Institute of Cell and Molecular Pathology, Hannover Medical School, Hannover, Germany.
Genes Chromosomes Cancer. 2010 Oct;49(10):885-900. doi: 10.1002/gcc.20797.
To evaluate whether copy number alterations (CNAs) are present that may contribute to disease development and/or progression of childhood myelodysplastic syndromes (MDS), 36 pediatric MDS patients were analyzed using array-based comparative genome hybridization (aCGH). In addition to monosomy 7, the most frequent chromosome aberration in childhood MDS, novel recurrent CNAs were detected. They included a loss of 3p14.3-p12.3, which contains the putative tumor suppressor gene FHIT, a loss of 7p21.3-p15.3, a loss of 9q33.3-q34.3 (D184) and microdeletions in 17p11.2, 6q23 containing MYB, and 17p13 containing TP53. In this small patient cohort, patients without CNA, patients with monosomy 7 only and patients with one CNA in addition to monosomy 7 did not differ in their survival. As expected, all patients with complex karyotypes, including two patients with deletions of TP53, died. A challenge inherent to aCGH analysis of MDS is the low percentage of tumor cells. We evaluated several approaches to overcome this limitation. Genomic profiles from isolated granulocytes were of higher quality than those from bone marrow mononuclear cells. Decreased breakpoint calling stringency increased recognition of CNAs present in small clonal populations. However, further analysis using a custom-designed array showed that these CNAs often did not confirm the findings from 244k arrays. In contrast, constitutional CNVs were reliably detected on both arrays. Moreover, aCGH on amplified DNA from distinct myeloid clusters is a new approach to determine CNAs in small subpopulations. Our results clearly emphasize the need to verify array-CGH results by independent methods like FISH or quantitative PCR.
为了评估是否存在可能导致儿童骨髓增生异常综合征（MDS）发展和/或进展的拷贝数改变（CNAs），我们使用基于阵列的比较基因组杂交（aCGH）分析了 36 名儿科 MDS 患者。除了儿童 MDS 中最常见的染色体异常——单体 7 之外，还检测到了新的反复出现的 CNA。它们包括 3p14.3-p12.3 的缺失，该区域包含潜在的肿瘤抑制基因 FHIT；7p21.3-p15.3 的缺失，9q33.3-q34.3（D184）的缺失，17p11.2、6q23 中包含 MYB 的微缺失，以及 17p13 中包含 TP53 的微缺失。在这个小患者队列中，没有 CNA 的患者、仅单体 7 的患者和除单体 7 之外还有一个 CNA 的患者在生存方面没有差异。正如预期的那样，所有具有复杂核型的患者，包括两个缺失 TP53 的患者，都死亡了。aCGH 分析 MDS 所固有的一个挑战是肿瘤细胞的百分比低。我们评估了几种克服这一限制的方法。从分离的粒细胞中获得的基因组图谱质量优于从骨髓单核细胞中获得的基因组图谱。降低断点调用严格性增加了对小克隆群体中存在的 CNA 的识别。然而，使用定制设计的阵列进行的进一步分析表明，这些 CNA 通常与 244k 阵列的结果不一致。相比之下，两种阵列都可靠地检测到了染色体结构变异。此外，从不同髓系簇扩增 DNA 的 aCGH 是一种确定小亚群中 CNA 的新方法。我们的结果清楚地强调了需要通过独立方法（如 FISH 或定量 PCR）验证阵列-CGH 结果的必要性。
