92. Characterization of an ultra-high-risk uveal melanoma copy number subtype
This study evaluated the genomic and clinical heterogeneity within established CNA subtypes of UM, and aimed to refine these subtypes based on CNA profiling in a large patient cohort. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2022 Category: Genetics & Stem Cells Authors: Emilie Lalonde, Kathryn Ewens, Jennifer Richards-Yutz, Jessica Ebrahimzedeh, Mizue Terai, Carin F. Gonsalves, Takami Sato, Carol L. Shields, Arupa Ganguly Source Type: research
93. Surveying the genomic landscape of Mantle Cell Lymphoma
Mantle Cell Lymphoma (MCL) is a B-cell non-Hodgkin Lymphoma that currently has poor prognosis and few effective treatments. This project was intended to explore the variants that characterize MCL, and potentially identify targets for novel treatments. The patient cohort included 28 individuals who contributed lymph node biopsies and matched skin normal samples. All 28 patients had whole exome sequencing (WES), 10 had whole genome sequencing (WGS), and 8 had RNA sequencing. We used established in-house DNA and RNA analysis pipelines to detect single-nucleotide variants and indels, structural variants, copy number alteration...
Source: Cancer Genetics and Cytogenetics - November 1, 2022 Category: Genetics & Stem Cells Authors: Brian Li, Felicia Gomez, Matthew Mosior, Vera Thornton, Zach Skidmore, Kelsy Cotto, Brad Kahl, Malachi Griffith, Obi L. Griffith Source Type: research
94. Comparison of FISH to whole exome/whole transcriptome detection of relevant structural alterations in Multiple Myeloma
In multiple myeloma and monoclonal gammopathies, single nucleotide variants (SNV), copy number variants (CNV) and IGH-rearrangements with prognostic/therapeutic relevance, are assessed by NGS, FISH, and karyotype. Recently, whole exome/transcriptome sequencing (WES/WTS) post CD138+-enrichment has been clinically implemented, thus we evaluated this approach to detect relevant alterations. Over 9 months, 160 aspirates were enriched including assessment of %CD138+ by flow cytometry post-enrichment. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2022 Category: Genetics & Stem Cells Authors: Bella Liu, William Lam Source Type: research
95. A novel comprehensive breakpoint-targeted assay for clinically actionable RNA fusions and aberrant RNAs in solid tumors
Accurate detection of gene fusions is key for supporting cancer diagnosis and therapy selection. Most assays are limited to select intronic DNA breakpoints capture assays or amplicon RNA panels querying only a small number of genes, while whole exome RNA capture or full transcriptome assays lack sensitivity. We developed a pair-ended, strand-specific hybridization-based RNA sequencing assay targeting 1194 unique known fusions pairs and 1104 genes involving 250 fusion genes clinically relevant to most solid tumors. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2022 Category: Genetics & Stem Cells Authors: Fernando Lopez-Diaz, Steven Rivera, Christophe Magnan, Brad Thomas, Yanglong Mou, Segun Jung, Sally Agersborg, Vincent Funari Source Type: research
96. Dissection of the expressed actionable fusions' repertoire in solid tumors in a clinical setting across 14 cancer types
Large studies based on DNA-based NGS testing alongside clinical trials have established the prevalence of clinically actionable gene fusions such as NTRK1/2/3. However, much less is known about the broader repertoire and prevalence of bonafide expressed gene fusions. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2022 Category: Genetics & Stem Cells Authors: Fernando Lopez-Diaz, Rachel Schell, Chaugiang Duong, Steven Rivera, Vincent Funari Source Type: research
97. The clinical implications of unbalanced CCND1::IGH rearrangement resulted from the 5 ′IGH deletion in multiple myeloma
