微阵列比较基因组杂交技术检测不明原因智力低下/发育迟缓患儿的基因组拷贝数变异

Genomic copy number variations in children with unexplained mental retardation and developmental delay detected by array-comparative genomic hybridization

目的应用高分辨微阵列比较基因组杂交技术(Array-CGH),对中国人群不明原因的智力低下/发育迟缓(MR/DD)患儿进行全基因组拷贝数变异(CNVs)筛查,获得在这些不明原因MR/DD患儿中CNVs的检出率,并分析其中的罕见CNVs与MR/DD的相关性,以此评估Array-CGH对不明原因MR/DD可能的遗传病因诊断作用。方法根据特定筛选条件收集在首都儿科研究所临床诊断为不明原因MR/DD患儿,用Oligo244KDNA芯片筛查全基因组CNVs。针对所发现的CNVs,首先将其与国际基因组CNVs多态性数据库(databaseofgenomicvariants)进行比对,剔除常见多态性CNVs,将获得的罕见CNVs应用美国波士顿儿童医院遗传诊断实验室的临床分子诊断平台,结合基因组异常拷贝数数据库(DECIPHER)进行核查并与既往相关文献比对,以发现罕见CNVs在不明原因MR/DD患儿中的检出率。结果2004年7月至2008年7月共收集111例不明原因MR/DD患儿,平均年龄为6岁,男女比例为1.775。28例患儿发现36个罕见CNVs,CNVs平均长度为1326kb(29～8760kb),这些CNVs均无法被常规染色体G带检查所识别。通过评估,19例患儿携带可能与MR/DD相关的CNVs,另1例患儿的CNVs临床意义不明确,Array-CGH在不明原因MR/DD患儿中发现携带与疾病相关的罕见CNVs的诊断率为17.1%(19/111例)。22/36个(66.1%)罕见CNVs曾被美国波士顿儿童医院Array-CGH数据库、DECIPHER数据库、既往MR/DD微阵列研究文献所报道。1例患儿在15q11.2-13.1存在2098kb的基因组缺失,覆盖Prader-Willi综合征/Angelman综合征关键区的多个候选基因,包括SNRPN、NECDIN、SnRNAs和UBE3A,结合该患儿面部表型、临床检查以及Array-CGH结果,诊断为非典型性Prader-Willi综合征。结论基因组CNVs相关的微缺失/重复是中国人群中不明原因MR/DD患儿的原因之一,高分辨Array-CGH技术可在不明原因MR/DD患儿中发现更多的遗传病因,帮助和提高不明原因MR/DD的分子诊断水平。

Objective To screen for genome-wide copy number variations（CNVs） in Chinese children with unexplained mental retardation or developmental delay（MR/DD） using high resolution array-comparative genomic hybridization（Array-CGH）,identify rare CNVs（microdeletions/duplications） which may associate with MR/DD,and evaluate the effectiveness of Array-CGH in clinical molecular diagnosis of children with unexplained MR/DD.Methods Children with unexplained MR/DD were recruited for this study by using a high resolution oligo 244 K array for detection of genomic copy number variations.All identified CNVs were analyzed with the references from database of genomic variants（DGV）,database of DECIPHER,and UCSC brower（build 18）,as well as an internal Array-CGH database from the Genetics Diagnostic Lab of Children＇s Hospital Boston,plus a comprehensive literature review,to determine if the rare CNVs found in these children were associated with MR/DD.Results One hundred and eleven children with unexplained MR/DD were collected from July 2004 to July 2008.The average age was 6 years old and the ratio of male to female was 1.775.Among them,36 rare CNVs were identified in 28 patients.The average size of CNVs was 1 326 kb（29-8 760 kb） which was undetectable by chromosome analysis.Nineteen patients carried CNVs that may be associated with MR/DD but 1 patient had a CNV with uncertain clinical significance.The diagnostic yield of Array-CGH for these MR/DD children is 17.1%（19/111）.22/36 CNVs（61.1%） found by this study was also reported at least in one of the database and/or literature reviews.A 2 098 kb deletion at 15q11.2-13.1 overlapping with PWS/AS critical region was found in a patient who had global developmental delay,feeding difficulty,tricuspid incompetence,hypotonia,cryptorchidism and foot deformity.His dysmorphism included flat face,sparse hair,hypertelorism,down-slanting eyes and small hands.The MRI showed prominent bilateral frontal and temporal lobe sulcus,enlarged lateral ventricles.Atypical PWS was diagnosed according to his clinic information and Array-CGH finding.The deletion included SNRPN,NECDIN,SnRNAs,UBE3A genes.Conclusions CNV associated with microdeletions/duplications found in Chinese patients was one of the causes for unexplained mental retardation and developmental delay.Array-CGH could detect disease associated rare CNVs effectively which should be applied to clinical molecular diagnostics as a useful evaluation to help differential diagnosis of children with unexplained MR/DD and other ambiguous medical conditions.