74. Genomic analyses of Hodgkin and non-Hodgkin composite lymphomas identifies shared somatic mutations indicative of common clonal origin
Composite lymphoma (CL) occurs when two lymphomas with distinct WHO subtypes arise in one patient. Here, we present two cases of CL. Case 1 presented with diffuse large B-cell lymphoma (DLBCL), Hodgkin lymphoma (HL), and follicular lymphoma (FL). Case 2 presented with FL and HL in two distinct areas of one lymph node. We performed exome sequencing on matched tumor/normal samples (mean depth per sample>70x) from each lymphoma, excluding the FL in case 1. SNVs and indels were filtered and manually reviewed. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Felicia Gomez, Lauren Shea, Matthew Mosior, Kilannin Krysiak, Yi-Shan Lee, Eric Duncavage, Michelle O'Laughlin, Nancy Bartlett, Amanda Cashen, Malachi Griffith, Todd Fehniger, Lukas Wartman, Obi Griffith Source Type: research
75. Novel complex translocation involving PDGFRA::PRKG2, in a myeloid neoplasm with basophilia sample by OGM
Myeloproliferative neoplasms are often characterized by genetic abnormalities which activate requested new titletyrosine kinases resulting in uncontrolled cell proliferation. Conventional cytogenetic techniques are used to identify these abnormalities but they have low resolution and/or are targeted in nature among other limitations. Optical genome mapping (OGM) overcomes these limitations, providing better detection of structural rearrangements of known clinical relevance. A case where multiple rearrangements which were identified via OGM, leading to a targeted therapy will be presented. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Alex Hastie, Sandeep Rao, Shruthi Neelamegam, Trilochan Sahoo, Alka Chaubey, Sachin Jadhav Source Type: research
76. Von Hippel-Lindau syndrome in a patient with negative germline testing
The VHL gene is a tumor suppressor gene that plays a critical role in regulating cell growth and division. Pathogenic variants in the VHL gene can lead to the development of tumors in various organs, including the kidneys, adrenal glands, and pancreas. The most well-known disease associated with VHL gene pathogenic variants is von Hippel-Lindau disease (VHL disease), an inherited disorder that increases the risk of developing multiple tumors and cysts in different parts of the body.Here, we present the case of an individual with a clinical diagnosis of VHL disease where germline NGS testing results were negative twice, usi...
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Patricia Hernandez, Andrea Stacy, Yang Cao Source Type: research
77. Mining COSMIC for frameshift neoantigens as `off-the-shelf' therapeutic cancer vaccine candidates
A frameshift mutation is an insertion or deletion which shifts the reading frame and consequently creates novel peptide sequences, usually resulting in premature termination but occasionally extension at the C-terminus. Since multiple frameshift mutations can give rise to the same alternate amino acid sequences, frameshift neoantigens are more commonly shared between different patients compared to many individual missense neoantigens. Frameshift peptides are also highly distinct from self, and hence more likely to induce robust immune responses. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: My Hoang, Bryan Fisk, Jon A. Weidanz, Georgios Alexandrakis, Obi L. Griffith, Malachi Griffith Source Type: research
78. Financially stratified diagnostic, prognostic and treatment response evaluation of ALL in LMIC
The prognosis for hematologic malignancies such as acute lymphoblastic leukemia has remarkably improved in the past decade. However, the financial burden of the ever-evolving evaluation and treatment guidelines is a source of strain for patients and caregivers in LMICs, who have limited insurance cover and thus, largely bear this burden with out-of-pocket expenses while also suffering loss of productivity, due to work absenteeism. In addition to this, the incremental improvement in clinical outcomes, vis-a-vis the financial toxicity of diagnostic and prognostic testing, has not been studied in a prospective manner, in a re...
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Sachin Jadhav, Yesheswini Naik, Sandeep Rao Source Type: research
79. Extraction of multiple analytes in liquid biopsy may improve the diagnosis of breast cancer
This study demonstrates an optimized extraction method for cfTNA (Cell-Free Total Nucleic Acid) and circulating tumor cells (CTC) from a single blood sample. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Nafiseh Jafari, Mayer Saidian, Jason Saenz, Cory Arnold, Andrew Dunnigan, Carlos Hernandez, Lauren Lee Source Type: research
80. Identification of a post-platinum NBN reversion in a pancreatic cancer patient with a co-occurring NTRK1 fusion
Pancreatic acinar cell carcinomas (PACCs) frequently harbor activating fusions in the MAPK pathway, and alterations in DNA damage response (DDR) and homologous recombination (HR) repair-related genes.Here we report the case of a 65-year-old white male with PACC. The patient initially received pancreaticoduodenectomy and adjuvant therapy, but later developed metastatic disease in the liver. Multimodal genomic analysis of the primary resection identified an in-frame SEL1L::NTRK1 fusion and a somatic pathogenic frameshift mutation in NBN exon 10 (c.1146del; p.E383Kfs*21) coupled with loss of heterozygosity, resulting in biall...