Multiple myeloma (MM) is cytogenetically heterogeneous. IGH translocation driving the over expression of the fusion partner gene is considered as a primary genomic event in the pathogenesis of MM. Most IGH fusions in MM are balanced, however, unbalanced IGH fusions are frequent. While the unbalanced translocation resulted from the 3 ′IGH deletion has clinical implications, the 5′IGH deletion is not well studied and often could be interpreted as physiological event due to the IGH locus somatic V-D-J recombination. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2022 Category: Genetics & Stem Cells Authors: Xinyan Lu, Amandeep Kaur, Barina Aqil, Juehua Gao, Madina Sukhanova, Yi-Hua Chen Source Type: research
98. Utility and feasibility of Molecular Profiling of Circulating Tumor RNA (ctRNA) from FNA Supernatants
In this study, we evaluated the feasibility of using ctRNA extracted from FNA supernatants for NGS-based fusion detection using three different extraction kits. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2022 Category: Genetics & Stem Cells Authors: Mohamed H. Maher, Dzifa Y. Duose, Gabrielle Carillo, Jessica Lan, Ignacio I. Wistuba, Rajyalakshmi Luthra, Sinchita Roy Chowdhuri Source Type: research
99. Histopathologic Correlation Somatic Variants in Non Small Cell Lung Cancer with High Tumor Mutation Burden
High tumor mutation burden (TMB), having at least 10 mutations/megabase (mut/Mb), is reported to be as high as 42% of non small cell lung adenocarcinoma (LADC). Micropapillary adenocarcinoma is one of the most aggressive histologic subtypes of lung adenocarcinoma (LADC) and is often associated with a poor prognosis. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2022 Category: Genetics & Stem Cells Authors: Elias Makhoul, Saleh Heneidi, Celeste Eno, Eric Vail Source Type: research
100. Identification of unique subtypes of pediatric high-grade glioma by comparative tumor transcriptomics
Pediatric high-grade glioma (pHGG) is a devastating and poorly understood cancer driven by numerous genetic and epigenetic mechanisms. Here, we use numerous bioinformatics approaches to analyze transcriptomic data of 1,543 pediatric brain tumor specimens from the UCSC Treehouse Childhood Cancer Initiative (Treehouse) and Open Pediatric Brain Tumor Atlas (OpenPBTA) to subtype pHGG patients. We find that approximately half (49.5%) of pHGG tumors from OpenPBTA can be partitioned into three subgroups defined by high outlier-level expression either of: mitochondrially-encoded 12S and 16S rRNAs; genes enriched in the HSF1-mediat...
Source: Cancer Genetics and Cytogenetics - November 1, 2022 Category: Genetics & Stem Cells Authors: Gina Mawla, Geoff Lyle, Ellen Kephart, Katrina Learned, Holly Beale, Joshua Goldford, Olena Vaske Source Type: research
101. Development of an analytical pipeline for detecting fusions of clinical relevance in liver cancer
Gene fusions play a crucial role in multiple cancers including cholangiocarcinoma (CCA) and hepatocellular carcinoma (HCC). To make unbiased gene-fusion discoveries for CCA and HCC, we studied tumor RNA-seq data from 51 CCA and 48 HCC patients treated at Mayo Clinic, and an additional 424 HCC and CCA cases from The Cancer Genome Atlas (TCGA). We developed an integrative fusion pipeline to annotate and identify high confidence, candidate gene fusions initially called by STAR-Fusion-v1.4.0. The pipeline considers exon boundaries, in-frame candidates, homologous genes, and the proximity of gene partners. (Source: Cancer Genet...
Source: Cancer Genetics and Cytogenetics - November 1, 2022 Category: Genetics & Stem Cells Authors: Chantal McCabe, Numrah Fadra, Daniel O'Brien, Asha Nair, Rory Smoot, Lewis Roberts, Mike Torbenson, Chen Wang Source Type: research
102. Elucidating the genomic landscape of Prostate Adenocarcinoma through whole genome and transcriptome sequencing
Whole Genome and Transcriptome Sequencing (WGTS) testing provides a comprehensive molecular profile of a patient's tumor. Genome sequencing was performed at the New York Genome Center CLIA laboratory, from frozen and FFPE tumor of two cases diagnosed with prostate adenocarcinoma and matched normal blood DNA. RNA sequencing of the two separate tumors was also performed using NYGC proprietary analysis pipeline. Results of the first specimen showed two biallelic inactivating CDK12 alterations, focal tandem duplications across entire genome and a high rate of DNA fusions likely due to DNA mismatch repair error. (Source: Cancer...
