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Performance of risk prediction for inflammatory bowel disease based on genotyping platform and genomic risk score method.

Abstract Predicting risk of disease from genotypes is being increasingly proposed for a variety of diagnostic and prognostic purposes. Genome-wide association studies (GWAS) have identified a large number of genome-wide significant susceptibility loci for Crohn's disease (CD) and ulcerative colitis (UC), two subtypes of inflammatory bowel disease (IBD). Recent studies have demonstrated that including only loci that are significantly associated with disease in the prediction model has low predictive power and that power can substantially be improved using a polygenic approach.
PMID
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Authors

Mayor MeshTerms
Keywords

Case-control study

Complex trait

Crohn’s disease

Inflammatory bowel disease

Risk score

SNP array

Ulcerative colitis

Journal Title bmc medical genetics
Publication Year Start




PMID- 28851283
OWN - NLM
STAT- In-Process
DA  - 20170830
LR  - 20170902
IS  - 1471-2350 (Electronic)
IS  - 1471-2350 (Linking)
VI  - 18
IP  - 1
DP  - 2017 Aug 29
TI  - Performance of risk prediction for inflammatory bowel disease based on genotyping
      platform and genomic risk score method.
PG  - 94
LID - 10.1186/s12881-017-0451-2 [doi]
AB  - BACKGROUND: Predicting risk of disease from genotypes is being increasingly
      proposed for a variety of diagnostic and prognostic purposes. Genome-wide
      association studies (GWAS) have identified a large number of genome-wide
      significant susceptibility loci for Crohn's disease (CD) and ulcerative colitis
      (UC), two subtypes of inflammatory bowel disease (IBD). Recent studies have
      demonstrated that including only loci that are significantly associated with
      disease in the prediction model has low predictive power and that power can
      substantially be improved using a polygenic approach. METHODS: We performed a
      comprehensive analysis of risk prediction models using large case-control cohorts
      genotyped for 909,763 GWAS SNPs or 123,437 SNPs on the custom designed Immunochip
      using four prediction methods (polygenic score, best linear genomic prediction,
      elastic-net regularization and a Bayesian mixture model). We used the area under 
      the curve (AUC) to assess prediction performance for discovery populations with
      different sample sizes and number of SNPs within cross-validation. RESULTS: On
      average, the Bayesian mixture approach had the best prediction performance. Using
      cross-validation we found little differences in prediction performance between
      GWAS and Immunochip, despite the GWAS array providing a 10 times larger effective
      genome-wide coverage. The prediction performance using Immunochip is largely due 
      to the power of the initial GWAS for its marker selection and its low cost that
      enabled larger sample sizes. The predictive ability of the genomic risk score
      based on Immunochip was replicated in external data, with AUC of 0.75 for CD and 
      0.70 for UC. CD patients with higher risk scores demonstrated clinical
      characteristics typically associated with a more severe disease course including 
      ileal location and earlier age at diagnosis. CONCLUSIONS: Our analyses
      demonstrate that the power of genomic risk prediction for IBD is mainly due to
      strongly associated SNPs with considerable effect sizes. Additional SNPs that are
      only tagged by high-density GWAS arrays and low or rare-variants over-represented
      in the high-density region on the Immunochip contribute little to prediction
      accuracy. Although a quantitative assessment of IBD risk for an individual is not
      currently possible, we show sufficient power of genomic risk scores to stratify
      IBD risk among individuals at diagnosis.
FAU - Chen, Guo-Bo
AU  - Chen GB
AD  - Queensland Brain Institute, The University of Queensland, Brisbane, Australia.
