Article
Oncology
Juan A. Santamaria-Barria, Chikako Matsuba, Adam Khader, Anthony J. Scholar, Mary Garland-Kledzik, Trevan D. Fischer, Richard Essner, Matthew P. Salomon, Joshua M. V. Mammen, Melanie Goldfarb
Summary: This study analyzed melanoma samples and identified age-related mutational differences, as well as potential targetable mutations for personalized therapies.
JOURNAL OF SURGICAL ONCOLOGY
(2023)
Article
Biochemical Research Methods
Christopher Paul Wardell, Cody Ashby, Michael Anton Bauer
Summary: FiNGS is a software developed to improve the precision of variant caller outputs for somatic variants, with demonstrated reliability and better performance than other tools for the same task. It provides researchers with a simple, configurable, and reproducible tool for filtering somatic variants in sequencing data.
BMC BIOINFORMATICS
(2021)
Article
Immunology
Arun Kumar Arunachalam, Madhavi Maddali, Fouzia N. Aboobacker, Anu Korula, Biju George, Vikram Mathews, Eunice Sindhuvi Edison
Summary: This study characterized the clinical and genetic spectrum of PID patients in India, identifying BTK and IL12RB1 as the most common mutated genes, with autosomal recessive and X-linked recessive inheritance in 51.6% and 23.7% of patients, respectively. MSMD and IL12RB1 mutations were more common in this population compared to the Western world and the Middle East.
JOURNAL OF CLINICAL IMMUNOLOGY
(2021)
Article
Oncology
Angeliki Andrikopoulou, Eleni Zografos, Kleoniki Apostolidou, Anastasios Kyriazoglou, Alksistis-Maria Papatheodoridi, Maria Kaparelou, Konstantinos Koutsoukos, Michalis Liontos, Meletios-Athanasios Dimopoulos, Flora Zagouri
Summary: This study aimed to identify the molecular landscape of germline and somatic mutations in ovarian cancer patients through NGS analysis. The results revealed that TP53 and BRCA1 were the most common somatic mutations in high grade serous carcinoma patients, while BRCA1 and BRCA2 were the most common genes with pathogenic alterations in germline mutations.
FRONTIERS IN ONCOLOGY
(2022)
Article
Genetics & Heredity
Yu Jeong Choi, Hongkyung Kim, Won Kee Ahn, Seung-Tae Lee, Jung Woo Han, Jong Rak Choi, Chuhl Joo Lyu, Seungmin Hahn, Saeam Shin
Summary: Hereditary hemolytic anemia (HHA) is a group of genetic disorders characterized by the destruction of circulating red blood cells. Incorporation of next-generation sequencing (NGS) has proven to be a valuable tool in the diagnostic process of HHA.
BMC MEDICAL GENOMICS
(2023)
Article
Oncology
Ta-Chung Chao, Yi-Fang Tsai, Chun-Yu Liu, Pei-Ju Lien, Yen-Shu Lin, Chin-Jung Feng, Yen-Jen Chen, Jiun-I. Lai, Chih-Yi Hsu, Jiun Jen Lynn, Chi-Cheng Huang, Ling-Ming Tseng
Summary: This study examined the frequency of PIK3CA mutations in Taiwanese breast cancer patients. It found that PIK3CA mutations were common in these patients, and early detection of this mutation may impact treatment decisions and improve outcomes.
FRONTIERS IN ONCOLOGY
(2023)
Article
Genetics & Heredity
Yunlong Li, Jie Su, Jingman Zhang, Jiahong Pei, Dongmei Li, Yinhong Zhang, Jingyu Li, Menglang Chen, Baosheng Zhu
Summary: This study used targeted next-generation sequencing to identify pathogenic mutations in 84 deaf patients in southwestern China. Common and novel causative genes were found, highlighting the importance of further studying the spectrum of deafness genes in this region.
