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Sequencing-Related US Patents Granted November 2007

US Patent 7,300,755. Methods for haplotyping genomic DNA.
Inventors: Effie Petersdorf, Zhen Guo, Leroy Hood. Assignees: Fred Hutchinson Cancer Research Center, Institute for Systems Biology.
The invention provides a novel method for specifically isolating and separating large segments of genomic DNA that can subsequently be used to determine a genomic haplotype. The invention relies on using a solid phase with a flat surface arrayed with oligonucleotides designed to specifically hybridize to each particular haplotype of an individual sample, e.g., oligonucleotides designed to specifically hybridize with each of the two HLA-B haplotypes, HLA-A, HLA-C, HLA-DR, HLA-DQ, and the like. The genomic DNA is contacted and hybridized to the arrayed oligonucleotides to form a genomic DNA/oligonucleotide complex. The excess genomic DNA is washed away and the haplotype-separated genomic DNA is denatured from the oligonucleotide probe and collected. The method of the invention allows for the separation of genomic DNA fragments of between approximately 2 to about 4 megabases. Separation of the haplotypes of large genomic DNA fragments allows for linkage analysis of other HLA alleles and polymorphisms, microsatellite, SNPs, and the like across a large span of the HLA region. This linkage analysis is particularly useful when HLA typing for an individual with limited family HLA typing available, according to the patent abstract.

US Patent 7,297,518. Methods and apparatus for analyzing polynucleotide sequences by asynchronous base extension.
Inventors: Stephen Quake, Ido Braslavsky, Benedict Hebert, Emil Kartalov. Assignee: California Institute of Technology.
Provides methods for analyzing the sequence of a target polynucleotide. The methods include a primed target polynucleotide immobilized to a surface of a substrate, where the target polynucleotide is attached to the surface with single molecule resolution. In the presence of a polymerase, a first fluorescently labeled nucleotide is added to the surface of the substrate under conditions whereby the first nucleotide attaches to the primer, if a complementary nucleotide is present to serve as a template in the target polynucleotide. The presence or absence of a fluorescence signal on the surface where the target polynucleotide is immobilized is determined. The presence of a signal indicates that the first nucleotide was incorporated into the primer, and identifies the complementary base that served as a template in the target polynucleotide. In some methods of the invention, the presence or absence of a fluorescence signal is determined with total internal reflection fluorescence microscopy. In some methods, the target polynucleotide is primed with a fluorescently labeled primer (e.g., with Cy5 or Cy3). Some methods of the invention employ nucleotides that are labeled with Cy3 or Cy5.

US Patent 7,297,485. Method for nucleic acid amplification that results in low amplification bias.
Inventors: Carole Bornarth, Michele Wisniewski, Seiyu Hosono, Arumugham Raghunathan, Roger Lasken. Assignee: Qiagen.
Provides compositions and methods for amplification of nucleic acid sequences of interest. It has been discovered that amplification reactions can produce amplification products of high quality, such as low amplification bias, if performed on an amount of nucleic acid at or over a threshold amount and/or on nucleic acids at or below a threshold concentration. The threshold amount and concentration can vary depending on the nature and source of the nucleic acids to be amplified and the type of amplification reaction employed. Disclosed is a method of determining the threshold amount and/or threshold concentration of nucleic acids that can be used with nucleic acid samples of interest in amplification reactions of interest.

US Patent 7,294,461. Methods and compositions for transcription-based nucleic acid amplification.
Inventors: Nurith Kurn. Assignee: Nugen Technologies.
Methods for isothermal exponential amplification of a target polynucleotide are disclosed. The methods employ two transcription modules, the first module providing linear amplification resulting in RNA transcripts, and a second module providing for further, generally cyclical, amplification resulting in more RNA transcripts.

US Patent 7,292,742. Waveguides for performing enzymatic reactions.
Inventors: Michael Levene, Jonas Korlach, Stephen Turner, Harold Craighead, Watt Webb. Assignee: Cornell Research Foundation.
The invention is directed to a method and an apparatus for the analysis of an analyte. The method involves providing a zero-mode waveguide that includes a cladding surrounding a core where the cladding is configured to preclude propagation of electromagnetic energy of a frequency less than a cutoff frequency longitudinally through the core of the zero-mode waveguide. The analyte is positioned in the core of the zero-mode waveguide and is then subjected, in the core of the zero-mode wave guide, to activating electromagnetic radiation of a frequency less than the cut-off frequency under conditions effective to permit analysis of the analyte in an effective observation volume which is more compact than if the analysis were carried out in the absence of the zero-mode waveguide.

US Patent 7,291,471. Cleavable oligonucleotide arrays.
Inventors: Jeffrey Sampson, Joel Myerson. Assignee: Agilent Technologies.
Discloses oligonucleotide arrays with features that include cleavable oligonucleotides, as well as methods of making such arrays. Methods of synthesizing an oligonucleotide on a surface of a substrate are described as well.

US Patent 7,291,468 and US Patent 7,291,467. Systems and methods of analyzing nucleic acid polymers and related components.
Inventor: William Glover, III. Assignee: ZS Genetics.
Systems and methods of identifying, sequencing and/or detecting nucleic acid polymers, as well as related components, such as substrates and software are disclosed. The methods include forming a complementary strand of the nucleic acid polymer and identifying a sequence of nucleotides in the nucleic acid polymer and/or in the complementary strand using a particle beam. In preferred embodiments, the nucleotides of the nucleic acid polymer and/or the complementary strand are modified to include labels. Preferably the labels are specific for each type of nucleotide. The labels can include one or more atoms, preferably three or fewer atoms, preferably a single atom.

US Patent 7,291,460. Multiplexed systems for nucleic acid sequencing.
Inventors: Mike Lafferty, Charles Tweedy, James Butler. Assignee: Verenium.

Provides methods for the sequencing of polynucleotides as well as multiplex systems for sequencing polynucleotides, kits, and methods for diagnosing diseases and adverse drug reactions using the disclosed methods. Includes a method for determining the sequence of a polynucleotide, providing at least one population of polynucleotides wherein the members of the population share a nucleotide sequence. In addition, at least 4x sets of sequencing adaptors are provided, where each set of sequencing adaptors comprises one of 4x possible combinations of nucleotides in a single-stranded region of x nucleotides long, a nuclease recognition site for a nuclease that produces a single-stranded region of x nucleotides long, but does not cleave within its recognition site, and a detectable optical marker that is unique to that set of sequencing adaptors, where x is an integer equal to 2 or greater. Thus, for a given single-stranded region, each set of sequencing adaptors contains a different nucleotide sequence within the single-stranded region, such that all possible nucleotide sequences are represented by the sets of sequencing adaptors. In another embodiment, the sequencing adaptors also comprise a spacer region. In one embodiment, the unique optical marker comprises a microbead. In yet another embodiment, the microbead is a fluorescent microbead.

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.