming sites;
• (b) producing fragments of the modified nucleic acid polymer in a fluid that is in contact with the solid support surface, thereby releasing fragments that each comprise at least a portion of the inserts having the priming sites;
• (c) capturing the fragments from the fluid randomly at locations on a solid support surface;
• (d) determining nucleotide sequences from the fragments by extension of primers hybridized to the priming sites at the locations;
• (e) determining relative physical distances between the fragments at the locations;
• and
• (f) producing a representation of the nucleotide sequence for the target nucleic acid polymer based on the nucleotide sequences from the fragments and the determined relative physical distances between the locations on the solid support surface, wherein the relative physical distances are indicative of distances between sequence regions along a given strand of the target nucleic acid polymer.

A method of sequencing a target nucleic acid polymer, comprising:

• (a) adding inserts into a target nucleic acid polymer to form a modified nucleic acid polymer comprising a plurality of internal inserts;
• (b) attaching the modified nucleic acid polymer to a solid support surface;
• (c) producing fragments of the modified nucleic acid polymer that is attached to the solid support surface, wherein the fragments are attached to locations on the solid support surface and wherein the fragments each comprise at least a portion of the inserts;
• (d) determining nucleotide sequences from the fragments by detecting the fragments at the locations;
• (e) determining relative physical distances between the fragments at the locations;
• and
• (f) producing a representation of the nucleotide sequence for the target nucleic acid polymer based on the nucleotide sequences from the fragments and the determined relative physical distances between the locations on the solid support surface, wherein the relative physical distances are indicative of distances between sequence regions along a given strand of the target nucleic acid polymer.

A method of determining the source of individual sequences in a mixture of sequences from different sources, comprising:

• (a) providing a mixture of target nucleic acid polymers from a plurality of different sources;
• (b) modifying the mixture of target nucleic acid polymers to produce a mixture of modified nucleic acid polymers, wherein the mixture of modified nucleic acid polymers comprises a plurality of sequence regions from the different sources;
• (c) producing fragments of the modified nucleic acid polymers in a vessel having a solid support surface, each fragment comprising a sequence region from a single one of the different sources;
• (d) capturing the fragments randomly at locations of the solid support surface, under conditions wherein fragments from a common target nucleic acid polymer preferentially localize to proximal locations on the solid support surface;
• (e) determining nucleotide sequences of the fragments at the locations;
• (f) determining relative physical distances between the fragments at the locations;
• and
• (g) identifying the nucleotide sequences from the mixture of target nucleic acid polymers that are derived from a common source from the plurality of different sources based on the nucleotide sequences from the fragments and the determined relative physical distances between the locations on the solid support surface, wherein the relative physical distances are indicative of distances between the sequence regions along a given strand of a target nucleic acid polymer from the mixture of target nucleic acid polymers.

A method of determining the source for individual sequences in a mixture of sequences from different sources, comprising:

• (a) providing a mixture of target nucleic acid polymers from a plurality of different sources;
• (b) modifying the mixture of target nucleic acid polymers to produce a mixture of modified nucleic acid polymers, wherein the mixture of modified nucleic acid polymers comprises a plurality of sequence regions from the different sources;
• (c) attaching the modified nucleic acid polymers to a solid support surface;
• (d) producing fragments of the modified nucleic acid polymers that are attached to the solid support surface, wherein fragments from a common source of the plurality of sources are attached to locations that are proximal on the solid support surface;
• (e) determining nucleotide sequences of the fragments at the locations;
• (f) determining relative physical distances between the fragments at the locations;
• and
• (g) identifying the nucleotide sequences from the mixture of target nucleic acid polymers that are derived from a common source from the plurality of different sources based on the nucleotide sequences from the fragments and the determined relative physical distances between the locations on the solid support surface, wherein the relative physical distances are indicative of distances between the sequence regions along a given strand of a target nucleic acid polymer from the mixture of target nucleic acid polymers.

A method of determining the source for individual sequences in a mixture of sequences from different sources, comprising:

• (a) providing a mixture of target nucleic acid polymers from a plurality of different sources;
• (b) adding inserts into the target nucleic acid polymers in the mixture to form a mixture of modified nucleic acid polymers, each polymer including a plurality of internal inserts;
• (c) producing fragments of the modified nucleic acid polymers in a fluid that is in contact with a solid support surface, thereby releasing fragments that each include at least a portion of each of the inserts;
• (d) capturing the fragments from the fluid randomly at locations on the solid support surface;
• (e) determining nucleotide sequences from the fragments by detecting the fragments at the locations;
• (f) determining relative physical distances between the fragments at the locations;
• (g) identifying the nucleotide sequences from the mixture of target nucleic acid polymers that are derived from a common source from the plurality of different sources based on the nucleotide sequences from the fragments and the determined relative physical distances between the locations on the solid support surface, wherein the relative physical distances are indicative of distances between sequence regions along a given strand of a target nucleic acid polymer from the mixture of target nucleic acid polymers.

A method of determining the source for individual sequences in a mixture of sequences from different sources, comprising:

• (a) providing a mixture of target nucleic acid polymers from a plurality of different sources;
• (b) adding inserts into the target nucleic acid polymers in the mixture to form a mixture of modified nucleic acid polymers, each polymer comprising a plurality of internal inserts;
• (c) attaching the modified nucleic acid polymer to a solid support surface;
• (d) producing fragments of the modified nucleic acid polymers that are attached to the solid support surface, wherein fragments from a common source of the plurality of sources are attached to locations that are proximal on the solid support surface;
• (e) determining nucleotide sequences from the fragments by detecting the fragments at the locations;
• (f) determining relative physical distances between the fragments at the locations;
• and
• (g) identifying the nucleotide sequences from the mixture of target nucleic acid polymers that are derived from a common source from the plurality of different sources based on the nucleotide sequences from the fragments and the determined relative physical distances between the locations on the solid support surface, wherein the relative physical distances are indicative of distances between sequence regions along a given strand of a target nucleic acid polymer from the mixture of target nucleic acid polymers.