Systems, methods, and gene signatures for predicting a biological status of an individual

A biological state and gene technology, applied in the fields of biochemical equipment and methods, biostatistics, and microbial determination/examination, which can solve problems such as complex blood analysis

Pending Publication Date: 2019-04-16
PHILIP MORRIS PROD SA
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

Blood is complex to analyze due to the many different cell subsets it contains

Method used

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  • Systems, methods, and gene signatures for predicting a biological status of an individual
  • Systems, methods, and gene signatures for predicting a biological status of an individual
  • Systems, methods, and gene signatures for predicting a biological status of an individual

Examples

Experimental program
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example 1

[0096] Example 1 - Study Population and Design

[0097] Whole blood samples are collected at PAXgene during clinical and in vivo studies TM tubes, or purchase whole blood samples from Biobank. exist Image 6 The sample cohorts / categories, sizes and characteristics of the different studies are summarized in the tables shown. Briefly, human blood samples were obtained from: (i) a clinical case-control study conducted at the Queen Ann Street Medical Center (QASMC) in London, UK and registered with ClinicalTrials.gov with identification number NCT01780298; (ii) Biobank (BioServe Biotechnologies Ltd., Batesville, MD, USA) (Dataset BLD-SMK-01). Samples from these sources included smokers (S), former smokers (FS), and never smokers (NS) selected based on well-defined inclusion criteria ( Image 6 ); and (iii) the clinical ZRHR Reduced Exposure (REX) C-03-EU and -04-JP studies corresponding to randomized, controlled, 3-arm parallel cohort and single center studies. The REX stud...

example

[0136] Example 1 - Gene signature length, gene expression collinearity grade and classification method from the top six panels Performance analysis of all gene panels affected by consensus signatures of smoking exposure in humans

[0137] method

[0138] Consider all possible gene combinations from the consensus signature. Due to the limitations imposed by the computer-intensive calculations required for this analysis, the extraction of a consensus signature of human smoking exposure based on 18 genes was limited to the first six panels (instead of the 12 eligible panels). A consensus signature based on 18 genes containing DSC2, FSTL1, GPR63, GSE1, GUCY1A3, RGL1, CTTNBP2, F2R, SEMA6B, CDKN1C, CLEC10A, GPR15, LINC00599, P2RY6, PID1, SASH1, AHRR, and LRRN3 in blood was obtained by selecting spanning Genes whose signatures co-occurred at least twice in the six panels were identified. The effect of gene label size and collinearity rank on classification performance was investi...

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Abstract

Systems and methods for assessing a subject's sample to predict the subject's biological status, such as a smoker status. The computer-implemented method includes receiving, by a computer system including at least one hardware processor, a data set associated with the sample. The data set comprises quantitative expression data for a set of genes less than a whole genome, the set of genes comprising AHHR, CDKN1C, LRRN3, PID1, GPR15, SASH1, CLEC10A, LINC00599, P2RY6, DSC2, F2R, SEMA6B, and TLR5. The at least one hardware processor generates a score based on the quantitative expression data for the set of genes in the received data set, wherein the score is based on fewer than 40 genes and is indicative of a predicted smoking status of the subject.

Description

[0001] References to related applications [0002] This application claims priority under 35 U.S.C. §119 to U.S. Provisional Patent Application No. 62 / 394,551, filed September 14, 2016, which is hereby incorporated by reference in its entirety. This application is related to PCT Application No. PCT / EP2014 / 077473, filed December 11, 2014, and PCT Application No. PCT / EP2014 / 067276, filed August 12, 2014, each of which is incorporated by reference in its entirety In this article. Background technique [0003] People are constantly exposed to external toxic substances (eg, cigarette smoke, pesticides) that may trigger harmful molecular changes. Risk assessment in 21st century toxicology relies on the elucidation of mechanisms of toxicity and the identification of markers of exposure response from high-throughput data. New technologies such as whole-genome microarrays have been incorporated into toxicity testing to improve efficiency and provide a more data-driven approach to ex...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16H70/60G16B20/00G16B40/00C12Q1/68G16B20/20G16B40/20
CPCC12Q1/6876C12Q2600/158G16H70/60G16B40/00G16B20/00G16B40/20G16B20/20Y02A90/10G16B25/10A24F42/00
Inventor C·普森V·贝尔卡斯特罗F·马丁S·布韦M·C·派奇
Owner PHILIP MORRIS PROD SA
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