MOLECULAR GENETICS & GENOMIC MEDICINE
(2021)
Article
Respiratory System
Ya-Sian Chang, Siang-Jyun Tu, Yu-Chia Chen, Ting-Yuan Liu, Ya-Ting Lee, Ju-Chen Yen, Hsin-Yuan Fang, Jan-Gowth Chang
Summary: This study identified 19 known driver mutations and new variants in Taiwanese patients with non-small cell lung cancer. EGFR mutations were found at a higher frequency compared to Caucasians, while KRAS and TP53 mutations were less common. All ClinVar pathogenic variants were trunk mutations present in the tumor regions.
RESPIRATORY RESEARCH
(2021)
Article
Medicine, General & Internal
Deborah Malvi, Francesco Vasuri, Thais Maloberti, Viviana Sanza, Antonio De Leo, Adele Fornelli, Michele Masetti, Claudia Benini, Raffaele Lombardi, Maria Fortuna Offi, Mariacristina Di Marco, Matteo Ravaioli, Sirio Fiorino, Enrico Franceschi, Alba A. Brandes, Elio Jovine, Antonietta D'Errico, Giovanni Tallini, Dario de Biase
Summary: Despite efforts, the 5-year survival rate for PDAC remains very low. Precision oncology is not yet ready for PDAC, despite studies on molecular and genetic alterations. This study used next-generation sequencing to analyze PDAC samples and found that KRAS and TP53 mutations were common, with KRAS mutation associated with shorter time to tumor recurrence.
Review
Genetics & Heredity
Aleksandra Mroczkowska-Bekarciak, Tomasz Wrobel
Summary: BCR::ABL1-negative myeloproliferative neoplasms are clonal diseases with characteristic driver mutations in genes including JAK2, CALR, or MPL. The diagnosis of these neoplasms relies on the detection of mutations in these genes. New technologies like next-generation sequencing have opened up new possibilities for finding additional mutations, which can aid in risk stratification, disease progression assessment, transformation to AML, and treatment selection.
FRONTIERS IN GENETICS
(2023)
Review
Oncology
Hanadi El Achi, Rashmi Kanagal-Shamanna
Summary: NGS is routinely used for mutation profiling in acute myeloid leukemia, with results driving AML phenotype and guiding targeted therapies. Molecular findings have been incorporated into WHO sub-classifications and integrated into treatment guidelines by the European Leukemia Net. NGS mutation profiling provides essential information for diagnosis and treatment in AML, and offers valuable insights into disease ontogeny, resistance monitoring, and other aspects beyond routine clinical applications.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Tyler Shugg, Reynold C. Ly, Wilberforce Osei, Elizabeth J. Rowe, Caitlin A. Granfield, Ty C. Lynnes, Elizabeth B. Medeiros, Jennelle C. Hodge, Amy M. Breman, Bryan P. Schneider, S. Cenk Sahinalp, Ibrahim Numanagic, Benjamin A. Salisbury, Steven M. Bray, Ryan Ratcliff, Todd C. Skaar
Summary: This study assessed the accuracy of the Aldy computational method in extracting pharmacogenomics genotypes from whole genome sequencing (WGS) and whole exome sequencing (WES) data. The results showed that Aldy achieved over 99% accuracy in calling diplotypes for major pharmacogenes from both WGS and WES data, supporting its importance in clinical applications.
FRONTIERS IN ONCOLOGY
(2023)
Article
Microbiology
Ilayda Akacin, Seymanur Ersoy, Osman Doluca, Mine Gungormusler
Summary: This review provides a comprehensive overview of recent literature on the utilization of TGS and NGS technologies in microbial metagenomics research. It discusses the advantages and limitations of these technologies and presents real-time examples of novel applications in clinical microbiology and public health, food and agriculture, energy and environment, arts and space.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Oncology
Xuan Pei, Libing Xiang, Wei Chen, Wei Jiang, Lina Yin, Xuxia Shen, Xiaoyan Zhou, Huijuan Yang
Summary: Small cell neuroendocrine carcinoma of the cervix (SCNEC) is specifically associated with HPV 18 infection and characterized by a high genetic mutation rate, with mutations in genes related to the p53 pathway potentially affecting prognosis. Some patients harbor mutations in homogeneous recombination repair (HRR) genes, providing therapeutic targets. The study suggests that targeted therapies against certain mutated genes may have potential efficacy in SCNEC patients.
