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Developing polygenic risk models for complex traits and diseases

Principal Investigator
Name
Jianxin Shi
Degrees
PhD
Institution
NCI
Position Title
Senior Investigator
Email
About this CDAS Project
Study
PLCO (Learn more about this study)
Project ID
PLCO-1577
Initial CDAS Request Approval
Jun 7, 2024
Title
Developing polygenic risk models for complex traits and diseases
Summary
Dr. Bin Zhu and I are developing novel statistical methods for building polygenic risk score (PRS) models for predicting genetic risk of complex traits and diseases. We request data from PLCO to validate our PRS models by calculating area of ROC (AUC) based on the PLCO data. We are interested in obtaining the phenotype data for the following traits:

entryage_bq
ph_X_bq (here, X= lung, breast, prostate, ovarian, colorectal, melanoma, pancreatic)
fstcan_exitstat
X_exitstat (X= lung, breast, prostate, ovarian, colorectal, melanoma, pancreatic)

age
Sex
X_cancer (X= lung, breast, prostate, ovarian, colorectal, melanoma, pancreatic)
X_stage (X= lung, breast, prostate, ovarian, colorectal, melanoma, pancreatic)

bq_age
race7
cig_stat
fh_cancer
bmi_curr
height_f
weight_f
arthrit_f
bronchit_f
colon_comorbidity
diabetes_f
divertic_f
emphys_f
gallblad_f
hearta_f
hyperten_f
liver_comorbidity
osteopor_f
polyps_f
stroke_f

lmenstr
benign_ovcyst
endometriosis

infpros_f
infprosa
prosprob_f
Aims

We have built PRS models using data from public GWAS summary statistics and would like to evaluate the performance using PLCO data (the listed traits) by calculating AUC. A separate application was submitted to access PLCO genotype data for calculating PRS.

Collaborators

Bin Zhu, BB/DCEG/NCI
Difei Wang, CGR/DCEG/NCI
Kevin Wang, CGR/DCEG/NCI
Xing Hua, CGR/DCEG/NCI