Patents Assigned to Perlegen Sciences, Inc.
  • Patent number: 7127355
    Abstract: Several methods are described for assessing an individual's likelihood of developing or exhibiting a multifactorial trait. The methods include determining a plurality of genotypes for the individual at a plurality of biallelic polymorphic loci, using the genotypes to compute a score for the individual, and comparing the score to at least one threshold value.
    Type: Grant
    Filed: September 30, 2004
    Date of Patent: October 24, 2006
    Assignee: Perlegen Sciences, Inc.
    Inventors: David Cox, Mark McCamish
  • Publication number: 20060234216
    Abstract: The present invention includes the use of any of the polymorphisms, SNP haplotype blocks or SNP haplotype patterns. In one embodiment, susceptibility to a phenotype resulting from an allele or marker in linkage disequilibrium with such polymorphic forms is evaluated. Novel therapeutic and diagnostic compounds and methods are also disclosed.
    Type: Application
    Filed: August 22, 2002
    Publication date: October 19, 2006
    Applicant: Perlegen Sciences, Inc.
    Inventors: David Cox, Deana Arnold
  • Patent number: 7124033
    Abstract: Methods, code, and apparatus are used to ensure that groups of experimental subjects selected for inclusion in a study are matched. Individuals are genotyped and the genotype data is used to determine the extent of mismatch between study groups. If groups show evidence of poor matching, then the genotype data is used to better match the study groups.
    Type: Grant
    Filed: April 30, 2003
    Date of Patent: October 17, 2006
    Assignee: Perlegen Sciences, Inc.
    Inventors: David Hinds, Renee Stokowski
  • Publication number: 20060228728
    Abstract: A collection of polymorphic sites having resistance or susceptibility to Alzheimer's disease is provided. The sites are useful in methods of diagnosing and treating Alzheimer's disease and related conditions.
    Type: Application
    Filed: January 31, 2006
    Publication date: October 12, 2006
    Applicant: Perlegen Sciences, Inc.
    Inventors: David Cox, Dennis Ballinger, Erica Beilharz, Karel Konvicka, Laura Stuve
  • Publication number: 20060223058
    Abstract: Cell and tissue autonomous phenotypes are correlated with genotype information. Correlated genotype information is used to screen individual traits. Methods and systems for correlating cell and tissue autonomous phenotypes to genotype information are provided.
    Type: Application
    Filed: March 9, 2006
    Publication date: October 5, 2006
    Applicant: Perlegen Sciences, Inc.
    Inventors: David Cox, Brad Margus
  • Patent number: 7115726
    Abstract: The present invention includes the use of any of the polymorphisms, SNP haplotype blocks or SNP haplotype patterns. In one embodiment, susceptibility to a phenotype resulting from an allele or marker in linkage disequilibrium with such polymorphic forms is evaluated. Novel therapeutic and diagnostic compounds and methods are also disclosed.
    Type: Grant
    Filed: August 22, 2002
    Date of Patent: October 3, 2006
    Assignee: Perlegen Sciences, Inc.
    Inventors: David R. Cox, Deana A. Arnold
  • Publication number: 20060211684
    Abstract: The present invention provides a strategy to compensate for deficiency in the alpha-2C receptor by administering an agonist of different receptors; the alpha-2A and/or dopamine d2 receptors. These receptors are fully functional and receptive to stimulation by an agonist. Agonism of the alpha-2A and/or dopamine d2 receptors by clonidine, Nolomirole or other suitable agonist may down regulate epinephrine production, and hence compensate for the deficiency in the alpha-2C receptor. Such methods are useful for treating a variety of cardiovascular disorders.
    Type: Application
    Filed: January 13, 2006
    Publication date: September 21, 2006
    Applicant: Perlegen Sciences, Inc.
    Inventor: Mark McCamish
  • Publication number: 20060188875
    Abstract: The invention provides nucleic acid segments of the human genome including polymorphic sites, SNP haplotype blocks, SNP haplotype patterns for each block and informative SNPs for each pattern. Allele-specific primers and probes hybridizing to regions flanking these sites are also provided. The nucleic acids, primers and probes are used in applications such as association studies and other genetic analyses.
