Genetic Analysis Systems and Methods

Abstract

The present invention provides methods of assessing an individual's genotype correlations by analyzing the individual's genomic profile to a database of medically relevant genetic variations that have been established to correlate to a phenotype.

1 . A method of assessing genotype correlations of an individual comprising:
 a) obtaining a genetic sample of the individual;   b) generating a genomic profile for the individual;   c) determining the individual's genotype correlations with phenotypes by comparing the individual's genomic profile to a current database of human genotype correlations with phenotypes;   d) reporting the results from step c) to the individual or a health care manager of the individual;   e) updating the database of human genotype correlations with an additional human genotype correlation as the additional human genotype correlation becomes known; and   f) updating the individual's genotype correlations by comparing the individual's genomic profile of step c) or a portion thereof to the additional human genotype correlation and determining an additional genotype correlation of the individual; and   g) reporting the results from step f) to the individual or the health care manager of the individual.   
     
     
         2 . The method of  claim 1 , wherein the reporting comprises transmission of the results over a network. 
     
     
         3 . The method of  claim 1 , wherein the reporting of the results is through an on-line portal. 
     
     
         4 . The method of  claim 1 , wherein the reporting of the results is by paper or by e-mail. 
     
     
         5 . The method of  claim 1 , wherein the reporting comprises reporting the results in a secure manner. 
     
     
         6 . The method of  claim 1 , wherein the reporting comprises reporting the results in a non-secure manner. 
     
     
         7 . The method of  claim 1 , wherein the individual's genomic profile is deposited into a secure database or vault. 
     
     
         8 . The method of  claim 1 , wherein the individual is a subscriber. 
     
     
         9 . The method of  claim 1 , wherein the individual is not a subscriber. 
     
     
         10 . The method of  claim 1 , wherein the genetic sample is DNA. 
     
     
         11 . The method of  claim 1 , wherein the genetic sample is RNA. 
     
     
         12 . The method of  claim 1 , wherein the genomic profile is a single nucleotide polymorphism genomic profile, the database of human genotype correlations are human single nucleotide polymorphism correlations, and the additional human genotype correlation is a single nucleotide polymorphism correlation. 
     
     
         13 . The method of  claim 1 , wherein the genomic profile comprises truncations, insertions, deletions or repeats, the database of human genotype correlations are human truncations, insertions, deletions or repeats correlations, and the additional human genotype correlation is a truncation, insertion, deletion or repeat correlation. 
     
     
         14 . The method of  claim 1 , wherein the genomic profile is of the individual's entire genome. 
     
     
         15 . The method of  claim 1 , wherein the method comprises assessing 2 or more genotype correlations. 
     
     
         16 . The method of  claim 1 , wherein the method comprises assessing 10 or more genotype correlations. 
     
     
         17 . The method of  claim 1 , wherein the database of human genotype correlations contains genetic variants in one or more genes listed in Table 1 and phenotypes correlated with the genetic variants. 
     
     
         18 . The method of  claim 1 , wherein the database of human genotype correlations contains genetic variants in one or more genes listed in  FIGS. 4 ,  5 , or  6  and phenotypes correlated with the genetic variants. 
     
     
         19 . The method of  claim 1 , wherein the database of human genotype correlations contains genetic variants determined from the genomic profiles of the individuals and previously determined phenotypes disclosed by the individuals. 
     
     
         20 . The method of  claim 1 , wherein the database of human genotype correlations contains single nucleotide polymorphisms in the genes listed in Table 1 or  FIGS. 4 ,  5 , or  6 , and phenotypes correlated with the single nucleotide polymorphisms. 
     
     
         21 . The method of  claim 1 , wherein the genetic sample is from a biological sample selected from the group consisting of blood, hair, skin, saliva, semen, urine, fecal material, sweat, and buccal sample. 
     
     
         22 . The method of  claim 12 , wherein the genotype correlations are correlations of single nucleotide polymorphisms to diseases and conditions. 
     
     
         23 . The method of  claim 12 , wherein the genotype correlations are correlations of single nucleotide polymorphisms to phenotypes that are not medical conditions. 
     
     
         24 . The method of  claim 13 , wherein the genotype correlations are correlations of truncations, insertions, deletions or repeats to diseases and conditions. 
     
     
         25 . The method of  claim 13 , wherein the genotype correlations are correlations of truncations, insertions, deletions or repeats to phenotypes that are not medical conditions. 
     
