Double-minute MYC amplification and deletion of MTAP, CDKN2A, CDKN2B, and ELAVL2 in an acute myeloid leukemia characterized by oligonucleotide-array comparative genomic hybridization

Kamath, Anitha; Tara, Harold; Xiang, Bixia; Bajaj, Renu; He, Wanping; Li, Peining

doi:10.1016/j.cancergencyto.2008.02.011

Cited by 22 publications

(17 citation statements)

References 14 publications

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“…Two out of the three cases with 7q deletions in our patients had the 7q21.3 deletion. As reported in the literature [16,27,28] and also shown from our cases #1, #13, # 19 and #23, genomic analysis has been used effectively to define dmin chromosomes of 8q24 and complex 11q rearrangements with or without the MLL gene amplification in simple or complex karyotype. The presence of cytogenetic unresolved marker chromosome in our case #23 and the reported hidden abnormalities associated with t(15;17) justified further genomic analysis for this obvious balanced rearrangements [29,30].…”

Section: Discussionsupporting

confidence: 63%

“…To confirm significant cryptic genomic aberrations, DNA samples from two BAC clones, RP11-1107G21 ( NF1 gene at 17q11.2, chr17:26,415,260-26,627,398, sequence designation per NCBI36/hg18 assembly of the UCSC Human Genome browser http://genome.ucsc.edu/ and RP11-55J8 ( RHOT1 gene at 17q11.2, chr17:27,462,203-27,654,151), were purchased from Roswell Park Cancer Institute (Buffalo, NY). The labeling of BAC DNA with fluorescent nucleotides by nick translation, the hybridization and the image analysis were performed as previously described [4,16]. …”

Section: Methodsmentioning

confidence: 99%

“…This laboratory has validated the aCGH procedure to offer 99% sensitivity and 99% specificity with an average analytical resolution of 300-500 Kb using the log 2 ratio from five to seven contiguous probes, and also demonstrated its capacity in detecting 25%, 33% and 50% level of mosaicism [4]. The differential labeling of test and control DNAs, comparative hybridization onto 4x44K Agilent slides, post-hybridization wash, slide scanning, image feature extraction were processed as previously described [4,16]. Data was analyzed using Agilent's DNA Analytical (version 4.0) with the built-in ADM-2 algorithm set at threshold value of 6, a cut off value of 0.25, and a filter of six probes.…”

Section: Methodsmentioning

confidence: 99%

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Evidence-based genomic diagnosis characterized chromosomal and cryptic imbalances in 30 elderly patients with myelodysplastic syndrome and acute myeloid leukemia

Bajaj

Xiang

et al. 2011

Mol Cytogenet

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BackgroundTo evaluate the clinical validity of genome-wide oligonucleotide array comparative genomic hybridization (aCGH) for detecting somatic abnormalities, we have applied this genomic analysis to 30 cases (13 MDS and 17 AML) with clonal chromosomal abnormalities detected in more than 50% of analyzed metaphase cells.ResultsThe aCGH detected all numerical chromosomal gains and losses from the mainline clones and 113 copy number alterations (CNAs) ranging from 0.257 to 102.519 megabases (Mb). Clinically significant recurrent deletions of 5q (involving the RPS14 gene), 12p12.3 (ETV6 gene), 17p13 (TP53 gene), 17q11.2 (NF1 gene) and 20q, double minutes containing the MYC gene and segmental amplification involving the MLL gene were further characterized with defined breakpoints and gene contents. Genomic features of microdeletions at 17q11.2 were confirmed by FISH using targeted BAC clones. The aCGH also defined break points in a derivative chromosome 6, der(6)t(3;6)(q21.3;p22.2), and an isodicentric X chromosome. However, chromosomally observed sideline clonal abnormalities in five cases were not detected by aCGH.ConclusionsOur data indicated that an integrated cytogenomic analysis will be a better diagnostic scheme to delineate genomic contents of chromosomal and cryptic abnormalities in patients with MDS and AML. An evidence-based approach to interpret somatic genomic findings was proposed.

