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Genomic imbalances are confined to non-proliferating cells in paediatric patients with acute myeloid leukaemia and a normal or incomplete karyotype.

Ballabio E, Regan R, Garimberti E, Harbott J, Bradtke J, Teigler-Schlegel A, Biondi A, Cazzaniga G, Giudici G, Wainscoat JS, Boultwood J, Bridger JM, Knight SJ, Tosi S - PLoS ONE (2011)

Bottom Line: Leukaemia is often associated with genetic alterations such as translocations, amplifications and deletions, and recurrent chromosome abnormalities are used as markers of diagnostic and prognostic relevance.The majority of these copy number alterations (CNAs) were confirmed by FISH and found to localize to the interphase rather than metaphase nuclei.Interestingly, these experiments showed that, in the vast majority of cases, the changes appeared to be confined to interphase nuclei in a non-proliferative status.

View Article: PubMed Central - PubMed

Affiliation: Centre for Cell and Chromosome Biology and Brunel Institute of Cancer Genetics and Pharmacogenomics, Division of Biosciences, Brunel University, West London, United Kingdom.

ABSTRACT
Leukaemia is often associated with genetic alterations such as translocations, amplifications and deletions, and recurrent chromosome abnormalities are used as markers of diagnostic and prognostic relevance. However, a proportion of acute myeloid leukaemia (AML) cases have an apparently normal karyotype despite comprehensive cytogenetic analysis. Based on conventional cytogenetic analysis of banded chromosomes, we selected a series of 23 paediatric patients with acute myeloid leukaemia and performed whole genome array comparative genome hybridization (aCGH) using DNA samples derived from the same patients. Imbalances involving large chromosomal regions or entire chromosomes were detected by aCGH in seven of the patients studied. Results were validated by fluorescence in situ hybridization (FISH) to both interphase nuclei and metaphase chromosomes using appropriate bacterial artificial chromosome (BAC) probes. The majority of these copy number alterations (CNAs) were confirmed by FISH and found to localize to the interphase rather than metaphase nuclei. Furthermore, the proliferative states of the cells analyzed by FISH were tested by immunofluorescence using an antibody against the proliferation marker pKi67. Interestingly, these experiments showed that, in the vast majority of cases, the changes appeared to be confined to interphase nuclei in a non-proliferative status.

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aCGH results of patients no. 1 (A) and 11 (B).On the Y-axis: mean fluorescence ratio; on the X-axis: ordered chromosomal location. Results from the test versus reference and dye-swap experiments are shown in blue and pink, respectively. (A): genomic gains involving chromosomes 7 and 8 are detected in the sample from patient no. 1 and are indicated by the red arrows. The subtle ratio changes are attributable to mosaicism (see FISH results). (B): genomic losses involving 7q and 16p12 are detected in the sample from patient no. 11 and are indicated by the green arrows; a gain involving 8q is indicated by the red arrow.
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pone-0020607-g001: aCGH results of patients no. 1 (A) and 11 (B).On the Y-axis: mean fluorescence ratio; on the X-axis: ordered chromosomal location. Results from the test versus reference and dye-swap experiments are shown in blue and pink, respectively. (A): genomic gains involving chromosomes 7 and 8 are detected in the sample from patient no. 1 and are indicated by the red arrows. The subtle ratio changes are attributable to mosaicism (see FISH results). (B): genomic losses involving 7q and 16p12 are detected in the sample from patient no. 11 and are indicated by the green arrows; a gain involving 8q is indicated by the red arrow.

Mentions: A total of 23 paediatric patients with AML and reported normal karyotype were analyzed for CNAs by aCGH. The karyotypes had been assessed previously either by Q-banding (patient nos. 1–5) or by G-banding (patient nos. 6–23). A number of 20 metaphases were analyzed for each patients, when possible, before a diagnosis of normal karyotype was made. In patients no. 1–3, 5 and 18, diagnosis of normal karyotype was made based on the analysis of the few metaphases that were retrieved from the samples (<20). The clinical and cytogenetic data for the patients and the aCGH results are documented in Table 1 and described according to the International System for Human Cytogenetic Nomenclature [17]. In total, 15 large CNAs were identified in seven of the 23 paediatric patient samples; gains were detected in six of the seven cases and losses in three cases, the majority involving entire chromosomes or large chromosomal regions. To summarize the aCGH results: three copies of chromosome 7 and three copies of chromosome 8 were detected in patient no. 1; three copies of chromosome 19 were detected in patient no. 2; a gain of 1p36.2p32.3 together with a gain of 11q12.3q13.4 were detected in patient no. 4; a gain of regions 1p36.2p32.3, 9q33.3q34.3, 13q34 and 22q13.1q13.3 were detected in patient 5; a loss of 7q31.2q36.3 and 16p12.2p12.1 together with a gain of 8q24.12q24.3 were detected in patient no. 11; a loss of 15q13.3q21.1 was detected in patient 12 and a loss of 4q35.2 together with a gain of 13q31.1q33.1 were detected in patient no. 19 (Table 1). One of the gains, the 13q34 gain noted in patient no. 5, encompassed a region of polymorphism documented in the Database of Genomic Variants (DGV) and was excluded from follow-up studies. The remaining 16 samples revealed small putative aberrations that were also excluded from the follow-up studies. Examples of the plots showing the CNAs detected in patients no. 1 and no. 11 are shown in Figure 1.


