105. Machine learning for automated tumor classification based on mutation repertoire
A cornerstone of oncologic treatment is accurate tumor type and tissue of origin (TT/TO) identification. Nevertheless, histological analysis is occasionally inconclusive. As comprehensive genomic profiling has become prevalent in cancer care, a method to identify the TT/TO based on tumor mutations would be valuable for clinical practice. Our goal was to develop a machine learning model to identify TT/TO based on the repertoire of mutations restricted to genes present in the Trusight Oncology 500 Assay (Illumina) (TSO500). (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Qiao Xuanyuan, Matthew Inkman, Victoria Tomaz, Rafael Lucas Muniz Guedes, Michael Waters, Jin Zhang, Paulo Campregher Source Type: research
106. Three-way translocation t(8;14;18) leading to rearrangements of MYC and BCL2 with single IGH in high-grade B-cell lymphoma
The 5th edition of WHO classification and the 2022 International Consensus Classification of mature lymphoid neoplasms have reframed the double-hit lymphoma as high-grade B-cell lymphoma (HGBCL) with MYC and BCL2 rearrangements (HGBCL-MYC/BCL2). This aggressive lymphoma is relatively rare (4-10% of large/HGBCL), mostly found in older adults, and associated with poor outcomes. There are no reliable morphologic or immunophenotypic criteria to predict HGBCL-MYC/BCL2. Therefore, it is recommended to evaluate MYC and BCL2 translocation status for all large/HGBCL to enable modified management, including CAR-T cell therapy, or ta...
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Chen Yang, Chen Yang, Jiong Yang, Alysia Sanchez, Hong Xiao, Turquessa Brown-Krajewski, Anamarija Perry, Lina Shao Source Type: research
107. MyVariant.info: a gateway to integrated resource of variant annotations
The depth and breadth of knowledges on genetic variation are growing exponentially. At the same time, the latest web API technology revamps the way we collect, manage and publish the fast-growing variant annotations. First, users can fetch annotation data from web APIs with much lower latency compared to downloading and analyzing data sources separately. Second, web APIs return data in standard formats (e.g., JSON or XML), which enables easy integration with other applications such as knowledge discoveries. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: Yao Yao, Everaldo Rodolpho, Sebastien Lelong, Xinghua Zhou, Cyrus Afrasiabi, Zhongchao Qian, Marco Alvarado Cano, Ginger Tsueng, Andrew I. Su, Chunlei Wu Source Type: research
108. Optical genome mapping for detection of biomarkers in residual disease monitoring research of hematologic malignancies
Cancer disease monitoring and detection of biomarkers associated with relapse are critical for the appropriate therapeutic management of such diseases. Currently, karyotyping, fluorescent in situ hybridization (FISH), flow cytometry, PCR, and next-generation sequencing are often used for these applications. PCR is sensitive but it's a targeted approach requiring identification of a biomarker. Karyotyping and FISH are used to detect structural variants (SVs); however, karyotype has low sensitivity and FISH is only targeted. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - November 1, 2023 Category: Genetics & Stem Cells Authors: James Yu, Alex Chitsazan, Andy Pang, Alex Hastie Source Type: research
Breast and colorectal cancer risks among over 6,000 CHEK2 pathogenic variant carriers: A comparison of missense versus truncating variants
CHEK2, a cell-cycle checkpoint regulator gene involved in DNA damage repair, is well established as a moderate-risk susceptibility gene in hereditary breast cancer.[1] Those who carry a heterozygous germline pathogenic variant (PV) in CHEK2 have a 1.5- to 3-fold increase in breast cancer risk up to age 80.[2 –5] Breast cancer risk is higher among women with biallelic PVs in CHEK2, with a nearly 9-fold increased risk of ductal invasive breast cancer reported.[6] Heterozygous PVs in CHEK2 have also been associated with an increased risk of colorectal cancer. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - October 10, 2023 Category: Genetics & Stem Cells Authors: Erin Mundt, Brent Mabey, Irene Rainville, Charite Ricker, Nanda Singh, Anna Gardiner, Susan Manley, Thomas Slavin Tags: Original Article Source Type: research
Pan-cancer genetic analysis of disulfidptosis-related gene set
In recent years, cancer has become a major public health concern across the world, with a projected 1,918,030 new cancer cases and 609,360 cancer deaths in the United States alone in 2022 according to the American Cancer Society[1]. Cancer is a complex and multifaceted disease that requires comprehensive research in order to improve early detection and treatment methods. By doing so, it is possible to reduce the number of cancer-related deaths and help more individuals to achieve successful treatment outcomes. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - October 9, 2023 Category: Genetics & Stem Cells Authors: Hengrui Liu, Tao Tang Tags: Original Article Source Type: research