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Section: Discussionsupporting

confidence: 63%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Evidence-based genomic diagnosis characterized chromosomal and cryptic imbalances in 30 elderly patients with myelodysplastic syndrome and acute myeloid leukemia

Bajaj

Xiang

et al. 2011

Mol Cytogenet

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“…PVT1 copy number gain (e.g. double * This work was supported, in whole or in part, by National Institutes of Health minutes, amplifications) or overexpression of PVT1 has been demonstrated in breast cancer, ovarian cancer, pediatric malignant astrocytomas, acute myeloid leukemia, and Hodgkin lymphoma (25)(26)(27)(28)(29)(30). In congruence with such observations, PVT1 expression has been reported to be low in normal tissue but highly expressed in many transformed cell lines (31).…”

mentioning

confidence: 99%

p53-dependent Induction of PVT1 and miR-1204

Barsotti

Beckerman

Laptenko

et al. 2012

Journal of Biological Chemistry

168

165

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“…For many cryptic rearrangements undetectable by routine chromosome analysis, such as t(12;21)(p13;q22) with ETV6/RUNX1 gene fusions, t(4;14)(p16.3;q32) with FGFR3/IGH gene fusions, deletions of 12p13 (ETV6), 13q14 (RB1), and 17p13 (TP53), FISH tests are considered a stand-alone diagnostic assay. Adjunctive use of FISH probes to further define ambiguous or hidden chromosomal abnormalities is required for many cases (Kamath et al, 2008; Massaro et al, 2011). Additionally, FISH is a sensitive and timely method to monitor residual diseases with known clonal abnormality and bone marrow transplantation by sex-mismatch donor at cellular level.…”

Section: Cell Based Genetic Diagnosis By Fishmentioning

confidence: 99%

Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications

Cui

Shu

2016

Front. Cell Dev. Biol.

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165

125

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Fluorescence in situ hybridization (FISH) is a macromolecule recognition technology based on the complementary nature of DNA or DNA/RNA double strands. Selected DNA strands incorporated with fluorophore-coupled nucleotides can be used as probes to hybridize onto the complementary sequences in tested cells and tissues and then visualized through a fluorescence microscope or an imaging system. This technology was initially developed as a physical mapping tool to delineate genes within chromosomes. Its high analytical resolution to a single gene level and high sensitivity and specificity enabled an immediate application for genetic diagnosis of constitutional common aneuploidies, microdeletion/microduplication syndromes, and subtelomeric rearrangements. FISH tests using panels of gene-specific probes for somatic recurrent losses, gains, and translocations have been routinely applied for hematologic and solid tumors and are one of the fastest-growing areas in cancer diagnosis. FISH has also been used to detect infectious microbias and parasites like malaria in human blood cells. Recent advances in FISH technology involve various methods for improving probe labeling efficiency and the use of super resolution imaging systems for direct visualization of intra-nuclear chromosomal organization and profiling of RNA transcription in single cells. Cas9-mediated FISH (CASFISH) allowed in situ labeling of repetitive sequences and single-copy sequences without the disruption of nuclear genomic organization in fixed or living cells. Using oligopaint-FISH and super-resolution imaging enabled in situ visualization of chromosome haplotypes from differentially specified single-nucleotide polymorphism loci. Single molecule RNA FISH (smRNA-FISH) using combinatorial labeling or sequential barcoding by multiple round of hybridization were applied to measure mRNA expression of multiple genes within single cells. Research applications of these single molecule single cells DNA and RNA FISH techniques have visualized intra-nuclear genomic structure and sub-cellular transcriptional dynamics of many genes and revealed their functions in various biological processes.

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Double-minute MYC amplification and deletion of MTAP, CDKN2A, CDKN2B, and ELAVL2 in an acute myeloid leukemia characterized by oligonucleotide-array comparative genomic hybridization

Cited by 22 publications

References 14 publications

Evidence-based genomic diagnosis characterized chromosomal and cryptic imbalances in 30 elderly patients with myelodysplastic syndrome and acute myeloid leukemia

Evidence-based genomic diagnosis characterized chromosomal and cryptic imbalances in 30 elderly patients with myelodysplastic syndrome and acute myeloid leukemia

p53-dependent Induction of PVT1 and miR-1204

Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications

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