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Ultra-High Density SNParray in Neuroblastoma Molecular Diagnostics.

Ambros IM, Brunner C, Abbasi R, Frech C, Ambros PF - Front Oncol (2014)

Bottom Line: However, MYCN amplification is by far not the only genetic change associated with unfavorable clinical courses.However, these genomic aberrations need to be scrutinized in larger studies applying the most appropriate techniques.Single nucleotide polymorphism arrays have proven successful in deciphering genomic aberrations of cancer cells; these techniques, however, are usually not applied in the daily routine.

View Article: PubMed Central - PubMed

Affiliation: Children's Cancer Research Institute, St. Anna Kinderkrebsforschung , Vienna , Austria.

ABSTRACT
Neuroblastoma serves as a paradigm for applying tumor genomic data for determining patient prognosis and thus for treatment allocation. MYCN status, i.e., amplified vs. non-amplified, was one of the very first biomarkers in oncology to discriminate aggressive from less aggressive or even favorable clinical courses of neuroblastoma. However, MYCN amplification is by far not the only genetic change associated with unfavorable clinical courses. So called "segmental chromosomal aberrations," (SCAs) i.e., gains or losses of chromosomal fragments, can also indicate tumor aggressiveness. The clinical use of these genomic aberrations has, however, been hampered for many years by methodical and interpretational problems. Only after reaching worldwide consensus on markers, methodology, and data interpretation, information on SCAs has recently been implemented in clinical studies. Now, a number of collaborative studies within COG, GPOH, and SIOPEN use genomic information to stratify therapy for patients with localized and metastatic disease. Recently, new types of DNA based aberrations influencing the clinical behavior of neuroblastomas have been described. Deletions or mutations of genes like ATRX and a phenomenon referred to as "chromothripsis" are all assumed to correlate with an unfavorable clinical behavior. However, these genomic aberrations need to be scrutinized in larger studies applying the most appropriate techniques. Single nucleotide polymorphism arrays have proven successful in deciphering genomic aberrations of cancer cells; these techniques, however, are usually not applied in the daily routine. Here, we present an ultra-high density (UHD) SNParray technique which is, because of its high specificity and sensitivity and the combined copy number and allele information, highly appropriate for the genomic diagnosis of neuroblastoma and other malignancies.

No MeSH data available.


Related in: MedlinePlus

Depicts examples of homogenous “classical” and heterogeneous MYCN amplified tumors. The FISH picture, (A) (MYCN FISH probe in green, 2p probe in red), shows tumor cell nuclei with a varying number of MYCN signals ranging from approximately 30 signals up to hundreds distributed randomly within the nuclei. The large size of some of the MYCN hybridization spots can be explained by repeated amplicon units. The SNParray profile of a segment of the short arm of chromosome 2 from a homogeneously amplified neuroblastoma is given in (B) which shows a clear peak for the MYCN locus (copy number ~48). (C,D) Examples of a so called hetMNA tumor. In the I-FISH picture (C), one tumor cell nucleus clearly displays MYCN amplification (arrow), while the others do have a balanced number of MYCN and reference probe hybridization signals. The SNParray profile (D) shows an example of a heterogeneous MYCN amplified tumor with much lower peaks (copy number < 3 of the smooth signals, lower line) than compared to the profile given in (B) and could easily be missed if the number of tumor cell nuclei with MYCN amplification is too small in the sample under examination.
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Figure 4: Depicts examples of homogenous “classical” and heterogeneous MYCN amplified tumors. The FISH picture, (A) (MYCN FISH probe in green, 2p probe in red), shows tumor cell nuclei with a varying number of MYCN signals ranging from approximately 30 signals up to hundreds distributed randomly within the nuclei. The large size of some of the MYCN hybridization spots can be explained by repeated amplicon units. The SNParray profile of a segment of the short arm of chromosome 2 from a homogeneously amplified neuroblastoma is given in (B) which shows a clear peak for the MYCN locus (copy number ~48). (C,D) Examples of a so called hetMNA tumor. In the I-FISH picture (C), one tumor cell nucleus clearly displays MYCN amplification (arrow), while the others do have a balanced number of MYCN and reference probe hybridization signals. The SNParray profile (D) shows an example of a heterogeneous MYCN amplified tumor with much lower peaks (copy number < 3 of the smooth signals, lower line) than compared to the profile given in (B) and could easily be missed if the number of tumor cell nuclei with MYCN amplification is too small in the sample under examination.

Mentions: Interphase FISH used for the detection of gene amplifications can be considered as classical diagnostic tool for such purposes, as it is a quick and reliable technique and allows analyses at the single cell level. As seen in Figure 4A, the number of FISH spots varies markedly from cell to cell, ranging from hundreds per nucleus to a small excess of signals in comparison to the reference probe (in red) located on the short arm of chromosome 2. This variation is caused by the random distribution of double minute chromosomes (dmin) to the daughter cells during cell divisions. Despite this unequal dmin distribution among the different cells, we call this a homogeneously amplified tumor, since virtually all tumor cells show supernumerary MYCN signals, with a mostly more than four-fold increase in the MYCN signal number compared to the reference probe (thus being well above the threshold value as it was defined for neuroblastoma diagnostics). Array based techniques, as well, show distinct peaks, surpassing by far the four times ratio of the fluorescence intensities.