Hypomethylation of DRD2 promotes breast cancer through the FLNA-ERK pathway
The treatment of breast cancer is still challenging [1]. Some tumor cells have a strong ability for self-renewal and produce heterogeneous cells as stem cells [2], which were defined as cancer stem cells (CSCs) by some scholars [3]. Although controversy about their surface markers for isolation and identification remains, these CSC-like cells were tumor cells with highly malignant tumors. Experimental evidence shows that traditional chemotherapy drugs are ineffective on these highly malignant human cancer cells [4]. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - September 9, 2023 Category: Genetics & Stem Cells Authors: Shuoyi Zhang, Ming Zhong, Hongbo Zhu, Qinghua You, Hao Yuan, Yongping Li Tags: Original Article Source Type: research
Paediatric B lymphoblastic leukaemia with hyperdiploidy and a false-positive KMT2A fluorescence in situ hybridization result
Acute lymphoblastic leukaemia (ALL) is the most common cause of childhood cancer. [1 –4] Paediatric ALL event-free survival (EFS) has improved dramatically, with EFS of over 85%.[5] With improved understanding of leukaemia biology, patients now receive risk stratified treatment based on a combination of clinical features, cytogenetic abnormalities and response to treatment. High h yperdiploidy, defined as>50 chromosomes, is seen in 25-30% of paediatric B-lymphoblastic leukaemia (B-ALL). [6,7] The presence of high hyperdiploidy is considered a favourable disease feature, however the underlying pathways that account for th...
Source: Cancer Genetics and Cytogenetics - September 6, 2023 Category: Genetics & Stem Cells Authors: Jenna Nunn, Nandini Adayapalam, Sarbjit Riyat, Louise Seymour, Bronwyn Williams, Jacqueline Rehn, Deborah White, Andrew S. Moore, Karen Tsuchiya Tags: Short Communication Source Type: research
Effects of concurrent TP53 mutations on the efficacy and prognosis of targeted therapy for advanced EGFR mutant lung adenocarcinoma
Lung cancer has high mortality rates caused by the low early diagnostic rate, being prone to distant metastasis and drug resistance during treatment[1]. EGFR is the most frequent driving gene in lung adenocarcinoma, and it has been detected in almost 40-50% Asian lung adenocarcinoma patients[2]. 19 exon deletion (19del) and 21 exon L858R mutations (L858R) are the most common EGFR mutation types and considered sensitive to EGFR-TKIs[3]. Although having EGFR mutations can predict a favorable TKIs response, acquired resistance will eventually develop. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - August 26, 2023 Category: Genetics & Stem Cells Authors: Huiwen Qian, Chunqi Hou, Yi Zhang, Shundong Ji, Chongke Zhong, Juan Li, Qianqian Zhang, Jianan Huang, Chong Li, ChengJi Source Type: research
Acute Myeloid Leukemia with LRRFIP1::FGFR1 Rearrangement and a Complex Karyotype
We report a case of a 20-year-old man who presented with splenomegaly, hyperleukocytosis, anemia, and thrombocytopenia. A diagnosis of acute myeloid leukemia (AML) with LRRFIP1::FGFR1 rearrangement with complex karyotype was determined. Chromosome analysis showed a male karyotype: 46,XY,i(1)(q10),t(2;8)(q37;p11.2),der(5)t(1;5) (p22;q13)[17]46,XY[3]. Fluorescence in situ hybridization (FISH) analysis using the Cytocell FGFR1 break apart/amplification probe detected FGFR1 rearrangement with t(2:8) in 126/200 cells analyzed. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - August 14, 2023 Category: Genetics & Stem Cells Authors: You-Wen Qian, Eunice S. Wang, Sheila Jani Sait, Sean T. Glenn Tags: Original Article Source Type: research
Evaluation of Chromosome 1p/19q deletion by Fluorescence in Situ Hybridization (FISH) as prognostic factors in malignant glioma patients on treatment with alkylating chemotherapy
Glioma, the most frequent brain tumor occurs at a frequency of 1.6% as per Global Cancer Statistics, male: female ratio of age-standardized risk as 3.9:3.1 [1]. Glioma displays a widespread heterogeneity at morphological site, genetic model and response to chemo-radiotherapy. Glioblastoma (GBM) is mainly the most frequent among the different types of malignant glioma with aggressive nature [2,3]. In addition to epigenetic alterations like mutations in IDH and MGMT gene hypermethylation respectively, chromosomal variations mostly in chromosome 1p/19q deletion have been detected in malignant gliomas [4]. (Source: Cancer Gene...