GYNECOLOGIC ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Paolo Rosa, Elena De Falco, Luca Pacini, Amedeo Piazza, Paolo Ciraci, Luca Ricciardi, Francesco Fiorentino, Sokol Trungu, Massimo Miscusi, Antonino Raco, Antonella Calogero
Summary: This study investigated the feasibility of analyzing the genomic profile of grade IV glioblastoma patients using circulating extracellular vesicles (EVs). The findings revealed lower DNA content in EVs of glioblastoma patients compared to controls, and consistent mutations in the NF1 gene. These results support the clinical utility of EVs as a tool for personalized medicine in glioblastoma.
Letter
Dermatology
Aurelie Halle, Alix De Becdelievre, Benoit Funalot, Christine Labreze, Fanny Morice-Picard, Franck Boralevi
BRITISH JOURNAL OF DERMATOLOGY
(2022)
Article
Genetics & Heredity
Guillaume Jouret, Matthieu Egloff, Emilie Landais, Olivier Tassy, Fabienne Giuliano, Houda Karmous-Benailly, Charles Coutton, Veronique Satre, Francoise Devillard, Klaus Dieterich, Gaelle Vieville, Paul Kuentz, Cedric le Caignec, Claire Beneteau, Bertrand Isidor, Mathilde Nizon, Patrick Callier, Valentine Marquet, Eric Bieth, Jonathan Levy, Anne-Claude Tabet, Stanislas Lyonnet, Genevieve Baujat, Marlene Rio, Francois Cartault, Sophie Scheidecker, Aurelie Gouronc, Audrey Schalk, Clemence Jacquin, Marta Spodenkiewicz, Chloe Angelini, Perrine Pennamen, Caroline Rooryck, Martine Doco-Fenzy, Celine Poirsier
Summary: This study aims to better characterize the syndrome associated with duplications in the proximal 19p13.3 region. A large cohort of patients with 19p13.3 duplications was collected and analyzed to identify a new critical region. The findings suggest that these duplications may lead to structural abnormalities and gene misregulation, impacting the control of head circumference during development.
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
(2023)
Article
Genetics & Heredity
Anne-Sophie Denomme-Pichon, Leslie Matalonga, Elke de Boer, Adam Jackson, Elisa Benetti, Siddharth Banka, Ange-Line Bruel, Andrea Ciolfi, Jill Clayton-Smith, Bruno Dallapiccola, Yannis Duffourd, Kornelia Ellwanger, Chiara Fallerini, Christian Gilissen, Holm Graessner, Tobias B. Haack, Marketa Havlovicova, Alexander Hoischen, Nolwenn Jean-Marcais, Tjitske Kleefstra, Estrella Lopez-Martin, Milan Macek, Maria Antonietta Mencarelli, Sebastien Moutton, Rolph Pfundt, Simone Pizzi, Manuel Posada, Francesca Clementina Radio, Alessandra Renieri, Caroline Rooryck, Lukas Ryba, Hana Safraou, Martin Schwarz, Marco Tartaglia, Christel Thauvin-Robinet, Julien Thevenon, Frederic Tran Mau-Them, Aurelien Trimouille, Pavel Votypka, Bert B. A. de Vries, Marjolein H. Willemsen, Birte Zurek, Alain Verloes, Christophe Philippe, Antonio Vitobello, Lisenka E. L. M. Vissers, Laurence Faivre
Summary: Within the Solve-RD project, the European Reference Network aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. The results of the ClinVar low-hanging fruit reanalysis, reasons for previous analysis failure, and lessons learned are presented.
