Article
Biology
Maria Guarnaccia, Laura Guarnaccia, Valentina La Cognata, Stefania Elena Navone, Rolando Campanella, Antonella Ampollini, Marco Locatelli, Monica Miozzo, Giovanni Marfia, Sebastiano Cavallaro
Summary: The study developed a targeted next-generation sequencing approach for analyzing genetic variations and chromosomal aberrations in gliomas, which can provide accurate and specific assessment of tumor pathogenesis, prognosis, and treatment response. This has important implications for the diagnosis and treatment of gliomas.
Review
Biochemistry & Molecular Biology
Alissa Drees, Markus Fischer
Summary: The HiTS-FLIP technology improves the efficiency of aptamer selection, providing insights into the relationship between sequence, structure, and function, which supports the evolution of aptamers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Arnaud Bayle, Debora Basile, Simon Garinet, Bastien Rance, Pierre Laurent-Puig, Helene Blons, Julien Taieb, Geraldine Perkins
Summary: This study evaluated the role of NGS targeted panels in digestive oncology, showing that it allows for an exhaustive search for molecular abnormalities and provides patients with more opportunities for targeted therapies. Regular updates and further studies are needed for better analysis of prognostic factors.
Review
Medicine, General & Internal
Rajesh R. Singh
Summary: Screening for genomic sequence variants is crucial in precision medicine and next-generation sequencing technologies have become the preferred platforms due to their capacity for massively parallel sequencing. Targeted NGS workflow involves enrichment of the regions of interest, improving the accuracy and cost-effectiveness of screening.
Article
Biochemistry & Molecular Biology
Markus Pfenninger, Philipp Schoennenbeck, Tilman Schell
Summary: Accurate estimation of genome sizes is essential in biodiversity genomics, and this study introduces a method that can estimate genome size from the number of sequenced bases and mean sequencing depth. Simulations demonstrate that even from low-coverage genome drafts, reasonable estimates can be obtained using this method. Comparison with flow cytometry estimates suggests that both methods provide similar and interchangeable results.
MOLECULAR ECOLOGY RESOURCES
(2022)
Review
Biology
Konstantina Athanasopoulou, Glykeria N. Daneva, Michaela A. Boti, Georgios Dimitroulis, Panagiotis G. Adamopoulos, Andreas Scorilas
Summary: Deciphering the etiopathogenesis of cancer is a complex task that requires a multidimensional approach. The introduction of next- and third-generation sequencing technologies has provided powerful tools for cancer research and has expanded the scope of personalized cancer medicine and pharmacogenomics.
Article
Microbiology
Changwoo Park, Seung Bum Kim, Sang Ho Choi, Seil Kim
Summary: Microbial community analysis based on the 16S rRNA-gene is important for studying microorganisms, and next-generation sequencing technology has improved the accuracy and speed of analysis. However, biases can still occur in the results due to factors like sample handling and sequencing platforms. Different primer pairs and sequencing platforms can lead to varying levels of bias in microbial community analysis.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Pei-Ling Yu, James C. Fulton, Owen H. Hudson, Jose C. Huguet-Tapia, Jeremy T. Brawner
Summary: This study developed a broad-spectrum fungal identification tool using high-throughput Nanopore sequencing and enrichment probes. It provides a fast and accurate method for fungal identification, and also offers a platform for identifying other plant pathogens.
Article
Oncology
Angeli Ambayya, Rozaimi Razali, Sarina Sulong, Ezzanie Suffya Zulkefli, Yee Yee Yap, Jameela Sathar, Rosline Hassan
Summary: This study identified genomic biomarkers in AML-NK patients by DNA and RNA sequencing, revealing potential variants affecting gene regulation and functional enrichments. These variants dysregulated transcription and DNA-binding transcription activator activity RNA polymerase II-specific. Characterising genomic variants is crucial for understanding the pathogenesis and heterogeneity of AML-NK.
Review
Agronomy
Balakrishnan Marudamuthu, Tamanna Sharma, Supriya Purru, S. K. Soam, Ch. Srinivasa Rao
Summary: Next-generation sequencing (NGS) is a game-changing technology in genomic research, enabling massively parallel sequencing. In agriculture, NGS has transformed enhancement strategies and simplified genetic modification approaches. This review highlights the available NGS platforms and their applications in agricultural genomics.
