REPORT Whole-Genome Analysis Reveals that Mutations in Inositol Polyphosphate Phosphatase-like 1 Cause Opsismodysplasia Jennifer E. Below, 1 Dawn L. Earl, 2,3 Kathryn M. Shively, 3 Margaret J. McMillin, 3 Joshua D. Smith, 1 Emily H. Turner, 1 Mark J. Stephan, 4 Lihadh I. Al-Gazali, 5 Jozef L. Hertecant, 5 David Chitayat, 6 Sheila Unger, 7 Daniel H. Cohn, 8,9 Deborah Krakow, 9,10 James M. Swanson, 11 Elaine M. Faustman, 12 Jay Shendure, 1 Deborah A. Nickerson, 1 Michael J. Bamshad, 1,2,3, * and University of Washington Center for Mendelian Genomics Opsismodysplasia is a rare, autosomal-recessive skeletal dysplasia characterized by short stature, characteristic facial features, and in some cases severe renal phosphate wasting. We used linkage analysis and whole-genome sequencing of a consanguineous trio to discover that mutations in inositol polyphosphate phosphatase-like 1 (INPPL1) cause opsismodysplasia with or without renal phosphate wasting. Evaluation of 12 families with opsismodysplasia revealed that INPPL1 mutations explain ~60% of cases overall, including both of the families in our cohort with more than one affected child and 50% of the simplex cases. Opsismodysplasia (MIM 258480) is a rare skeletal dysplasia with delayed bone maturation (from ‘‘opsismos,’’ Greek for ‘‘late’’). 1–3 The clinical signs observed at birth include short limbs, small hands and feet, relative macrocephaly with a large anterior fontanel, and characteristic craniofacial abnormalities including a prominent brow, depressed nasal bridge, a small anteverted nose, and a relatively long philtrum. Death secondary to respiratory failure during the first few years of life was reported in the cases originally described but the outcome is now known to be highly variable with multiple long-term survivors. 3 Typical radiographic findings include shortened long bones with very delayed epiphyseal ossification, severe platyspondyly, metaphyseal cupping, and characteristic abnormalities of the metacarpals and phalanges. Recurrence within sibships and incidence in consanguineous pedigrees suggest that the mode of inheritance of opsismodysplasia is autosomal recessive. 1–6 To determine the genetic basis of opsismodysplasia, one of two siblings with opsismodysplasia and severe hypo- phosphatemia because of renal phosphate wasting (AII-1 in Table 1, Figures 1 and 2, and Figure S1 available online) and his consanguineous parents were genotyped with the HumanCytoSNP-12 DNA Analysis BeadChip, at nearly 300,000 single-nucleotide polymorphisms (SNPs). All studies were approved by the institutional review boards of the University of Washington and Seattle Children’s Hospital and informed consent was obtained from partici- pants or their parents. Self-reported Hispanic and Native American ancestry was first confirmed with EIGENSTRAT. Parametric linkage analysis by a fully penetrant rare reces- sive model (f 2 ¼ 1; q ¼ 0.0001) and allele frequencies esti- mated from unrelated members of the HapMap CEPH, European, Chinese, Japanese, and Mexican American pop- ulations (Figure S2) was performed with ALLEGRO on an approximately 0.2 cM SNP map in an 11 person pedigree that included the consanguineous parents of the proband. Ten genomic regions reached a maximum LOD score of 1.5 (Figure S3). Homozygosity mapping via PLINK and default parameters (length ¼ 1 Mb, # SNPs [n] ¼ 100, density [kb/SNP] ¼ 50, largest gap [kb] ¼ 1 Mb) detected six of the regions also implicated via linkage analysis. Next, whole-genome sequencing was performed on both parents and the same affected sibling used in the linkage studies. In brief, 1 mg of genomic DNA was subjected to a series of shotgun library construction steps, including fragmentation through acoustic sonication (Covaris), end-polishing (NEBNext End Repair kit), A-tailing (NEBNext dA Tailing kit), and ligation of 8 bp barcoded sequencing adaptors (Enzymatics Ultrapure T4 Ligase). Libraries were automatically size selected for fragments 350–550 bp in length with the automated PippinPrep cartridge system, which provides for fine control over the insert size and physically isolates each size fraction in separate chambers. Prior to sequencing, the library was amplified via PCR (Kapa HiFi Hotsart). To facilitate optimal 1 Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; 2 Division of Genetic Medicine, Seattle Children’s Hospital, Seattle, WA 98105, USA; 3 Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; 4 Department of Pediatrics, Madigan Army Medical Center, Tacoma, WA 98431, USA; 5 Department of Pediatrics, United Arab Emirates University, PO Box 17666, Al Ain, United Arab Emirates; 6 Department of Obstetrics and Gynecology, The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, University of Toronto, Toronto, ON M5G 1Z5, Canada; 7 Department of Genetics, University of Lausanne, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland; 8 Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; 9 Department of Ortho- paedic Surgery, University of California, Los Angeles, Los Angeles, CA 90095, USA; 10 Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; 11 Department of Pediatrics, University of California, Irvine, Irvine, CA 92697, USA; 12 Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA *Correspondence: mbamshad@uw.edu http://dx.doi.org/10.1016/j.ajhg.2012.11.011. Ó2013 by The American Society of Human Genetics. All rights reserved. The American Journal of Human Genetics 92, 137–143, January 10, 2013 137