Methods and systems for medical sequencing analysis
First Claim
1. A computer-implemented method of identifying elements associated with a trait, the method comprisingselecting a set of discovery samples, wherein the set of discovery samples consist of samples from a single individual, samples from a single pedigree, samples from a subset of a single cohort, or samples from a single cohort;
- identifying, by the computer, variant genetic elements in the discovery samples;
filtering, by the computer, the variant genetic elements to select candidate variant genetic elements, wherein the variant genetic elements are filtered by selecting variant genetic elements that are present in a threshold number of sequence reads, are present in a threshold percentage of sequence reads, are represented by a threshold read quality score at variant base(s), are present in sequence reads from in a threshold number of strands, are aligned at a threshold level to a reference sequence, are aligned at a threshold level to a second reference sequence, are variants that do not have biasing features bases within a threshold number of nucleotides of the variant or a combination;
prioritizing, by the computer, the candidate variant genetic elements to select relevant variant genetic elements; and
identifying, by the computer, an association of a relevant element with a relevant component phenotype of the trait, wherein the relevant element is selected from the relevant variant genetic elements and wherein the relevant element is an element having a threshold value of importance of the element to homeostatis relevant to the trait, intensity of the perturbation of the element, duration of the effect of the element, or a combination, wherein the relevant component phenotype is a component phenotype having a threshold value of severity, age of onset, specificity to the trait, or a combination, and wherein the association of the relevant element with the relevant component phenotype identifies the relevant element as an element associated with the trait.
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Accused Products
Abstract
Disclosed are methods of identifying elements associated with a trait, such as a disease. The methods can comprise, for example, identifying the association of a relevant element (such as a genetic variant) with a relevant component phenotype (such as a disease symptom) of the trait, wherein the association of the relevant element with the relevant component phenotype identifies the relevant element as an element associated with the trait, wherein the relevant component phenotype is a component phenotype having a threshold value of severity, age of onset, specificity to the trait or disease, or a combination, wherein the relevant element is an element having a threshold value of importance of the element to homeostasis relevant to the trait, intensity of the perturbation of the element, duration of the effect of the element, or a combination. The disclosed methods are based on a model of how elements affect complex diseases. The disclosed model is based on the existence of significant genetic and environmental heterogeneity in complex diseases. Thus, the specific combinations of genetic and environmental elements that cause disease vary widely among the affected individuals in a cohort. The disclosed model is an effective, general experimental design and analysis approach for the identification of causal variants in common, complex diseases by medical sequencing. The disclosed model and the disclosed methods based on the model can be used to generate valuable and useful information.
69 Citations
37 Claims
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1. A computer-implemented method of identifying elements associated with a trait, the method comprising
selecting a set of discovery samples, wherein the set of discovery samples consist of samples from a single individual, samples from a single pedigree, samples from a subset of a single cohort, or samples from a single cohort; -
identifying, by the computer, variant genetic elements in the discovery samples; filtering, by the computer, the variant genetic elements to select candidate variant genetic elements, wherein the variant genetic elements are filtered by selecting variant genetic elements that are present in a threshold number of sequence reads, are present in a threshold percentage of sequence reads, are represented by a threshold read quality score at variant base(s), are present in sequence reads from in a threshold number of strands, are aligned at a threshold level to a reference sequence, are aligned at a threshold level to a second reference sequence, are variants that do not have biasing features bases within a threshold number of nucleotides of the variant or a combination; prioritizing, by the computer, the candidate variant genetic elements to select relevant variant genetic elements; and identifying, by the computer, an association of a relevant element with a relevant component phenotype of the trait, wherein the relevant element is selected from the relevant variant genetic elements and wherein the relevant element is an element having a threshold value of importance of the element to homeostatis relevant to the trait, intensity of the perturbation of the element, duration of the effect of the element, or a combination, wherein the relevant component phenotype is a component phenotype having a threshold value of severity, age of onset, specificity to the trait, or a combination, and wherein the association of the relevant element with the relevant component phenotype identifies the relevant element as an element associated with the trait. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37)
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Specification