Rare coding variants in RCN3 are associated with blood pressure

He, Karen Y.; Kelly, Tanika N.; Wang, Heming; Liang, Jingjing; Zhu, Luke; Cade, Brian E.; Assimes, Themistocles L.; Becker, Lewis C.; Beitelshees, Amber L.; Bielak, Lawrence F.; Bress, Adam P.; Brody, Jennifer A.; Chang, Yen-Pei C.; Chang, Yi-Cheng; de Vries, Paul S.; Duggirala, Ravindranath; Fox, Ervin R.; Franceschini, Nora; Furniss, Anna L.; Gao, Yan; Guo, Xiuqing; Haessler, Jeffrey; Hung, Yi-Jen; Hwang, Shih-Jen; Irvin, Marguerite R.; Kalyani, Rita R.; Liu, Ching-Ti; Liu, Chunyu; Martin, Lisa W.; Montasser, May E.; Muntner, Paul M.; Mwasongwe, Stanford; Naseri, Take; Palmas, Walter; Reupena, Muagututi’a S.; Rice, Kenneth M.; Sheu, Wayne H.; Shimbo, Daichi; Smith, Jennifer A.; Snively, Beverly M.; Yanek, Lisa R.; Zhao, Wei; Blangero, John; Boerwinkle, Eric; Chen, Yii-Der I.; Correa, Adolfo; Cupples, L. A.; Curran, Joanne E.; Fornage, Myriam; He, Jiang; Hou, Lifang; Kaplan, Robert C.; Kardia, Sharon L. R.; Kenny, Eimear E.; Kooperberg, Charles; Lloyd-Jones, Donald; Loos, Ruth J. F.; Mathias, Rasika A.; McGarvey, Stephen T.; Mitchell, Braxton D.; North, Kari E.; Peyser, Patricia A.; Psaty, Bruce M.; Raffield, Laura M.; Rao, D. C.; Redline, Susan; Reiner, Alex P.; Rich, Stephen S.; Rotter, Jerome I.; Taylor, Kent D.; Tracy, Russell; Vasan, Ramachandran S.; Morrison, Alanna C.; Levy, Daniel; Chakravarti, Aravinda; Arnett, Donna K.; Zhu, Xiaofeng

While large genome-wide association studies have identified nearly one thousand loci associated with variation in blood pressure, rare variant identification is still a challenge. In family-based cohorts, genome-wide linkage scans have been successful in identifying rare genetic variants for blood pressure. This study aims to identify low frequency and rare genetic variants within previously reported linkage regions on chromosomes 1 and 19 in African American families from the Trans-Omics for Precision Medicine (TOPMed) program. Genetic association analyses weighted by linkage evidence were completed with whole genome sequencing data within and across TOPMed ancestral groups consisting of 60,388 individuals of European, African, East Asian, Hispanic, and Samoan ancestries.

Associations of low frequency and rare variants in RCN3 and multiple other genes were observed for blood pressure traits in TOPMed samples. The association of low frequency and rare coding variants in RCN3 was further replicated in UK Biobank samples (N = 403,522), and reached genome-wide significance for diastolic blood pressure (p = 2.01 × 10− 7).

Low frequency and rare variants in RCN3 contributes blood pressure variation. This study demonstrates that focusing association analyses in linkage regions greatly reduces multiple-testing burden and improves power to identify novel rare variants associated with blood pressure traits.


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September 22, 2023


Rare variant analysis, Blood pressure, Whole genome sequencing