Article
Biochemistry & Molecular Biology
Soragia Athina Gkazi, Emma Gravett, Carla Bautista, Jack Bartram, Sara Ghorashian, Stuart Paul Adams
Summary: Chimeric antigen receptor (CAR) T cell therapy has proven to be effective in treating cancers in both children and adults, and some CAR T cell therapies have been approved for clinical use. This study focuses on a recently approved CAR T therapy called tisagenlecleucel, which targets B-cell acute lymphoblastic leukemia (B-ALL). Accurate monitoring of these CAR T cells in patients is crucial, but a standardized method with high reproducibility and efficiency has not been described in routine clinical laboratories. The study introduces a novel digital droplet PCR-based methodology for assessing copy number variant (CNV) of CAR T cell products, which can be universally applied in clinical diagnostic laboratories.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Samuel Terkper Ahuno, Anna-Lisa Doebley, Thomas U. Ahearn, Joel Yarney, Nicholas Titiloye, Nancy Hamel, Ernest Adjei, Joe-Nat Clegg-Lamptey, Lawrence Edusei, Baffour Awuah, Xiaoyu Song, Verna Vanderpuye, Mustapha Abubakar, Maire Duggan, Daniel G. Stover, Kofi Nyarko, John M. S. Bartlett, Francis Aitpillah, Daniel Ansong, Kevin L. Gardner, Felix Andy Boateng, Anne M. Bowcock, Carlos Caldas, William D. Foulkes, Seth Wiafe, Beatrice Wiafe-Addai, Montserrat Garcia-Closas, Alexander Kwarteng, Gavin Ha, Jonine D. Figueroa, Paz Polak
Summary: ctDNA sequencing studies conducted on patients in sub-Saharan Africa revealed the detection of ctDNA in a majority of patients, despite not being selected for tumor grade and subtype. Additionally, breast cancer driver copy number alterations were observed in the majority of patients.
NPJ PRECISION ONCOLOGY
(2021)
Editorial Material
Multidisciplinary Sciences
Roberto H. Herai, Ryan A. Szeto, Cleber A. Trujillo, Alysson R. Muotri
Summary: Researchers conducted an undisclosed in silico-only whole-exome sequencing analysis of the data, identifying genomic alterations in some clones previously undetected. However, most of these alterations could not be experimentally validated, with only one alteration remaining unconfirmed and having no impact on previous results or data interpretation.
Article
Oncology
Li Sun, Meijun Du, Manish Kohli, Chiang-Ching Huang, Xiaoxiang Chen, Mu Xu, Hongbing Shen, Shukui Wang, Liang Wang
Summary: Circulating tumor DNA (ctDNA) in plasma is used as a biomarker for cancer detection, with this study showing significant differences in ctDNA content among different fractions of plasma, with the highest levels found in EV-depleted plasma. Mutational analysis further confirmed higher detection rates in fraction 6 compared to whole plasma, suggesting the potential for improved ctDNA detection using fractionated plasma.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Ariane Hallermayr, Tobias Wohlfrom, Verena Steinke-Lange, Anna Benet-Pages, Florentine Scharf, Ellen Heitzer, Ulrich Mansmann, Christopher Haberl, Maike de Wit, Holger Vogelsang, Markus Rentsch, Elke Holinski-Feder, Julia M. A. Pickl
Summary: This study developed and validated a sensitive and cost-effective method for untargeted detection of circulating tumor DNA (ctDNA) in colorectal cancer (CRC) patients based on genetic and non-genetic cfDNA features. The method showed potential for diagnosis and treatment monitoring in CRC patients.
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Jonathan R. Belyeu, Murad Chowdhury, Joseph Brown, Brent S. Pedersen, Michael J. Cormier, Aaron R. Quinlan, Ryan M. Layer
Summary: Samplot is a tool for creating images that display read depth and sequence alignments to adjudicate purported SVs, which can be rapidly reviewed to curate large SV call sets. It includes a machine learning package that decreases false positives without human review and is applicable to various biological problems.
Article
Medicine, General & Internal
Giorgia Gurioli, Vincenza Conteduca, Nicole Brighi, Emanuela Scarpi, Umberto Basso, Giuseppe Fornarini, Alessandra Mosca, Maurizio Nicodemo, Giuseppe Luigi Banna, Cristian Lolli, Giuseppe Schepisi, Giorgia Ravaglia, Isabella Bondi, Paola Ulivi, Ugo De Giorgi
Summary: This study evaluated the prognostic role of CTC gene expression in cabazitaxel-treated mCRPC patients and its association with plasma AR copy number. The results showed that CTC gene expression was significantly associated with overall survival and disease progression. AR-V7 was identified as an important prognostic biomarker, and patients with AR-V7 positivity had poorer outcomes with lower dose cabazitaxel treatment.