GENETICS IN MEDICINE
(2023)
Article
Genetics & Heredity
Tristan Celse, Angele Tingaud-Sequeira, Klaus Dieterich, Geraldine Siegfried, Cedric Lecaignec, Laurence Bouneau, Madeleine Fannemel, Gaelle Salaun, Fanny Laffargue, Guillaume Martinez, Veronique Satre, Gaelle Vieville, Marie Bidart, Cecilia Soussi Zander, Ann-Charlotte Turesson, Miranda Splitt, Dorothee Reboul, Jean Chiesa, Philippe Khau Van Kien, Manon Godin, Nicolas Gruchy, Himanshu Goel, Elizabeth Palmer, Kalliope Demetriou, Carolyn Shalhoub, Caroline Rooryck-Thambo, Charles Coutton
Summary: Oculo-auriculo-vertebral spectrum (OAVS) is a common cause of head and neck malformations in children. This study identified OTX2 gene duplications as a recurrent cause of OAVS, with proper dosage of OTX2 being critical for normal development. The findings highlight the importance of understanding the genetic factors underlying OAVS.
JOURNAL OF MEDICAL GENETICS
(2023)
Letter
Dermatology
O. Letertre, M. L. Jullie, M. P. Reboul, S. Leclerc-Mercier, F. Charbit, F. Boralevi, C. Labreze, S. Hadj-Rabia, F. Morice-Picard
JOURNAL OF THE EUROPEAN ACADEMY OF DERMATOLOGY AND VENEREOLOGY
(2023)
Article
Genetics & Heredity
Ester Moreno-Artero, Fanny Morice-Picard, Eulalie Lasseaux, Matthieu P. P. Robert, Valentine Coste, Vincent Michaud, Stephanie Leclerc-Mercier, Dominique Bremond-Gignac, Benoit Arveiler, Smail Hadj-Rabia
Summary: Albinism is a genetic disorder caused by mutations in genes affecting melanin production or transport in the skin, hair, and eyes. At least 20 different genes have been identified to be involved in albinism. This study analyzed 30 OCA4 patients and found two main phenotypes, with a correlation between genotype and phenotype.
Article
Cell Biology
Nathalie Vadrot, Flavie Ader, Maryline Moulin, Marie Merlant, Francoise Chapon, Estelle Gandjbakhch, Fabien Labombarda, Pascale Maragnes, Patricia Reant, Caroline Rooryck, Vincent Probst, Erwan Donal, Pascale Richard, Ana Ferreiro, Brigitte Buendia
Summary: A missense variant of the TMPO/LAP2 alpha gene has been linked to cardiomyopathy. This study identified three novel rare TMPO heterozygous variants in hypertrophic or dilated cardiomyopathy patients. The variants were found to alter cell proliferation, chromatin structure, and gene expression-regulation pathways.
Article
Genetics & Heredity
Eva Kohaut, Flavie Ader, Caroline Rooryck, Fanny Pelluard, Maryse Bonniere, Gwenaelle Andre, Fanny Sauvestre, Philippe Roth, Diala Khraiche, Bettina Bessieres, Tania Attie-Bitach, Pascale Richard
Summary: Cardiomyopathies are heart muscle diseases with various clinical presentations. Most forms are inherited and have incomplete penetrance until adulthood. Severe forms of cardiomyopathies can occur before birth and result in fetal death or medical termination of pregnancy. Genetic testing was able to identify the genetic cause of cardiomyopathy in 8 out of 11 families, highlighting the diagnostic value of genetic testing for severe antenatal cardiomyopathy.
Article
Genetics & Heredity
Cecile Courdier, John Boudjarane, Valerie Malan, Christine Muti, Brian Sperelakis-Beedham, Sylvie Odent, Sylvie Jaillard, Chloe Quelin, Cedric Le Caignec, Olivier Patat, Charlotte Dubucs, Sophie Julia, Caroline Schluth-Bolard, Carole Goumy, Sylvia Redon, Jean-Baptiste Gaillard, Minh Tuan Huynh, Celine Dupont, Anne-Claude Tabet, Guillaume Cogan, Francois Vialard, Rodolphe Dard, Guillaume Jedraszak, Florence Jobic, Mathilde Lefebvre, Genevieve Quenum, Saori Inai, Melanie Rama, Fanny Sauvestre, Frederic Coatleven, Julie Thomas, Caroline Rooryck
Summary: This study aimed to collect fetal cases carrying a 7q11.23 copy number variation (CNV) and gather detailed clinical data to expand knowledge of antenatal features in these syndromes. The researchers retrospectively recruited unrelated cases with 7q11.23 deletion or duplication who had prenatal ultrasound findings and collected data from multiple diagnostic centers in France. The results showed a broad spectrum of prenatal presentations associated with 7q11.23 CNVs, with intra-uterine growth retardation and cardiovascular defects being the most common ultrasound signs. By reporting the largest series of antenatal Williams-Beuren syndrome cases, the study aims to better understand the distinctive signs in fetuses with 7q11.23 CNVs.