     
         26 . The method of  claim 1 , wherein the genomic profile is generated using a high density DNA micro array. 
     
     
         27 . The method of  claim 12 , wherein the single nucleotide polymorphism genomic profile is generated using a high density DNA microarray. 
     
     
         28 . The method of  claim 1 , wherein the genomic profile is generated using genomic DNA sequencing. 
     
     
         29 . The method of  claim 12 , wherein the single nucleotide polymorphism genomic profile is generated using genomic DNA sequencing. 
     
     
         30 . The method of  claim 21 , wherein the genetic sample is genomic DNA and the biological sample is saliva. 
     
     
         31 . A business method of assessing genotype correlations of an individual comprising:
 a) obtaining a genetic sample of the individual;   b) generating a genomic profile for the individual;   c) determining the individual's genotype correlations by comparing the individual's genomic profile to a database of human genotype correlations;   d) providing results of the determining of the individual's genotype correlations to the individual or a health care manager of the individual;   e) updating the database of human genotype correlations with an additional human genotype correlation as the additional human genotype correlation becomes known;   f) updating the individual's genotype correlations by comparing the individual's genomic profile of step c) or a portion thereof to the additional human genotype correlation and determining an additional genotype correlation of the individual; and   g) providing results of the updating of the individual's genotype correlations to the individual or a health care manager of the individual.   
     
     
         32 . The method of  claim 31 , wherein the providing results comprises transmission of the results over a network. 
     
     
         33 . The method of  claim 31 , wherein the results are provided through an on-line portal. 
     
     
         34 . The method of  claim 31 , wherein the results are provided by paper or by e-mail. 
     
     
         35 . The method of  claim 33 , wherein providing the results comprises providing the results in a secure manner. 
     
     
         36 . The method of  claim 33 , wherein the reporting comprises reporting the results in a non-secure manner. 
     
     
         37 . The method of  claim 31 , wherein the individual's genomic profile is deposited into a secure database or vault. 
     
     
         38 . The method of  claim 31 , wherein the individual is a subscriber. 
     
     
         39 . The method of  claim 31 , wherein the individual is not a subscriber. 
     
     
         40 . The method of  claim 31 , wherein the individual or the health care manager sets preferences for the results that are provided to the individual or the health care manager. 
     
     
         41 . The method of  claim 31 , comprising further providing the individual or the health care manager with interpretative and supportive information of the results. 
     
     
         42 . The method of  claim 31 , wherein the genomic profile is a single nucleotide polymorphism genomic profile, the database of human genotype correlations are human single nucleotide polymorphism correlations, and the additional human genotype correlation is a single nucleotide polymorphism correlation. 
     
     
         43 . The method of  claim 31 , wherein the genomic profile comprises truncations, insertions, deletions or repeats, the database of human genotype correlations are human truncations, insertions, deletions or repeats correlations, and the additional human genotype correlation is a truncation, insertion, deletion or repeat correlation. 
     
     
         44 . The method of  claim 31 , wherein the genomic profile is of the individual's entire genome. 
     
     
         45 . The method of  claim 31 , wherein the method comprises assessing 2 or more genotype correlations. 
     
     
         46 . The method of  claim 31 , wherein the method comprises assessing 10 or more genotype correlations. 
     
     
         47 . The method of  claim 31 , wherein the genetic sample is obtained from a biological sample selected from the group consisting of blood, hair, skin, saliva, semen, urine, fecal material, sweat, and buccal sample. 
     
     
         48 . The method of  claim 31 , wherein the database of human genotype correlations contains genetic variants in the genes listed in Table 1 and phenotypes correlated with the genetic variants. 
     
     
         49 . The method of  claim 31 , wherein the database of human genotype correlations contains genetic variants in the genes listed in  FIGS. 4 ,  5 , or  6  and phenotypes correlated with the genetic variants. 
     
     
         50 . The method of  claim 31 , wherein the database of human genotype correlations contains genetic variants determined from the genomic profiles of the individuals and previously determined phenotypes disclosed by the individuals. 
     
     
         51 . The method of  claim 42 , wherein the genotype correlations are correlations of single nucleotide polymorphisms to diseases and conditions. 
     
     
         52 . The method of  claim 42 , wherein the genotype correlations are correlations of single nucleotide polymorphisms to phenotypes that are not medical conditions. 
     
