A multicenter, cross-platform clinical validation study of cancer cytogenomic arrays

Li, Marilyn M.; Monzon, Federico A.; Biegel, Jaclyn A.; Jobanputra, Vaidehi; Laffin, Jennifer; Levy, Brynn; Leon, Annette; Miron, Patricia M.; Rossi, Michael R.; Toruner, Gokce; Alvarez, Karla; Doho, Gregory; Dougherty, Margaret; Hu, Xiaofeng; Kash, Shera; Streck, Deanna; Znoyko, Iya; Hagenkord, Jill; Wolff, Daynna J.

doi:10.1016/j.cancergen.2015.08.002

Cited by 12 publications

(12 citation statements)

References 31 publications

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“…Despite a substantial amount of clinically relevant data revealed in recent years that support the integration of CMA into the diagnostic workup of hematological malignancies and the establishment of technical guidelines and standards for diagnosis of neoplastic disorders by CMA by the American College of Medical Genetics and Genomics, hematologists tend to request CC and FISH tests only because CMA is not utilized in the diagnosis/treatment guidelines (eg, National Comprehensive Cancer Network Guidelines). Through the results of this study, we are confident that, firstly, CMA benchwork is significantly automated compared to CC and is much less labor intensive.…”

Section: Discussionmentioning

confidence: 99%

“…Despite a substantial amount of clinically relevant data revealed in recent years that support the integration of CMA into the diagnostic workup of hematological malignancies [33][34][35] genes in ALL patients 31,37 ; and in cases with suspected gene amplification of unknown origin. Lastly, with the advantage of obviating the need for cell culture, CMA is useful in samples with a normal karyotype or culture failure.…”

Section: Discussionmentioning

confidence: 99%

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Chromosomal microarray analysis is superior in identifying cryptic aberrations in patients with acute lymphoblastic leukemia at diagnosis/relapse as a single assay

Chen

Heng

Lim

et al. 2019

Int J Lab Hematology

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Introduction Conventional cytogenetics (CC) is important in diagnosis, therapy, monitoring of post‐transplant bone marrow, and prognosis assessment of acute lymphoblastic leukemia (ALL). However, due to the nature of ALL, CC often encounters difficulties of complex karyotype, poor chromosome morphology, low mitotic index, or normal cells dividing only. In contrast, chromosomal microarray analysis (CMA) showed a specificity >99% and a sensitivity of 100% in chronic lymphocytic leukemia (CLL) patients. Here, we report our experience with CMA on adult ALL patients. Methods Thirty‐three bone marrow/blood samples from ALL patients (aged 18‐79 years, median 44) at diagnosis/relapse, analyzed by CC and/or fluorescence in situ hybridization (FISH), were recruited. Chromosomal microarray analysis results were compared with CC. Fluorescence in situ hybridization analysis, if available, was applied when there was a discrepancy. Results Copy‐neutral loss‐of‐heterozygosity (CN‐LOH) was found in 8 cases (24.2%). Only CN‐LOH at 9p was recurrent (3 cases, 9.1%). Copy number alterations (CNAs) were detected in 6 of 9 cases (66.7%) with normal karyotypes, in 3 of 5 cases (60.0%) with sole “balanced” translocations, and in 18 of 19 cases (94.7%) with complex karyotypes. Common CNAs involved CDKN2A/2B (30.3%), IKZF1 (27.3%), PAX5 (9.1%), RB1 (9.1%), BTG1 (6.7%), and ETV6 (6.7%), which regulate cell cycle, B lymphopoiesis, or act as tumor suppressors in ALL. Copy number alteration detection rate by CMA was 81.8% (27 of 33 cases) as compared to 57.6% (19 of 33 cases) by CC. Conclusion Incorporation of CMA as a routine clinical test at the time of diagnosis/relapse, in conjunction with CC and/or FISH, is highly recommended.

