Article
Multidisciplinary Sciences
Laurel A. Keefer, James R. White, Derrick E. Wood, Kelly M. R. Gerding, Kenneth C. Valkenburg, David Riley, Christopher Gault, Eniko Papp, Christine M. Vollmer, Amy Greer, James Hernandez, Paul M. McGregor, Adriana Zingone, Brid M. Ryan, Kristen Deak, Shannon J. McCall, Michael B. Datto, James L. Prescott, John F. Thompson, Gustavo C. Cerqueira, Sian Jones, John K. Simmons, Abigail McElhinny, Jennifer Dickey, Samuel Angiuoli, Luis A. Diaz, Victor E. Velculescu, Mark Sausen
Summary: This study describes a comprehensive genomic profiling assay with high analytical performance and provides validation of its accuracy and reliability using clinically and biologically relevant samples.
NATURE COMMUNICATIONS
(2022)
Article
Pathology
Ching-Yeuh Yanga, Yi-Che Yeh, Lei-Chi Wanga, Yen-Yu Lina, Shin-Ying Lina, Shu-Ying Wanga, Ping-Yuan Chua, Zih-Yu Liua, Yu-Chi Sua, Hsiang-Ling Ho, Teh-Ying Choua
Summary: This study aimed to investigate the value of large-scale next-generation sequencing (NGS) panels in distinguishing between separate primary lung cancers (SPLCs) and intrapulmonary metastases (IPMs). With NGS and a molecular classification algorithm, 97.6% of tumor pairs can be accurately classified as SPLCs or IPMs. The molecular classification was predictive of postoperative clinical outcomes in terms of overall survival and recurrence-free interval, providing accurate risk stratification.
Letter
Oncology
Steven Olsen, Yoshiaki Nakamura
Summary: A comprehensive genomic profiling (CGP) using plasma-based next-generation sequencing was conducted in a real-world database of metastatic colorectal cancer (mCRC) in the United States. The study revealed potentially actionable genomic profiles for approximately one-third of the patients, and around 60% of all tested patients received treatment consistent with the CGP results in each line of treatment. These findings suggest the potential role of CGP prior to multiple lines of mCRC treatment.
Article
Multidisciplinary Sciences
Jeffrey M. Conroy, Sarabjot Pabla, Sean T. Glenn, R. J. Seager, Erik Van Roey, Shuang Gao, Blake Burgher, Jonathan Andreas, Vincent Giamo, Melissa Mallon, Yong Hee Lee, Paul DePietro, Mary Nesline, Yirong Wang, Felicia L. Lenzo, Roger Klein, Shengle Zhang
Summary: The study assessed the analytical performance of the TruSight Oncology 500 High-Throughput assay for detection of molecular alterations in solid tumors. Supporting software and automated sample preparation systems were developed to process up to 70 clinical samples in a single sequencing run within 7 days. Results showed that the scalable assay accurately detects various molecular alterations and gene fusions, demonstrating high analytical performance for precision therapeutics in oncology.
Article
Oncology
Pratibha Bhai, Jacob Turowec, Stephanie Santos, Jennifer Kerkhof, LeeAnne Pickard, Aidin Foroutan, Daniel Breadner, Matthew Cecchini, Michael A. Levy, Alan Stuart, Stephen Welch, Christopher Howlett, Hanxin Lin, Bekim Sadikovic
Summary: Personalized targeted therapies are important in the management of solid tumors. The use of targeted next-generation sequencing assays has been shown to be a valuable tool for accurate molecular testing in solid tumors. This study provides an overview of the technical validation, diagnostic yields, and spectrum of variants observed in 3,164 solid tumor samples over a period of 2 years.
FRONTIERS IN ONCOLOGY
(2023)
Article
Oncology
Zeyun Lin, Yuqin Li, Shiqi Tang, Qiuhua Deng, Juhong Jiang, Chengzhi Zhou
Summary: This study compared the molecular profiles of tissue and plasma samples, and found that tissue-NGS has a higher sensitivity in detecting genetic alterations compared to plasma-NGS. Tissue-NGS remains the preferred method for evaluating the molecular profile of NSCLC patients when tumor tissue is available, but plasma can be used as substitute material when tissue is unavailable.