GENETIC RESOURCES AND CROP EVOLUTION
(2023)
Review
Immunology
Tapoka T. Mkandawire, Adam Sateriale
Summary: This review discusses the significance of using long read DNA and RNA sequencing technologies to provide novel insights into the biology of Cryptosporidium, and highlights that the widespread adoption of these technologies will help fill key gaps in the understanding of Cryptosporidium biology.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Medicine, General & Internal
Cienne Morton, Debashis Sarker, Paul Ross
Summary: Cancers contain numerous mutations, but only a few are critical for malignancy. Targeted therapies and immunotherapy have shown great success in various cancer types. Next-generation sequencing enables the detection of potentially actionable mutations and contributes to the identification of new biomarkers. However, technical challenges and the development of targeted therapies against common genomic aberrations need to be overcome for personalized medicine to become more widely available.
Article
Biotechnology & Applied Microbiology
Songbai Zheng, Xiaodan Wang, Ying Fu, Beibei Li, Jianhua Xu, Haifang Wang, Zhen Huang, Hui Xu, Yurong Qiu, Yaozhou Shi, Kui Li
Summary: This study investigated genetic variations in Chinese NSCLC patients using next-generation sequencing, identifying common mutated genes and genes with copy number variation. GO and KEGG analyses revealed that these genes were mainly involved in tumor-related signaling pathways such as PI3K-Akt, FoxO, and Ras.
Article
Biochemistry & Molecular Biology
Aleksander Salomon-Perzynski, Joanna Barankiewicz, Marcin Machnicki, Irena Misiewicz-Krzeminska, Michal Pawlak, Sylwia Radomska, Agnieszka Krzywdzinska, Aleksandra Bluszcz, Piotr Stawinski, Malgorzata Rydzanicz, Natalia Jakacka, Iwona Solarska, Katarzyna Borg, Zofia Spyra-Gorny, Tomasz Szpila, Bartosz Pula, Sebastian Grosicki, Tomasz Stoklosa, Rafal Ploski, Ewa Lech-Maranda, Jana Jakubikova, Krzysztof Jamroziak
Summary: Tracking genetic changes during multiple myeloma progression reveals different patterns of mutation evolution, with mutation loss pathway associated with better treatment response. Many druggable genes are mutated, even in heavily pre-treated patients. Redefining R-ISS at relapse is clinically valuable.
Review
Biochemistry & Molecular Biology
Payal Ganguly, Bradley Toghill, Shelly Pathak
Summary: This article discusses the importance and research progress of bone marrow aging, explores inflammaging, and the application of next-generation sequencing technology in research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Correction
Pathology
Rashmi Kanagal-Shamanna, Attilio Orazi, Robert P. Hasserjian, Daniel A. Arber, Kaaren Reichard, Eric D. Hsi, Adam Bagg, Heesun Joyce Rogers, Julia Geyer, Faezeh Darbaniyan, Kim-Anh Do, Kyle M. Devins, Olga Pozdnyakova, Tracy I. George, Paola Dal Cin, Patricia T. Greipp, Mark J. Routbort, Keyur Patel, Guillermo Garcia-Manero, Srdan Verstovsek, L. Jeffrey Medeiros, Sa A. Wang, Carlos Bueso-Ramos
Article
Hematology
Hua-Jay J. Cherng, Raamis Khwaja, Rashmi Kanagal-Shamanna, Guilin Tang, Jan Burger, Philip Thompson, Alessandra Ferrajoli, Zeev Estrov, Koji Sasaki, Deepa Sampath, Xuemei Wang, Hagop Kantarjian, Michael Keating, William G. Wierda, Nitin Jain
Summary: Long-term follow up of prospective studies has shown that continuous Bruton's tyrosine kinase inhibitor (BTKi) therapy leads to durable remissions in previously untreated patients with TP53-altered chronic lymphocytic leukemia (CLL). A retrospective analysis of patients with CLL treated with BTKi was performed, and the results showed that variant allele frequency (VAF) of TP53 mutation (TP53-m) or percentage of cells with deletion of chromosome 17p [del(17p)] did not significantly influence the efficacy of first-line BTKi, although there was a trend towards shorter progression-free survival (PFS) with increasing karyotypic complexity.
AMERICAN JOURNAL OF HEMATOLOGY
(2022)
Article
Hematology
Adam C. Smith, Kornelia Neveling, Rashmi Kanagal-Shamanna
Summary: Optical genome mapping (OGM) is a rapidly adopted technology in clinical genetics laboratories that can detect structural variation and replace multiple standard techniques, simplifying the lab workflow. OGM has superior ability in detecting structural variation across the genome, reducing the need for reflex studies and decreasing cost and turnaround time. Compared to karyotyping or fluorescence in situ hybridization, OGM can detect more abnormalities.
