Stevens-Kroef Marian Jpl, van den Berg Eva, Olde Weghuis Daniel, Geurts van Kessel Ad, Pfundt Rolph, Linssen-Wiersma Matty, Benjamins Marloes, Dijkhuizen Trijnie, Groenen Patricia Jta, Simons Annet
Department of Human Genetics, Radboud university medical center, P,O, Box 9101, Nijmegen 6500 HB, The Netherlands.
Mol Cytogenet. 2014 Jan 9;7(1):3. doi: 10.1186/1755-8166-7-3.
Characteristic genomic abnormalities in patients with B cell chronic lymphocytic leukemia (CLL) have been shown to provide important prognostic information. Fluorescence in situ hybridization (FISH) and multiplex ligation-dependent probe amplification (MLPA), currently used in clinical diagnostics of CLL, are targeted tests aimed at specific genomic loci. Microarray-based genomic profiling is a new high-resolution tool that enables genome-wide analyses. The aim of this study was to compare two recently launched genomic microarray platforms, i.e., the CytoScan HD Array (Affymetrix) and the HumanOmniExpress Array (Illumina), with FISH and MLPA to ascertain whether these latter tests can be replaced by either one of the microarray platforms in a clinical diagnostic setting.
Microarray-based genomic profiling and FISH were performed in all 28 CLL patients. For an unbiased comparison of the performance of both microarray platforms 9 patients were evaluated on both platforms, resulting in the identification of exactly identical genomic aberrations. To evaluate the detection limit of the microarray platforms we included 7 patients in which the genomic abnormalities were present in a relatively low percentage of the cells (range 5-28%) as previously determined by FISH. We found that both microarray platforms allowed the detection of copy number abnormalities present in as few as 16% of the cells. In addition, we found that microarray-based genomic profiling allowed the identification of genomic abnormalities that could not be detected by FISH and/or MLPA, including a focal TP53 loss and copy neutral losses of heterozygosity of chromosome 17p.
From our results we conclude that although the microarray platforms exhibit a somewhat lower limit of detection compared to FISH, they still allow the detection of copy number abnormalities present in as few as 16% of the cells. By applying similar interpretation criteria, the results obtained from both platforms were comparable. In addition, we conclude that both microarray platforms allow the identification of additional potential prognostic relevant abnormalities such as focal TP53 deletions and copy neutral losses of heterozygosity of chromosome 17p, which would have remained undetected by FISH or MLPA. The prognostic relevance of these novel genomic alterations requires further evaluation in prospective clinical trials.
B细胞慢性淋巴细胞白血病（CLL）患者的特征性基因组异常已被证明可提供重要的预后信息。荧光原位杂交（FISH）和多重连接依赖探针扩增（MLPA）目前用于CLL的临床诊断，是针对特定基因组位点的靶向检测。基于微阵列的基因组分析是一种新的高分辨率工具，能够进行全基因组分析。本研究的目的是将两种最近推出的基因组微阵列平台，即CytoScan HD Array（Affymetrix）和HumanOmniExpress Array（Illumina），与FISH和MLPA进行比较，以确定在临床诊断环境中后两种检测是否可以被微阵列平台之一所取代。
对所有28例CLL患者进行了基于微阵列的基因组分析和FISH检测。为了对两个微阵列平台的性能进行无偏比较，对9例患者在两个平台上进行了评估，结果发现完全相同的基因组畸变。为了评估微阵列平台的检测限，我们纳入了7例患者，这些患者的基因组异常细胞百分比相对较低（范围为5%-28%），这是之前通过FISH确定的。我们发现两个微阵列平台都能够检测到仅存在于16%细胞中的拷贝数异常。此外，我们发现基于微阵列的基因组分析能够识别FISH和/或MLPA无法检测到的基因组异常，包括局部TP53缺失和17号染色体杂合性的拷贝中性缺失。
从我们的结果可以得出结论，虽然微阵列平台与FISH相比检测限略低，但它们仍然能够检测到仅存在于16%细胞中的拷贝数异常。通过应用相似的解释标准，两个平台获得的结果具有可比性。此外，我们得出结论，两个微阵列平台都能够识别其他潜在的预后相关异常，如局部TP53缺失和17号染色体杂合性的拷贝中性缺失，而这些异常FISH或MLPA无法检测到。这些新的基因组改变的预后相关性需要在前瞻性临床试验中进一步评估。
