Analysis of copy number variants on chromosome 21 in Down syndrome-associated congenital heart defects

One in five people with Down syndrome (DS) are born with an atrioventricular septal defect (AVSD), an incidence 2,000 times higher than in the euploid population. The genetic loci that contribute to this risk are poorly understood. In this study, we tested two hypotheses: 1) individuals with DS carrying chromosome 21 copy number variants (CNVs) that interrupt exons may be protected from AVSD, because these CNVs return AVSD susceptibility loci back to disomy, and 2) individuals with DS carrying chromosome 21 genes spanned by microduplications are at greater risk for AVSD because these microduplications boost the dosage of AVSD susceptibility loci beyond a tolerable threshold. We tested 236 case individuals with DS+AVSD and 290 control individuals with DS and a normal heart using a custom microarray with dense probes tiled on chromosome 21 for array CGH. We found that neither an individual chromosome 21 CNV nor any individual gene intersected by a CNV was associated with AVSD in DS. Burden analyses revealed that African American controls had more bases covered by rare deletions than did African American cases. Inversely, we found that Caucasian cases had more genes intersected by rare duplications than did Caucasian controls. Pathway analyses indicated copy number perturbtations of genes involved in protein heterotrimerization and histone methylating proteins. Finally, we showed that previously DS+AVSD-associated common CNVs on chromosome 21 are likely false positives. This research adds to the swell of evidence indicating that DS-associated AVSD is similarly heterogeneous, as is AVSD in the euploid population. aCGH for CNV detection. A single reference individual with Down Syndrome was used for all samples, labeled with Cy3 (Channel 2).

每5名唐氏综合征（Down syndrome）患者中即有1名先天合并房室间隔缺损（atrioventricular septal defect, AVSD），其发病率较整倍体人群高出2000倍。目前学界对该风险相关的遗传位点仍知之甚少。本研究验证了两项假说：其一，携带可打断外显子的21号染色体拷贝数变异（copy number variants, CNVs）的唐氏综合征患者或可免受房室间隔缺损困扰，因为此类CNVs可使房室间隔缺损易感位点恢复为二体状态；其二，携带21号染色体上被微重复区域覆盖的基因的唐氏综合征患者，其房室间隔缺损风险更高，因为这些微重复会将易感位点的剂量提升至超出耐受阈值的水平。
本研究采用定制的、在21号染色体上高密度铺设计探针的比较基因组杂交芯片（array comparative genomic hybridization, aCGH），对236例唐氏综合征合并房室间隔缺损（DS+AVSD）的病例组个体与290例唐氏综合征但心脏结构正常的对照组个体进行了检测。结果显示，无论是单个21号染色体CNV，还是CNV所覆盖的任意单个基因，均与唐氏综合征患者的房室间隔缺损无关联。负担分析结果表明，非裔美国人对照组中罕见缺失覆盖的碱基数量多于非裔美国人病例组。与之相反，高加索裔病例组中被罕见重复覆盖的基因数量多于高加索裔对照组。通路分析显示，涉及蛋白质异源三聚化与组蛋白甲基化蛋白的基因存在拷贝数扰动。最后，本研究证实，此前报道的与唐氏综合征合并房室间隔缺损相关的21号染色体常见CNVs大概率为假阳性结果。本研究进一步佐证了唐氏综合征相关房室间隔缺损与整倍体人群的房室间隔缺损一样，具有显著异质性。
用于拷贝数变异检测的比较基因组杂交芯片（aCGH）：本研究所有样本均使用1名唐氏综合征参考个体，以Cy3（通道2）进行标记。