Ultra-High Density SNParray in Neuroblastoma Molecular Diagnostics.

Ambros IM, Brunner C, Abbasi R, Frech C, Ambros PF - Front Oncol (2014)

Depicts examples of homogenous “classical” and heterogeneous MYCN amplified tumors. The FISH picture, (A) (MYCN FISH probe in green, 2p probe in red), shows tumor cell nuclei with a varying number of MYCN signals ranging from approximately 30 signals up to hundreds distributed randomly within the nuclei. The large size of some of the MYCN hybridization spots can be explained by repeated amplicon units. The SNParray profile of a segment of the short arm of chromosome 2 from a homogeneously amplified neuroblastoma is given in (B) which shows a clear peak for the MYCN locus (copy number ~48). (C,D) Examples of a so called hetMNA tumor. In the I-FISH picture (C), one tumor cell nucleus clearly displays MYCN amplification (arrow), while the others do have a balanced number of MYCN and reference probe hybridization signals. The SNParray profile (D) shows an example of a heterogeneous MYCN amplified tumor with much lower peaks (copy number < 3 of the smooth signals, lower line) than compared to the profile given in (B) and could easily be missed if the number of tumor cell nuclei with MYCN amplification is too small in the sample under examination.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4129917&req=5

Figure 4: Depicts examples of homogenous “classical” and heterogeneous MYCN amplified tumors. The FISH picture, (A) (MYCN FISH probe in green, 2p probe in red), shows tumor cell nuclei with a varying number of MYCN signals ranging from approximately 30 signals up to hundreds distributed randomly within the nuclei. The large size of some of the MYCN hybridization spots can be explained by repeated amplicon units. The SNParray profile of a segment of the short arm of chromosome 2 from a homogeneously amplified neuroblastoma is given in (B) which shows a clear peak for the MYCN locus (copy number ~48). (C,D) Examples of a so called hetMNA tumor. In the I-FISH picture (C), one tumor cell nucleus clearly displays MYCN amplification (arrow), while the others do have a balanced number of MYCN and reference probe hybridization signals. The SNParray profile (D) shows an example of a heterogeneous MYCN amplified tumor with much lower peaks (copy number < 3 of the smooth signals, lower line) than compared to the profile given in (B) and could easily be missed if the number of tumor cell nuclei with MYCN amplification is too small in the sample under examination.
Mentions: Interphase FISH used for the detection of gene amplifications can be considered as classical diagnostic tool for such purposes, as it is a quick and reliable technique and allows analyses at the single cell level. As seen in Figure 4A, the number of FISH spots varies markedly from cell to cell, ranging from hundreds per nucleus to a small excess of signals in comparison to the reference probe (in red) located on the short arm of chromosome 2. This variation is caused by the random distribution of double minute chromosomes (dmin) to the daughter cells during cell divisions. Despite this unequal dmin distribution among the different cells, we call this a homogeneously amplified tumor, since virtually all tumor cells show supernumerary MYCN signals, with a mostly more than four-fold increase in the MYCN signal number compared to the reference probe (thus being well above the threshold value as it was defined for neuroblastoma diagnostics). Array based techniques, as well, show distinct peaks, surpassing by far the four times ratio of the fluorescence intensities.

Bottom Line: However, MYCN amplification is by far not the only genetic change associated with unfavorable clinical courses.However, these genomic aberrations need to be scrutinized in larger studies applying the most appropriate techniques.Single nucleotide polymorphism arrays have proven successful in deciphering genomic aberrations of cancer cells; these techniques, however, are usually not applied in the daily routine.

View Article: PubMed Central - PubMed

Affiliation: Children's Cancer Research Institute, St. Anna Kinderkrebsforschung , Vienna , Austria.

ABSTRACT
Neuroblastoma serves as a paradigm for applying tumor genomic data for determining patient prognosis and thus for treatment allocation. MYCN status, i.e., amplified vs. non-amplified, was one of the very first biomarkers in oncology to discriminate aggressive from less aggressive or even favorable clinical courses of neuroblastoma. However, MYCN amplification is by far not the only genetic change associated with unfavorable clinical courses. So called "segmental chromosomal aberrations," (SCAs) i.e., gains or losses of chromosomal fragments, can also indicate tumor aggressiveness. The clinical use of these genomic aberrations has, however, been hampered for many years by methodical and interpretational problems. Only after reaching worldwide consensus on markers, methodology, and data interpretation, information on SCAs has recently been implemented in clinical studies. Now, a number of collaborative studies within COG, GPOH, and SIOPEN use genomic information to stratify therapy for patients with localized and metastatic disease. Recently, new types of DNA based aberrations influencing the clinical behavior of neuroblastomas have been described. Deletions or mutations of genes like ATRX and a phenomenon referred to as "chromothripsis" are all assumed to correlate with an unfavorable clinical behavior. However, these genomic aberrations need to be scrutinized in larger studies applying the most appropriate techniques. Single nucleotide polymorphism arrays have proven successful in deciphering genomic aberrations of cancer cells; these techniques, however, are usually not applied in the daily routine. Here, we present an ultra-high density (UHD) SNParray technique which is, because of its high specificity and sensitivity and the combined copy number and allele information, highly appropriate for the genomic diagnosis of neuroblastoma and other malignancies.

No MeSH data available.


Related in: MedlinePlus