Positive predictive value highlights four novel candidates for actionable genetic screening from analysis of 220,000 clinicogenomic records

• Published in: Genetics in medicine Vol. 23; no. 12; pp. 2300 - 2308
• Main Authors: Schiabor Barrett, Kelly M., Bolze, Alexandre, Ni, Yunyun, White, Simon, Isaksson, Magnus, Sharma, Lavania, Levin, Elissa, Lee, William, Grzymski, Joseph J., Lu, James T., Washington, Nicole L., Cirulli, Elizabeth T.
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01-12-2021; Elsevier Limited
• Subjects: Biomedical and Life Sciences; Biomedicine; Exome; Exome Sequencing; Genes; Genes, BRCA2; Genetic Predisposition to Disease; Genetic Testing; Human Genetics; Humans; Laboratory Medicine; Population; Predictive Value of Tests
• ISSN: 1098-3600; 1530-0366; 1530-0366
• DOI: 10.1038/s41436-021-01293-9

Purpose
To identify conditions that are candidates for population genetic screening based on population prevalence, penetrance of rare variants, and actionability.
Methods
We analyzed exome and medical record data from >220,000 participants across two large population health cohorts with different demographics. We performed a gene-based collapsing analysis of rare variants to identify genes significantly associated with disease status.
Results
We identify 74 statistically significant gene–disease associations across 27 genes. Seven of these conditions have a positive predictive value (PPV) of at least 30% in both cohorts. Three are already used in population screening programs (
BRCA1
,
BRCA2
,
LDLR
), and we also identify four new candidates for population screening:
GCK
with diabetes mellitus,
HBB
with β-thalassemia minor and intermedia,
PKD1
with cystic kidney disease, and
MIP
with cataracts. Importantly, the associations are actionable in that early genetic screening of each of these conditions is expected to improve outcomes.
Conclusion
We identify seven genetic conditions where rare variation appears appropriate to assess in population screening, four of which are not yet used in screening programs. The addition of
GCK
,
HBB
,
PKD1
, and
MIP
rare variants into genetic screening programs would reach an additional 0.21% of participants with actionable disease risk, depending on the population.