Article
Oncology
Xiaoxi Dong, Tiantian Zheng, Minhua Zhang, Chao Dai, Lili Wang, Lei Wang, Ruipeng Zhang, Yuan Long, Danyi Wen, Feng Xie, Yue Zhang, Yong Huang, Jianguo Dong, Huan Liu, Pan Du, Bonnie L. King, Winston Tan, Shidong Jia, Chris X. Lu, Manish Kohli, Haitao Wang, Jianjun Yu
Summary: This study introduces a liquid biopsy assay with improved sensitivity for detecting copy number loss in blood samples with low levels of circulating tumor DNA, and demonstrates its utility by profiling PTEN, RB1, and TP53 genetic loss in metastatic prostate cancer patients.
FRONTIERS IN ONCOLOGY
(2021)
Review
Oncology
Hao Xie, Richard D. Kim
Summary: Liquid biopsy with circulating tumor DNA provides genetic and epigenetic information from both primary and metastatic colorectal cancer, capturing tumor heterogeneity and evolution effectively. It is minimally invasive, rapid, easily repeatable, and highly compliant with real-time molecular information.
ANNALS OF SURGICAL ONCOLOGY
(2021)
Article
Biochemical Research Methods
Rosa Barcelona-Cabeza, Walter Sanseverino, Riccardo Aiese Cigliano
Summary: The article introduces a tool called isoCNV, which improves the sensitivity of CNV detection by optimizing the parameters of the DECoN algorithm, using an in silico CNV validated dataset from overlapping calls of three algorithms. It has been shown to perform well in TS and WES real datasets, increasing the accuracy of CNV detection.
BMC BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Iris J. M. Levink, Malgorzata I. Srebniak, Walter G. De Valk, Monique M. van Veghel-Plandsoen, Anja Wagner, Djuna L. Cahen, Gwenny M. Fuhler, Marco J. Bruno
Summary: This study evaluates the feasibility and performance of shallow sequencing for detecting copy number variations in cell-free DNA from pancreatic juice for pancreatic cancer detection. The presence of an 8q24 gain in pancreatic juice shows promise as a biomarker for the detection of pancreatic cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medical Laboratory Technology
Wenlong Guo, Lei Jin, Jianhao Liang, Guowang Lin, Jiantao Zheng, Dong Zhou, Shengquan Zhan, Haitao Sun, Xiaodan Jiang
Summary: This study tested the application of cerebrospinal fluid (CSF)-derived ctDNA in the detection and diagnosis of glioma. The results showed a high detection rate of ctDNA in CSF and a high concordance rate with tumor DNA. Additionally, CSF ctDNA TMB exhibited a strong correlation with tumor DNA TMB, and age was significantly associated with CSF ctDNA TMB in glioma patients.
CLINICA CHIMICA ACTA
(2022)
Article
Biochemistry & Molecular Biology
David R. Porubsky, Mitchell T. Vollger, William N. Harvey, Allison Rozanski, Peter Ebert, Glenn Hickey, Patrick D. Hasenfeld, Ashley Sanders, Catherine O. Stober, Jan Korbel, Benedict E. Paten, Tobias Marschall, Evan Eichler
Summary: There has been significant progress in phased genome assembly by combining long-read data with parental information or linked-read data. However, the typical phased genome assembly still has over 140 gaps. A detailed analysis of 182 haploid assemblies reveals that the majority of assembly gaps cluster near large and identical repeats, resulting in disrupted protein-coding genes. Misorientations and alignment discontinuities are also identified, highlighting the need for algorithmic development and pangenome representation.
Article
Biochemical Research Methods
Junping Li, Lin Gao, Yusen Ye
Summary: The researchers developed a control-free method called HiSV for identifying large-scale structural variations from Hi-C samples. HiSV achieved superior accuracy and sensitivity through evaluations on simulated data sets and cancer cell lines, and effectively captured complex SVs. HiSV can also supplement the results of WGS methods.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Brittany Rupp, Sarah Owen, Harrison Ball, Kaylee Judith Smith, Valerie Gunchick, Evan T. Keller, Vaibhav Sahai, Sunitha Nagrath
Summary: As pancreatic cancer is the third deadliest cancer in the U.S., studying genetic alterations is crucial for understanding potential targets for cancer treatment. This study presents the Labyrinth-DEPArray pipeline for isolating and analyzing single circulating tumor cells (CTCs). Sequencing reveals copy number variations (CNVs) in single cells, including gains and losses of cancer-related genes. The pipeline combines antigen-free CTC isolation with single cell genomic analysis, offering a validated workflow for pancreatic cancer research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)