30. Chromosomal microarray analysis work-up for hypocellular MDS patients with inconclusive cytogenetics
Identification of chromosomal abnormalities is essential for diagnosis, prognosis, and therapeutic decision-making in myelodysplastic neoplasms (MDS). Hypocellular MDS (h-MDS), is a newly recognized diagnostic sub-entity under the 2022 WHO classification ( (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Ha Nguyen, Fangling Xu, Sherin Raju, Nazneen Ahmed, Christopher Bowman, Hector Alvarez, Hyvan Dang, Awdhesh Kalia, Peter Hu, Rajyalakshmi Luthra, Diana Rush, Guilin Tang, Kunhwa Kim, Kelly Chien, Guillermo Garcia-Manero Source Type: research
31. Prognostic significance of copy number gain of MYC detected by FISH analysis in large B-cell lymphoma
Current diagnostic workup of large B-cell lymphomas (LBCLs) includes FISH and immunohistochemistry (IHC) results. MYC translocations have negative effect on survival, are recurrent in LBCL and if detected together with BCL2 and/or BCL6 translocations, define a distinct entity of high-grade B-cell lymphoma based on the WHO classification, whereas lymphomas with high Myc and Bcl2 protein levels without MYC translocations (double-expressors) remain in the category of LBCLs. Currently there is no consensus on prognostic significance of gains of extra MYC copies, also frequently detected by FISH assay. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Madina Sukhanova, Lucas Santana-Santos, Juehua Gao, Xinyan Lu, Reem Karmali, Taylor Zak Source Type: research
32. Whole transcriptome sequencing as a diagnostic tool for AML
Next generation sequencing (NGS) has revolutionized the field of genomics by enabling the rapid and cost-effective sequencing of entire genomes, exomes, and transcriptomes. Genomic profiling has become an indispensable tool for diagnosis and risk stratification in Acute Myeloid Leukemia (AML). While targeted DNA sequencing has become the gold standard to detect driver mutations in AML, transcriptome sequencing offers relevant advantages, such as: the possibility of gene expression profiling evaluation, detection of alternative splicing and gene fusions. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Victoria Tomaz, Paulo Campregher Source Type: research
33. Optical Genome Mapping identifies additional cytogenetic abnormalities in patients with hematologic malignancies
Chromosomal and genetic abnormalities are important prognostic factors in most hematologic malignancies and most clinically relevant aberrations are detectable by conventional cytogenetic and/FISH (CK) analysis. One limitation of cytogenetics is failure due to a lack of analysable metaphases. (1) We have investigated the use of optical genome mapping (OGM) in these disorders and are reporting the advantage of this techinique over CK. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Sachin Jadhav, Sandeep Rao, Alex Hastie, Alka Chaubey Source Type: research
34. Comprehensive genomic characterization of infantile cancers reveals high yield of therapeutically targetable alterations
Our pediatric tertiary care center has established a patient-focused translational protocol supporting genomic profiling of rare or treatment refractory cancers. Infantile and congenital cancers represent a unique cohort among our study group due to disease spectrum, complexity, and associated co-morbidities. Comprehensive genomic profiling was initiated to aid in diagnosis, prognostication, treatment, and detection of germline disease predisposition in this patient cohort.Enhanced exome sequencing of disease and comparator tissue was coupled with RNA sequencing of the disease-involved specimen to assess for single nucleot...
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Mariam Mathew, Samara Potter, Brianna Bucknor, Kathleen Schieffer, Elizabeth Varga, Katherine Miller, Benjamin Kelly, Peter White, Richard Wilson, Elaine Mardis, Catherine Cottrell Source Type: research
35. Evolution of a variant curation procedures in the open-access cancer variant interpretation knowledgebase CIViC
The open-access, literature-based cancer variant knowledgebase CIViC (Clinical Interpretation of Variants in Cancer), was designed to be an expert-moderated, crowd-sourced variant curation platform. By providing structured and editable data, updates can be made in real time as the field grows and emerging evidence is published. Now supporting abstracts from both the American Society of Hematology (ASH) and the American Society of Clinical Oncology (ASCO), CIViC supports early discoveries that can be updated with more detail when studies are later published. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Kilannin Krysiak, Arpad Danos, Jason Saliba, Susanna Kiwala, Adam Coffman, Joshua McMichael, Cameron Grisdale, Mariam Khanfar, Alex Wagner, Malachi Griffith, Obi Griffith Source Type: research
36. Gene Normalizer: A tool to resolve genetic ambiguity through data harmonization
Gene symbols, maintained by gene naming authorities such as HGNC, are error-prone when used as identifiers for describing genes in databases and biomedical literature. Gene symbols are subject to changes over time, and may conflict with community aliases for gene loci, leading to potential errors. We investigated the scale of this issue by evaluating the gene symbols and aliases of two authoritative gene sets: NCBI Gene and HGNC. We found 3,940 gene records (2.3%) containing aliases that identically matched the primary symbol of another gene record. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Anastasia Smith, James Stevenson, Kori Kuzma, Wesley Goar, Matthew Cannon, Alex Wagner Source Type: research
37. Cell-type-specific genetic-to-epigenetic relationships in the human breast
Interplay between the genome and the epigenome is fundamental to cell type functionality and the mechanisms of associated diseases. Most studies that have explored these interactions have leveraged population-scale genotype surveys to associate genetic polymorphisms with epigenetic states in whole blood or other heterogenous tissue types. Epigenetic states differ by cell type, raising the possibly of cell-type-specific genetic-to-epigenetic relationships that could drive specific functional states and disease predisposition. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Axel Hauduc, Misha Bilenky, Annaick Carles, Jonathan Steif, Michelle Moksa, Qi Cao, Connie Eaves, Martin Hirst Source Type: research
38. Assessment of TRG and TRB clonality by NGS of dermatologic specimens is impacted by biopsy type, DNA and amplicon sizes
Molecular testing to detect clonal T-cell populations is commonly applied to dermatologic specimens to support cutaneous T-cell lymphoma diagnosis. With clinical implementation of TRG and TRB clonality by NGS using Lymphotrack (Invivoscribe) sequenced on the Miseq (Illumina), increased specimen numbers have been submitted for testing. For 66 specimens (50 patients) received to date, high insufficiency rates were found for TRG (30%) and TRB (56%). Thus, to improve testing efficiency and effect better specimen triage, we examined tissue features, DNA size by fragment analysis, library concentration, reads and overall call. (...
