Data_Sheet_1_Rare Copy Number Variants in Array-Based Comparative Genomic Hybridization in Early-Onset Skeletal Fragility.XLSX

Early-onset osteoporosis is characterized by low bone mineral density (BMD) and fractures since childhood or young adulthood. Several monogenic forms have been identified but the contributing genes remain inadequately characterized. In search for novel variants and novel candidate loci, we screened a cohort of 70 young subjects with mild to severe skeletal fragility for rare copy-number variants (CNVs). Our study cohort included 15 subjects with primary osteoporosis before age 30 years and 55 subjects with a pathological fracture history and low or normal BMD before age 16 years. A custom-made high-resolution comparative genomic hybridization array with enriched probe density in >1,150 genes important for bone metabolism and ciliary function was used to search for CNVs. We identified altogether 14 rare CNVs. Seven intronic aberrations were classified as likely benign. Five CNVs of unknown clinical significance affected coding regions of genes not previously associated with skeletal fragility (ETV1-DGKB, AGBL2, ATM, RPS6KL1-PGF, and SCN4A). Finally, two CNVs were pathogenic and likely pathogenic, respectively: a 4 kb deletion involving exons 1–4 of COL1A2 (NM_000089.3) and a 12.5 kb duplication of exon 3 in PLS3 (NM_005032.6). Although both genes have been linked to monogenic forms of osteoporosis, COL1A2 deletions are rare and PLS3 duplications have not been described previously. Both CNVs were identified in subjects with significant osteoporosis and segregated with osteoporosis within the families. Our study expands the number of pathogenic CNVs in monogenic skeletal fragility and shows the validity of targeted CNV screening to potentially pinpoint novel candidate loci in early-onset osteoporosis.

早发性骨质疏松症以骨矿物质密度（BMD）降低及自幼年或年轻成年期开始出现的骨折为特征。尽管已鉴定出多种单基因形式，但相关基因的功能特征描述尚不充分。为探寻新型变异及新的候选位点，我们对70名骨骼脆弱程度从轻度到重度的年轻受试者进行了罕见拷贝数变异（CNVs）的筛查。研究队列中包括15名在30岁之前患有原发性骨质疏松症的受试者和55名在16岁之前有病理性骨折病史且骨矿物质密度低或正常的受试者。本研究采用了富含超过1,150个对骨代谢和纤毛功能至关重要的基因探针的高分辨率比较基因组杂交阵列，以寻找CNVs。我们总共鉴定出14种罕见CNVs。其中7种内含子异常被归类为可能良性。5种未知临床意义的CNVs影响了与骨骼脆弱性无关的基因的编码区（ETV1-DGKB、AGBL2、ATM、RPS6KL1-PGF和SCN4A）。最终，两种CNVs分别被归类为致病性和可能致病性：一种涉及COL1A2（NM_000089.3）外显子1至4的4 kb缺失，另一种涉及PLS3（NM_005032.6）外显子3的12.5 kb重复。尽管这两个基因均与单基因骨质疏松症形式有关联，但COL1A2的缺失极为罕见，而PLS3的重复尚未有报道。这两种CNVs均出现在具有显著骨质疏松症的受试者中，并在家族中与骨质疏松症相关联。本研究扩展了单基因骨骼脆弱性中的致病性CNVs数量，并证明了针对CNV的靶向筛查在潜在地定位早发性骨质疏松症的新候选位点方面的有效性。