AMERICAN JOURNAL OF HEMATOLOGY
(2022)
Article
Hematology
Mehrnoosh Tashakori, Tapan Kadia, Sanam Loghavi, Naval Daver, Rashmi Kanagal-Shamanna, Sherry Pierce, Dawen Sui, Peng Wei, Farnoosh Khodakarami, Zhenya Tang, Mark Routbort, Carol A. Bivins, Elias J. Jabbour, L. Jeffrey Medeiros, Kapil Bhalla, Hagop M. Kantarjian, Farhad Ravandi, Joseph D. Khoury
Summary: Mutant TP53 is a risk factor in AML, but there is limited analysis of TP53 alterations in AML patients. Our study analyzed TP53 mutational status, copy number, and protein expression in AML patients and identified different hotspots and novel pathogenic variants involving TP53 splice sites. We found TP53 CN loss in TP53-mutated AML cases and copy neutral loss of heterozygosity in AML patients with intact TP53 CN. We also demonstrated that mutant p53 protein expression patterns can provide a readout that integrates TP53 mutation and allelic states in AML patients, regardless of TP53 CN status. Additionally, genomic analysis of comutations in TP53-mutant AML showed mutations in genes involved in epigenetic regulation, RAS/MAPK signaling, and RNA splicing. This study provides insights for risk stratification of AML patients based on integrated molecular and protein-level TP53 analyses.
Letter
Hematology
Hussein A. Abbas, Hanxiao Sun, Sherry Pierce, Rashmi Kanagal-Shamanna, Ziyi Li, Musa Yilmaz, Gautam Borthakur, Adam J. DiPippo, Elias Jabbour, Marina Konopleva, Nicholas J. Short, Courtney DiNardo, Naval Daver, Farhad Ravandi, Tapan M. Kadia
Article
Hematology
Nicholas J. Short, Hagop Kantarjian, Farhad Ravandi, Marina Konopleva, Nitin Jain, Rashmi Kanagal-Shamanna, Keyur P. Patel, Walid Macaron, Tapan M. Kadia, Sa Wang, Jeffrey L. Jorgensen, Joseph D. Khoury, Musa Yilmaz, Partow Kebriaei, Koichi Takahashi, Guillermo Garcia-Manero, Naval Daver, Sean M. Post, Xuelin Huang, Steven M. Kornblau, Sara Pelletier, Wilmer Flores, Jairo Matthews, Rebecca Garris, Elias Jabbour
Summary: This study evaluated the clinical impact of a highly sensitive next-generation sequencing (NGS) MRD assay in acute lymphoblastic leukemia (ALL) patients. The study found that NGS detection could identify patients with a significant risk of relapse, even if they were considered MRD negative by multiparameter flow cytometry (MFC). Early assessment of MRD using NGS provides important prognostic information for predicting relapse risk and long-term survival in ALL patients.
Article
Oncology
Alexandre Bazinet, Faezeh Darbaniyan, Tapan M. Kadia, Sangeetha Venugopal, Rashmi Kanagal-Shamanna, Courtney D. DiNardo, Gautam Borthakur, Elias J. Jabbour, Naval G. Daver, Naveen Pemmaraju, Marina Y. Konopleva, Farhad Ravandi, Koji Sasaki, Kelly S. Chien, Danielle Hammond, Sherry A. Pierce, Hagop M. Kantarjian, Guillermo Garcia-Manero, Guillermo Montalban-Bravo
Summary: CLAD/LDAC/HMA-based regimens are effective in a subset of patients with higher risk CMML and sAML arising from CMML who have not previously experienced HMA failure.
Letter
Hematology
Fatima Zahra Jelloul, Mark. J. Routbort, Courtney D. DiNardo, Carlos E. Bueso-Ramos, Rashmi Kanagal-Shamanna, Beenu Thakral, Zhuang Zuo, C. Cameron Yin, Sanam Loghavi, Chi Young. Ok, Sa A. Wang, Zhenya Tang, M. James You, Keyur P. Patel, L. Jeffrey Medeiros, Andres E. Quesada
AMERICAN JOURNAL OF HEMATOLOGY
(2023)
Article
Hematology
Nicholas J. Short, Elias Jabbour, Walid Macaron, Farhad Ravandi, Nitin Jain, Rashmi Kanagal-Shamanna, Keyur P. Patel, Sanam Loghavi, Fadi G. Haddad, Musa Yilmaz, Ghayas C. Issa, Partow Kebriaei, Steven M. Kornblau, Sarah Pelletier, Wilmer Flores, Jairo Matthews, Rebecca Garris, Hagop Kantarjian
Summary: Reverse transcription polymerase chain reaction (RT-PCR) is commonly used for measurable residual disease (MRD) assessment in Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph+ ALL), but it may not be optimal for all cases. A highly sensitive next-generation sequencing (NGS) MRD assay was evaluated and showed a discordance with RT-PCR in 32% of patients with Ph+ ALL. Patients with long-term detectable BCR::ABL1 by PCR had stable levels and did not relapse, while patients who were PCR+/NGS+ had variable PCR values that responded to therapeutic intervention. NGS-based assessment of MRD is prognostic in Ph+ ALL and identifies patients with low-level detectable BCR::ABL1 who are unlikely to relapse nor to benefit from therapeutic interventions.