    Type: Application
    Filed: October 31, 2002
    Publication date: August 24, 2006
    Applicant: Perlegen Sciences, Inc.
    Inventors: David Cox, Nila Patil, Anthony Berno, David Hinds
  • Publication number: 20060183132
    Abstract: Multiple unique selection probes are provided in a single medium. Each selection probe has a sequence that is complementary to a unique target sequence that may be present in a sample under consideration. For example, each selection probe may be complementary to a sequence that includes one of the SNPs used to genotype an organism. Single-stranded selection probes anneal or hybridize with sample sequences having the unique target sequences specified by the selection probe sequences. Sequences from the sample that do not anneal or hybridize with the selection probes are separated from the bound sequences by an appropriate technique. The bound sequences can then be freed to provide a mixture of isolated target sequences, which can be used as needed for the application at hand.
    Type: Application
    Filed: February 14, 2005
    Publication date: August 17, 2006
    Applicant: Perlegen Sciences, Inc.
    Inventors: Glenn Fu, Laura Stuve, John Sheehan, Amy Ollmann, Naiping Shen, Andrew Sparks, Dennis Ballinger
  • Publication number: 20060177847
    Abstract: Correlations between polymorphisms and metabolic syndrome, obesity, treatment-emergent weight gain and insulin resistance are provided. Methods of diagnosing and treating metabolic syndrome, obesity, treatment-emergent weight gain and insulin resistance are provided. Systems and kits for disgnosis and treatment of metabolic syndrome, treatment-emergent weight gain, obesity and insulin resistance are provided.
    Type: Application
    Filed: December 8, 2005
    Publication date: August 10, 2006
    Applicant: Perlegen Sciences, Inc.
    Inventors: David Cox, Dennis Ballinger, Richard Hockett, Sandra Kirkwood
  • Patent number: 7058657
    Abstract: An interactive and dynamic data analysis tool that helps interactive analysis in real time on medium size datasets having complex structure is described. In one aspect, the data analysis tool is capable of being configured to act as a data producer tool arranged to provide a data source. The data analysis tool can also be configured as a data consumer tool capable of receiving and processing a particular data source. The data source tool and the data consumer tool are connected together to form a framework that takes the form of a data mapping context that mediates the data provided by the data source and a particular data role.
    Type: Grant
    Filed: January 7, 2003
    Date of Patent: June 6, 2006
    Assignee: Perlegen Sciences, Inc.
    Inventor: Anthony J. Berno
  • Publication number: 20060008834
    Abstract: Improved life sciences business systems and methods are disclosed. One or more genomes are scanned for single nucleotide polymorphisms. The polymorphisms are assigned to haplotype blocks, and representative SNPs from the haplotype blocks are used in association studies for pharmaceutical and diagnostic developments.
    Type: Application
    Filed: July 13, 2005
    Publication date: January 12, 2006
    Applicant: Perlegen Sciences, Inc.
    Inventors: Bradley Margus, David Cox
  • Publication number: 20050272086
    Abstract: The present invention relates to methods for identifying variations that occur in the human genome and relating these variations to the genetic basis of disease and drug response. In particular, the present invention relates to identifying individual SNPs, determining SNP haplotype blocks and patterns, and, further, using the SNP haplotype blocks and patterns to dissect the genetic bases of disease and drug response. The methods of the present invention are useful in whole genome analysis.
    Type: Application
    Filed: June 29, 2005
    Publication date: December 8, 2005
    Applicant: Perlegen Sciences, Inc.
    Inventors: Nila Patil, David Cox, Anthony Berno, David Hinds
  • Patent number: 6969589
    Abstract: The present invention relates to methods for identifying variations that occur in the human genome and relating these variations to the genetic basis of disease and drug response. In particular, the present invention relates to identifying individual SNPs, determining SNP haplotype blocks and patterns, and, further, using the SNP haplotype blocks and patterns to dissect the genetic bases of disease and drug response. The methods of the present invention are useful in whole genome analysis.