Genomic imbalances are confined to non-proliferating cells in paediatric patients with acute myeloid leukaemia and a normal or incomplete karyotype.

Ballabio E, Regan R, Garimberti E, Harbott J, Bradtke J, Teigler-Schlegel A, Biondi A, Cazzaniga G, Giudici G, Wainscoat JS, Boultwood J, Bridger JM, Knight SJ, Tosi S - PLoS ONE (2011)

aCGH results of patients no. 1 (A) and 11 (B).On the Y-axis: mean fluorescence ratio; on the X-axis: ordered chromosomal location. Results from the test versus reference and dye-swap experiments are shown in blue and pink, respectively. (A): genomic gains involving chromosomes 7 and 8 are detected in the sample from patient no. 1 and are indicated by the red arrows. The subtle ratio changes are attributable to mosaicism (see FISH results). (B): genomic losses involving 7q and 16p12 are detected in the sample from patient no. 11 and are indicated by the green arrows; a gain involving 8q is indicated by the red arrow.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3111408&req=5

pone-0020607-g001: aCGH results of patients no. 1 (A) and 11 (B).On the Y-axis: mean fluorescence ratio; on the X-axis: ordered chromosomal location. Results from the test versus reference and dye-swap experiments are shown in blue and pink, respectively. (A): genomic gains involving chromosomes 7 and 8 are detected in the sample from patient no. 1 and are indicated by the red arrows. The subtle ratio changes are attributable to mosaicism (see FISH results). (B): genomic losses involving 7q and 16p12 are detected in the sample from patient no. 11 and are indicated by the green arrows; a gain involving 8q is indicated by the red arrow.
Mentions: A total of 23 paediatric patients with AML and reported normal karyotype were analyzed for CNAs by aCGH. The karyotypes had been assessed previously either by Q-banding (patient nos. 1–5) or by G-banding (patient nos. 6–23). A number of 20 metaphases were analyzed for each patients, when possible, before a diagnosis of normal karyotype was made. In patients no. 1–3, 5 and 18, diagnosis of normal karyotype was made based on the analysis of the few metaphases that were retrieved from the samples (<20). The clinical and cytogenetic data for the patients and the aCGH results are documented in Table 1 and described according to the International System for Human Cytogenetic Nomenclature [17]. In total, 15 large CNAs were identified in seven of the 23 paediatric patient samples; gains were detected in six of the seven cases and losses in three cases, the majority involving entire chromosomes or large chromosomal regions. To summarize the aCGH results: three copies of chromosome 7 and three copies of chromosome 8 were detected in patient no. 1; three copies of chromosome 19 were detected in patient no. 2; a gain of 1p36.2p32.3 together with a gain of 11q12.3q13.4 were detected in patient no. 4; a gain of regions 1p36.2p32.3, 9q33.3q34.3, 13q34 and 22q13.1q13.3 were detected in patient 5; a loss of 7q31.2q36.3 and 16p12.2p12.1 together with a gain of 8q24.12q24.3 were detected in patient no. 11; a loss of 15q13.3q21.1 was detected in patient 12 and a loss of 4q35.2 together with a gain of 13q31.1q33.1 were detected in patient no. 19 (Table 1). One of the gains, the 13q34 gain noted in patient no. 5, encompassed a region of polymorphism documented in the Database of Genomic Variants (DGV) and was excluded from follow-up studies. The remaining 16 samples revealed small putative aberrations that were also excluded from the follow-up studies. Examples of the plots showing the CNAs detected in patients no. 1 and no. 11 are shown in Figure 1.

Bottom Line: Leukaemia is often associated with genetic alterations such as translocations, amplifications and deletions, and recurrent chromosome abnormalities are used as markers of diagnostic and prognostic relevance.The majority of these copy number alterations (CNAs) were confirmed by FISH and found to localize to the interphase rather than metaphase nuclei.Interestingly, these experiments showed that, in the vast majority of cases, the changes appeared to be confined to interphase nuclei in a non-proliferative status.

View Article: PubMed Central - PubMed

Affiliation: Centre for Cell and Chromosome Biology and Brunel Institute of Cancer Genetics and Pharmacogenomics, Division of Biosciences, Brunel University, West London, United Kingdom.

ABSTRACT
Leukaemia is often associated with genetic alterations such as translocations, amplifications and deletions, and recurrent chromosome abnormalities are used as markers of diagnostic and prognostic relevance. However, a proportion of acute myeloid leukaemia (AML) cases have an apparently normal karyotype despite comprehensive cytogenetic analysis. Based on conventional cytogenetic analysis of banded chromosomes, we selected a series of 23 paediatric patients with acute myeloid leukaemia and performed whole genome array comparative genome hybridization (aCGH) using DNA samples derived from the same patients. Imbalances involving large chromosomal regions or entire chromosomes were detected by aCGH in seven of the patients studied. Results were validated by fluorescence in situ hybridization (FISH) to both interphase nuclei and metaphase chromosomes using appropriate bacterial artificial chromosome (BAC) probes. The majority of these copy number alterations (CNAs) were confirmed by FISH and found to localize to the interphase rather than metaphase nuclei. Furthermore, the proliferative states of the cells analyzed by FISH were tested by immunofluorescence using an antibody against the proliferation marker pKi67. Interestingly, these experiments showed that, in the vast majority of cases, the changes appeared to be confined to interphase nuclei in a non-proliferative status.

Show MeSH
Related in: MedlinePlus