Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR (Mapping250K_Nsp and Mapping250K_Sty)

Clinical laboratories are adopting array comparative genomic hybridization (AGH) as a standard clinical test. A number of whole genome AGH systems are available, but little is known about the comparative performance in a clinical context. We prospectively studied 30 children with idiopathic MR and both unaffected parents of each child using Affymetrix 500K GeneChip SNP arrays, Agilent Human Genome 244K oligonucleotide arrays and NimbleGen 385K Whole-Genome oligonucleotide arrays. We determined whether CNVs called on these platforms were detected by Illumina Hap550 beadchips or SMRT 32K BAC whole genome tiling arrays and tested 15 of the 30 trios on Affymetrix 6.0 SNP array. The Affymetrix 500K, Agilent and NimbleGen platforms identified 3061 autosomal and 117 X chromosome CNVs in 30 trios. 147 of these CNVs were de novo, but only 33 (22%) of the de novo CNVs were found on more than one platform. Performing genotype-phenotype correlations, we identified 7 pathogenic and 4 possibly pathogenic CNVs for MR. All 11 of these CNVs were detected by both the Agilent and NimbleGen arrays, 9 by the Affymetrix 500K and Illumina beadchips, and 5 by the SMRT BAC array. Two of the 4 pathogenic or possibly pathogenic CNVs present in the trios tested with the Affymetrix 6.0 array were identified. Our findings demonstrate that different results are obtained with different AGH platforms and illustrate the trade-off that exists between sensitivity and specificity. The large number of apparently false positive CNV calls supports the need for validating clinically important findings with a different methodology. 45 trios were analysed consisting of child (proband) and both normal parents.

临床实验室正将阵列比较基因组杂交（array comparative genomic hybridization, AGH）作为标准临床检测手段。目前已有多款全基因组AGH系统投入应用，但针对其在临床场景中的比较性能，现有认知仍较为匮乏。本研究前瞻性纳入30名特发性智力障碍（idiopathic mental retardation, MR）患儿及其每名患儿的健康双亲，采用Affymetrix 500K GeneChip SNP阵列、安捷伦（Agilent）人类基因组244K寡核苷酸阵列及尼姆博真（NimbleGen）385K全基因组寡核苷酸阵列开展检测。我们评估了上述平台检出的拷贝数变异（copy number variations, CNVs）是否可通过因美纳（Illumina）Hap550微珠芯片或SMRT 32K细菌人工染色体（bacterial artificial chromosome, BAC）全基因组铺瓦阵列予以验证，并对30个核心家系中的15个采用Affymetrix 6.0 SNP阵列进行了检测。在30个核心家系中，Affymetrix 500K、安捷伦及尼姆博真平台共检出3061个常染色体拷贝数变异及117个X染色体拷贝数变异。其中147个为新发（de novo）拷贝数变异，但仅33个（22%）的新发拷贝数变异可在多个平台上被检出。通过开展基因型-表型关联分析，我们共鉴定出7个与MR相关的致病性（pathogenic）拷贝数变异及4个可能致病性（possibly pathogenic）拷贝数变异。上述11个拷贝数变异均可通过安捷伦及尼姆博真阵列检出，其中9个可通过Affymetrix 500K及因美纳微珠芯片检出，5个可通过SMRT BAC阵列检出。在采用Affymetrix 6.0阵列检测的核心家系中，4个致病性或可能致病性拷贝数变异中的2个被成功鉴定。本研究结果表明，不同AGH平台可得出不同的检测结果，同时阐明了灵敏度与特异性之间存在的权衡关系。大量疑似假阳性拷贝数变异检出结果提示，有必要采用不同的检测方法对具有临床意义的发现进行验证。本研究共分析了45个核心家系，每个家系均包含先证者（proband，患儿）及其健康双亲。