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Jane Houldsworth, Ekaterina Bogdanova, Tatyana Sidorenko, Zinnia Mai, Avisek Parajuli, Meenakshi Mehrotra, Brett Baskovich Source Type: research
39. Genomic microarray analysis reveals heterogeneity in high hyperdiploid B-cell acute lymphoblastic leukemia
High hyperdiploidy (HHD) is the most common cytogenetic abnormality in childhood B-cell acute lymphoblastic leukemia (B-ALL) and is generally associated with a favorable prognosis; however, 10-20% of patients with HHD B-ALL will ultimately relapse. Although certain trisomy combinations including chromosomes 4, 10, 17 and 18 have previously been reported to be associated with a superior outcome, recent studies redefined the relapse predictive chromosome trisomy combination. The role of clonal heterogeneity has become important for predicting outcomes in HHD B-ALL. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Julie Feusier, Rotem Fishel Ben-Kenan, Denise Quigley, Erica Andersen, Bo Hong Source Type: research
40. Cell-free DNA fragmentation profiling as a method for tumor fraction assessment and treatment monitoring in NSCLC
Available cfDNA assays have shown potential for tracking tumor progression during therapy in patients with metastatic cancers. However, these approaches typically require deep-targeted sequencing to detect cancer-specific mutations at low mutant allele frequency (MAF) levels in the circulating blood. We developed DELFI-Tumor Fraction (DELFI-TF), a mutation-independent approach that utilizes low-coverage whole genome sequencing (WGS) to predict plasma tumor fractions based on genome-wide fragmentation-related features. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Zachary Skidmore, Bahar Alipanahi, Lorenzo Rinaldi, Nicholas Dracopoli, Alessandro Leal Source Type: research
41. Resolving ambiguities in copy number variation representation
Representation of copy number variations (CNV) in biomedical databases and literature represent a variety of closely related concepts, some of which are not representable under all variant nomenclatures. One common example of this is representing the number of copies of a genetic locus in a genome, a concept that is not directly supported by the widely-used Human Genome Variation Society (HGVS) variant nomenclature. For example, HGVS expressions such as NC_000001.10:g. (?_143134063)_(143284670_?)dup are used to convey a systemic gain of a stretch of sequence, but this syntax technically represents a tandem duplication with...
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Kori Kuzma, Kyle Ferriter, Tristan Nelson, Michael Baudis, Lawrence Babb, Alex Wagner Source Type: research
42. Automated deep aberration detection from chromosome karyotype images
Chromosome analysis is essential for diagnosing genetic disorders. For hematologic malignancies, identification of somatic clonal aberrations by karyotype analysis remains the standard of care, with the advantage to identify global genomic aberrations at a single-cell basis. However, karyotyping is costly and time-consuming because of the largely manual process and the expertise required in identifying and annotating aberrations. Efforts to automate karyotype analysis to date fell short in aberration detection. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Min Fang, Zahra Shamsi, Drew Bryant, Jacob Wilson, Xiaoyu Qu, Avinava Dubey, Konik Kothari, Mostafa Dehghani, Mariya Chavarha, Valerii Likhosherstov, Brian Williams, Michael Frumkin, Fred Appelbaum, Krzysztof Choromanski, Ali Bashir Source Type: research
43. Fusion Curation Interface: an educational tool to explore a unified framework for representing & curating gene fusions
Gene fusions are a highly important, but often conflated and ambiguous concept in genomics. Gene fusions hold clinical significance in the understanding of cancers, so contradictory representations of fusion events hinder the ability of the genomics community to effectively share and find knowledge in this area.To overcome the challenges posed by misaligned gene fusion definitions, a cross-consortia panel of experts from the Variant Interpretation for Cancer Consortium (VICC), Cancer Genomics Consortium (CGC), ClinGen, and the CAP/ACMG Cytogenetics Committee developed a unified framework for representing gene fusions, name...
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Kathryn Stahl, James Stevenson, Kori Kuzma, Jeremy Arbesfeld, Alex Wagner Source Type: research
44. Frequency and etiology of cytogenetically cryptic oncogenic fusions in pediatric AML
Fusion genes created by chromosomal rearrangements are the most common oncogenic drivers in pediatric AML. Identifying the primary driver is critical for risk stratification and for developing therapeutic targets. In a series of 600 patients enrolled on Children's Oncology Group AML trial AAML1831 in progress, we determined the frequency of cryptic oncogenic fusions (COFs) in each of the major subgroups of recurring genetic abnormalities. Fusions detected by RNA sequencing and/or FISH were cryptic by karyotype analysis in 12.7% of cases. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Gordana Raca, Todd Cooper, Todd Alonzo, Edward Kolb, Matthew Kutny, Wendy Lee, Soheil Meshinchi, Jessica Pollard, Betsy Hirsch Source Type: research