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Adrienne Johnson, Pier Selenica, Joseph Schonhoft, Danielle Ulanet, Victoria Rimkunas, Jorge Reis-Filho, Ian Silverman, Meredith Pelster Source Type: research
81. Prediction of plant based EGFR inhibitors against breast cancer (EGFR) using machine learning model
In this study, we applied machine learning techniques to predict potential inhibitors for EGFR in breast cancer. We utilized a dataset of compounds and their inhibitory activities against EGFR, as well as molecular descriptors, such as structural and physicochemical properties of the compounds. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Abraham Peele Karlapudi Source Type: research
82. Can mitochondrial DNA mutations be used as a biomarker for endometrial cancer?
Endometrial cancer (EC) is one of the most common forms of gynecological cancer, with death rates from this disease doubling over the past 20 years. Most solid tumors harbor at least one mtDNA mutation, and cancer cells can have mixtures of polyploid wild-type and mutant mtDNA genomes, so-called heteroplasmy. We compared mtDNA genomes from three matched sets of peri-normal and EC tumor specimens and determined that each tumor harbors tumor-specific mtDNA mutations. Furthermore, somatic EC mtDNA mutations were investigated in aggregate from several published studies. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Pabitra Khadka, Carolyn Young, Taryn Sauerbrunn, Kathleen Groesch, Kathy Robinson, Andrea Braundmeier-Fleming, Ravi Sachidanandam, Dale Buck Hales, Laurent Brard, Matthew Young Source Type: research
83. Cytogenetic and molecular characterization of IDH-mutant adult-type diffuse gliomas with near-total 1p/19q co-deletions
Whole-arm 1p/19q co-deletion is a diagnostic criterion for oligodendroglioma, IDH-mutant and 1p/19q-codeleted. The significance of near-total co-deletions of 1p and 19q arms (( ≥75%) is unclear. We cytogenetically and molecularly characterized 15 IDH-mutant adult-type diffuse gliomas with near-total 1p/19q co-deletions encountered in routine testing by a single reference laboratory using OncoScanTM CNV Plus and targeted neuro-oncology NGS panels (2017-2021). Median age a t surgery was 51 years (range 34-74). (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Cinthya Zepeda Mendoza, Thomas Kollmeyer, Corinne Praska, Katherine Geiersbach, William Sukov, Patricia Greipp, Aditya Raghunathan, Caterina Giannini, Robert Jenkins, Cristiane Ida Source Type: research
84. Challenges in the clinical implementation of the large next-generation sequencing oncomine comprehensive plus assay
Technical barriers, panel complexity and bioinformatics are major challenges for the clinical implementation of large NGS panels. For optimization of the 500+ gene Oncomine comprehensive plus targeted amplicon based NGS assay to detect SNVs, Indels, CNVs, fusions and TMB, 40ng DNA and RNA from 115 specimens from different tumor types (tumor cellularity ≥10%) were used for library preparation and sequenced on the Ion S5XL sequencer. Ion Reporter 5.18 (IR) and Alissa custom classification trees were optimized for known variants. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Meenakshi Mehrotra, William Lam, Evelyne Kouame, Michelle Guan, Brett Baskovich, Matthew Croken, Jane Houldsworth Source Type: research
85. Microfilter enrichment of Hodgkin and Reed-Sternberg (HRS) cells
Hodgkin lymphoma (HL) is a rare B-cell derived hematologic malignancy that affects the lymph nodes. Large, multinucleated Reed-Sternberg (50-100 µm) and mononuclear Hodgkin cells (20-30 µm) are pathognomonic features of HL. These cells are rare and associated with T-cell aggregates making isolation and characterization challenging. Previous methods employed to isolate Hodgkin and Reed-Sternberg (HRS) cells are technically challenging, time consuming, and produce limited outputs unsuitable for clinical assays, making an alternative methodology imperative for the continued study of HL. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Brianna Munnich, Becca Brown, Abdulrahman Saadalla, Richard Cote, Todd Fehniger, Siddarth Rawal, Kilannin Krysiak Source Type: research
86. Diagnostic challenges of high-grade myeloid malignancies with partial plasmacytoid dendritic cell differentiation
We describe a rare case of chronic myelomonocytic leukemia (CMML) showing an unusual pattern of progression to myeloid sarcoma with partial plasmacytoid dendritic cell (pDC) differentiation which is previously not been well-described in literature. A 71-year-old man, diagnosed with CMML five years back, developed progressive lymphadenopathy. Lymph node (LN) biopsy confirmed myeloid sarcoma with prominent ( ∼40%) pDC differentiation [dual TCF4/CD123 positivity by immunohistochemistry (IHC) and flow cytometry (FC) analysis (CD123bright/HLA-DR+/CD303+/CD2partial/CD7partial)]. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Karen Nahmod, Roberto Miranda, Francisco Vega, Beenu Thakral, Naveen Pemmaraju, Sanam Loghavi, Fatima Jelloul, Wei Wang, Sa Wang, Tariq Muzzafar, Keyur Patel, Carlos Bueso-Ramos, L. Jeffrey Medeiros, Rashmi Kanagal-Shamanna Source Type: research
87. A tale of two aspirates: sequential pulls of bone marrow yield discordant results in hepatosplenic T-cell lymphoma
We present a case of a 33-year-old female with a recent diagnosis of HSTCL from an outside institution referred to Vanderbilt University Medical Center (VUMC) in late 2022. Bone marrow (BM) biopsies from VUMC and the outside institution-performed 16 days apart-had similar immunophenotypic and morphologic findings: an abnormal T-cell lymphocyte population positive for CD3, CD56, and gamma delta, negative for CD5 and alpha beta, and an intrasinusoidal distribution. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Barbara Nelson, Rebecca Smith, Cindy Vnencak-Jones, Laura Lee, Aaron Shaver, Mary Ann Thompson Arildsen, Barbara Sommer, Yingda Wang, Ashwini Yenamandra Source Type: research
88. Clinical impact of targeted genomic profiling
Next-generation sequencing (NGS) assays for solid tumors range from those that assess dozens of genes with actionable clinical utility (targeted genomic profiling, TGP) to assays that evaluate hundreds of genes (comprehensive genomic profiling, CGP). Genes included in TGP are limited in number and carefully chosen based on their clinical actionability with prognostic and/or therapeutic impact. Our goal is to determine the degree of difference in clinical impact of TGP as compared with CGP.We analyzed 775 unique CGP cases. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Thuy Phung, Christian Manganti, Mohan Kasukurthi, Kelly Hebert, Jingshan Huang Source Type: research
