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Sequencing-Related US Patents, Granted May — June 2007

US Patent 7,232,656. Arrayed biomolecules and their use in sequencing. Inventors: Shankar Balasubramanian, David Klenerman, Colin Barnes, Mark Allen Osborne. Assignee: Solexa.
The patent covers a method for analyzing genome-wide variation in an individual based on randomly fragmenting the individual's genome and generating sequence reads of multiple bases on all the fragments, then aligning the sequence reads generated with a known genomic reference sequence, and finally analyzing variations between the sequence reads derived from the individual's genome and a genomic reference sequence.

US Patent 7,230,093. Method of sequencing by hybridization of oligonucleotide probes. Inventors: Radoje Drmanac, Radornir Crkvenjakov. Assignee: Callida Genomics.
The patent describes conditions under which oligonucleotide probes “hybridize preferentially with entirely complementary and homologous nucleic acid targets.” Using these hybridization conditions, overlapping oligonucleotide probes associate with a target nucleic acid. Following washes, positive hybridization signals are used to assemble the sequence of a given nucleic acid fragment. Up to 100,000 probes are used to determine sequence information by simultaneous hybridization with nucleic acid molecules bound to a filter. Additional hybridization conditions are provided that allow stringent hybridization of 6 to 10 nucleotide long oligomers. “Sequence generation can be obtained for a large complex mammalian genome in a single process,” according to the patent abstract.

US Patent 7,229,799. System and method for nucleic acid sequencing by polymerase synthesis. Inventors: John Williams. Assignee: Li-Cor.
The patent covers improved methods for sequencing and genotyping nucleic acid in a single molecule configuration. The method involves single-molecule detection of fluorescent labeled pyrophosphate moieties released from nucleoside triphosphates as a polymerase extension product is created.

US Patent 7,229,798. Transposon mediated multiplex sequencing. Inventors: Paul August, Pamela Keagle, Henry Long, Anna Wiencis Montmayeur, Katherine Call, Michael Draper. Assignee: Aventis Pharmaceuticals.
The patent protects an automated method of transposon-mediated multiplex sequencing of DNA fragments inserted into a vector. According to the patent abstract, the method offers increase efficiency by screening out constructs in which the transposon inserted into the vector sequence. “This prevents a waste of time and resources in performing reactions sequencing the vector instead of the DNA fragments of interest,” the abstract states.

US Patent 7,229,767. Genomics applications for modified oligonucleotides. Inventors: Eric Kmiec, Howard Gamper, Michael Rice, Michael Usher. Assignee: University of Delaware.
The patent covers methods for producing and using stable complexes of duplex nucleic acid molecules and oligonucleotides. The complexes can be used to detect and purify a known nucleic acid target as well as to manipulate a defined nucleic acid target sequence, according to the patent abstract.

The Scan

Follow-Up Data Requests to Biobank Participants Ineffective, Study Finds

An effort to recontact biobank enrollees for additional information reports low participation in a new BMJ Open study.

Study Finds Widespread Transmission of Resistant Bacteria in Vietnam Hospitals

A sequencing study in The Lancet Microbe finds widespread transmission of drug-resistant Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii in two Vietnam ICUs.

Novel Brain Cell Organoids Show Promise for Autism Research

University of Utah researchers report in Nature Communications on their development of brain cell organoids to study SHANK3-related autism.

Study Finds Few FDA Post-Market Regulatory Actions Backed by Research, Public Assessments

A Yale University-led team examines in The BMJ safety signals from the US FDA Adverse Event Reporting System and whether they led to regulatory action.