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Sequencing-Related US Patents, Granted July — September 2007

US Patent 7,264,934. Rapid parallel nucleic acid analysis.
Inventor: Carl W. Fuller. Assignee: GE Healthcare Bio-Sciences.
Provides methods for massive parallel nucleic acid analysis. A closed complex of nucleic acid template, nucleotide, and polymerase can be formed during a polymerase reaction in the absence of divalent metal ions. This is used to trap the nucleotide complementary to the next template nucleotide in the closed complex. Detection of the trapped nucleotide allows determination of the sequence of the next correct nucleotide. In this way, sequential nucleotides of a nucleic acid template can be identified, effectively determining the sequence. This method is applied to sequence multiple templates in parallel, particularly if they are immobilized on a solid support.

US Patent 7,264,931. Method for sequencing nucleic acid sequences without chain termination.
Inventors: Abram Gabriel, Yoshifumi Kobayashi. Assignee: Rutgers, the State University of New Jersey.
Provides a method for determining the sequence of a nucleic acid sequence via incubation of a primer-extended product of the nucleic acid sequence in separate pools of semi-random oligonucleotides of 5'(N)nA3', 5'(N)nG3', and 5'(N)nT3', wherein N is A, C, G or T and n is selected so that the oligonucleotides will optimally anneal to all complementary sequences.

US Patent 7,264,929. Method of sequencing a nucleic acid.
Inventors: Jonathan M. Rothberg, Joel S. Bader, Scott B. Dewell, Keith McDade, John W. Simpson, Jan Berka, Christopher M. Colangelo. Assignee: 454 Life Sciences.
Discloses methods and apparatuses for sequencing a nucleic acid. These methods permit a very large number of independent sequencing reactions to be arrayed in parallel, permitting simultaneous sequencing of more than 10,000 different oligonucleotides. One method involves a primed anchor primer-circular template complex and combining the complex with a polymerase and nucleotides to generate concatenated, linear, complementary copies (CLCC) of the circular template. One or more sequencing primers are then annealed to the CLCC and are extended with a polymerase and a predetermined nucleotide triphosphate to yield a sequencing product and a sequencing reaction byproduct, e.g., inorganic pyrophosphate. The invention also includes a method for sequencing a nucleic acid by providing one or more nucleic acid templates linked to a plurality of anchor primers linked to a fiber optic surface substrate.

US Patent 7,262,030. Multiple sequencible and ligatible structures for genomic analysis.
Inventor: Xiangning Chen. Assignee: Virginia Commonwealth University.
Protects high-throughput methods and kits for single nucleotide polymorphism genotyping. The methods involve nested PCR amplification reactions, which produce sequencible and ligatible structures. An outer PCR primer set amplifies the SNP, and an inner PCR primer set amplifies a portion of the DNA amplified by the outer primer set, but does not amplify the SNP itself.

US Patent 7,262,013. Bisulfite method.
Inventors: Victoria Boyd, Gerald Zon. Assignee: Applera.
The invention provides methods for purifying bisulfite-treated nucleic acid samples. Sample preparation comprises the steps of providing a nucleic acid comprising at least one cytosine nucleobase; contacting the sample with a bisulfite conversion reagent; and purifying the contacted sample using a size-exclusion device. Following desulfonation of the bisulfite-treated nucleic acid(s), the obtained product may be used in any of a wide variety of analytical or preparative procedures, such as amplification (e.g., by PCR, whole genome amplification, etc.), sequencing (which may optionally follow amplification), differential hybridization, mass spectrometry, or other techniques.

US Patent RE39,793. Compositions for sorting polynucleotides.
Inventor: Sydney Brenner. Assignee: Solexa.
Provides a method of tracking, identifying, and/or sorting classes or subpopulations of molecules by the use of oligonucleotide tags. Oligonucleotide tags of the invention each consist of a plurality of subunits three to six nucleotides in length selected from a minimally cross-hybridizing set. A subunit of a minimally cross-hybridizing set forms a duplex or triplex having two or more mismatches with the complement of any other subunit of the same set. The number of oligonucleotide tags available in a particular embodiment depends on the number of subunits per tag and on the length of the subunit. An important aspect of the invention is the use of the oligonucleotide tags for sorting polynucleotides by specifically hybridizing tags attached to the polynucleotides to their complements on solid phase supports. This embodiment provides a readily automated system for manipulating and sorting polynucleotides, particularly useful in large-scale parallel operations, such as large-scale DNA sequencing, mRNA fingerprinting, and the like, wherein many target polynucleotides or many segments of a single target polynucleotide are sequenced simultaneously.

US Patent 7,256,019. Terminal phosphate blocked nucleoside polyphosphates.
Inventors: Anup Sood, Shiv Kumar, Carl Fuller, John Nelson. Assignee: GE Healthcare Bio-Sciences.
Describes terminal phosphate blocked nucleoside polyphosphates that are stable at high temperature and their use in nucleic acid amplification and analysis. Further describes charge-modified terminal phosphate-blocked nucleoside polyphosphates for improved incorporation and direct loading of nucleic acid sequencing reactions onto separating media.

US Patent 7,255,994. Ligation assay.
Inventor: Kai Qin Lao. Assignee: Applera.
Protects methods and kits for detecting or quantifying one or more target polynucleotide sequences in a sample. Embodiments of the invention employ a first ligation reaction, a subsequent optional amplification reaction, and a second ligation reaction. Embodiments of the invention combine the specificity of both hybridization and ligation reactions along with universal probe polynucleotide sequences to achieve specific and multiplexed detection of a plurality of target polynucleotide sequences.

The Scan

Pig Organ Transplants Considered

The Wall Street Journal reports that the US Food and Drug Administration may soon allow clinical trials that involve transplanting pig organs into humans.

'Poo-Bank' Proposal

Harvard Medical School researchers suggest people should bank stool samples when they are young to transplant when they later develop age-related diseases.

Spurred to Develop Again

New Scientist reports that researchers may have uncovered why about 60 percent of in vitro fertilization embryos stop developing.

Science Papers Examine Breast Milk Cell Populations, Cerebral Cortex Cellular Diversity, Micronesia Population History

In Science this week: unique cell populations found within breast milk, 100 transcriptionally distinct cell populations uncovered in the cerebral cortex, and more.