SEQUENCE-CENTRIC SCIENTIFIC INFORMATION MANAGEMENT

• US 20100318528A1
• Filed: 06/08/2010
• Published: 12/16/2010
• Est. Priority Date: 12/16/2005
• Status: Active Grant

• Current Assignee: NextBio
• Original Assignee: NextBio
• Inventors: Kupershmidt, Ilya, Su, Qiaojuan Jane
• Granted Patent: US 9,183,349 B2
• Time in Patent Office: Days
• US Class Current: 707/756
• CPC Class Codes: G06F 16/24578 using ranking
• CPC Class Codes: G06F 16/248 Presentation of query results
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/10 Ploidy or copy number detection
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 20/40 Population genetics; Linkage disequilibrium
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/30 Data warehousing; Computing architectures

Abstract

According to various embodiments, aspects of the invention provide a highly efficient meta-analysis infrastructure for performing research queries across a large number of studies and experiments from diverse sequencing technologies as well as different biological and chemical assays, data types and organisms, as well as systems to build and add to such an infrastructure. The methods, systems and apparatuses described enable combining orthogonal types of data and available public knowledge to elucidate mechanisms governing normal development, disease progression, as well as susceptibility of individuals to disease or response to drug treatments.

Claims

1. A computer-implemented method of integrating a sequence-centric feature set into a knowledge base comprising sequence-centric feature sets and gene-centric feature sets, the sequence-centric feature sets comprising genomic sequence regions and associated statistics and the gene-centric feature sets comprising genes and associated statistics, the method comprising:

receiving a sequence-centric feature set comprising a plurality of sequence regions and associated statistics;

mapping the plurality of sequence regions to genes within the knowledge base to provide a set of mapped genes for the received sequence-centric feature set;

mapping said sequence regions to other sequence regions within the knowledge base to provide a set of mapped sequence regions for the received sequence-region feature set;

correlating the received sequence-centric feature set to other sequence-centric feature sets using the set of mapped sequence regions; and

correlating the received sequence-centric feature set to gene-centric feature sets using the set of mapped genes.

2. A computer-implemented method of integrating and querying orthogonal data, said data comprising gene-centric experimental data regarding genes in a sample and sequence-centric-data experimental data regarding sequence regions in a sample;

the method comprising mapping gene-centric data to sequence-centric data based on genomic coordinates.

3. A computer implemented method of conducting a query in a knowledge base comprising sequence-centric feature sets and gene-centric feature sets, the sequence-centric feature sets comprising genomic sequence regions and associated statistics based on experiments on samples containing the sequence regions and the gene-centric feature sets comprising genes and associated statistics based on experiments on samples containing the genes, the method comprising:

receiving a query identifying one or more sequence regions, genes, or feature sets, wherein the query is received from a user input to a computer system;

correlating the identified sequence region, gene or feature set with other information in the knowledge base comprising gene-centric feature sets and other sequence-centric feature sets to determine feature set rankings in reply to said query;

presenting the user with a ranked list of feature sets as determined by using the correlations; and

presenting the user with a graphical representation of an association between sequence-regions within a resulting feature set and other information in the knowledge base.