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Clinical Sequencing Patents of Note


Sequencing-Related US Patents Granted May 20 – June 23

US Patent 7,550,570. 4,7-dichlororhodamine dyes labeled polynucleotides
Inventors: Linda Lee, Scott Benson, Barnett Rosenblum, Sandra Spurgeon, Ronald Graham
Assignee: Applied Biosystems

Discloses a set of 4,7-dichlororhodamine compounds that are useful as fluorescent dyes In another aspect, the invention includes reagents labeled with the 4,7-dichlororhodamine dye compounds, including deoxynucleotides, dideoxynucleotides, and polynucleotides. In an additional aspect, the invention includes methods utilizing such dye compounds and reagents, including dideoxy polynucleotide sequencing and fragment analysis methods.

US Patent 7,547,530. Nucleotide compositions comprising photocleavable markers and methods of preparation thereof
Inventors: Jerzy Olejnik, Edyta Krzymanska-Olejnik, Kenneth Rothschild
Assignee: AmberGen

Describes labelled nucleotides and polynucleotides that are useful in the sequencing of nucleic acids, as well as methods of preparing photocleavable marker nucleotides and photocleavable marker-polynucleotide conjugates. Such photocleavable marker nucleotides can be incorporated into nucleic acids.

US Patent 7,544,794. Method for sequencing DNA and RNA by synthesis
Inventor: Steven Benner
Assignee: N/A

Relates to compositions that allow the sequencing of oligonucleotides by synthesis, and processes for sequencing by synthesis that exploit these compositions. More specifically, the invention discloses compositions of matter that are 5'-triphosphates of ribo- and 2'-deoxyribonucleosides wherein the 3'-OH group is replaced by a 3'-ONHR group in the alpha configuration, wherein R is either a H or CH3 group. Also disclosed are triphosphates where the nucleobase carries, via a linker, a reporter group, such as a fluorescent species that can be used in single- or multi-copy DNA sequencing, or a tag that can be visualized by ultramicroscopy. Also disclosed are processes that use these compositions to do sequencing by synthesis.

US Patent 7,544,473. Nucleic acid analysis using sequence tokens
Inventor: Sydney Brenner
Assignee: Population Genetics Technologies

Provides methods and compositions for tagging nucleic acid sequence fragments, for example a set of nucleic acid sequence fragments from a single genome, with one or more unique members of a collection of oligonucleotide tags, or sequence tokens, which, in turn, can be identified using a variety of readout platforms. As a general rule, a given sequence token is used once and only once in any tag sequence. In addition, the invention provides methods for using the sequence tokens to efficiently determine variations in nucleotide sequences in the associated nucleic acid sequence fragments.

US Patent 7,541,444. Modified nucleotides
Inventors: John Milton, Xiaolin Wu, Mark Smith, Joseph Brennan, Colin Barnes, Xiaohai Liu, Silke Ruediger
Assignee: Illumina

Provides modified nucleotide or nucleoside molecule comprising a purine or pyrimidine base and a ribose or deoxyribose sugar moiety having a removable 3'-OH blocking group covalently attached, such that the 3' carbon atom has attached a group of a certain structure.

US Patent 7,537,892. Method and sequences for determinate nucleic acid hybridization
Inventor: William Hillis
Assignee: Searete

Provides methods for using nucleic acid sequences with two or more degenerately pairing nucleotides, each having a partially overlapping set of complementarity, to reduce the number of hybridizing nucleotide sequences or probes used in biochemical and molecular biological operations with sequence specific hybridization. The method may be employed for various hybridization procedures with sequence specific hybridization, including sequencing methods measuring hybridization directly, and tagging by hybridization methods in which the sequence is determined by analyzing the pattern of tags that hybridize to it, and hybridization-dependent amplification methods.