Review
Plant Sciences
Philomena Chu, Sarah Zanon Agapito-Tenfen
Summary: Classical genetic engineering and new genome editing techniques, especially CRISPR/Cas technology, have increased the possibilities for modifying genetic material in organisms, potentially offering novel agricultural traits. However, concerns arise from unintended genetic modifications reported as side-effects. This systematic review of scientific literature on unintended genomic alterations in plants modified through various techniques reveals a wide range of effects, from small nucleotide polymorphisms to large structural variations, with a potential underestimation due to limited use of comprehensive sequencing methods. Future research should focus on more thorough examination of analytical methods to provide regulators with valuable information for detection and identification of genomic interventions.
Review
Biochemistry & Molecular Biology
Pasquale Tripodi
Summary: This review examines the application of genomic technologies in studying the diversity of tomatoes, with a focus on next-generation sequencing strategies and methods. It also discusses how genomics has provided insights into the domestication process of tomatoes and presents perspectives on utilizing natural variation for breeding purposes through pan-genome construction and graphical pan-genome development.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Review
Oncology
Albrecht Stenzinger, Arndt Vogel, Ulrich Lehmann, Angela Lamarca, Paul Hofman, Luigi Terracciano, Nicola Normanno
Summary: Cholangiocarcinomas are a heterogeneous group of tumors with distinct genomic alterations. Next-generation sequencing is a powerful tool for identifying gene variants and guiding personalized treatment for patients with cholangiocarcinomas. Understanding the use of NGS in molecular profiling is crucial for healthcare professionals to optimize treatment outcomes.
CANCER TREATMENT REVIEWS
(2024)
Article
Biochemistry & Molecular Biology
Raquel Lopes-Bras, Dolores Lopez-Presa, Miguel Esperanca-Martins, Cecilia Melo-Alvim, Lina Gallego, Luis Costa, Isabel Fernandes
Summary: This retrospective cohort study reports the findings of comprehensive genomic profiling in a group of sarcoma patients. The study identifies actionable genomic alterations in the majority of patients and provides targeted treatment options. The results suggest that next-generation sequencing is a feasible method for determining therapeutic options for sarcoma patients, and it is recommended to implement Molecular Tumor Boards in clinical practice to discuss genomic findings and inform targeted therapies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Debora Cabral de Carvalho Correa, Francine Tesser-Gamba, Indhira Dias Oliveira, Nasjla Saba da Silva, Andrea Maria Capellano, Maria Teresa de Seixas Alves, Frederico Adolfo Benevides Silva, Patricia Alessandra Dastoli, Sergio Cavalheiro, Silvia Regina Caminada de Toledo
Summary: The study identified novel genetic variants in pediatric and adolescent Ependymomas using a next-generation sequencing panel specific for pediatric neoplasms, highlighting the importance of genetic profiling for patient prognosis and therapeutic direction.
JOURNAL OF NEURO-ONCOLOGY
(2021)
Article
Cell Biology
Ekaterina Olkhov-Mitsel, Aurelia Busca, Carlos Parra-Herran, Yutaka Amemiya, Sharon Nofech-Mozes, Bojana Djordjevic, Marisa R. Nucci, Arun Seth, Jelena Mirkovic
Summary: This study investigated the molecular landscape of dedifferentiated endometrial carcinoma (DEC) by targeted genomic sequencing and immunohistochemical analysis on seven DEC-HG and four DEC-LG cases. The results showed similar frequency and spectrum of mutations between DEC-HG and DEC-LG. The findings support expanding the definition of DEC to include DEC-HG, a previously under-recognised phenomenon with genomic similarities to DEC-LG.
