Patent Document ID: 9946835
Application ID: 13592292
Patent Flag: 1

Claim One:
1. A computer-implemented method for analyzing genetic variants in transcription factor binding sites, comprising: performing a Chromatin Immunoprecipitation-DNA sequencing assay; storing the results of the Chromatin Immunoprecipitation-DNA sequencing assay in a first database; receiving variant data describing information regarding human genetic variants from the first database and storing the information regarding human genetic variants in memory of a computer system comprising a processor and a memory, where the information regarding human genetic variants comprises a genetic variant associated with a disease and a genetic variant coordinate identifying a location on a genetic sequence; receiving transcription factor data describing information regarding binding of transcription factor in a human genome and storing the information regarding binding of transcription factor in a human genome on a memory of a computer system comprising a processor and a memory, where the information regarding binding of transcription factor in a human genome comprises a transcription factor binding event and a transcription factor binding site, and where the transcription factor binding event has been experimentally characterized by a binding intensity indicated by Chromatin immunoprecipitation; determining whether the genetic variant coordinate is found within the transcription factor binding site by querying the transcription factor binding site for the genetic variant coordinate, wherein the transcription factor binding site is a regulatory region in the human genome; storing the determination whether the genetic variant coordinate is found within the transcription factor binding site on a computer system comprising a processor and a memory; determining whether the genetic variant associated with the disease affects the transcription factor binding event based on at least whether the genetic variant coordinate is found within (1) the transcription factor binding site, and (2) the information regarding binding of a transcription factor in a human genome, and (3) the binding intensity of the transcription factor binding event; storing the determination whether the genetic variant associated with the disease affects the transcription factor binding event on a computer system comprising a processor and a memory; annotating a record of a reference sequence stored in a database of experimental results in intergenic and non-coding regions in the human genome with a functional annotation indicating the human genetic variant at the genetic coordinate according to the determination whether the genetic variant associated with the disease affects the transcription factor binding event, where the functional annotation describes the function of a region of the reference sequence, and a clinical relevance of genes being regulated by the region of the reference sequence; obtaining a genetic sequence of a patient; querying the database of experimental results in intergenic and non-coding regions in the human genome for records containing functional annotations indicating human genetic variants that are present in the genetic sequence of the patient; and taking clinical action by treating the patient in accordance with the clinical relevance described by records containing functional annotations received by the query.