Method and system for genomic visualization

Abstract

A method and system for correlating genome data with EMR/MR data is disclosed herein. The method includes identifying a plurality of sources of genome data. The method also includes generating an index file for each of the plurality of genome files. The method also includes transmitting each index file to a central depository. The method also includes identifying electronic medical record (EMR) and/or personal health record (PHR) data at each source of the plurality of sources of genome data. The method also includes correlating each genome file of the plurality of genome files with a corresponding EMR/MR data.

We claim as our invention the following: 
     
         1 . A method for correlating genome data from a subject with one or more of electronic medical record (EMR) data and personal health record (PHR) data from the subject, the method comprising:
 receiving, at a distributed server, via an internet network connection, a genome file specific to the subject, the genome file comprising at least a variant call file (VCF);   indexing and encrypting, by the distributed server, the subject's genome file, the subject's genome file being associated with a first De-identified Identifier (DID);   generating and encrypting, by the distributed server, an index file for the genome file;   transmitting, via the internet network connection, one or more of the genome file and the index file to a central depository for storage thereby;   receiving, at the central depository, via the internet network connection, the one or more of EMR and PHR data for the subject;   generating, at the central depository, a second DID for the received one or more of EMR and PHR data, where the second DID corresponds to the first DID; and   correlating at least one of the genome file and the index file of the subject with one or more corresponding EMR and PHR data;   wherein an algorithm utilized to generate the DID for the genome file is also used for generating the DID for the one or more of the EMR and PHR data allowing for matching based on the DID.   
     
     
         2 . The method according to  claim 1 , wherein the one or more of EMR and PHR data comprises phenotypic data. 
     
     
         3 . The method according to  claim 1 , wherein the index file is searchable at a chromosome level, exome level, gene level, allele panel, or at an individual SNP or allele level. 
     
     
         4 . The method according to  claim 1 , wherein the genome file is capable of being tracked and controlled by an owner of the genome file. 
     
     
         5 . The method according to  claim 1 , wherein the genome file is generated by processing sequence data to generate a sequenced data file, processing the sequenced data file to generate mapped data file, processing the mapped data to generate an aligned data file, and processing the aligned data file to generate a variant called data file (VCF). 
     
     
         6 . The method according to  claim 5 , wherein generating the index file comprises processing sequence data to generate one or more of a BCL and a FASTQ file, processing the BCL or FASTQ file to generate one or more of a sequence alignment map (SAM) and a binary sequence alignment map (BAM) file, and processing one or more of the SAM and BAM file to generate a variant call file (VCF). 
     
     
         7 . The method according to  claim 6 , further comprising encrypting the VCF. 
     
     
         8 . The method according to  claim 1 , further comprises searching the index file for a specific anomaly. 
     
     
         9 . The method according to  claim 1 , further comprising brokering the index file and the one or more EMR and PHR data. 
     
     
         10 . A system for searching correlated genome data and one or more electronic medical record (EMR) data and personal health record (PHR) data from a subject, the system comprising:
 a distributed server for receiving genomic data from a subject, the genomic data being specific to the subject and comprising a variant call file, the distributed server being configured for indexing the subject's genomic data and for encrypting one or more of the genomic data and a generated index file, the genomic data and the index file of the subject being associated with a first DID, the distributed server having an internet network connection for receiving and transmitting the genomic data and the generated index file;   a source for the one or more EMR and PHR data files, comprising a database for encrypting and storing the EMR and PHR data files of the subject, the encrypted EMR and PHR data files having a second DID, the source having an internet network connection for transmitting the encrypted EMR and PHR files, wherein the first DID corresponds to the second DID; and   a central depository server, associated with both the distributed server and the source for EMR and PHR data files via the internet network connection, and configured for receiving and decrypting one or more of the genomic data and the index files from the distributed server, and for receiving and decrypting the EMR and PHR data files from the source, and further configured for associating the one or more of the genomic data and index file with one or more of the EMR and PHR files based on their respective DIDs;   a browser for searching one or more of the genomic data and the index file and the one or more EMR and PHR files;   wherein an algorithm utilized to generate the DID for the one or more of the genomic data and the index file is also used for generating the unique DID for the one or more EMR and PHR files allowing for matching based on the DID number.   
     
     
         11 . The system according to  claim 10 , wherein the EMR and PHR data comprises phenotypic data. 
     
     
         12 . The system according to  claim 10 , wherein the one or more of genomic data and index file is searchable at a chromosome level, exome level, gene level, allele panel, or at an individual SNP or allele level. 
     
     
         13 . The system according to  claim 10 , wherein one or more of the genomic data, the index file, the EMR and PHR data files is capable of being tracked and controlled by the subject. 
     
     
         14 . The system according to  claim 10 , wherein the genomic data is generated and received from one or more sources of genomic data. 
     
     
         15 . The system according to  claim 14 , wherein the generating of genomic data comprises processing sequence data to generate a sequenced data file, processing the sequenced data file to generate a mapped data file, and processing the mapped data file to generate an aligned data file, and processing the aligned data file to generate a variant called data file (VCF). 
     
     
         16 . The system according to  claim 15 , wherein the generating of the genomic data comprises processing sequence data to generate one or more of a BCL and FASTQ file, processing the BCL and FASTQ file to generate one or more of a binary sequence alignment map (BAM) or sequence alignment map (SAM) file, and processing the one or more BAM and SAM file to generate the variant call file (VCF). 
     
     
         17 . The system according to  claim 16 , wherein one or more of the BCL, FASTQ, BAM, SAM, and VCF is encrypted. 
     
     
         18 . The system according to  claim 11 , further comprising a privacy control engine configured to allow an owner of one or more of the encrypted genomic data, index file, EMR and PHR files to track and control access thereto. 
     
     
         19 . A system for searching correlated genomic data and one or more electronic medical record (EMR) data and personal health record (PHR) data files from a subject, the system comprising:
 a distributed server, having an internet network connection for receiving one or more of a FASTQ and a BCL file, the FASTQ or BCL file comprising genetic sequence data from a subject, the genetic sequence data comprising a first sequence of nucleotides, the distributed server being associated with a database storing a reference genome sequence, the reference genome sequence comprising a second sequence of nucleotides, and the distributed server being configured for performing each of a mapping operation, an alignment operation, and a variant calling operation on the genomic sequencing data in comparison to the reference genome sequence to produce a genome file, the genome file being specific to the subject and comprising a variant call file, the distributed server further being configured for encrypting the subject's genome file, associating the genome file with a first DID unique to the subject, and transmitting the encrypted file;   a source for encrypting and storing one or more EMR and PHR data files of the subject, the encrypted EMR and PHR data files having a second DID unique to the subject, the source having an internet network connection for transmitting the encrypted EMR and PHR data files, wherein the first DID matches the second DID; and   a central depository server, associated with both the distributed server and the source for EMR and PHR data files via the internet network connection, and configured for receiving and decrypting the genome file from the distributed server, and for receiving and decrypting the EMR and PHR files from the source, and further configured for associating the genome file with the one or more EMR and PHR data files based on their respective DIDs;   wherein, an algorithm utilized to generate the DID for the genome file is also used for generating the DID for the one or more EMR and PHR files allowing for matching based on the DID number.   
     
     
         20 . The system according to  claim 19 , wherein one or more of the genomic data, the index file, the EMR and PHR data files is capable of being tracked and controlled by the subject.