     
         53 . The method of  claim 43 , wherein the genotype correlations are correlations of truncations, insertions, deletions or repeats to diseases and conditions. 
     
     
         54 . The method of  claim 43 , wherein the genotype correlations are correlations of truncations, insertions, deletions or repeats to phenotypes that are not medical conditions. 
     
     
         55 . The method of  claim 31  wherein the genomic profile is generated using a high density DNA microarray. 
     
     
         56 . The method of  claim 42 , wherein the single nucleotide polymorphism genomic profile is generated using a high density DNA microarray. 
     
     
         57 . The method of  claim 31  wherein the genomic profile is generated using genomic DNA sequencing. 
     
     
         58 . The method of  claim 42 , wherein the single nucleotide polymorphism genomic profile is generated using genomic DNA sequencing. 
     
     
         59 . The method of  claim 47 , wherein the genetic sample is genomic DNA and the biological sample is saliva. 
     
     
         60 . A business method of assessing genotype correlations of an individual comprising:
 a) obtaining a genetic sample of the individual;   b) generating a genomic profile for the individual;   c) importing data of the individual's genomic profile;   d) determining the individual's genotype correlations by comparing the individual's genomic profile to a database of human genotype correlations;   e) providing results of the determining of the individual's genotype correlations to the individual of a health care manager of the individual;   f) updating the database of human genotype correlations with an additional human genotype correlation as the additional human genotype correlation becomes known;   g) updating the individual's genotype correlations by comparing the individual's genomic profile or a portion thereof to the additional human genotype correlation and determining an additional genotype correlation of the individual; and   h) providing results of the updating of the individual's genotype correlations to the individual or the health care manager of the individual.   
     
     
         61 . The method of  claim 60 , wherein providing the results comprises providing the results in a secure manner. 
     
     
         62 . The method of  claim 60 , wherein providing the results comprises transmission of the results over a network. 
     
     
         63 . A method comprising:
 a) providing a rule set comprising rules, each rule indicating a correlation between at least one genotype and at least one phenotype;   b) providing a data set comprising genomic profiles of each of a plurality of individuals, wherein each genomic profile comprises a plurality of genotypes;   c) periodically updating the rule set with at least one new rule, wherein the at least one new rule indicates a correlation between a genotype and a phenotype not previously correlated with each other in the rule set; and   d) applying each new rule to the genomic profile of at least one of the individuals, thereby correlating at least one genotype with at least one phenotype for the individual.   
     
     
         64 . The method of  claim 63  further comprising:
 e) generating a report comprising the phenotype profile of the individual.   
     
     
         65 . The method of  claim 63  further comprising, after step (b),
 i) applying the rules of the rule set to the genomic profiles of the individuals to determine a set of phenotype profiles for the individuals; and   ii) generating a report comprising an initial phenotype profile of the individual.   
     
     
         66 . The method of  claim 64  or  65 , wherein providing the report comprises transmission of the report over a network. 
     
     
         67 . The method of  claim 64  or  65 , wherein providing the report comprises transmission of the report over a network to the individual or a health care manager of the individual. 
     
     
         68 . The method of  claim 64  or  65 , wherein the report is provided in a secure manner. 
     
     
         69 . The method of  claim 64  or  65 , wherein the report is provided in a non-secure manner. 
     
     
         70 . The method of  claim 64  or  65 , wherein the report is provided through an on-line portal. 
     
     
         71 . The method of  claim 64  or  65 , wherein the report is provided by paper or e-mail. 
     
     
         72 . The method of  claim 63 , wherein the new rule correlates an uncorrelated genotype with a phenotype. 
     
     
         73 . The method of  claim 63 , wherein the new rule correlates a correlated genotype with a phenotype with which it was not previously correlated in the rule set. 
     
     
         74 . The method of  claim 63 , wherein the new rule modifies a rule in the rule set. 
     
     
         75 . The method of  claim 63 , wherein the new rule is generated by correlation of a genotype from the genomic profiles of the individuals and a previously determined phenotype of the individuals. 
     
     
         76 . The method of  claim 63 , wherein the rules correlate a plurality of genotypes with a phenotype. 
     
     
         77 . The method of  claim 63 , wherein applying the new rule further comprises determining the phenotype profile at least in part based on a characteristic of the individual selected from ethnicity, ancestry, geography, gender, age, family history, and previously determined phenotypes. 
     
