Targeted sequencing of genome wide significant loci associated with bone mineral density (BMD) reveals significant novel and rare variants: the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) targeted sequencing study.
Bone mineral density (BMD) is a heritable phenotype that predicts fracture risk. We performed fine-mapping by targeted sequencing at WLS, MEF2C, ARHGAP1/F2 and JAG1 loci prioritized by eQTL and bioinformatic approaches among 56 BMD loci from our previous GWAS meta-analysis. Targeted sequencing was conducted in 1,291 Caucasians from the Framingham Heart Study ( n =  925) and Cardiovascular Health Study ( n =  366), including 206 women and men with extreme low femoral neck (FN) BMD. A total of 4,964 sequence variants (SNVs) were observed and 80% were rare with MAF <1%. The associations between previously identified SNPs in these loci and BMD, while nominally significant in sequenced participants, were no longer significant after multiple testing corrections. Conditional analyses did not find protein-coding variants that may be responsible for GWAS signals. On the other hand, in the sequenced subjects, we identified novel associations in WLS , ARHGAP1 , and 5' of MEF2C ( P- values < 8x10  -   5 ; false discovery rate (FDR) q-values < 0.01) that were much more strongly associated with BMD compared to the GWAS SNPs. These associated SNVs are less-common; independent from previous GWAS signals in the same loci; and located in gene regulatory elements. Our findings suggest that protein-coding variants in selected GWAS loci did not contribute to GWAS signals. By performing targeted sequencing in GWAS loci, we identified less-common and rare non-coding SNVs associated with BMD independently from GWAS common SNPs, suggesting both common and less-common variants may associate with disease risks and phenotypes in the same loci.
The Institute for Aging Research Hebrew SeniorLife and the Department of Medicine Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.|Molecular and Integrative Physiological Sciences, Harvard School of Public Health, Boston, MA, USA.|BROAD Institute of MIT and Harvard, Cambridge, MA, USA.
Yi-Hsiang
YH
Hsu
Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA.
Guo
G
Li
Department of Biostatistics, Boston University School of Public Health, Boston, MA.
Ching-Ti
CT
Liu
Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA.
Jennifer A
JA
Brody
The Institute for Aging Research Hebrew SeniorLife and the Department of Medicine Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.|Faculty of Medicine in the Galilee, Bar Ilan University, Israel.
David
D
Karasik
BROAD Institute of MIT and Harvard, Cambridge, MA, USA.
Wen-Chi
WC
Chou
Department of Biostatistics, Boston University School of Public Health, Boston, MA.
Serkalem
S
Demissie
The Institute for Aging Research Hebrew SeniorLife and the Department of Medicine Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
Kannabiran
K
Nandakumar
Department of Biostatistics, Boston University School of Public Health, Boston, MA.
Yanhua
Y
Zhou
The Institute for Aging Research Hebrew SeniorLife and the Department of Medicine Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
Chia-Ho
CH
Cheng
BROAD Institute of MIT and Harvard, Cambridge, MA, USA.
Richard
R
Gill
Baylor College of Medicine, Human Genome Sequencing Center, Houston, TX, USA.
Richard A
RA
Gibbs
Baylor College of Medicine, Human Genome Sequencing Center, Houston, TX, USA.
Donna
D
Muzny
Baylor College of Medicine, Human Genome Sequencing Center, Houston, TX, USA.
Jireh
J
Santibanez
Department of Internal Medicine and Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.
Karol
K
Estrada
Department of Internal Medicine and Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.
Fernando
F
Rivadeneira
National Instute on Aging, National Institutes of Health, Bethesda, MD, USA.
Tamara
T
Harris
Icelandic Heart Association, Kopavogur, Iceland and Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
Vilmundur
V
Gudnason
Department of Internal Medicine and Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.
Andre
A
Uitterlinden
Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA; Group Health Research Institute, Group Health Cooperative, Seattle, WA, USA.
Bruce M
BM
Psaty
Department of Medicine, University of California, Davis, Sacramento, CA, USA.
John A
JA
Robbins
Department of Biostatistics, Boston University School of Public Health, Boston, MA.|Framingham Heart Study, Framingham, MA, USA.
L
L
Adrienne Cupples
The Institute for Aging Research Hebrew SeniorLife and the Department of Medicine Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.|BROAD Institute of MIT and Harvard, Cambridge, MA, USA.
Douglas P
DP
Kiel
D000375:Aging / Q000235:genetics / Q000473:pathology; D015519:Bone Density / Q000235:genetics*; D002318:Cardiovascular Diseases / Q000235:genetics* / Q000473:pathology; D015331:Cohort Studies; D016021:Epidemiologic Studies; D005260:Female; D005272:Femur Neck / Q000378:metabolism / Q000473:pathology; D020690:GTPase-Activating Proteins / Q000235:genetics*; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D006801:Humans; D064326:MEF2 Transcription Factors / Q000235:genetics; D008297:Male; D008875:Middle Aged; D020641:Polymorphism, Single Nucleotide
C000621391:ARHGAP1 protein, human; D020690:GTPase-Activating Proteins; D064326:MEF2 Transcription Factors; C578040:MEF2C protein, human