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）降低及自幼童或青年早期开始出现的骨折为特征。尽管已鉴定出几种单基因形式，但相关基因的功能描述仍不充分。为寻找新的变异和新候选位点，我们对70名患有轻度至重度骨骼脆弱的年轻受试者进行了稀有拷贝数变异（CNVs）的筛查。研究队列包括15名30岁前患有原发性骨质疏松症的受试者和55名在16岁前有病理性骨折病史且BMD低或正常的受试者。本研究采用了定制的高分辨率比较基因组杂交阵列，其中富含>1,150个对骨骼代谢和纤毛功能至关重要的基因的探针密度，以搜索CNVs。我们共鉴定出14种稀有CNVs。其中7种内含子异常被认为可能是良性的。5种临床意义未知的CNVs影响了以前未与骨骼脆弱相关的基因的编码区（ETV1-DGKB、AGBL2、ATM、RPS6KL1-PGF和SCN4A）。最终，两种CNVs分别被确认为致病性和可能致病性：一种涉及COL1A2（NM_000089.3）外显子1-4的4 kb缺失，另一种涉及PLS3（NM_005032.6）外显子3的12.5 kb重复。尽管这两个基因都与单基因形式的骨质疏松症有关，但COL1A2的缺失较为罕见，而PLS3的重复此前尚未有报道。这两种CNVs均发现于患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中的致病性CNVs数量，并证明了针对CNV筛查的有效性，这可能有助于在早发性骨质疏松症中定位新的候选位点。