{"search_session":{},"preferences":{"l":"en","queryLanguage":"en"},"patentId":"064-320-762-728-247","frontPageModel":{"patentViewModel":{"ref":{"entityRefId":"064-320-762-728-247","entityRefType":"PATENT"},"entityMetadata":{"linkedIds":{"empty":true},"tags":[],"collections":[{"id":11704,"type":"PATENT","title":"The Chinese University of Hong Kong - Patent Portfolio","description":"","access":"OPEN_ACCESS","displayAvatar":true,"attested":false,"itemCount":2452,"tags":[],"user":{"id":91044780,"username":"Cambialens","firstName":"","lastName":"","created":"2015-05-04T00:55:26.000Z","displayName":"Cambialens","preferences":"{\"usage\":\"public\",\"beta\":false}","accountType":"PERSONAL","isOauthOnly":false},"notes":[{"id":8358,"type":"COLLECTION","user":{"id":91044780,"username":"Cambialens","firstName":"","lastName":"","created":"2015-05-04T00:55:26.000Z","displayName":"Cambialens","preferences":"{\"usage\":\"public\",\"beta\":false}","accountType":"PERSONAL","isOauthOnly":false},"text":"
Search Applicants and Owners separately: chinese uni* Kong
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identifying a plurality of subpopulation informative genes including:\n\nat least one subpopulation target gene; and\nat least one subpopulation reference gene having a lower biological variation relative to the subpopulation target gene, each of the plurality of subpopulation informative genes identified as having at least a predetermined percentage of its transcripts in one or more calibration samples of the cell mixture contributed by the cells of the first subpopulation, the cell mixture containing a plurality of different subpopulations of cells, the predetermined percentage being equal to or greater than 50%;\n
performing one or more reactions involving the cell mixture sample;\n
measuring signals corresponding to the plurality of subpopulation informative genes from the one or more reactions involving the cell mixture sample, wherein the signals are proportional to amounts of transcripts of the plurality of subpopulation informative genes in the cell mixture sample;\n
receiving, at a computer system, the signals obtained from the measurement of the cell mixture sample;\n
using the signals to determine, with the computer system, a first amount of transcripts of the at least one subpopulation target gene in the cell mixture sample and a second amount of transcripts of the at least one subpopulation reference gene in the cell mixture sample; and\n
calculating a parameter that is a relative value of the first amount to the second amount, the parameter providing a measurement of an amount of genomic expression of the subpopulation target gene in the first subpopulation of cells of the cell mixture sample."],"number":1,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the one or more reactions involve polymerase chain reaction (PCR), microarray, or sequencing."],"number":2,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, further comprising:\n
comparing the parameter to one or more cutoff values to determine a classification of the cell mixture sample."],"number":3,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 3, wherein the classifications include whether the cell mixture sample is in a diseased state or a non-diseased state."],"number":4,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 4, wherein a range of values are associated with the non-diseased state."],"number":5,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein identifying the plurality of subpopulation informative genes for the first subpopulation includes:\n
receiving data regarding expression of a plurality of genes in the first subpopulation of cells and regarding expression of the plurality of genes in one or more calibration cell mixtures corresponding to the one or more calibration samples;\n
identifying a first set of genes that are expressed in the first subpopulation of cells based on the data;\n
receiving a proportional cell count of the first subpopulations of cells in the one or more calibration cell mixtures; and\n
analyzing the data to determine:\n\na first expression level for each of the first set of genes in the one or more calibration cell mixtures; and\na respective expression level for each of the first set of genes in the first subpopulation; and\n
for each of the genes in the first set:\n"],"number":6,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein identifying the plurality of subpopulation informative genes for the first subpopulation includes:\nusing the proportional cell count and the respective expression level to determine whether the first subpopulation contributes at least the predetermined percentage of transcripts of the respective gene in the one or more calibration cell mixtures relative to the first expression level.\n
receiving data regarding which of a plurality of genes are expressed in different subpopulations of cells in one or more calibration cell mixtures corresponding to the one or more calibration samples;\n
receiving a respective proportional cell count of each of the different subpopulations in the one or more calibration cell mixtures, the respective proportional cell counts including a first proportional cell count P(1) for the first subpopulation;\n
identifying a first set of genes that are expressed in the first subpopulation of cells based on the data;\n
for each of the genes in the first set:\n\n\nEP(1)*P(1)≥C%(1-C%)∑i=2NEp(i)*P(i)\nanalyzing the data to determine a respective expression level for the respective gene in each of the different subpopulations in which the respective gene is expressed, the respective expression level including a first expression level Ep(1) for the first subpopulation;\nusing the equation\n
\n"],"number":7,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the first subpopulation is selected from a group consisting of neutrophils, lymphocytes, monocytes, eosinophils, basophils, natural killer cells, CD3 total T cells, CD4 T cells, CD8 T cells, and , B cell lymphocytes."],"number":8,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the predetermined percentage is 66% or 75%."],"number":9,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the first subpopulation is B lymphocytes and the cell mixture sample is a blood sample, wherein the at least one subpopulation reference gene includes at least one selected from: TNFRSF13 C, KLHL14, and FREB."],"number":10,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the first subpopulation is T lymphocytes and the cell mixture sample is a blood sample, wherein the at least one subpopulation reference gene includes GIMAP7 and/or LRRN3."],"number":11,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the first subpopulation is granulocytes and the cell mixture sample is a blood sample, wherein the at least one subpopulation reference gene includes AQP1 and/or SOD2."],"number":12,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein identifying a subpopulation reference gene for the first subpopulation includes\nto determine whether the first subpopulation contributes at least the predetermined percentage of transcripts of the respective gene in the one or more calibration cell mixtures, where N is an integer corresponding to a number of subpopulation in which the respective gene is expressed, and C % is the predetermined percentage.\n
