The advantage of using SNP array in clinical testing for hematological malignancies—a comparative study of three genetic testing methods

Xu, Xinjie; Johnson, Eric B.; Leverton, Lisa; Arthur, Ashley; Watson, Quinn; Chang, Faye L.; Raca, Gordana; Laffin, Jennifer

doi:10.1016/j.cancergen.2013.09.001

Cited by 33 publications

(27 citation statements)

References 34 publications

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“…Similarly, our results suggest that FISH alone, irrespective of how comprehensive the FISH panel may be, is significantly ameliorated by the addition of karyotyping. Given the increasing use of chromosomal microarrays to detect aberrations in hematologic malignancies [26,27] and the clinical significance of recurrent mutations in CLL [28,29], the diagnostic approaches employed to evaluate genomic aberrations in this disease will undoubtedly change. In the interim, however, it remains important to maximize our understanding of the genomic aberrations that contribute to the pathogenesis of CLL.…”

Section: Discussionmentioning

confidence: 99%

FISHing in the dark: How the combination of FISH and conventional karyotyping improves the diagnostic yield in CpG‐stimulated chronic lymphocytic leukemia

et al. 2016

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Despite significant advances in molecular genetic approaches, fluorescence in situ hybridization (FISH) remains the gold standard for the diagnostic evaluation of genomic aberrations in patients with chronic lymphocytic leukemia (CLL). Efforts to improve the diagnostic utility of molecular cytogenetic testing have led to the expansion of the traditional 4-probe CLL FISH panel. Not only do these efforts increase the cost of testing, they remain hindered by the inherent limitations of FISH studies -namely the inability to evaluate genomic changes outside of the targeted loci. While array-based profiling and next generation sequencing (NGS) have critically expanded our understanding of the molecular pathogenesis of CLL, these methodologies are not routinely used by diagnostic laboratories to evaluate copy number changes or the mutational profile of this disease. Mitogenic stimulation of CLL specimens with CpG-oligonucleotide (CpG-ODN) has been identified as a reliable and reproducible means of obtaining a karyotype, facilitating a low-resolution genomewide analysis. Across a cohort of 1255 CpG-ODN-stimulated CLL specimens, we describe the clinical utility associated with the combinatorial use of FISH and karyotyping. Our testing algorithm achieves a higher diagnostic yield (~10%) through the detection of complex karyotypes, well-characterized chromosomal aberrations not covered by the traditional CLL FISH panel and through the detection of concurrent secondary malignancies. Moreover, the single cell nature of this approach permits the evaluation of emerging new clinical concepts including clonal dynamics and clonal evolution. This approach can be broadly applied by diagnostic laboratories to improve the utility of traditional and molecular cytogenetic studies of CLL.

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Section: Discussionmentioning

confidence: 99%

FISHing in the dark: How the combination of FISH and conventional karyotyping improves the diagnostic yield in CpG‐stimulated chronic lymphocytic leukemia

et al. 2016

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“…Molecular karyotyping by comparative genomic hybridization (CGH), array-CGH (aCGH) for copy number variation (CNV), and single nucleotide polymorphism (SNP) arrays (SNP-array) have resulted in superior resolution over conventional metaphase analysis, and thus, aCGH and SNP-array eliminates use of metaphases in malignant samples. A combined approach of SNP-array and conventional cytogenetics showed convincing results for prediction of OS, EFS and PFS [134]. Thus, karyotype analysis will continue to be essential, as abnormal karyotypes, including CK and MK, support clonality, and the consideration of specific karyotypic abnormalities in morphologically subtle cases will most likely remain unchanged in the proposed risk-classification of MDS, which is likely to be published in mid 2016 [135].…”

Section: Complex Chromosomal Aberrations (Ck) and Monosomal Karyotypementioning

confidence: 95%

Mutations of myelodysplastic syndromes (MDS): An update

Ganguly

Kadam

2016

Mutation Research/Reviews in Mutation Research

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“…Biallelic deletion of 13q14 was observed in 17% of the cases with both DNA probes D13S25 and D13S319, which is in the range reported previously [Garg et al, 2012]. The occurrence of trisomy 12, del (11) [Fabris et al, 2011;Ouilette et al, 2011;Véronèse et al, 2013;Xu et al, 2013;Puiggros et al, 2014;Stevens-Kroef et al, 2014]. However, these new assays share several limitations: the inability to detect balanced rearrangements, low-level mosaicism, and a clonal evolution of neoplastic B cells.…”

Section: Discussionmentioning

confidence: 84%

Detection of Clonal Aberrations by Cytogenetic Analysis after Different Culture Methods and by FISH in 129 Patients with Chronic Lymphocytic Leukemia

Jenderny¹,

Goldmann²,

Thede³

et al. 2014

Cytogenet Genome Res

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There are only a few cytogenetic analysis (CA) studies that directly compare the novel cultivation technique using immunostimulatory CpG-oligonucleotide DSP30/interleukin-2 (DSP30/IL2) with other culture methods. Therefore, parallel cultures of peripheral blood of 129 chronic lymphocytic leukemia (CLL) patients were set up in unstimulated cultures, in the presence of pokeweed medium (PWM), and with DSP30/IL2. Furthermore, CA results were compared with data obtained by FISH. Clonal aberrations were observed by CA in 6% of the cases in unstimulated cultures, in 27% of the cases with PWM, and in 40% of the cases with DSP30/IL2. Some clonal aberrations were detected by CA only with one culture method. Using 3 different culture methods, clonal aberrations were detected in 41% of the cases by CA and in 71% of the cases by FISH. Altogether, 78% of the cases exhibited clonal aberrations discovered by CA and FISH. Also, CA detected clonal aberrations not targeted by FISH in 7% of the cases, and FISH identified clonal aberrations not detected by CA in 36% of the cases. Our study demonstrates that the combined use of CA with different culture methods together with FISH increases our knowledge of the genetic complexity and heterogeneity in CLL pathogenesis.

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The advantage of using SNP array in clinical testing for hematological malignancies—a comparative study of three genetic testing methods

Cited by 33 publications

References 34 publications

FISHing in the dark: How the combination of FISH and conventional karyotyping improves the diagnostic yield in CpG‐stimulated chronic lymphocytic leukemia

FISHing in the dark: How the combination of FISH and conventional karyotyping improves the diagnostic yield in CpG‐stimulated chronic lymphocytic leukemia

Mutations of myelodysplastic syndromes (MDS): An update

Detection of Clonal Aberrations by Cytogenetic Analysis after Different Culture Methods and by FISH in 129 Patients with Chronic Lymphocytic Leukemia

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