System, method and apparatus to enhance privacy and enable broad sharing of bioinformatic data

Abstract

A system, method and apparatus for enabling individuals to determine their sharing, privacy, and data access preferences and conditions for disclosure of bioinformatic data, including whole genome sequence data over a network. In combination with a privacy preferences repository and policy repository for expressing legal and institutional criteria for accessing such information, a private access bureau enables such privacy requirements to be addressed while simultaneously enabling broad sharing of such data by and with properly authorized parties or applications. Through the use of various forms of metadata, encryption, and globally unique IDs that accompany such data elements, discrete segments of said data can be queried; and where permissible discovered, accessed, analyzed, viewed, linked with other health data and contact details, used, and/or exported based on pertinent privacy laws, institutional policies, and the individual's preferences that are associated with, and dynamically controlled through, an intuitive user interface.

What is claimed is: 
     
         1 . A computer implemented method for selectively designating segments of bioinformatic data in an electronic document, the method comprising the steps of:
 (a) receiving a command by at least one computer from a party wishing to designate such segments identifying at least one portion of an electronic document to be subject to access control;   (b) presenting, by said at least one computer, a set of selectable access control directives defining conditions for access to said at least one portion of said electronic document, said selectable access control directives selected and controlled by the holder of privacy rights of said document;   (c) receiving, from said party wishing to designate such segments by said at least one computer, selectable access control directives; and   (d) imposing access control of said at least one portion by said at least one computer in accordance with said conditions in response to receiving said selectable access control directives.   
     
     
         2 . The method of  claim 1 , wherein said selectable access control directives minimally consists of designate said at least one portion, allow access to at least one portion of said bioinformatic data, prohibit access to said at least one portion of said bioinformatic data, and query said holder of privacy rights of said document for direction as to whether to allow or prohibit access thereto. 
     
     
         3 . The method of  claim 1 , wherein said steps of presenting a set of selectable access control directives comprises providing a privacy menu on a document viewing user interface. 
     
     
         4 . The method of  claim 3 , wherein said step of receiving selective directives comprises receiving mouse clicks on said privacy menu to identify selected directives. 
     
     
         5 . The method of  claim 3 , further comprising: displaying, on a user interface display by said computer, said privacy menu in response to said holder of privacy rights of said document hovering a mouse over said at least one portion presented on said user interface display. 
     
     
         6 . A system for selectively designating segments of bioinformatic data in an electronic document comprising:
 (a) at least one computer configured to receive from a party wishing to designate segments of bioinformatic data, selected directives of a set of selectable access control directives;   (b) receive a command from the person to whom said bioinformatic data pertains or said person's designated representative designating such segments of said electronic document so as to identify at least one portion of said bioinformatic data to be subject to access control;   (c) present a set of selectable access control directives defining conditions for access to said at least one portion of said bioinformatic data;   (d) receive selected directives of said set of selectable access control directives; and   (e) impose access control of said at least one portion of said bioinformatic data in accordance with said conditions in response to receiving said selective access control directives.   
     
     
         7 . The system of  claim 6 , wherein said set of selectable access control directives defining conditions for access to said at least one portion of said bioinformatic data minimally consists of allow access to at least one portion of said bioinformatic data, prohibit access to said at least one portion of said bioinformatic data, and query the person to whom said bioinformatic data pertains (or that person's designated representative) for direction as to whether to allow or prohibit said proposed access. 
     
     
         8 . The system of  claim 6 , wherein said sat least one computer is further configured to present a privacy menu on a document viewing user interface. 
     
     
         9 . The method of  claim 8 , wherein said at least one computer is further configured to receive mouse clicks on said privacy menu to identify selected directives. 
     
     
         10 . The system of  claim 6 , wherein said bioinformatic data is a genome, and said designated segments are chromosomes comprising said genome. 
     
     
         11 . The system of  claim 10 , wherein said bioinformatic data is metadata concerning variants identified on the chromosomes, and said designated segments are the said metadata indicating for each of said chromosomes the name of any gene located on said chromosome wherein a variant is identified. 
     
     
         12 . The system of  claim 10 , wherein said bioinformatic data is meta-metadata concerning whether or not any variants are identified on the chromosomes, and said designated segments are the said meta-metadata indicating in a binary expression for each said chromosome if there is at least one gene located on said single chromosome wherein a variant is identified. 
     
     
         13 . The system of  claim 6 , wherein said bioinformatic data is a genome, and said designated segments are all of the sub-bands of all of the chromosomes comprising said genome. 
     
     
         14 . The system of  claim 13 , wherein said bioinformatic data is metadata concerning variants identified within the sub-bands of the chromosomes, and said designated segments are the said metadata indicating for each of said chromosomal sub-band the name of any gene located within said single chromosomal sub-band wherein a variant is identified. 
     
     
         15 . The system of  claim 13 , wherein said bioinformatic data is meta-metadata concerning whether or not any variants are identified within the sub-bands of the chromosomes, and said designated segments are the said meta-metadata indicating in a binary expression for each said chromosomal sub-band if there is at least one gene located within said single chromosomal sub-band wherein a variant is identified. 
     
