Abstract
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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 424-434 |
| Number of pages | 11 |
| Journal | Diabetes/Metabolism Research and Reviews |
| Volume | 30 |
| Issue number | 5 |
| DOIs | |
| State | Published - 2014 |
Keywords
- Batch effects
- Biomarker discovery
- Nested case-control design
- TEDDY
- Type 1 diabetes
ASJC Scopus subject areas
- Endocrinology
- Endocrinology, Diabetes and Metabolism
- Internal Medicine
- Medicine(all)
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Biomarker discovery study design for type 1 diabetes in The Environmental Determinants of Diabetes in the Young (TEDDY) study. / Lee, Hye Seung; Burkhardt, Brant R.; Mcleod, Wendy; Smith, Susan; Eberhard, Chris; Lynch, Kristian; Hadley, David; Rewers, Marian; Simell, Olli; She, Jin Xiong; Hagopian, Bill; Lernmark, Ake; Akolkar, Beena; Ziegler, Anette G.; Krischer, Jeffrey P.; Barriga, Katherine; Bautista, Kimberly; Baxter, Judith; Eisenbarth, George; Frank, Nicole; Gesualdo, Patricia; Hoffman, Michelle; Ide, Lisa; Karban, Rachel; Liu, Edwin; Norris, Jill; Waugh, Kathleen; Samper-Imaz, Adela; Steck, Andrea; Schatz, Desmond; Hopkins, Diane; Steed, Leigh; Thomas, Jamie; Silvis, Katherine; Haller, Michael; Shankar, Meena; Sheehan, Eleni; Gardiner, Melissa; McIndoe, Richard; Liu, Haitao; Nechtman, John; Sharma, Ashok; Williams, Joshua; Foghis, Gabriela; Anderson W., Stephen W.; Beyerlein, Andreas; Bonifacio, Ezio; Hummel, Michael; Hummel, Sandra; Foterek, Kristina; Kersting, Mathilde; Knopff, Annette; Koletzko, Sibylle; Peplow, Claudia; Roth, Roswith; Schenke, Julia; Stock, Joanna; Strauss, Elisabeth; Warncke, Katharina; Winkler, Christiane; Simell G., Olli G.; Hyoty, Heikki; Ilonen, Jorma; Knip, Mikael; Koivu, Annika; Koreasalo, Mirva; Kahonen, Miia; Lonnrot, Maria; Multasuo, Katja; Mantymaki, Elina; Mykkanen, Juha; Nanto-Salonen, Kirsti; Niininen, Tiina; Nyblom, Mia; Rautanen, Jenna; Riikonen, Anne; Romo, Minna; Simell, Aaro; Simell, Barbara; Simell, Tuula; Simell, Ville; Sjoberg, Maija; Stenius, Aino; Toppari, Jorma; Varjonen, Eeva; Veijola, Riitta; Virtanen M., Suvi M.; Akerlund, Mari; Agardh, Daniel; Andrén-Aronsson, Carin; Ask, Maria; Bremer, Jenny; Carlsson, Ulla Marie; Cilio, Corrado; Ericson-Hallstrom, Emilie; Fransson, Lina; Gard, Thomas; Gerardsson, Joanna; Hakansson, Rasmus; Hansen, Monica; Hansson, Gertie; Hyberg, Susanne; Johansen, Fredrik; Jonasdottir, Berglind; Jonsson, Linda; Larsson, Helena; Lernmark, Barbro; Mansson-Martinez, Maria; Markan, Maria; Massadakis, Theodosia; Melin, Jessica; Mestan, Zeliha; Nilsson, Anita; Nilsson, Emma; Rahmati, Kobra; Rosenquist, Anna; Salami, Falastin; Jarvirova, Monica Sedig; Sibthorpe, Sara; Sjoberg, Birgitta; Swartling, Ulrica; Trulsson, Erika; Torn, Carina; Wallin, Anne; Wimar, Asa; Aberg, Sofie; Hagopian A., William A.; Yan, Xiang; Killian, Michael; Crouch, Claire Cowen; Hay M., Kristen M.; Ayres, Stephen; Adams, Carissa; Bratrude, Brandi; Coughlin, David; Fowler, Greer; Franco, Czarina; Hammar, Carla; Heaney, Diana; Marcus, Patrick; Meyer, Arlene; Mulenga, Denise; Scott, Elizabeth; Skidmore, Jennifer; Stabbert, Joshua; Stepitova, Viktoria; Williams, Nancy; Becker, Dorothy; Franciscus, Margaret; Dalmagro-Elias, MaryEllen; Daftary, Ashi; Klein, Mary Beth; Abbondondolo, Michael; Austin-Gonzalez, Sarah; Brown, Rasheedah; Burkhardt, Brant; Butterworth, Martha; Cuthbertson, David; Eberhard, Christopher; Fiske, Steven; Gowda, Veena; Lane, Page; Liu, Shu; Liu, Xiang; Malloy, Jamie; McCarthy, Cristina; McLeod, Wendy; Smith, Laura; Tamura, Roy; Uusitalo, Ulla; Vehik, Kendra; Washington, Earnest; Yang, Jimin; Bourcier, Kasia; Briese, Thomas; Johnson, Suzanne Bennett; Oberste, Steve; Triplett, Eric; Yu, Liping; Miao, Dongmei; Bingley, Polly; Williams, Alistair; Chandler, Kyla; Rokni, Saba; Long, Anna; Boldison, Joanna; Butterly, Jacob; Broadhurst, Jessica; Carreno, Gabriella; Curnock, Rachel; Easton, Peter; Geoghan, Ivey; Goode, Julia; Pearson, James; Reed, Charles; Ridewood, Sophie; Wyatt, Rebecca; Eriksson, Elisabeth Aardal; Karlsson, Ewa Lonn; Erlund, Iris; Salminen, Irma; Sundvall, Jouko; Leiviska, Jaana; Lehtonen, Mari; Little R., Randie R.; Tennill L., Alethea L.; Erlich, Henry; Bugawan, Teodorica; Alejandrino, Maria; Fiehn, Oliver; Wikoff, Bill; Kind, Tobias; Palazoglu, Mine; Wong, Joyce; Wohlgemuth, Gert; Petrosino F., Joseph F.; Marcovina M., Santica M.; Higgins, Heather; Ke, Sandra; Zhao, Yansheng; Jiang, Na; Rich S., Stephen S.; Chen, Wei Min; Onengut-Gumuscu, Suna; Farber, Emily; Pickin, Rebecca Roche; Davis, Jordan; Gallo, Dan.
