SNP genotyping of cryptic complexity in structural chromosome abnormalities previously detected by cytogenetic analysis. Homo sapiens

Purpose: The purpose of this study was to evaluate SNP genotyping methodology as a means to detect chromosomal abnormalities previously diagnosed by G-band karyotype or fluorescence in situ hybridization (FISH) analysis and to determine the frequency of sub-microscopic (cryptic) chromosomal alterations in these subjects. Methods: We used the Illumina HumanHap Beadchip platform to genotype 40 individuals having previously detected chromosomal anomalies (by G-banded and/or FISH analysis). The resulting data were analyzed for signal intensity (log R ratio) and allelic composition (B allele frequency). Results: SNP array analysis detected 100% of previously identified cytogenetic abnormalities. Changes or clarifications of the ISCN karyotype designation assigned by conventional cytogenetic and/or FISH analysis were made in 82 % of the cases (32 of 39). Nine of the 39 cases (23%) involved a reassignment of an abnormal band while an additional 9 of the 39 (23%) resulted in a clarification of a sub-band assignment. In 8 more of the 39 cases (21%) the previously reported alterations were confirmed, however the SNP analysis also identified related cryptic alterations. SNP analysis not only confirmed FISH-detected abnormalities but also more precisely mapped the breakpoints of 6/6 patients. Investigations into the origin of de novo abnormalities in 15 trio families established that 12 /15 occurred on the paternal chromosome. Conclusions: SNP genotyping array analysis, confirmed all previously detected structural chromosomal abnormalities and provided additional, clinically-relevant genomic information in 82% of these alterations. Overall design: To evaluate potential chromosomal abnormalities in patients, we measured SNPs using Illumina 550K and 300K arrays. In some cases we also measured SNPs in parents to determine whether deletions or duplications occurred de novo or were inherited.

研究目的：本研究旨在评估SNP基因分型（SNP genotyping）方法，用于检测此前通过G带核型分析（G-band karyotype）或荧光原位杂交（fluorescence in situ hybridization, FISH）确诊的染色体异常，并明确上述受试者中亚显微（cryptic）染色体改变的发生频率。
研究方法：本研究采用Illumina HumanHap Beadchip基因分型平台，对40名此前经G带核型分析和/或荧光原位杂交（FISH）检测出染色体异常的个体进行基因分型。对所得数据的信号强度（对数比比值，log R ratio）及等位基因构成（B等位基因频率，B allele frequency）展开分析。
研究结果：SNP阵列（SNP array）分析可100%检出此前已明确的细胞遗传学异常。在39例病例中，82%的病例对传统细胞遗传学和/或荧光原位杂交（FISH）给出的国际细胞遗传学命名体系（ISCN）核型命名进行了修正或澄清。其中9例（23%）涉及异常条带的重新指定，另有9例（23%）明确了亚条带的命名。39例病例中有8例（21%）在确认此前报告的染色体改变的同时，SNP分析还检出了相关的隐匿性染色体改变。SNP阵列分析不仅确认了荧光原位杂交（FISH）检出的异常，还更精准地定位了6例患者的染色体断裂点。针对15个三人家庭的新发异常起源进行溯源分析后发现，12/15的新发异常发生于父源染色体。
研究结论：SNP基因分型阵列分析可确认所有此前检出的结构性染色体异常，并在82%的此类异常中提供了额外的、具有临床相关性的基因组学信息。
整体实验设计：为评估患者潜在的染色体异常，本研究使用Illumina 550K和300K芯片检测单核苷酸多态性（SNP）。在部分病例中，研究人员还对父母的SNP进行检测，以明确染色体缺失或重复属于新发变异还是遗传性变异。