AMERICAN JOURNAL OF HEMATOLOGY
(2023)
Letter
Hematology
Emmanuel Almanza-Huante, Alex Bataller, Samuel Urrutia, Georgina Gener-Ricos, Robert Edward Briski, Rashmi Kanagal-Shamanna, Karen H. Lu, Shannon N. Westin, Timothy A. Yap, Koichi Takahashi, Farhad Ravandi, Yesid Alvarado, Tapan Kadia, Koiji Sasaki, Hagop M. Kantarjian, Guillermo Garcia-Manero
BRITISH JOURNAL OF HAEMATOLOGY
(2023)
Letter
Oncology
Samuel Urrutia, Ziyi Li, Emmanuel Almanza, Alex Bataller, Rashmi Kanagal-Shamanna, Jayastu Senapati, Koji Sasaki, Kelly Chien, Guillermo Montalban-Bravo, Courtney DiNardo, Gautam Borthakur, Carlos Bueso-Ramos, Sherry Pierce, Hagop Kantarjian, Guillermo Garcia-Manero
Editorial Material
Oncology
Alex Bataller, Kelly S. Chien, Koji Sasaki, Guillermo Montalban-Bravo, Rashmi Kanagal-Shamanna, Samuel Urrutia, Emmanuel Almanza-Huante, Georgina Gener-Ricos, Farhad Ravandi, Elias Jabbour, Tapan Kadia, Gautam Borthakur, Guillermo Garcia-Manero
Article
Hematology
Guillermo Montalban-Bravo, Rashmi Kanagal-Shamanna, Ziyi Li, Danielle Hammond, Kelly Chien, Juan Jose Rodriguez-Sevilla, Koji Sasaki, Elias Jabbour, Courtney DiNardo, Koichi Takahashi, Nicholas Short, Ghayas C. Issa, Naveen Pemmaraju, Tapan Kadia, Farhad Ravandi, Naval Daver, Gautam Borthakur, Sanam Loghavi, Sherry Pierce, Carlos Bueso-Ramos, Hagop Kantarjian, Guillermo Garcia-Manero
Summary: Chronic myelomonocytic leukaemia (CMML) is a blood disorder that has a high risk of transforming into acute myeloid leukaemia (AML). A study on a cohort of 189 CMML patients with AML transformation revealed distinct trajectories of transformation characterized by genomic profiles and clonal evolution: monocytic, immature myeloid, or erythroid. Monocytic AML was defined by specific mutations and was more likely to evolve from a specific type of CMML, while immature myeloid AML exhibited different mutations and had a higher frequency of a specific mutation. The study also observed potential benefits of a certain combination therapy for immature myeloid AML. These findings contribute to the understanding of CMML progression and provide a basis for the development of phenotype-specific therapeutics.
BRITISH JOURNAL OF HAEMATOLOGY
(2023)
Review
Oncology
Erica F. F. Reinig, Jeremy D. D. Rubinstein, Apoorva T. T. Patil, Amanda L. L. Schussman, Vanessa L. L. Horner, Rashmi Kanagal-Shamanna, Jane E. E. Churpek, Daniel R. R. Matson
Summary: Myeloid malignancies associated with germline predisposition syndromes account for up to 10% of myeloid neoplasms. Identifying these syndromes in pathology practice is challenging, but crucial for tailored treatment and improved outcomes. This review aims to empower clinicians in recognizing and evaluating germline disorders in myeloid malignancies.
Letter
Oncology
Preetesh Jain, Krystle Nomie, Nikita Kotlov, Vitaiy Segodin, Holly Hill, Chi Young Ok, Ahmed Fetooh, Rashmi Kanagal-Shamanna, Francisco Vega, Alexander Bagaev, Nathan Fowler, Christopher R. Flowers, Michael Wang
BLOOD CANCER JOURNAL
(2023)