Supplementary Material for: Copy Number Variants in Short Children Born Small for Gestational Age

<b><i>Background/Aims:</i></b> In addition to genome-wide association studies (GWAS), height-associated genes may be uncovered by studying individuals with extreme short or tall stature. <b><i>Methods:</i></b> Genome-wide analysis for copy number variants (CNVs), using single nucleotide polymorphism (SNP) arrays, was performed in 49 index cases born small for gestational age with persistent short stature. Segregation analysis was performed, and genes in CNVs were compared with information from GWAS, gene expression in rodents' growth plates, and published information. <b><i>Results:</i></b> CNVs were detected in 13 cases. In 5 children a known cause of short stature was found: UPD7, UPD14, a duplication of the <i>SHOX</i> enhancer region, an<i> IGF1R</i> deletion, and a 22q11.21 deletion. In the remaining 8 cases, potential pathogenic CNVs were detected, either de novo (n = 1), segregating (n = 2), or not segregating with short stature (n = 5). Bioinformatic analysis of the de novo and segregating CNVs suggested that <i>HOXD4</i>, <i>AGPS</i>, <i>PDE11A</i>, <i>OSBPL6</i>, <i>PRKRA </i>and <i>PLEKHA3</i>, and possibly <i>DGKB</i> and <i>TNFRSF11B</i> are potential candidate genes<i>.</i> A <i>SERPINA7</i> or <i>NRK</i> defect may be associated with an X-linked form of short stature. <b><i>Conclusion:</i></b> SNP arrays detected 5 known causes of short stature with prenatal onset and suggested several potential candidate genes.