     
         16 . The system of  claim 6 , wherein said bioinformatic data is a genome or exome, and said designated segments are all of the genes located within said genome or exome. 
     
     
         17 . The system of  claim 16 , wherein said bioinformatic data is metadata concerning variants identified within said genes, and said designated segments are the said metadata indicating for each of said genes the name of any variants located within said genes wherein at least one variant is identified. 
     
     
         18 . The system of  claim 16 , wherein said bioinformatic data is meta-metadata concerning whether or not any variants are identified within said genes, and said designated segments are the said meta-metadata indicating in a binary expression for each one of said genes if there is at least one variant identified 
     
     
         19 . The system of  claim 6 , wherein said bioinformatic data is a genome or exome, and said designated segments are all of the SNPs located within said genome or exome. 
     
     
         20 . The system of  claim 19 , wherein said bioinformatic data is metadata concerning variants identified within the base pairs comprising said genome or exome, and said designated segments are the said metadata indicating for each of said SNPs any variants located within said base pairs wherein at least one variant is identified. 
     
     
         21 . The system of  claim 19 , wherein said bioinformatic data is meta-metadata concerning whether or not any variants are identified within said base pairs, and said designated segments are the said meta-metadata indicating in a binary expression for each one of said SNPs where there is at least one variant identified. 
     
     
         22 . The system of  claim 6 , wherein said bioinformatic data is a genome or exome, and said designated segments are the genes and SNPs that are suspected to be associated with a particular medical diagnosis, condition or disorder. 
     
     
         23 . The system of  claim 22 , wherein said bioinformatic data is metadata concerning variants identified within any of said genes or SNPs that are suspected to be associated with a particular medical diagnosis, condition or disorder, and said designated segments are the said metadata indicating for each of said diagnosis, condition or disorder the name of the genes and/or SNPs that are affected and the name of any variants located within said one or more genes or SNPs wherein at least one variant is identified. 
     
     
         24 . The system of  claim 22 , wherein said bioinformatic data is meta-metadata concerning whether or not any variants are identified within any of the genes or SNPs that are suspected to be associated with a particular medical diagnosis, condition or disorder, and said designated segments are the said meta-metadata indicating in a binary expression for each one of said diagnosis, condition or disorder, if there is at least one genes or SNP where a variant is identified. 
     
     
         25 . The system of  claim 6 , wherein said bioinformatic data is a genome or exome, and said designated segments are the genes and SNPs suspected to be associated with a particular symptom, medical sign, or relevance to drug responsiveness. 
     
     
         26 . The system of  claim 25 , wherein said bioinformatic data is metadata concerning variants identified within any of said genes or SNPs that are suspected to be associated with a particular symptom, medical sign, or relevance to drug responsiveness and said designated segments are the said metadata indicating for each of said symptom, medical sign, or relevance to drug responsiveness, the name of the genes and/or SNPs that are affected and the name of any variants located within said one or more genes or SNPs wherein at least one variant is identified. 
     
     
         27 . The system of  claim 25 , wherein said bioinformatic data is meta-metadata concerning whether or not any variants are identified within any of the genes or SNPs that are suspected to be associated with a particular symptom, medical sign, or relevance to drug responsiveness, and said designated segments are the said meta-metadata indicating in a binary expression for each one of said symptom, medical sign, or relevance to drug responsiveness, if there is at least one genes or SNP where a variant is identified. 
     
     
         28 . An apparatus for identifying segments of bioinformatic data and associating selectable access control directives as a step of a sequence analysis pipeline on genomic data, such apparatus comprising:
 (a) an integrated circuit comprising a set of hardwired digital logic circuits that are interconnected by a plurality of physical electrical interconnects, one or more of the plurality of physical electrical interconnects comprising an input for receiving the plurality of reads of genomic data;   (b) said set of hardwired digital logic circuits being in a wired configuration to access an index of the one or more genetic reference sequences via one of the plurality of physical electrical interconnects, and to map the plurality of reads to one or more segments of the one or more genetic reference sequences according to said index;   (c) configuring the set of hardwired digital logic circuits to extract one or more components of said genetic data from the plurality of reads of genetic data;   (d) configuring the set of hardwired digital logic circuits to encrypt said one or more components; and   (e) assigning a GUID to said encrypted one or more components to generate a globally-unique address for each of said one or more components.   
     
     
         29 . The apparatus of  claim 28 , wherein said one or more components include all of the chromosomes, each chromosome being assigned a GUID, and the unencrypted content of such GUIDs collectively comprising the subject's genome or exome; 
     
     
         30 . The apparatus of  claim 28 , wherein said one or more components include all of the regions, bands and sub-bands of all of the chromosomes, each such region, band and/or sub-band being assigned a GUID, and the unencrypted content of such GUIDs collectively comprising the subject's genome or exome; 
     
     
         31 . The apparatus of  claim 28 , wherein said one or more components include all of the genes, each such gene being assigned a GUID, and the unencrypted content of such genes collectively comprising the subject's genome or exome; 
     
     
         32 . The apparatus of  claim 28 , wherein said one or more components include all of the base pairs, each such base pair being assigned a GUID, and the unencrypted content of such base pairs collectively comprising the subject's genome or exome;