Cancer PRSweb

Polygenic risk scores

Scores Evaluation trait 172 Michigan Genomics Initiative

Skin cancer

ICD9 and ICD10 based PheWAS codes

Binary MGI Fixed threshold (5e-06) UKB GWAS (PheCode) nominally significant

Model details

PRS IDprsweb-phecode172-ukbb-saige-hrc-x172-p-5e-06-mgi-20200608
Legacy IDPRSWEB_PHECODE172_UKBB-SAIGE-HRC-X172_P_5e-06_MGI_20200608
Legacy modelP_5e-06
# SNPs159
Discovery GWAS trait/source UKB GWAS (PheCode)
Genome buildGRCh37/hg19
Tuning parameterP<=5e-06
Reference Publication UKB_GWAS
PubMed 30104761
Last updated2020-06-08

Evaluation details

Evaluation cohortMichigan Genomics Initiative
Evaluation trait Skin cancer
172
Trait typeBinary
SexBoth
Cases3557
Controls14050

PRS performance

P value4.1e-58
Pseudo-R²0.026
Brier score0.146
AAUC0.586
AAUC CI0.576-0.597
Percentile effect metricOR
Top percentile OR 95% CI
1%2.061.53-2.77
2%2.361.91-2.92
5%2.121.84-2.44
10%1.901.70-2.12
25%1.761.62-1.91

How to use this score page

  • Start with P value and the main performance metrics above to judge whether this model is useful in this cohort.
  • Use the top-percentile rows to see how strongly the score separates the upper PRS tail.
  • Use the main Scores table to compare alternative models for the same trait when no preserved PheWAS follow-up is attached.

Flag guide: nominally significant passed the preserved release's nominal threshold; reversed effect means the observed direction ran opposite to the expected effect direction in the preserved evaluation.

Files and next steps

This release keeps the score metadata and performance summary for this model, but it does not preserve a rendered PheWAS result set or downloadable scan tables for it. Use the main Scores table to compare alternative models for the same trait, and see the Method page for cohort and metric definitions.

Related links and downloads

This release does not preserve direct weight links or PheWAS artifacts for this model. Use the main Scores table to compare alternative models for the same trait.