Biomarker discovery study design for type 1 diabetes in The Environmental Determinants of Diabetes in the Young (TEDDY) study

被引：41

作者：

Lee, Hye-Seung ^{[1
]}

Burkhardt, Brant R. ^{[2
]}

McLeod, Wendy ^{[1
]}

Smith, Susan ^{[1
]}

Eberhard, Chris ^{[1
]}

Lynch, Kristian ^{[1
]}

Hadley, David ^{[1
]}

Rewers, Marian ^{[3
]}

Simell, Olli ^{[4
]}

She, Jin-Xiong ^{[5
]}

Hagopian, Bill ^{[6
]}

Lernmark, Ake ^{[7
]}

Akolkar, Beena ^{[8
]}

Ziegler, Anette G. ^{[9
,10
,11
]}

Krischer, Jeffrey P. ^{[1
]}

机构：

[1] Univ S Florida, Dept Pediat, Pediat Epidemiol Ctr, Tampa, FL 33620 USA

[2] Univ S Florida, Dept Cell Biol Microbiol & Mol Biol, Tampa, FL 33620 USA

[3] Univ Colorado Denver, Barbara Davis Ctr Childhood Diabet, Aurora, CO USA

[4] Turku Univ, Cent Hosp, Dept Pediat, Turku, Finland

[5] Georgia Regents Univ, Med Coll Georgia, Ctr Biotechnol & Genom Med, Augusta, GA USA

[6] Pacific Northwest Diabet Res Inst, Seattle, WA USA

[7] Lund Univ, Dept Clin Sci, Malmo, Sweden

[8] NIDDK, Bethesda, MD USA

[9] Helmholtz Zentrum Munchen, Inst Diabet Res, Munich, Germany

[10] Tech Univ Munich, Klinikum Rechts Isar, D-80290 Munich, Germany

[11] Forschergrp Diabet eV Neuherberg, Neuherberg, Germany

来源：

DIABETES-METABOLISM RESEARCH AND REVIEWS | 2014年 / 30卷 / 05期

关键词：

batch effects; biomarker discovery; nested case-control design; TEDDY; type; 1; diabetes; SELECTION; COHORT;

D O I：

10.1002/dmrr.2510

中图分类号：

R5 [内科学];

学科分类号：

1002 ; 100201 ;

摘要：

Aims The Environmental Determinants of Diabetes in the Young planned biomarker discovery studies on longitudinal samples for persistent confirmed islet cell autoantibodies and type 1 diabetes using dietary biomarkers, metabolomics, microbiome/viral metagenomics and gene expression. Methods This article describes the details of planning The Environmental Determinants of Diabetes in the Young biomarker discovery studies using a nested case-control design that was chosen as an alternative to the full cohort analysis. In the frame of a nested case-control design, it guides the choice of matching factors, selection of controls, preparation of external quality control samples and reduction of batch effects along with proper sample allocation. Results and conclusion Our design is to reduce potential bias and retain study power while reducing the costs by limiting the numbers of samples requiring laboratory analyses. It also covers two primary end points (the occurrence of diabetes-related autoantibodies and the diagnosis of type 1 diabetes). The resulting list of case-control matched samples for each laboratory was augmented with external quality control samples. Copyright (C) 2013 John Wiley & Sons, Ltd.

引用

页码：424 / 434

页数：11

共 25 条

[1] Singular value decomposition for genome-wide expression data processing and modeling [J].

Alter, O ;

Brown, PO ;

Botstein, D .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (18) :10101-10106

[2]

[Anonymous], 1993, MOL EPIDEMIOLOGY PRI

[3] Improving the Biomarker Pipeline to Develop and Evaluate Cancer Screening Tests [J].

Baker, Stuart G. .

JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE, 2009, 101 (16) :1116-1119

[4] Analysis of case-cohort designs [J].

Barlow, WE ;

Ichikawa, L ;

Rosner, D ;

Izumi, S .

JOURNAL OF CLINICAL EPIDEMIOLOGY, 1999, 52 (12) :1165-1172

[5] Adjustment of systematic microarray data biases [J].

Benito, M ;

Parker, J ;

Du, Q ;

Wu, JY ;

Xang, D ;

Perou, CM ;

Marron, JS .

BIOINFORMATICS, 2004, 20 (01) :105-114

[6] Harmonization of Glutamic Acid Decarboxylase and Islet Antigen-2 Autoantibody Assays for National Institute of Diabetes and Digestive and Kidney Diseases Consortia [J].

Bonifacio, Ezio ;

Yu, Liping ;

Williams, Alastair K. ;

Eisenbarth, George S. ;

Bingley, Polly J. ;

Marcovina, Santica M. ;

Adler, Kerstin ;

Ziegler, Anette G. ;

Mueller, Patricia W. ;

Schatz, Desmond A. ;

Krischer, Jeffrey P. ;

Steffes, Michael W. ;

Akolkar, Beena .

JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM, 2010, 95 (07) :3360-3367

[7]

Diabetes Vehik K, 2013, DIABETES-METAB RES, V29, P557

[8] Adjusting batch effects in microarray expression data using empirical Bayes methods [J].

Johnson, W. Evan ;

Li, Cheng ;

Rabinovic, Ariel .

BIOSTATISTICS, 2007, 8 (01) :118-127

[9]

Krischer J, 2007, PEDIATR DIABETES, V8, P286

[10] Sample size evaluation for a multiply matched case-control study using the score test from a conditional logistic (discrete Cox PH) regression model [J].

Lachin, John M. .

STATISTICS IN MEDICINE, 2008, 27 (14) :2509-2523

← 1 2 3 →