Genome-phenome analyzer and methods of using same
First Claim
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1. A method comprising the steps of:
- (a) providing a plurality of patient findings for a patient being diagnosed in a physical computing device having a representation of a set of candidate diseases,wherein each said patient finding in said plurality is representative of clinical or laboratory information gathered about said patient, and wherein said patient findings comprise genetic sequencing information associated with said patient comprising identification of one or more genetic variants, and for each of said one or more genetic variants, a measure of zygosity for said patient, wherein for each of said one or more genetic variants, a severity score is provided in said plurality of patient findings or said computing device generates said severity score;
(b) using said computing device to generate estimated probabilities of said candidate diseases using said plurality of patient findings and said severity scores for each of said one or more genetic variants;
(c) generating the pertinence of said plurality of patient findings; and
(d) outputting a candidate disease list capable of being displayed and ranked by highest said estimated probabilities and outputting a patient finding list capable of being displayed and ranked by pertinence.
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Abstract
The present invention features methods, devices, and systems, e.g., for providing diagnostic or treatment decision support to a clinician for the diagnosis or treatment of a patient in need thereof or for diagnosing or treating a patient in need thereof.
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Citations
34 Claims
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1. A method comprising the steps of:
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(a) providing a plurality of patient findings for a patient being diagnosed in a physical computing device having a representation of a set of candidate diseases, wherein each said patient finding in said plurality is representative of clinical or laboratory information gathered about said patient, and wherein said patient findings comprise genetic sequencing information associated with said patient comprising identification of one or more genetic variants, and for each of said one or more genetic variants, a measure of zygosity for said patient, wherein for each of said one or more genetic variants, a severity score is provided in said plurality of patient findings or said computing device generates said severity score; (b) using said computing device to generate estimated probabilities of said candidate diseases using said plurality of patient findings and said severity scores for each of said one or more genetic variants; (c) generating the pertinence of said plurality of patient findings; and (d) outputting a candidate disease list capable of being displayed and ranked by highest said estimated probabilities and outputting a patient finding list capable of being displayed and ranked by pertinence. - 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)
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29. A computer readable medium having stored thereon executable instructions for directing a physical computing device to implement a method comprising the steps of:
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(a) providing a plurality of patient findings for a patient being diagnosed, in said physical computing device having a representation of a set of candidate diseases, wherein each said patient finding in said plurality is representative of clinical or laboratory information gathered about said patient, and wherein said patient findings comprise genetic sequencing information associated with said patient comprising identification of one or more genetic variants, and for each of said one or more genetic variants, a measure of zygosity for said patient; (b) generating a severity score for each of said one or more genetic variants; (c) generating estimated probabilities of said candidate diseases using said plurality of patient findings and said severity scores for each of said one or more genetic variants; (d) generating the pertinence of said plurality of patient findings; and (e) outputting a candidate disease list capable of being displayed ranked by highest said estimated probabilities and outputting a patient finding list capable of being displayed and ranked by pertinence.
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30. A physical computing device having a representation of a set of candidate diseases and programmed with executable instructions for directing the device to implement a method comprising the steps of:
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(a) providing a plurality of patient findings for a patient being diagnosed, wherein each said patient finding in said plurality is representative of clinical or laboratory information gathered about said patient, and wherein said patient findings comprise genetic sequencing information associated with said patient comprising identification of one or more genetic variants, and for each of said one or more genetic variants, a measure of zygosity for said patient; (b) generating a severity score for each of said one or more genetic variants; (c) generating estimated probabilities of said candidate diseases using said plurality of patient findings and said severity scores for each of said one or more genetic variants; (d) generating the pertinence of said plurality of patient findings; and (e) outputting a candidate disease list capable of being displayed ranked by highest said estimated probabilities and outputting a patient finding list capable of being displayed and ranked by pertinence.