Article
Immunology
Yanmin He, Xiaozhen Hong, Jingjing Zhang, Ji He, Faming Zhu, He Huang
Summary: In this study, we established an NGS method for analyzing the sequence of the start codon to the stop codon in the ABO gene. Through analysis of 110 individuals, we identified two novel ABO alleles and confirmed the presence of DNA recombination in ABO alleles.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Veterinary Sciences
Kristina M. Kruglyak, Jason Chibuk, Lisa McLennan, Prachi Nakashe, Gilberto E. Hernandez, Rita Motalli-Pepio, Donna M. Fath, John A. Tynan, Lauren E. Holtvoigt, Ilya Chorny, Daniel S. Grosu, Dana W. Y. Tsui, Andi Flory
Summary: This proof-of-concept study demonstrates that blood-based liquid biopsy using next generation sequencing of cell-free DNA can non-invasively detect multiple classes of genomic alterations in dogs with cancer, including alterations that originate from spatially separated tumor sites. The study showed the potential of blood-based testing for comprehensive genomic profiling of heterogeneous tumors in dogs.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Review
Microbiology
Chi-Ching Tsang, Jade L. L. Teng, Susanna K. P. Lau, Patrick C. Y. Woo
Summary: NGS technology has matured into clinical applications, showing potential advantages in diagnosing difficult-to-grow fungi and cases with low fungal loads. Studies have revealed that fungal infections diagnosed by NGS present some different characteristics from general epidemiology, such as a low HIV-positive rate among patients with P.jirovecii infections.
Article
Pathology
Friederike Kullmann, Pamela L. Strissel, Reiner Strick, Robert Stoehr, Markus Eckstein, Simone Bertz, Bernd Wullich, Danijel Sikic, Sven Wach, Helge Taubert, Peter Olbert, Hendrik Heers, Maria Fernanda Lara, Maria Luisa Macias, Elisa Matas-Rico, Maria Jose Lozano, Daniel Prieto, Isabel Hierro, Thomas van Doeveren, Ivan Bieche, Julien Masliah-Planchon, Romane Beaurepere, Joost L. Boormans, Yves Allory, Bernardo Herrera-Imbroda, Arndt Hartmann, Veronika Weyerer
Summary: This study investigated the incidence rate of MSI in UTUC and compared the results between standard methodology and Idylla MSI Assay. The results showed a low incidence rate of MSI tumors in UTUC and highlighted the potential of Idylla MSI Assay as an alternative method for MSI analysis in UTUC.
JOURNAL OF CLINICAL PATHOLOGY
(2023)
Article
Hematology
Thomas Pincez, Ken Sin Lo, Melanie E. Garrett, Carlo Brugnara, Allison E. Ashley-Koch, Marilyn J. Telen, Philippe Joly, Pablo Bartolucci, Guillaume Lettre
Summary: This study investigated the influence of genetic variation on hematologic traits in sickle cell disease patients and found that multi-ancestry polygenic trait scores had limited predictive power for complications. However, a simple polygenic trait score consisting of 6 variants accurately explained the variation in fetal hemoglobin and was associated with complications. The results highlight the importance of validating polygenic trait scores in diseased populations before implementing them in precision medicine.
Article
Genetics & Heredity
Roseline Vibert, Jessica Le Gall, Bruno Buecher, Emmanuelle Mouret-Fourme, Guillaume Bataillon, Veronique Becette, Olfa Trabelsi-Grati, Virginie Moncoutier, Catherine Dehainault, Jennifer Carriere, Mathias Schwartz, Voreak Suybeng, Ivan Bieche, Chrystelle Colas, Anne Vincent-Salomon, Dominique Stoppa-Lyonnet, Lisa Golmard
Summary: Germline pathogenic variants in APC have been associated with familial adenomatous polyposis and various extraintestinal tumors, including ovarian cancer. This study identified APC germline pathogenic variants in two premenopausal ovarian cancer patients, suggesting a possible role of APC in ovarian carcinogenesis. Further research is needed to elucidate the contribution of APC to ovarian cancer predisposition.
JOURNAL OF MEDICAL GENETICS
(2023)
Article
Oncology
Danielle Awounou, Brigitte Lacour, Emmanuel Desandes, Sandra Guissou, Nathalie Cassoux, Francois Doz, Christelle Dufour, Veronique Minard-Colin, Gudrun Schleiermacher, Sophie Taque, Arnauld Verschuur, Jacqueline Clavel, Stephanie Goujon
Summary: This study aimed to investigate seasonal variations in the incidence rates of embryonal tumors by the month of birth and diagnosis. The findings showed a seasonal variation in the incidence rates of retinoblastoma and rhabdomyosarcoma by the month of diagnosis. These results may be due to delayed consultation during the summer months, but the potential role of seasonally varying environmental exposures cannot be ruled out.
