An individualized predictor of health and disease using paired reference and target samples

BMC Bioinformatics
Tzu-Yu LiuAlfred O Hero

Abstract

Consider the problem of designing a panel of complex biomarkers to predict a patient's health or disease state when one can pair his or her current test sample, called a target sample, with the patient's previously acquired healthy sample, called a reference sample. As contrasted to a population averaged reference this reference sample is individualized. Automated predictor algorithms that compare and contrast the paired samples to each other could result in a new generation of test panels that compare to a person's healthy reference to enhance predictive accuracy. This paper develops such an individualized predictor and illustrates the added value of including the healthy reference for design of predictive gene expression panels. The objective is to predict each subject's state of infection, e.g., neither exposed nor infected, exposed but not infected, pre-acute phase of infection, acute phase of infection, post-acute phase of infection. Using gene microarray data collected in a large scale serially sampled respiratory virus challenge study we quantify the diagnostic advantage of pairing a person's baseline reference with his or her target sample. The full study consists of 2886 microarray chips assaying 12,023 genes of 151 hu...Continue Reading

References

Oct 5, 2001·Clinical Microbiology Reviews·C E Samuel
Nov 3, 2001·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·R B Turner
May 27, 2003·Apoptosis : an International Journal on Programmed Cell Death·M Chawla-SarkarE C Borden
Mar 23, 2004·Annual Review of Immunology·Anthony P MandersonMark J Walport
Aug 17, 2004·The Journal of Biological Chemistry·Betsy J BarnesPaula M Pitha
Nov 9, 2004·Nature Medicine·Kenneth J RitchieDong-Er Zhang
Jan 21, 2006·Nature Immunology·Taro Kawai, Shizuo Akira
Feb 4, 2006·The Journal of Immunology : Official Journal of the American Association of Immunologists·Allison L MillerNicholas W Lukacs
Sep 19, 2006·Immunity·Daniel B Stetson, Ruslan Medzhitov
Feb 5, 2008·IEEE Transactions on Neural Networks·Chih-Wei Hsu, Chih-Jen Lin
Nov 26, 2008·Nature Immunology·Troy D QuerecBali Pulendran
Apr 10, 2010·IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society·Manya V AfonsoMário A T Figueiredo
May 4, 2010·Lancet·Euan A AshleyRuss B Altman
Jul 12, 2011·Nature Immunology·Helder I NakayaBali Pulendran
Oct 26, 2011·Genome Medicine·Eric Bortz, Adolfo García-Sastre
Mar 27, 2012·Nature·Aaron R EverittPaul Kellam
Sep 21, 2013·Science Translational Medicine·Aimee K ZaasGeoffrey S Ginsburg
Mar 19, 2014·Frontiers in Cellular and Infection Microbiology·Marc Lecuit, Marc Eloit

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Citations

Dec 10, 2017·Scientific Reports·Jigar S DesaiColleen J Doherty
Jan 9, 2019·Frontiers in Microbiology·Gregory D PooreEphraim L Tsalik
Jun 15, 2018·Genome Medicine·Erika BongenPurvesh Khatri
Jul 30, 2019·Clinical Therapeutics·Melissa H RossEphraim L Tsalik
Aug 11, 2019·Schizophrenia Research·Eunkyoung KimGregory F Payne
Mar 6, 2021·International Journal of Infectious Diseases : IJID : Official Publication of the International Society for Infectious Diseases·Hongxing LeiJiankui Chen

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Datasets Mentioned

BETA
GSE73072

Methods Mentioned

BETA
chips

Software Mentioned

RMA package

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