# US 2019/0172556 A1 · Method and System for Assessment of Regulatory Variants in a Genome > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2019/0172556 A1 - Document ID: US20190172556A1 - Status: Published application - Kind: A1 - Application number: 16/201,913 - Filed: 2018-11-27 - Published: 2019-06-06 - Earliest claimed: 2011-08-22 - Assignees: The Board of Trustees of the Leland Stanford Junior University - Applicants: The Board of Trustees of the Leland Stanford Junior University - Inventors: Konrad J. Karczewski; Joel T. Dudley; Michael P. Snyder; Atul J. Butte - Web page: https://patentgrep.com/patent/US20190172556A1 ## CPC - 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 - G16B 20/00: ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations - G16B 20/20: Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection - G16B 20/30: Detection of binding sites or motifs - G16B 20/40: Population genetics; Linkage disequilibrium - G16B 40/20: Supervised data analysis - G16B 99/00: Subject matter not provided for in other groups of this subclass - Y02A 90/10: Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation - G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY - Y02A: TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE ## Abstract The present invention provides methods embodied in a system that can be applied to genetic information comprising an individual genome to assess the regulatory impact of specific genetic variants and their possible impact on biological function or disease pathology. ## Claims ### Claim 1 A method of treating an individual based on genetic variants in transcription factor binding sites, comprising: obtaining genetic data from an individual by sequencing genetic material of the individual; identifying at least one disease in the individual using a computer system comprising a processor and a memory, wherein the at least one disease is associated with gene regulation, wherein the at least one disease is identified by: receiving information regarding genome-wide quantitative and genetic profiles, information regarding genetic variants associated with disease conditions, information regarding DNA motifs associated with transcription factor binding, and molecular profiles of disease pathologies and storing this information using a computer system comprising a processor and a memory, wherein the quantitative and genetic profiles describe transcription factor binding and gene expression measured across a multitude of individual human genomes; identifying a set of candidate variants using a computer system with a processor and a memory, wherein the set of candidate variants are identified by: mapping the genetic variants associated with disease conditions to the DNA motifs associated with transcription factor binding; and determining whether the genetic variants associated with disease conditions affect gene expression by identifying the effect on gene expression of the mapped genetic variants from the quantitative and genetic profiles; generating regulatory impact data for the set of candidate variants using a computer system comprising a processor and a memory, wherein the regulatory impact data indicates the clinical significance of the set of candidate variants, where the clinical significance identifies a disease associated with the effect of the set of candidate variants on gene expression based on the received molecular profiles of disease pathology; and identifying the presence of at least one candidate variant from the set of candidate variants in the obtained genetic sequence data of the individual using a computer system comprising a processor and a memory; and treating the individual for the at least one identified disease based on the clinical significance described by the regulatory impact data associated with the identified at least one candidate variant. ### Claim 2 (depends on 1) The method of claim 1, wherein the quantitative and genetic profiles describe NFkB binding measured across a multitude of individual human genomes, and the DNA motifs associated with transcription factor binding are NFkB motifs. ### Claim 3 (depends on 1) The method of claim 1, further comprising performing genome-wide expression profiling of the individual to confirm the clinical significance of the at least one candidate variant. ### Claim 4 (depends on 9) The method of claim 9, wherein the genome-wide expression profiling includes an RNA sequencing analysis. ### Claim 5 (depends on 1) The method of claim 1, further comprising: determining the impact of the at least one candidate disease variant on disease pathology by comparing the at least one candidate variant to the molecular profiles of disease pathologies using a computer system comprising a processor and a memory. ### Claim 6 (depends on 1) The method of claim 1, wherein the disease is at least one of an autoimmune disease and an inflammatory disease. ### Claim 7 (depends on 1) The method of claim 1, wherein the disease is at least one of Alzheimer's disease, rheumatoid arthritis, type 1 diabetes, systemic lupus erythematosus, asthma, alopecia areata, non-Hodgkin's lymphoma, malaria, drug-induced liver injury, myocardial infarction, and atherosclerosis. ### Claim 8 (depends on 1) The method of claim 1, wherein the genetic material comprises at least one of immunoprecipitated chromatin, genomic DNA, and RNA.