    Type: Grant
    Filed: March 26, 2002
    Date of Patent: November 29, 2005
    Assignee: Perlegen Sciences, Inc.
    Inventors: Nila Patil, David R. Cox, Anthony J. Berno, David A. Hinds
  • Patent number: 6963805
    Abstract: The present invention provides methods for determining sequence similarity (conserved sequences) between nucleic acids from a first organism and nucleic acids from a second, different organism without having to know a priori the nucleic acid sequence from the second, different organism. The first nucleic acid can be from any organism where the sequence of the nucleic acid is known and the second nucleic acid can be from any organism. The method involves determining which bases from the second nucleic acid are identical to the first nucleic acid, and allows one to determine the sequence of portions of the second nucleic acid. The invention is useful for identifying putative functional regions or putative organism-sequences in a genome.
    Type: Grant
    Filed: October 5, 2001
    Date of Patent: November 8, 2005
    Assignee: Perlegen Sciences, Inc.
    Inventors: Kelly A. Frazer, Nila Patil, John Sheehan
  • Patent number: 6955883
    Abstract: Improved life sciences business systems and methods are disclosed. One or more genomes are scanned for single nucleotide polymorphisms. The polymorphisms are assigned to haplotype blocks, and representative SNPs from the haplotype blocks are used in association studies for pharmaceutical and diagnostic developments.
    Type: Grant
    Filed: March 26, 2003
    Date of Patent: October 18, 2005
    Assignee: Perlegen Sciences, Inc.
    Inventors: Bradley A. Margus, David R. Cox, Stephen P. A. Fodor
  • Publication number: 20050196770
    Abstract: Several methods are described for assessing an individual's likelihood of developing or exhibiting a multifactorial trait. The methods include determining a plurality of genotypes for the individual at a plurality of biallelic polymorphic loci, using the genotypes to compute a score for the individual, and comparing the score to at least one threshold value.
    Type: Application
    Filed: September 30, 2004
    Publication date: September 8, 2005
    Applicant: Perlegen Sciences, Inc.
    Inventors: David Cox, Mark McCamish
  • Patent number: 6897025
    Abstract: Improved systems and methods for performing genetic analyses. Full genomic DNA scans are performed on the genetic DNA from a plurality of individuals to identify genetic variants. For those variants, but not based on a full genetic DNA scan, the variants alone are scanned in additional individuals to identify blocks of the variants that tend to be inherited together.
    Type: Grant
    Filed: January 7, 2002
    Date of Patent: May 24, 2005
    Assignee: Perlegen Sciences, Inc.
    Inventors: David R. Cox, Bradley A. Margus, Nila Patil
  • Patent number: 6898531
    Abstract: The presently claimed invention provides methods for amplifying a DNA target sequence. One embodiment of the present invention provides robust methods for amplification of target sequences. In a first aspect of the invention, a method for designing primer pairs for the amplification reaction is provided. In a further aspect of the invention, reagents and cycling parameters for the amplification reaction are provided.
    Type: Grant
    Filed: January 9, 2002
    Date of Patent: May 24, 2005
    Assignee: Perlegen Sciences, Inc.
    Inventors: John B. Sheehan, Daryl J. Thomas, Wade A. Barrett
  • Publication number: 20050100911
    Abstract: The invention provides several methods for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids on a nucleic acid probe array. The methods result in a subset of the initial population enriched for a desired property, or lacking nucleic acids having an undesired properly. The resulting nucleic acids in the subset are then applied to the array for various types of analysis. The methods are particularly useful for analyzing populations having a high decree of complexity, for example, chromosomal-derived DNA, or whole genomic DNA, or mRNA population. In addition, such methods allow for analysis of pooled samples.
    Type: Application
    Filed: August 6, 2003
    Publication date: May 12, 2005
    Applicant: Perlegen Sciences, Inc.
    Inventors: Nila Patil, David Cox, Charit Pethiyagoda, Andrew Sparks, Huang-Tsu Chen