title: Evaluation of IRX Genes and Conserved Noncoding Elements in a Region on 5p13.3 Linked to Families with Familial Idiopathic Scoliosis and Kyphosis.
abstract: Because of genetic heterogeneity present in idiopathic scoliosis, we previously defined clinical subsets (a priori) from a sample of families with idiopathic scoliosis to find genes involved with spinal curvature. Previous genome-wide linkage analysis of seven families with at least two individuals with kyphoscoliosis found linkage (P-value = 0.002) in a 3.5-Mb region on 5p13.3 containing only three known genes, IRX1, IRX2, and IRX4 In this study, the exons of IRX1, IRX2, and IRX4, the conserved noncoding elements in the region, and the exons of a nonprotein coding RNA, LOC285577, were sequenced. No functional sequence variants were identified. An intrafamilial test of association found several associated noncoding single nucleotide variants. The strongest association was with rs12517904 (P = 0.00004), located 6.5 kb downstream from IRX1 In one family, the genotypes of nine variants differed from the reference allele in all individuals with kyphoscoliosis, and two of three individuals with scoliosis, but did not differ from the reference allele in all other genotyped individuals. One of these variants, rs117273909, was located in a conserved noncoding region that functions as an enhancer in mice. To test whether the variant allele at rs117273909 had an effect on enhancer activity, zebrafish transgenesis was performed with overlapping fragments of 198 and 687 bp containing either the wild type or the variant allele. Our data suggests that this region acts as a regulatory element; however, its size and target gene(s) need to be identified to determine its role in idiopathic scoliosis.
authors.affiliation: Genometrics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland 21224 cmj@mail.nih.gov.
authors.forename: Cristina M
authors.identifier: 0000-0002-6190-6821
authors.initials: CM
authors.lastname: Justice
authors.affiliation: Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892.
authors.forename: Kevin
authors.initials: K
authors.lastname: Bishop
authors.affiliation: Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892.
authors.forename: Blake
authors.initials: B
authors.lastname: Carrington
authors.affiliation: National Institutes of Health Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland 20852.
authors.forename: Jim C
authors.initials: JC
authors.lastname: Mullikin
authors.affiliation: Department of Orthopedic Surgery, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045.
authors.forename: Kandice
authors.initials: K
authors.lastname: Swindle
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21224.
authors.forename: Beth
authors.initials: B
authors.lastname: Marosy
authors.affiliation: Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892.
authors.forename: Raman
authors.initials: R
authors.lastname: Sood
authors.affiliation: Department of Orthopedic Surgery, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045.
authors.forename: Nancy H
authors.initials: NH
authors.lastname: Miller
authors.affiliation: Genometrics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland 21224.
authors.forename: Alexander F
authors.initials: AF
authors.lastname: Wilson
mesh_terms: D000818:Animals; D030801:Animals, Genetically Modified; D002895:Chromosomes, Human, Pair 5; D017124:Conserved Sequence; D005091:Exons; D015870:Gene Expression; D017930:Genes, Reporter; D056726:Genetic Association Studies; D020022:Genetic Predisposition to Disease; D005838:Genotype; D018398:Homeodomain Proteins / Q000737:chemistry / Q000235:genetics*; D006801:Humans; D007738:Kyphosis / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D012600:Scoliosis / Q000235:genetics*; D015027:Zebrafish
chemical_list: D018398:Homeodomain Proteins
keywords: IRX genes; conserved noncoding regions; idiopathic scoliosis; kyphoscoliosis; zebrafish transgenesis