Article
Hematology
Thomas Pincez, Helder Fernandes, Marlene Pasquet, Wadih Abou Chahla, Jerome Granel, Sebastien Heritier, Mony Fahd, Stephane Ducassou, Caroline Thomas, Nathalie Garnier, Vincent Barlogis, Eric Jeziorski, Sophie Bayart, Pascal Chastagner, Nathalie Cheikh, Corinne Guitton, Catherine Paillard, Julien Lejeune, Frederic Millot, Valerie Li-Thiao Te, Coralie Mallebranche, Isabelle Pellier, Benedicte Neven, Corinne Armari-Alla, Liana Carausu, Christophe Piguet, Joy Benadiba, Claire Pluchart, Jean-Louis Stephan, Marianna Deparis, Claire Briandet, Eric Dore, Aude Marie-Cardine, Thierry Leblanc, Guy Leverger, Nathalie Aladjidi
Summary: This study investigated the long-term outcomes of pediatric chronic immune thrombocytopenia (cITP) and found that age at diagnosis, sex, and immunopathological manifestations (IMs) impacted the results. Adolescents with cITP had a higher risk of severe bleeding, second-line treatment use, clinical and biological IMs, and diagnosis of systemic lupus erythematosus (SLE). Female sex and biological IMs were independently associated with higher risks of biological IMs and SLE diagnosis, second-line treatment use, and SLE diagnosis.
AMERICAN JOURNAL OF HEMATOLOGY
(2023)
Article
Oncology
Lucas Moreno, Steven G. DuBois, Julia Glade Bender, Audrey Mauguen, Nick Bird, Vickie Buenger, Michela Casanova, Francois Doz, Elizabeth Fox, Lia Gore, Douglas S. Hawkins, Shai Izraeli, David T. W. Jones, Pamela R. Kearns, Jan J. Molenaar, Karsten Nysom, Stefan Pfister, Gregory Reaman, Malcolm Smith, Brenda Weigel, Gilles Vassal, Christian Michel Zwaan, Xavier Paoletti, Alexia Iasonos, Andrew D. J. Pearson
Summary: There is a growing need to evaluate innovative drugs for childhood cancer using combination strategies. Combinations of anticancer therapies should be developed on the basis of mechanism of action and robust preclinical evaluation. An optimized, agreed approach to the design and evaluation of early-phase pediatric combination trials will accelerate drug development and benefit all stakeholders.
JOURNAL OF CLINICAL ONCOLOGY
(2023)
Letter
Oncology
Noemie de Cacqueray, Lara Mayrand, Leticia Vaccaroni, Stefania Querciagrossa, Cecile Lozach, Paul Vergnaud, Yasmine Benadjaoud, Gudrun Schleiermacher, Daniel Orbach, Sabine Sarnacki
PEDIATRIC BLOOD & CANCER
(2023)
Article
Multidisciplinary Sciences
Manuel Rodrigues, Giulia Vanoni, Pierre Loap, Coraline Dubot, Eleonora Timperi, Mathieu Minsat, Louis Bazire, Catherine Durdux, Virginie Fourchotte, Enora Laas, Nicolas Pouget, Zahra Castel-Ajgal, Gregoire Marret, Laetitia Lesage, Didier Meseure, Anne Vincent-Salomon, Lolita Lecompte, Nicolas Servant, Sophie Vacher, Ivan Bieche, Caroline Malhaire, Virginie Huchet, Laurence Champion, Maud Kamal, Sebastian Amigorena, Olivier Lantz, Marion Chevrier, Emanuela Romano
Summary: Concurrent chemoradiotherapy with blockade of the PD-1 pathway shows promising results in treating locally advanced cervical cancer, with high response rates and improved progression-free survival.
