Section E6.1–6.4 of the ACMG technical standards and guidelines: chromosome studies of neoplastic blood and bone marrow–acquired chromosomal abnormalities

Mikhail, Fady M.; Heerema, Nyla A.; Rao, Kathleen W.; Burnside, Rachel D.; Cherry, Athena M.; Cooley, Linda D.

doi:10.1038/gim.2016.50

Cited by 43 publications

(30 citation statements)

References 33 publications

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“…In total, cell harvest, slide making, analysis, interpretation, and reporting generally necessitate about 1 week. Standard analysis requires 20 metaphase nuclei (Cooley, Morton, Sanger, Saxe, & Mikhail, 2016; Mikhail et al., 2016; The International Stem Cell Banking Initiative, 2009). Specifically, 20 cells will have their chromosomes counted, 4 to 8 of these cells will have their chromosomes analyzed band‐to‐band, and 2 to 4 cells will be made into karyogram images.…”

Section: Assays To Test Psc Genomic Stabilitymentioning

confidence: 99%

Genomic Stability Testing of Pluripotent Stem Cells

McIntire

Taapken

Leonhard

et al. 2020

CP Stem Cell Biology

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Pluripotent stem cell (PSC) cultures are subjected to selective pressures that can result in acquisition and expansion of recurrent genetic abnormalities at any time. These recurrent abnormalities enhance the variant cells harboring them with a competitive advantage over wild‐type cells. Variant cells can eventually supplant wild‐type cells entirely and become fixed in culture. Such variants can impact the efficacy of PSCs in research and clinical applications. Therefore, routine genomic characterization is required for reliable and effective use of PSCs. In this article we describe the capabilities and limitations of several assays commonly used for assessing PSC genomic stability. Based on this analysis, we provide a recommendation for integrating assays into a comprehensive testing regimen that maximizes coverage while minimizing cost. © 2020 by John Wiley & Sons, Inc.

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Section: Assays To Test Psc Genomic Stabilitymentioning

confidence: 99%

Genomic Stability Testing of Pluripotent Stem Cells

McIntire

Taapken

Leonhard

et al. 2020

CP Stem Cell Biology

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“…The two main pathogenetic pathways for hallmarks of cancer development are the inactivation of tumor suppressor genes by deletions, mutations, miRNA upregulation, or epigenetic mechanisms, and the activation or deregulation of oncogenes as a consequence of point mutations, amplification or balanced cytogenetic abnormalities (Vogelstein and Kinzler, 2004; Hanahan and Weinberg, 2011). Recurrent chromosomal abnormalities including translocations, deletions, duplications, and gene amplifications associated with distinct tumor entities have been characterized; specifically designed FISH panels have been widely used in the diagnosis and monitoring of acquired chromosomal abnormalities in hematologic and solid tumors (Hu et al, 2014; Liehr et al, 2015; Mikhail et al, 2016). …”

Section: Cell Based Genetic Diagnosis By Fishmentioning

confidence: 99%

“…Shaded for recurrent abnormalities detected by a primary FISH panel, unshaded for secondary FISH probes for specific abnormalities. For references see (Hu et al, 2014; Liehr et al, 2015), and (Mikhail et al, 2016) .…”

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.

175

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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“…Various molecular biology techniques are used clinically to detect these alterations. Chromosomal analysis, fluorescent in situ hybridization (FISH), and targeted Sanger sequencing have been the primary tools of detecting these alterations and remain part of the standard care ( 6 ). In recent years, high-throughput molecular technologies, including chromosomal microarray analysis (CMA) and NGS, have enhanced the capability to characterize critical genomic variations, and a combination of both classic and novel molecular technologies are used to assess clinically relevant mutations.…”

Section: Molecular Strategies For Genetic Testing In Leukemiamentioning

confidence: 99%

Clinical Impact of Genomic Information in Pediatric Leukemia

Lalonde

Wertheim

2017

Front. Pediatr.

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Pediatric leukemia remains a significant contributor to childhood lethality rates. However, recent development of new technologies including next-generation sequencing (NGS) has increased our understanding of the biological and genetic underpinnings of leukemia, resulting in novel diagnostic and treatment paradigms. The most prevalent pediatric leukemias include B-cell acute lymphoblastic leukemia (B-ALL) and acute myeloid leukemia (AML). These leukemias are highly heterogeneous, both clinically and genetically. There are multiple genetic subgroups defined by the World Health Organization, each with distinct clinical management. Clinical laboratories have started adopting genomic testing strategies to include high-throughput sequencing assays which, together with conventional cytogenetic techniques, enable optimal patient care. This review summarizes genetic and genomic techniques used in clinical laboratories to support management of pediatric leukemia, highlighting technical, biological, and clinical advances. We illustrate clinical utilities of comprehensive genomic evaluation of leukemia genomes through clinical case examples, which includes the interrogations of hundreds of genes and multiple mutation mechanisms using NGS technologies. Finally, we provide a future perspective on clinical genomics and precision medicine.

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Section E6.1–6.4 of the ACMG technical standards and guidelines: chromosome studies of neoplastic blood and bone marrow–acquired chromosomal abnormalities

Cited by 43 publications

References 33 publications

Genomic Stability Testing of Pluripotent Stem Cells

Genomic Stability Testing of Pluripotent Stem Cells

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

Clinical Impact of Genomic Information in Pediatric Leukemia

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