     
         78 . The method of  claim 63 , wherein the genotypes comprise nucleotide repeats, nucleotide insertions, nucleotide deletions, chromosomal translocations, chromosomal duplications, or copy number variations. 
     
     
         79 . The method of  claim 78 , wherein the copy number variations are microsatellite repeats, nucleotide repeats, centromeric repeats, or telomeric repeats. 
     
     
         80 . The method of  claim 63 , wherein the genotypes comprise single nucleotide polymorphisms. 
     
     
         81 . The method of  claim 63 , wherein the genotypes comprise haplotypes and diplotypes. 
     
     
         82 . The method of  claim 63 , wherein the genotypes comprise genetic markers in linkage disequilibrium with single nucleotide polymorphisms correlated with a phenotype. 
     
     
         83 . The method of  claim 63 , wherein the phenotype profile indicates a presence or absence of the quantitative trait or a risk developing the quantitative trait. 
     
     
         84 . The method of  claim 63 , wherein the phenotype profile indicates a probability that an individual with a genotype has or will have a phenotype. 
     
     
         85 . The method of  claim 84 , wherein the probability is high, moderate, or low. 
     
     
         86 . The method of  claim 63 , wherein the correlations are curated. 
     
     
         87 . The method of  claim 63  wherein the rule set comprises at least  20  rules. 
     
     
         88 . The method of  claim 63  wherein the rule set comprises at least  50  rules. 
     
     
         89 . The method of  claim 63  wherein the rule set comprises rules based on the genotype correlations in Table 1. 
     
     
         90 . The method of  claim 63  wherein the rule set comprises rules based on the genotype correlations in  FIGS. 4 ,  5 , or  6 . 
     
     
         91 . The method of  claim 63 , wherein the phenotype comprises a quantitative trait. 
     
     
         92 . The method of  claim 91 , wherein the quantitative trait comprises a medical condition. 
     
     
         93 . The method of  claim 92 , wherein the phenotype profiles indicates a presence or absence of the medical condition, a risk of developing the medical condition, a prognosis of the medical condition, an effectiveness of a treatment for the medical condition, or a response to a treatment of the medical condition. 
     
     
         94 . The method of  claim 91 , wherein the quantitative trait comprises a phenotype that is not a medical condition. 
     
     
         95 . The method of  claim 91 , wherein the quantitative trait is selected from the group consisting of: physical trait, physiological trait, mental trait, emotional trait, ethnicity, ancestry, or age. 
     
     
         96 . The method of  claim 63 , wherein the individuals are humans. 
     
     
         97 . The method of  claim 63 , wherein the individuals are subscribers. 
     
     
         98 . The method of  claim 63 , wherein the individuals are not subscribers. 
     
     
         99 . The method of  claim 63 , wherein the individuals are non-humans. 
     
     
         100 . The method of  claim 63 , wherein the genomic profile comprises at least 100,000 genotypes. 
     
     
         101 . The method of  claim 63 , wherein the genomic profile comprises at least 400,000 genotypes. 
     
     
         102 . The method of  claim 63 , wherein the genomic profile comprises at least 900,000 genotypes. 
     
     
         103 . The method of  claim 63 , wherein the genomic profile comprises at least 1,000,000 genotypes. 
     
     
         104 . The method of  claim 63 , wherein the genomic profile comprises a substantially complete entire genomic sequence. 
     
     
         105 . The method of  claim 63 , wherein the data set comprises a plurality of data points, wherein each data point relates to an individual and comprises a plurality of data elements, wherein the data elements include at least one element selected from a unique identifier, genotype information, microarray SNP identification number, SNP rs number, chromosome position, polymorphic nucleotide, quality metrics, raw data files, images, extracted intensity scores, physical data, medical data, ethnicity, ancestry, geography, gender, age, family history, known phenotypes, demographic data, exposure data, lifestyle data, and behavior data, of the individual. 
     
     
         106 . The method of  claim 63 , wherein periodically updating and applying occurs at least once a year. 
     
     
         107 . The method of  claim 63 , wherein providing the data set comprises obtaining a genomic profile of each of a plurality of individuals by:
 (i) performing a genetic analysis on a genetic sample from the individuals and   (ii) encoding the analysis in computer readable format.   
     
     
         108 . The method of  claim 63 , wherein the phenotype profile comprises a monogenic phenotype. 
     
     
         109 . The method of  claim 63 , wherein the phenotype profile comprises a multigenic phenotype. 
     
