Frequently asked questions

Clarity on reasons for and benefits of chromosomal microarray  

While chromosomal microarray (Mayo ID: CMAPT) is appropriate for many tumor types, it’s particularly beneficial in the characterization of gliomas. Our microarray’s platform (Affymetrix Oncoscan) contains 220,000 unique single nucleotide polymorphisms (SNPs) to target cancer genes of relevance with a resolution of approximately 50 kb for copy number variants (CNV) in targeted genes and approximately 500 kb for genome-wide CNVs. In addition, chromosomal microarray detects loss of heterozygosity (LOH) at approximately 5 Mb.

What are the indications for ordering a chromosomal microarray on formalin-fixed paraffin-embedded (FFPE) tumor specimens?

Identifying chromosomal abnormalities in malignant neoplasms can provide diagnostic, prognostic, and therapeutic information critical to proper patient care and management. While the level of resolution available through conventional chromosome analysis can identify many chromosomal abnormalities, it is not sufficient to detect copy-neutral loss of heterozygosity. Chromosomal microarray improves diagnostic yield through the use of single nucleotide polymorphism probes, which detect small copy number changes and regions of copy-neutral loss of heterozygosity.

What is the diagnostic benefit of chromosomal microarray for gliomas?

Chromosomal microarray facilitates molecular subclassification of all possible types of high- and low-grade adult gliomas by detecting distinct patterns of copy number alterations. Among the subclassifications of common and rare gliomas named by the World Health Organization (WHO) are astrocytoma, oligodendroglioma, oligoastrocytoma, high-grade astrocytoma with piloid features (HGAP), and pediatric glioblastoma H3K27 IDH wild type. Associations between these molecular subclassifications may further predict prognosis and response to chemotherapy and radiation treatment.

For example, what appears to be an oligodendroglioma by histological evaluation and positive molecular study for an IDH mutation, could be accurately diagnosed as an astrocytoma, IDH-mutant and not oligodendroglioma, IDH-mutant, 1p/19q codeleted, through microarray identification of associated chromosome anomalies. Another example is the use of microarray to correctly classify low-grade lesions with glial atypia as glioblastoma when histology alone is unclear.

What is the benefit of using chromosomal microarray rather than traditional FISH testing to detect 1p/19q co-deletions?

For many years FISH was the standard method to detect co-deletion of 1p/19q, which predicts gliomas of oligodendroglial lineage shown to have a better prognosis and therapeutic response. Microarray analysis, however, is a more sensitive approach to detect whole arm 1p/19q co-deletion.

Because FISH analysis cannot differentiate between different types of deletions, it is not recommended for detection of whole arm 1p/19q deletions. Microarray testing can detect copy number changes across the entire genome in a single assay, easily differentiating between whole-arm co-deletions versus partial-arm deletions of 1p and 19q, and is better for determining prognosis and response to treatment.

Are there additional applications of chromosomal microarray for brain tumors? 

  • New alterations named in the WHO 2021 glioma classification guidelines1 can be easily identified through chromosomal microarray.
  • Identification of CDKN2A homozygous deletion, which is essential for determining the prognosis of both astrocytoma, IDH-mutant and not oligodendroglioma, IDH-mutant, 1p/19q codeletions.
  • Clarifies +7/-10 and EGFR amplification, which are diagnostic of glioblastoma and included in 2021 WHO guidelines.

What is the value of using microarray in tandem with next-generation sequencing? 

Chromosomal microarray and next-generation sequencing (NGS) are complementary tests in specific clinical scenarios. Several entities named in the 2021 WHO guidelines are challenging to distinguish from one another. The use of NGS (Mayo ID: NONCP) test results can be used to assist with the interpretation of array results, and vice versa, which improves diagnostic confidence, especially in complicated cases.

How are the results of microarray testing used in patient care? 

Due to differing prognoses based on tumor type, accurate diagnosis is critical to guide appropriate treatment and disease management. For instance, a patient with a low-grade oligo glioma that is difficult to surgically remove and lacking in adverse genetic features would likely be watched, since chemotherapy and/or radiation could generate a more aggressive recurrent tumor. Conversely, patients who have tumors with high-grade pathological features or CDKN2A homozygous deletions would receive chemotherapy and radiation therapy earlier in the disease course.

  1. Sejda A, Grajkowska W, Trubicka J, Szutowicz E, Wojdacz T, Kloc W, Iżycka-Świeszewska E. WHO CNS5 2021 classification of gliomas: a practical review and road signs for diagnosing pathologists and proper patho-clinical and neuro-oncological cooperation. Folia Neuropathol. 2022;60(2):137-152. doi:10.5114/fn.2022.118183. PMID: 35950467.

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