FAU - Lee, Sang Hong
AU  - Lee SH
AD  - Queensland Brain Institute, The University of Queensland, Brisbane, Australia.
AD  - School of Environmental and Rural Science, The University of New England,
      Armidale, Australia.
FAU - Montgomery, Grant W
AU  - Montgomery GW
AD  - Institute for Molecular Bioscience, The University of Queensland, Brisbane,
      Australia.
FAU - Wray, Naomi R
AU  - Wray NR
AD  - Queensland Brain Institute, The University of Queensland, Brisbane, Australia.
FAU - Visscher, Peter M
AU  - Visscher PM
AD  - Queensland Brain Institute, The University of Queensland, Brisbane, Australia.
AD  - University of Queensland Diamantina Institute, Translational Research Institute, 
      The University of Queensland, Brisbane, Australia.
FAU - Gearry, Richard B
AU  - Gearry RB
AD  - Department of Medicine, University of Otago, Christchurch, New Zealand.
AD  - Department of Gastroenterology, Christchurch Hospital, Christchurch, New Zealand.
FAU - Lawrance, Ian C
AU  - Lawrance IC
AD  - Harry Perkins Institute of Medical Research, School of Medicine and Pharmacology,
      University of Western Australia, Murdoch, Australia.
AD  - Centre for Inflammatory Bowel Diseases, Saint John of God Hospital, Subiaco,
      Australia.
FAU - Andrews, Jane M
AU  - Andrews JM
AD  - Inflammatory Bowel Disease Service, Department of Gastroenterology and
      Hepatology, Royal Adelaide Hospital, School of Medicine, University of Adelaide, 
      Adelaide, Australia.
FAU - Bampton, Peter
AU  - Bampton P
AD  - Department of Gastroenterology and Hepatology, Flinders Medical Centre, Adelaide,
      Australia.
FAU - Mahy, Gillian
AU  - Mahy G
AD  - Department of Gastroenterology, Townsville Hospital, Townsville, Australia.
FAU - Bell, Sally
AU  - Bell S
AD  - Department of Gastroenterology, St Vincent's Hospital, Melbourne, Australia.
FAU - Walsh, Alissa
AU  - Walsh A
AD  - Department of Gastroenterology and Hepatology, St Vincent's Hospital, Sydney,
      Australia.
FAU - Connor, Susan
AU  - Connor S
AD  - Department of Gastroenterology and Hepatology, Liverpool Hospital, Sydney,
      Australia.
AD  - University of NSW, Sydney, Australia.
FAU - Sparrow, Miles
AU  - Sparrow M
AD  - Department of Gastroenterology, Alfred Health, Melbourne, Australia.
FAU - Bowdler, Lisa M
AU  - Bowdler LM
AD  - Institute for Molecular Bioscience, The University of Queensland, Brisbane,
      Australia.
FAU - Simms, Lisa A
AU  - Simms LA
AD  - Inflammatory Bowel Disease Research Group, Immunology Division, QIMR Berghofer
      Medical Research Institute, Brisbane, Australia.
FAU - Krishnaprasad, Krupa
AU  - Krishnaprasad K
AD  - Inflammatory Bowel Disease Research Group, Immunology Division, QIMR Berghofer
      Medical Research Institute, Brisbane, Australia.
CN  - International IBD Genetics Consortium
FAU - Radford-Smith, Graham L
AU  - Radford-Smith GL
AD  - School of Medicine, The University of Queensland, Brisbane, Australia.
AD  - Inflammatory Bowel Disease Research Group, Immunology Division, QIMR Berghofer
      Medical Research Institute, Brisbane, Australia.
AD  - Department of Gastroenterology, Royal Brisbane and Women's Hospital, Brisbane,
      Australia.
FAU - Moser, Gerhard
AU  - Moser G
AUID- ORCID: http://orcid.org/0000-0003-3104-5730
AD  - Queensland Brain Institute, The University of Queensland, Brisbane, Australia.
      [email protected]
LA  - eng
GR  - P01 GM099568/GM/NIGMS NIH HHS/United States
PT  - Journal Article
DEP - 20170829
PL  - England
TA  - BMC Med Genet
JT  - BMC medical genetics
JID - 100968552
PMC - PMC5576242
OTO - NOTNLM
OT  - Case-control study
OT  - Complex trait
OT  - Crohn's disease
OT  - Inflammatory bowel disease
OT  - Risk score
OT  - SNP array
OT  - Ulcerative colitis
EDAT- 2017/08/31 06:00
MHDA- 2017/08/31 06:00
CRDT- 2017/08/31 06:00
PHST- 2016/05/08 [received]
PHST- 2017/08/14 [accepted]
AID - 10.1186/s12881-017-0451-2 [doi]
AID - 10.1186/s12881-017-0451-2 [pii]
PST - epublish
SO  - BMC Med Genet. 2017 Aug 29;18(1):94. doi: 10.1186/s12881-017-0451-2.