     
         110 . The method of  claim 63 , wherein the report comprises an initial phenotype profile. 
     
     
         111 . The method of  claim 63 , wherein the report comprises an updated phenotype profile. 
     
     
         112 . The method of  claim 63 , wherein the report further comprises information on the phenotypes of the phenotype profile selected from one or more of the following: prevention strategies, wellness information, therapies, symptom awareness, early detection schemes, intervention schemes, and refined identification and sub-classification of the phenotypes in the phenotype profile. 
     
     
         113 . The method of  claim 63 , further comprising:
 a) adding a new genomic profile of a new individual into the individual data set;   b) applying the rule set to the genomic profile of the new individual; and   c) generating an initial report of a phenotype profile for the new individual.   
     
     
         114 . The method of  claim 63 , further comprising:
 a) adding a new genomic profile of the individual;   b) applying the rule set to the new genomic profile the individual; and   c) generating a new report of a phenotype profile for the individual.   
     
     
         115 . A system comprising:
 a) a rule set comprising rules, each rule indicating a correlation between at least one genotype and at least one phenotype;   b) code that periodically updates the rule set with at least one new rule, wherein the at least one new rule indicates a correlation between a genotype and a phenotype not previously correlated with each other in the rule set;   c) a database comprising genomic profiles of a plurality of individuals;   d) code that applies the rule set to the genomic profiles of individuals to determine phenotype profiles for the individuals; and   e) code that generates reports for each individual.   
     
     
         116 . The system of  claim 115 , wherein the report is transmitted over a network. 
     
     
         117 . The system of  claim 115 , wherein the report is transmitted over a network to the individual or health care manager of the individual. 
     
     
         118 . The system of  claim 115 , wherein the report is provided in a secure manner. 
     
     
         119 . The system of  claim 115 , wherein the reports is provided in a non-secure manner. 
     
     
         120 . The system of  claim 115 , wherein the report is provided through an on-line portal. 
     
     
         121 . The system of  claim 115 , wherein the report is provided by paper or e-mail. 
     
     
         122 . The system of  claim 115 , further comprising code that notifies the individual of new or revised correlations. 
     
     
         123 . The system of  claim 115 , further comprising code that notifies the individual of new or revised rules that can be applied to the genomic profile of the individual. 
     
     
         124 . The system of  claim 115 , further comprising code that notifies the individual of new or revised prevention and wellness information for the phenotypes of the phenotype profile of the individual. 
     
     
         125 . A kit comprising:
 a) at least one sample collection container;   b) instructions for obtaining a sample from an individual;   c) instructions for accessing a genomic profile of the individual obtained from the sample through an on-line portal;   d) instructions for accessing a phenotype profile of the individual obtained from the sample through an on-line portal; and   e) packaging for delivery of the sample collection container to the sample processing facility.   
     
     
         126 . An on-line portal comprising a website where a individual can access their phenotype profile, wherein the website allows the individual to do at least one of the following:
 a) choose the rules to be applied to the individual's genomic profile;   b) view initial and updated reports on the website;   c) print initial and updated reports from the website;   d) save initial and updated reports from the website onto the individual's computer;   e) obtain prevention and wellness information on the individual's phenotype profile;   f) obtain on-line or telephone-linked genetic counseling;   g) extract information to share with physicians/genetic counselors;   h) access to partner service and product offerings.   
     
     
         127 . The on-line portal of  claim 126 , wherein the information is transmitted over a network. 
     
     
         128 . The on-line portal of  claim 126 , wherein the information is transmitted over a network to the individual or health care manager of the individual. 
     
     
         129 . The on-line portal of  claim 126  wherein the website is secure. 
     
     
         130 . The on-line portal of  claim 126  wherein the website is not secure. 
     
     
         131 . The on-line portal of  claim 126  wherein the individual is presented with one or more options regarding the level of security of such individuals' information or one or more portions thereof. 
     
     
         132 . The on-line portal of  claim 126  wherein the phenotype profile comprises an actionable medical condition. 
     
     
         133 . The on-line portal of  claim 126  wherein the phenotype profile comprises a medical condition with no existing preventive actions or existing therapies. 
     
     
         134 . The on-line portal of  claim 126  wherein the phenotype profile comprises non medical conditions. 
     
     
         135 . The on-line portal of  claim 126  further comprising a search engine.