A genome-wide association study implicates the BMP7 locus as a risk factor for nonsyndromic metopic craniosynostosis.

Cristina M Justice, Araceli Cuellar, Krithi Bala, Jeremy A Sabourin, Michael L Cunningham, Karen Crawford, Julie M Phipps, Yan Zhou, Deirdre Cilliers, Jo C Byren, David Johnson, Steven A Wall, Jenny E V Morton, Peter Noons, Elizabeth Sweeney, Astrid Weber, Katie E M Rees, Louise C Wilson, Emil Simeonov, Radka Kaneva, Nadezhda Yaneva, Kiril Georgiev, Assen Bussarsky, Craig Senders, Marike Zwienenberg, James Boggan, Tony Roscioli, Gianpiero Tamburrini, Marta Barba, Kristin Conway, Val C Sheffield, Lawrence Brody, James L Mills, Denise Kay, Robert J Sicko, Peter H Langlois, Rachel K Tittle, Lorenzo D Botto, Mary M Jenkins, Janine M LaSalle, Wanda Lattanzi, Andrew O M Wilkie, Alexander F Wilson, Paul A Romitti, Simeon A Boyadjiev

Journal: Human genetics 2020;139(8):1077-1090

PMID: 32266521

Abstract

Our previous genome-wide association study (GWAS) for sagittal nonsyndromic craniosynostosis (sNCS) provided important insights into the genetics of midline CS. In this study, we performed a GWAS for a second midline NCS, metopic NCS (mNCS), using 215 non-Hispanic white case-parent triads. We identified six variants with genome-wide significance (P ≤ 5 × 10): rs781716 (P = 4.71 × 10; odds ratio [OR] = 2.44) intronic to SPRY3; rs6127972 (P = 4.41 × 10; OR = 2.17) intronic to BMP7; rs62590971 (P = 6.22 × 10; OR = 0.34), located ~ 155 kb upstream from TGIF2LX; and rs2522623, rs2573826, and rs2754857, all intronic to PCDH11X (P = 1.76 × 10, OR = 0.45; P = 3.31 × 10, OR = 0.45; P = 1.09 × 10, OR = 0.44, respectively). We performed a replication study of these variants using an independent non-Hispanic white sample of 194 unrelated mNCS cases and 333 unaffected controls; only the association for rs6127972 (P = 0.004, OR = 1.45; meta-analysis P = 1.27 × 10, OR = 1.74) was replicated. Our meta-analysis examining single nucleotide polymorphisms common to both our mNCS and sNCS studies showed the strongest association for rs6127972 (P = 1.16 × 10). Our imputation analysis identified a linkage disequilibrium block encompassing rs6127972, which contained an enhancer overlapping a CTCF transcription factor binding site (chr20:55,798,821-55,798,917) that was significantly hypomethylated in mesenchymal stem cells derived from fused metopic compared to open sutures from the same probands. This study provides additional insights into genetic factors in midline CS.

Address: Genometrics Section, Computational and Statistical Genomics Branch, Division of Intramural Research, NHGRI, NIH, Baltimore, MD, USA.; Department of Pediatrics, University of California Davis, 4625 2nd Avenue, Research Building II, Sacramento, CA, 95817, USA.; Department of Pediatrics, Division of Craniofacial Medicine, Seattle Children's Craniofacial Center, Seattle Children's Research Institute, University of Washington, Seattle, WA, USA.; MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.; MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.; Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.; Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.; Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.; West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK.; Birmingham Craniofacial Unit, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK.; Birmingham Craniofacial Unit, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK.; Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, England, UK.; Clinical Genetics Service, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK.; National Institute of Pediatrics, Sofia Medical University, Sofia, Bulgaria.; Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria.; National Genetic Laboratory, University Hospital of Obstetrics and Gynecology "Maichin Dom", Medical University of Sofia, Sofia, Bulgaria.; Department of Neurosurgery, University Hospital 'St. Ivan Rilski', Medical University of Sofia, Sofia, Bulgaria.; Department of Otolaryngology, Head and Neck Surgery, University of California Davis, Sacramento, CA, USA.; Department of Neurosurgery, University of California Davis, Sacramento, CA, USA.; Neuroscience Research Australia, University of New South Wales, Sydney, Australia.; Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.; Section of Neurosurgery, Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy.; Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.; Section of Experimental Biology, Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy.; Department of Epidemiology, College of Public Health, The University of Iowa, 145 N Riverside Dr, S416 CPHB, Iowa City, IA, 52242, USA.; Department of Pediatrics, Division of Medical Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA.; Gene and Environment Interaction Section, NHGRI, Bethesda, NIHMD, USA.; Epidemiology Branch, Eunice Kennedy Shriver NICHD, NIH, Bethesda, MD, USA.; Division of Genetics, NYS Department of Health, Wadsworth CenterAlbany, NY, USA.; Birth Defects Epidemiology and Surveillance Branch, Texas Department of State Health Services, Austin, TX, USA.; Department of Nutritional Sciences, University of Texas at Austin, Austin, TX, USA.; Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA.; National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA.; Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA, USA.; MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.; Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.; Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.; Department of Epidemiology, College of Public Health, The University of Iowa, 145 N Riverside Dr, S416 CPHB, Iowa City, IA, 52242, USA. [email protected].; Department of Pediatrics, University of California Davis, 4625 2nd Avenue, Research Building II, Sacramento, CA, 95817, USA. [email protected].
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