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Section: Discussionmentioning

confidence: 99%

“…Despite a substantial amount of clinically relevant data revealed in recent years that support the integration of CMA into the diagnostic workup of hematological malignancies [33][34][35] genes in ALL patients 31,37 ; and in cases with suspected gene amplification of unknown origin. Lastly, with the advantage of obviating the need for cell culture, CMA is useful in samples with a normal karyotype or culture failure.…”

Section: Discussionmentioning

confidence: 99%

Chromosomal microarray analysis is superior in identifying cryptic aberrations in patients with acute lymphoblastic leukemia at diagnosis/relapse as a single assay

Chen

Heng

Lim

et al. 2019

Int J Lab Hematology

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“…Microarrays, which aided the development of cancer genomics, have been identified as an effective tool for the detection of cytogenetic aberrations, including copy number, altered gene expression and single nucleotide polymorphism (70,71). Effective novel biotechnologies, such as next-generation sequencing, have aided significant advances in the comprehensive analysis of cancer genomic alterations that has a single-base resolution, is genome-wide and is high-throughput (21,22,27).…”

Section: Discussionmentioning

confidence: 99%

The context of prostate cancer genomics in personalized medicine

Liu

2017

Oncology Letters

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Abstract. Prostate cancer is one of the most common types of cancer in males. Heterogeneous genomic aberrations may lead to prostate cancer onset, progression and metastasis. This heterogeneity also contributes to the variety in cancer risk and outcomes, different drug responses and progression, observed between individual patients. Classical prognostic factors, including prostate-specific antigen, Gleason Score and clinical tumor staging, are not sufficient to portray the complexity of a clinically relevant cancer diagnosis, risk prognosis, treatment choice and therapy monitoring. There is a requirement for novel genetic biomarkers in order to understand the oncogenic heterogeneity in a patient-personalized clinical setting and to improve the efficacy of risk prognosis and treatment choice. A number of biomarkers and gene panels have been established from patient sample cohort studies. These previous studies have provided distinct information to the investigation of heterogeneous malignancy in prostate cancer, which aids in clinical decision-making. Biomarker-guided therapies may facilitate the effective selection of drugs during early treatment; therefore, are beneficial to the individual patient. A non-invasive approach allows for convenient and repeated sampling to screen for cancer and monitor treatment response without the requirement for invasive tissue biopsies. With the current availability of numerous advanced technologies, reliable detection of the minimal tumor residues present following treatment may become clinical practice and, therefore, inform further in the field of personalized medicine.

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“…1 While conventional karyotype is the gold standard for detection of genomic abnormalities in both diagnostic and prognostic settings, single nucleotide polymorphism arrays (SNP-As) have emerged as potential means of further categorizing prognostic risk beyond traditional karyotyping in many hematologic malignancies due to the assay's greater sensitivity in detecting unbalanced chromosomal defects and copy-neutral loss of heterozygosity (CN-LOH). [2][3][4][5][6] However, widespread adoption and incorporation into prognostic algorithms has not yet occurred despite evidence of the clinical significance of SNP-A in combination with already established karyotypic features. [5][6][7][8] We therefore sought to refine our understanding of the significance of additional SNP-A abnormalities and their impact on prognosis and ultimately risk of death.…”

Section: Introductionmentioning

confidence: 99%

Cytogenomic array detects a subset of myelodysplastic syndrome with increased risk that is invisible to conventional karyotype

Choi

Norman

Bixby

et al. 2019

Genes Chromosomes & Cancer

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Conventional karyotyping is essential standard practice in the initial evaluation of myelodysplastic syndrome (MDS) and is the most impactful single component of the Revised International Prognostic Scoring System (IPSS‐R). While single nucleotide polymorphism array (SNP‐A) has demonstrated the ability to detect chromosomal defects with greater sensitivity than conventional karyotype, widespread adoption is limited by the unknown additional prognostic impact of SNP‐A analysis. Here, we investigate the significance of additional SNP‐A abnormalities in the setting of MDS and demonstrate differences in survival of patients with additional abnormalities, even those initially characterized as relatively lower risk either by cytogenetic score or IPSS‐R. Our findings identify specific abnormalities, particularly KMT2A partial tandem duplication, that are invisible to conventional karyotype and potentially contribute to the poor prognosis of MDS patients. Furthermore, these results demonstrate the added value of SNP‐A analysis in identifying patients who may benefit from more aggressive therapy, particularly those who would otherwise be classified into lower risk categories.

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A multicenter, cross-platform clinical validation study of cancer cytogenomic arrays

Cited by 12 publications

References 31 publications

Chromosomal microarray analysis is superior in identifying cryptic aberrations in patients with acute lymphoblastic leukemia at diagnosis/relapse as a single assay

Chromosomal microarray analysis is superior in identifying cryptic aberrations in patients with acute lymphoblastic leukemia at diagnosis/relapse as a single assay

The context of prostate cancer genomics in personalized medicine

Cytogenomic array detects a subset of myelodysplastic syndrome with increased risk that is invisible to conventional karyotype

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