Source: Cancer Genetics and Cytogenetics - August 10, 2023 Category: Genetics & Stem Cells Authors: Arshad A. Pandith, Wani Zahoor, Usma Manzoor, Syed Nisar, Faisal R. Guru, Niyaz A. Naikoo, Qurat ul Aein, Shahid M. Baba, Abdul R Bhat, Farooq Ganai, Parveen Shah Source Type: research
Identification of a novel RSRC1-ALK (R6: A20) fusion using next-generation sequencing technique
Anaplastic lymphoma kinase (ALK) gene, initially discovered in 1994, is reported as a fusion gene in anaplastic large cell lymphoma [1]. It is located on the short arm of chromosome 2 (2p23), belonging to the insulin receptor superfamily [2]. The prevalence of ALK gene fusion and/or rearrangement is approximately 5%-6% among the non-small-cell lung cancer (NSCLC) patients [3,4], especially the never-smoking adenocarcinoma patients with no other oncogenic driver mutations [5]. To date, ALK fusion screening contributes to the identification of patients that may benefit from the ALK-targeted therapies. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - August 8, 2023 Category: Genetics & Stem Cells Authors: Jingjing Xia, Sheng Chen, Zhujian Zhang, Jipeng Wang Source Type: research
Clinical characterization of the mutational landscape of 24,639 real-world samples from patients with myeloid malignancies
Myeloid neoplasms are disorders of the blood arising from clonal mutations in hematopoietic stem cells and include diseases such as myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN) and acute myeloid leukemia (AML) [1]. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - August 7, 2023 Category: Genetics & Stem Cells Authors: Grant Hogg, Eric Severson, Li Cai, Heidi M. Hoffmann, Kimberly A. Holden, Kerry Fitzgerald, Angela Kenyon, Qian Zeng, Michael Mooney, Sabrina Gardner, Wenjie Chen, Narasimhan Nagan, Deborah Boles, Scott Parker, Tamara J. Richman, Stanley Letovsky, Henry D Tags: Original Article Source Type: research
Prognostic impact of molecular profiles and molecular signatures in clear cell ovarian cancer
Ovarian Clear Cell Carcinomas (OCCC) account for 5-25% of all Epithelial Ovarian Cancer (EOC). It represents distinct molecular, clinical, and pathological characteristics compared with other EOC subtypes [1 –3]. Next Generation Sequencing (NGS) studies have demonstrated that OCCC comprise several molecular heterogeneous subtypes [4,5]. Still, all OCCC patients are treated with primary surgery followed by adjuvant platin/taxane-based chemotherapy despite low response rates and thus, a poor prognosis o f patients diagnosed in advanced stages [1,2]. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - August 3, 2023 Category: Genetics & Stem Cells Authors: Tine Henrichsen Schnack, Douglas-V.N.P. Oliveira, Anne Pernille Christiansen, Claus H øgdall, Estrid Høgdall Source Type: research
Construction of a genomic instability-derived predictive prognostic signature for non-small cell lung cancer patients
Non-small cell lung cancer (NSCLC) is the most common histologic subtype of lung cancer, accounting for over 80% of all cases[1,2]. The two common types of NSCLC are lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) [3]. Recently, monoclonal antibodies targeting the PD-1/PD-L1 axis have emerged as a primary treatment approach for advanced NSCLC [4]. However, despite the use of these antibodies, treatment outcomes remain suboptimal due to the development of drug resistance in a majority of patients. (Source: Cancer Genetics and Cytogenetics)
Source: Cancer Genetics and Cytogenetics - August 2, 2023 Category: Genetics & Stem Cells Authors: Wei Li, Huaman Wu, Juan Xu Tags: Original Article Source Type: research