receiving, at a computer, data regarding which of a plurality of genes are expressed in the first subpopulation of cells in a plurality of cell-mixture samples corresponding to the calibration samples, each cell-mixture sample containing a plurality of different subpopulations of cells;\n
identifying, by the computer, a first set of genes that are expressed in the first subpopulation of cells based on the data;\n
analyzing, with the computer, the data to determine a respective expression level for each of the first set of genes in each of a plurality of first subpopulation samples, each first subpopulation sample being from a different cell-mixture sample of a different subject;\n
identifying a subset of subpopulation genes that each have at least a predetermined percentage of their respective transcripts in the plurality of cell-mixture samples contributed by the cells of the first subpopulation, the predetermined percentage being equal to or greater than 50%, wherein the identifying uses the respective expression levels; and\n
analyzing respective expression levels of the subset of subpopulation genes to identify at least one subpopulation reference gene that has a variance of expression levels among the first subpopulation samples of less than a threshold."],"number":13,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 13, further comprising:\n
determining a coefficient of variance of the gene expression level as the variance of expression level, wherein threshold is predetermined and is one hundred percent."],"number":14,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 13, further comprising:\n
determining a coefficient of variance of the gene expression level as the variance of expression level, wherein threshold is predetermined and in the range of 20% to 200%."],"number":15,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 13, wherein the subpopulation reference gene has the lowest variance of expression levels among the subset of subpopulation genes."],"number":16,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 13, wherein identifying the subset of subpopulation genes includes using expression levels of the subpopulation genes that are measured relative to expression levels of a housekeeping gene that has uniform expression over multiple subpopulations."],"number":17,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 13, wherein identifying the subset of subpopulation genes for the first subpopulation includes:\n
receiving a proportional cell count of the first subpopulations of cells in the plurality of cell-mixture samples;\n
analyzing the data to determine a first expression level for each the first set of genes in the cell-mixture samples;\n
for each of the genes in the first set:\n"],"number":18,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 13, wherein identifying the subset of subpopulation genes for the first subpopulation includes:\nusing the proportional cell count and the respective expression level to determine whether the first subpopulation contributes at least the predetermined percentage of transcripts of the respective gene in the cell-mixture samples relative to the first expression level.\n
receiving data regarding which of a plurality of genes are expressed in different subpopulations of cells in the plurality of cell-mixture samples;\n
receiving a respective proportional cell count of each of the different subpopulations of cells in the plurality of cell mixtures, the respective proportional cell counts including a first proportional cell count P(1) for the first subpopulation;\n
for each of the genes in the first set:\n\n\nEP(1)*P(1)≥C%(1-C%)∑i=2NEp(i)*P(i)\nanalyzing the data to determine a respective expression level for the respective gene in each of the different subpopulations in which the respective gene is expressed, the respective expression level including a first expression level Ep(1) for the first subpopulation;\nusing the equation\n
to determine whether the first subpopulation contributes at least the predetermined percentage of transcripts of the respective gene in the plurality of cell mixtures, where N is an integer corresponding to a number of subpopulation in which the respective gene is expressed, and C % is the predetermined percentage."],"number":19,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the plurality of different subpopulations of cells includes at least three different subpopulations of cells."],"number":20,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 13, wherein the plurality of different subpopulations of cells includes at least three different subpopulations of cells."],"number":21,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the at least one subpopulation reference gene is selected from Table II and wherein the first subpopulation of cells is B lymphocytes."],"number":22,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the at least one subpopulation reference gene is selected from Table III and wherein the first subpopulation of cells is CD4 T lymphocytes."],"number":23,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the at least one subpopulation reference gene is selected from Table IV and wherein the first subpopulation of cells is CD8 T lymphocytes."],"number":24,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the at least one subpopulation reference gene is selected from Table V and wherein the first subpopulation of cells is granulocytes."],"number":25,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the at least one subpopulation reference gene is selected from Table VI and wherein the first subpopulation of cells is T lymphocytes."],"number":26,"annotation":false,"claim":true,"title":false}]}},"filters":{"npl":[],"notNpl":[],"applicant":[],"notApplicant":[],"inventor":[],"notInventor":[],"owner":[],"notOwner":[],"tags":[],"dates":[],"types":[],"notTypes":[],"j":[],"notJ":[],"fj":[],"notFj":[],"classIpcr":[],"notClassIpcr":[],"classNat":[],"notClassNat":[],"classCpc":[],"notClassCpc":[],"so":[],"notSo":[],"sat":[]},"sequenceFilters":{"s":"SEQIDNO","d":"ASCENDING","p":0,"n":10,"sp":[],"si":[],"len":[],"t":[],"loc":[]}}