NATURE COMMUNICATIONS
(2023)
Review
Hematology
Nathalie Aladjidi, Thomas Pincez, Frederic Rieux-Laucat, Diane Nugent
Summary: This paper presents a new perspective on Evans syndrome (ES) based on recent advances in genomics, which classify patients based on their underlying molecular variants in previously described primary immune disorders. Targeted therapy or bone marrow transplant are potential alternatives to long-term immune suppression or splenectomy. Moreover, long-term follow-up and monitoring are important for pediatric patients as they may develop various immunopathological manifestations despite the resolution of cytopenias.
BRITISH JOURNAL OF HAEMATOLOGY
(2023)
Article
Oncology
Francois Sevrin, Helene Kolesnikov-Gauthier, Olivier Cougnenc, Emilie Bogart, Gudrun Schleiermacher, Frederic Courbon, Marion Gambart, Anne-Laure Giraudet, Nadege Corradini, Jean-Noel Badel, Erwann Rault, Aurore Oudoux, Marie Cecile Le Deley, Dominique Valteau-Couanet, Anne-Sophie Defachelles
Summary: This study evaluated the tandem infusions of I-131-metaiodobenzylguanidine (mIBG) and topotecan in children with relapsed/refractory metastatic neuroblastoma (NBL). The results showed that MIITOP had acceptable tolerability in this heavily pretreated population and encouraging survival rates in VHR-NBL when followed by busulfan-melphalan.
PEDIATRIC BLOOD & CANCER
(2023)
Article
Oncology
Mathieu Chicard, Yasmine Iddir, Julien Masliah Planchon, Valerie Combaret, Valery Attignon, Alexandra Saint-Charles, Didier Frappaz, Cecile Faure-Conter, Kevin Beccaria, Pascale Varlet, Birgit Geoerger, Sylvain Baulande, Gaelle Pierron, Yassine Bouchoucha, Francois Doz, Olivier Delattre, Joshua J. Waterfall, Franck Bourdeaut, Gudrun Schleiermacher
Summary: We demonstrated that cell-free DNA extracted from CSF can be used for whole exome sequencing in pediatric embryonal brain tumors, with informative results in 83% of samples. Clonal heterogeneity was identified in most cases compared to primary tumor tissue sequencing. Nucleosome footprinting at transcription start sites of genes of interest enabled the inference of gene expression. These findings pave the way for the use of CSF cfDNA in molecular diagnosis and disease monitoring.
Article
Oncology
Ines Debbabi, Sophie Vacher, Cindy Neuzillet, Jerome Cros, Francoise Revillon, Ambre Petitalot, Anthony Turpin, Samantha Antonio, Elodie Girard, Celia Dupain, Maud Kamal, Pascal Hammel, Ivan Bieche, Julien Masliah-Planchon, Sandrine M. M. Caputo
Summary: By 2030, pancreatic cancer will become the second leading cause of cancer-related deaths in the United States and in Europe. The management of patients with advanced pancreatic cancer relies on chemotherapy and poly (ADP-ribose) polymerase inhibitors for patients who carry BRCA1/2 inactivating alterations. A 47-year-old patient with pancreatic cancer was found to have a large somatic intra-exonic deletion of BRCA2, which could be pathogenic and affect tumorigenesis. The optimized bioinformatics algorithm enabled the identification of this intermediate size deletion, leading to personalized patient management through inclusion in a clinical trial.
THERAPEUTIC ADVANCES IN MEDICAL ONCOLOGY
(2023)
Article
Environmental Sciences
Danielle Awounou, Matthieu Mancini, Brigitte Lacour, Perrine de Crouy-Chanel, Isabelle Aerts, Veronique Minard-Colin, Gudrun Schleiermacher, Arnauld Verschuur, Sandra Guissou, Emmanuel Desandes, Laurence Guldner, Jacqueline Clavel, Stephanie Goujon
Summary: The study found a slight increase in the risk of neuroblastoma in children living close to vineyards, indicating a potential link between residential exposure to agricultural pesticides and the occurrence of these tumors. Proximity to vineyards did not show an association with other non-CNS embryonal tumors.
ENVIRONMENTAL RESEARCH
(2024)