In: Diabetes/Metabolism Research and Reviews, Vol. 30, No. 5, 2014, p. 424-434.Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - Biomarker discovery study design for type 1 diabetes in The Environmental Determinants of Diabetes in the Young (TEDDY) study
AU - Lee, Hye Seung
AU - Burkhardt, Brant R.
AU - Mcleod, Wendy
AU - Smith, Susan
AU - Eberhard, Chris
AU - Lynch, Kristian
AU - Hadley, David
AU - Rewers, Marian
AU - Simell, Olli
AU - She, Jin Xiong
AU - Hagopian, Bill
AU - Lernmark, Ake
AU - Akolkar, Beena
AU - Ziegler, Anette G.
AU - Krischer, Jeffrey P.
AU - Barriga, Katherine
AU - Bautista, Kimberly
AU - Baxter, Judith
AU - Eisenbarth, George
AU - Frank, Nicole
AU - Gesualdo, Patricia
AU - Hoffman, Michelle
AU - Ide, Lisa
AU - Karban, Rachel
AU - Liu, Edwin
AU - Norris, Jill
AU - Waugh, Kathleen
AU - Samper-Imaz, Adela
AU - Steck, Andrea
AU - Schatz, Desmond
AU - Hopkins, Diane
AU - Steed, Leigh
AU - Thomas, Jamie
AU - Silvis, Katherine
AU - Haller, Michael
AU - Shankar, Meena
AU - Sheehan, Eleni
AU - Gardiner, Melissa
AU - McIndoe, Richard
AU - Liu, Haitao
AU - Nechtman, John
AU - Sharma, Ashok
AU - Williams, Joshua
AU - Foghis, Gabriela
AU - Anderson W., Stephen W.
AU - Beyerlein, Andreas
AU - Bonifacio, Ezio
AU - Hummel, Michael
AU - Hummel, Sandra
AU - Foterek, Kristina
AU - Kersting, Mathilde
AU - Knopff, Annette
AU - Koletzko, Sibylle
AU - Peplow, Claudia
AU - Roth, Roswith
AU - Schenke, Julia
AU - Stock, Joanna
AU - Strauss, Elisabeth
AU - Warncke, Katharina
AU - Winkler, Christiane
AU - Simell G., Olli G.
AU - Hyoty, Heikki
AU - Ilonen, Jorma
AU - Knip, Mikael
AU - Koivu, Annika
AU - Koreasalo, Mirva
AU - Kahonen, Miia
AU - Lonnrot, Maria
AU - Multasuo, Katja
AU - Mantymaki, Elina
AU - Mykkanen, Juha
AU - Nanto-Salonen, Kirsti
AU - Niininen, Tiina
AU - Nyblom, Mia
AU - Rautanen, Jenna
AU - Riikonen, Anne
AU - Romo, Minna
AU - Simell, Aaro
AU - Simell, Barbara
AU - Simell, Tuula
AU - Simell, Ville
AU - Sjoberg, Maija
AU - Stenius, Aino
AU - Toppari, Jorma
AU - Varjonen, Eeva
AU - Veijola, Riitta
AU - Virtanen M., Suvi M.