Source: Cancer Genetics and Cytogenetics - November 1, 2022 Category: Genetics & Stem Cells Authors: Marilena Melas, Heather Geiger, Sowmya T. Srinivasa, Saurav Guha, Vanessa Felice, Lena Fielding, Amanda Thomas-Wilson, Ashley Wilson, Theresa MacDonald, Ryan Smith, Jyothi Manohar, Michelle Primiano, Olivier Elemento, Ravi Sharaf, Kazimierz O. Wrzeszczyns Source Type: research
103. Formation of a ClinGen Variant Curation Expert Panel (VCEP) dedicated to Oncohistone H3 Variants in Pediatric Gliomas
Mutations in histone H3 (oncohistones) result in widespread epigenetic dysregulation and are increasingly recognized as oncogenic events in many different cancer types. In particular, H3.1/3 K27M and G34R/V oncohistones define a subset of highly aggressive pediatric gliomas arising in the midline ('diffuse midline glioma, H3 K27-altered') and cerebral hemispheres ('diffuse hemispheric glioma, H3 G34-mutant'). Recently, other glioma subtypes with non-infiltrative or low-grade histomorphologies have been identified with H3 K27M mutations and less aggressive clinical courses, some harboring co-occurring driver events characte...
Source: Cancer Genetics and Cytogenetics - November 1, 2022 Category: Genetics & Stem Cells Authors: David Meredith, Jason Saliba, Yassmine Akkari, Wan-Hsin Lin, Jianling Ji, Elizabeth Spiteri, Cam Grisdale, Arpad Danos, Rushil Dua, Erin McMullin, Jeanine Ruggeri, Eldar Dudic, Donald Parsons, Daniel Brat, Sebastian Waszak, Sabine Mueller, Obi L. Griffith Source Type: research
104. H3K27-altered diffuse midline gliomas with secondary driver molecular alterations
Large-scale sequencing efforts have identified co-occurring driver events, such as activating mutations in FGFR1 and BRAF, in occasional diffuse midline gliomas (DMGs) H3K27-altered, but their significance is incompletely explored. To better understand the clinicopathologic features of these tumors, we identified all H3K27-mutant gliomas from our internal sequencing database (2013-2021) of over 2,000 gliomas and collected detailed clinical information, pathologic features, mutational signatures, and copy number profiles for the resulting cohort. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2022 Category: Genetics & Stem Cells Authors: David Meredith, Catherine Gestrich, Kristina Grieco, Hart Lidov, Keith Ligon, Sandro Santagata, Kee Kiat Yeo, Sanda Alexandrescu Source Type: research
105. Clinical whole-genome sequencing identifies NSD3 as the correct fusion partner of NUP98 in a patient with acute myeloid
Only rare cases of acute myeloid leukemia (AML) have been shown to harbor a t(8;11)(p11.2;p15.4). This translocation is believed to involve the fusion of NSD3 or FGFR1 with NUP98; however, apart from targeted mRNA quantitative PCR analysis, no molecular approaches have been utilized to define the chimeric fusions present in these rare cases. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2022 Category: Genetics & Stem Cells Authors: Bahareh Mojarad, Zachary Crees, Molly Schroeder, Zhifu Xiang, Justin Vader, Jason Sina, John Frater, Eric Duncavage, David Spencer, Julie Neidich, Kory Lavine, Ina Amarillo Source Type: research
106. Genotype of Human Papilloma virus in Male Genital Warts in Korean men and review of literature
Genital warts are one of the most common sexually transmitted infections and are known to develop due to human papilloma virus (HPV) infection, especially HPV types 6 and 11. However, their prevalence in male genital warts remains poorly defined. HPV vaccine is administered to both sexes and it is important to investigate their expected impact in male anogenital warts. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2022 Category: Genetics & Stem Cells Authors: Jung Joo Moon, Woo Chul Moon Source Type: research