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31. A method of diagnosing a patient in need thereof, said method comprising the steps of:
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(a) accessing a physical computing device comprising a representation of a set of candidate diseases, wherein; (i) said computing device receives a plurality of patient findings for said patient being diagnosed, wherein each said patient finding in said plurality is representative of clinical or laboratory information gathered about said patient, and wherein said patient findings comprise genetic sequencing information associated with said patient comprising identification of one or more genetic variants, and for each of said one or more genetic variants, a measure of zygosity for said patient, wherein for each of said one or more genetic variants, a severity score is provided in said plurality of patient findings or said computing device generates said severity score; (ii) said computing device generates estimated probabilities of said candidate diseases using said plurality of patient findings and said severity scores for each of said one or more genetic variants; and (iii) said computing device generates the pertinence of said plurality of patient findings; (b) receiving, from said physical computing device, a candidate disease list capable of being displayed ranked by highest said estimated probabilities and a patient finding list ranked by pertinence; and (c) diagnosing said patient as having one or more of said candidate diseases having highest said estimated probabilities.
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32. A method of treating a patient in need thereof, said method comprising the steps of:
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(a) accessing a physical computing device comprising a representation of a set of candidate diseases, wherein; (i) said computing device receives a plurality of patient findings for a patient being diagnosed, wherein each said patient finding in said plurality is representative of clinical or laboratory information gathered about said patient, and wherein said patient findings comprise genetic sequencing information associated with said patient comprising identification of one or more genetic variants, and for each of said one or more genetic variants, a measure of zygosity for said patient, wherein for each of said one or more genetic variants, a severity score is provided in said plurality of patient findings or said computing device generates said severity score; and (ii) said computing device generates estimated probabilities of said candidate diseases using said plurality of patient findings and said severity scores for each of said one or more genetic variants; and (iii) said computing device generates the pertinence of said plurality of patient findings; (b) receiving, from said physical computing device, a candidate disease list capable of being displayed ranked by highest said estimated probabilities and a patient finding list ranked by pertinence; (c) diagnosing said patient as having one or more of said candidate diseases having highest said estimated probabilities; and (d) treating said patient for said one or more of said candidate diseases having highest said estimated probabilities as determined in step (c).
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33. A method comprising providing, in a physical computing device, a representation of a set of candidate diseases, wherein:
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(i) said computing device receives a plurality of patient findings for a patient being diagnosed, wherein each said patient finding in said plurality is representative of clinical or laboratory information gathered about said patient, and wherein said patient findings comprise genetic sequencing information associated with said patient comprising identification of one or more genetic variants, and for each of said one or more genetic variants, a measure of zygosity for said patient, wherein for each of said one or more genetic variants, a severity score is provided in said plurality of patient findings or said computing device generates said severity score; (ii) said computing device generates estimated probabilities of said candidate diseases using said plurality of patient findings and said severity scores for each of said one or more genetic variants; and (iii) said computing device generates the pertinence of said plurality of patient findings; (iv) said computing device outputs a candidate disease list capable of being displayed, ranked by highest said estimated probabilities and outputs a patient finding list capable of being displayed and ranked by pertinence.
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34. A method comprising the steps of:
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(a) receiving, in a physical computing device, a plurality of patient findings for a patient being diagnosed, wherein said patient findings comprise genetic sequencing information associated with said patient comprising identification of one or more genetic variants associated with a gene, and for each, a measure of zygosity for said patient, wherein for each of said one or more genetic variants, a severity score is provided in said plurality of patient findings or said computing device generates said severity score; (b) using said measure of zygosity for each said genetic variant to categorize said one or more genetic variants, in said computing device, as autosomal monoallelic, autosomal biallelic, X-linked monoallelic, X-linked biallelic, Y-linked, or mitochondrial; (c) using said computing device to identify two or more genetic variants each associated with the same gene, said two genetic variants each having monoallelic zygosity, wherein said two or more genetic variants are collectively categorized as possibly having compound heterozygosity; (d) using said computing device to determine a combined severity score for said gene in step (c) corresponding to the lesser of the highest two severity scores of said two or more genetic variants in step (c); (e) repeating steps (c) and (d) for each gene having two or more associated genetic variants; and (f) outputting a list comprising all or a subset of; (i) each said gene having an associated genetic variant identified in step (a), and; (ii) for each said gene having two or more genetic variants identified in step (c), said combined severity score associated with said gene determined in step (d); and
for each said gene having only one genetic variant identified in step (a), said severity score associated with said genetic variant,wherein said list comprises genes with no previously described clinical findings, and wherein said list is capable of being displayed.
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Specification