AU - Akerlund, Mari
AU - Agardh, Daniel
AU - Andrén-Aronsson, Carin
AU - Ask, Maria
AU - Bremer, Jenny
AU - Carlsson, Ulla Marie
AU - Cilio, Corrado
AU - Ericson-Hallstrom, Emilie
AU - Fransson, Lina
AU - Gard, Thomas
AU - Gerardsson, Joanna
AU - Hakansson, Rasmus
AU - Hansen, Monica
AU - Hansson, Gertie
AU - Hyberg, Susanne
AU - Johansen, Fredrik
AU - Jonasdottir, Berglind
AU - Jonsson, Linda
AU - Larsson, Helena
AU - Lernmark, Barbro
AU - Mansson-Martinez, Maria
AU - Markan, Maria
AU - Massadakis, Theodosia
AU - Melin, Jessica
AU - Mestan, Zeliha
AU - Nilsson, Anita
AU - Nilsson, Emma
AU - Rahmati, Kobra
AU - Rosenquist, Anna
AU - Salami, Falastin
AU - Jarvirova, Monica Sedig
AU - Sibthorpe, Sara
AU - Sjoberg, Birgitta
AU - Swartling, Ulrica
AU - Trulsson, Erika
AU - Torn, Carina
AU - Wallin, Anne
AU - Wimar, Asa
AU - Aberg, Sofie
AU - Hagopian A., William A.
AU - Yan, Xiang
AU - Killian, Michael
AU - Crouch, Claire Cowen
AU - Hay M., Kristen M.
AU - Ayres, Stephen
AU - Adams, Carissa
AU - Bratrude, Brandi
AU - Coughlin, David
AU - Fowler, Greer
AU - Franco, Czarina
AU - Hammar, Carla
AU - Heaney, Diana
AU - Marcus, Patrick
AU - Meyer, Arlene
AU - Mulenga, Denise
AU - Scott, Elizabeth
AU - Skidmore, Jennifer
AU - Stabbert, Joshua
AU - Stepitova, Viktoria
AU - Williams, Nancy
AU - Becker, Dorothy
AU - Franciscus, Margaret
AU - Dalmagro-Elias, MaryEllen
AU - Daftary, Ashi
AU - Klein, Mary Beth
AU - Abbondondolo, Michael
AU - Austin-Gonzalez, Sarah
AU - Brown, Rasheedah
AU - Burkhardt, Brant
AU - Butterworth, Martha
AU - Cuthbertson, David
AU - Eberhard, Christopher
AU - Fiske, Steven
AU - Gowda, Veena
AU - Lane, Page
AU - Liu, Shu
AU - Liu, Xiang
AU - Malloy, Jamie
AU - McCarthy, Cristina
AU - McLeod, Wendy
AU - Smith, Laura
AU - Tamura, Roy
AU - Uusitalo, Ulla
AU - Vehik, Kendra
AU - Washington, Earnest
AU - Yang, Jimin
AU - Bourcier, Kasia
AU - Briese, Thomas
AU - Johnson, Suzanne Bennett
AU - Oberste, Steve
AU - Triplett, Eric
AU - Yu, Liping
AU - Miao, Dongmei
AU - Bingley, Polly
AU - Williams, Alistair
AU - Chandler, Kyla
AU - Rokni, Saba
AU - Long, Anna
AU - Boldison, Joanna
AU - Butterly, Jacob
AU - Broadhurst, Jessica
AU - Carreno, Gabriella
AU - Curnock, Rachel
AU - Easton, Peter
AU - Geoghan, Ivey
AU - Goode, Julia
AU - Pearson, James
AU - Reed, Charles
AU - Ridewood, Sophie
AU - Wyatt, Rebecca
AU - Eriksson, Elisabeth Aardal
AU - Karlsson, Ewa Lonn
AU - Erlund, Iris
AU - Salminen, Irma
AU - Sundvall, Jouko
AU - Leiviska, Jaana
AU - Lehtonen, Mari
AU - Little R., Randie R.
AU - Tennill L., Alethea L.
AU - Erlich, Henry
AU - Bugawan, Teodorica
AU - Alejandrino, Maria
AU - Fiehn, Oliver
AU - Wikoff, Bill
AU - Kind, Tobias
AU - Palazoglu, Mine
AU - Wong, Joyce
AU - Wohlgemuth, Gert
AU - Petrosino F., Joseph F.
AU - Marcovina M., Santica M.
AU - Higgins, Heather
AU - Ke, Sandra
AU - Zhao, Yansheng
AU - Jiang, Na
AU - Rich S., Stephen S.
AU - Chen, Wei Min
AU - Onengut-Gumuscu, Suna
AU - Farber, Emily
AU - Pickin, Rebecca Roche
AU - Davis, Jordan
AU - Gallo, Dan
PY - 2014
Y1 - 2014
N2 - 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.
AB - 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.
KW - Batch effects
KW - Biomarker discovery
KW - Nested case-control design
KW - TEDDY
KW - Type 1 diabetes
UR - http://www.scopus.com/inward/record.url?scp=84903691108&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84903691108&partnerID=8YFLogxK
U2 - 10.1002/dmrr.2510
DO - 10.1002/dmrr.2510
M3 - Article
C2 - 24339168
AN - SCOPUS:84903691108
VL - 30
SP - 424
EP - 434
JO - Diabetes/Metabolism Research and Reviews
JF - Diabetes/Metabolism Research and Reviews
SN - 1520-7552
IS - 5
ER -