PRENATAL DIAGNOSIS
(2023)
Article
Genetics & Heredity
Frederic Tran Mau-Them, Julian Delanne, Anne-Sophie Denomme-Pichon, Hana Safraou, Ange-Line Bruel, Antonio Vitobello, Aurore Garde, Sophie Nambot, Nicolas Bourgon, Caroline Racine, Arthur Sorlin, Sebastien Moutton, Nathalie Marle, Thierry Rousseau, Paul Sagot, Emmanuel Simon, Catherine Vincent-Delorme, Odile Boute, Cindy Colson, Florence Petit, Marine Legendre, Sophie Naudion, Caroline Rooryck, Clement Prouteau, Estelle Colin, Agnes Guichet, Alban Ziegler, Dominique Bonneau, Godelieve Morel, Melanie Fradin, Alinoe Lavillaureix, Chloe Quelin, Laurent Pasquier, Sylvie Odent, Gabriella Vera, Alice Goldenberg, Anne-Marie Guerrot, Anne-Claire Brehin, Audrey Putoux, Jocelyne Attia, Carine Abel, Patricia Blanchet, Constance F. Wells, Caroline Deiller, Mathilde Nizon, Sandra Mercier, Marie Vincent, Bertrand Isidor, Jeanne Amiel, Rodolphe Dard, Manon Godin, Nicolas Gruchy, Mederic Jeanne, Elise Schaeffer, Pierre-Yves Maillard, Frederique Payet, Marie-Line Jacquemont, Christine Francannet, Sabine Sigaudy, Marine Bergot, Emilie Tisserant, Marie-Laure Ascencio, Christine Binquet, Yannis Duffourd, Christophe Philippe, Laurence Faivre, Christel Thauvin-Robinet
Summary: This study describes the implementation of exome sequencing in prenatal diagnosis in France after the detection of anomalies on prenatal ultrasound. The study found that trio-exome sequencing provided a high diagnostic yield with a median turnaround time of 28 days. Trio-exome sequencing and chromosomal microarray analysis were concordant for identifying pathogenic CNVs.
FRONTIERS IN GENETICS
(2023)
Article
Genetics & Heredity
Adam Jackson, Sheng-Jia Lin, Elizabeth A. Jones, Kate E. Chandler, David Orr, Celia Moss, Zahra Haider, Gavin Ryan, Simon Holden, Mike Harrison, Nigel Burrows, Wendy D. Jones, Mary Loveless, Cassidy Petree, Helen Stewart, Karen Low, Deirdre Donnelly, Simon Lovell, Konstantina Drosou, Gaurav K. Varshney, Siddharth Banka
Summary: TSPEAR variants lead to autosomal recessive ectodermal dysplasia (ARED) 14. The function of TSPEAR is unknown and the understanding of clinical features, mutation spectrum, and underlying mechanisms of ARED14 is limited. Dental anomalies, similar to WNT10A-related odontoonychodermal dysplasia, were identified as the primary characteristics of ARED14. Mutational and recombination clock analyses suggested the origin of founder TSPEAR variants in non-Finnish European populations. TSPEAR was found to be an ortholog of drosophila Closca and its role in enamel knot was hypothesized. The tspeara-/-;tspearb-/- double knockout zebrafish model supported the interaction between tspear and wnt10a. This study provides insights into the role of TSPEAR in ectodermal development and the evolutionary history, epidemiology, mechanisms, and consequences of its loss of function variants.
HUMAN GENETICS AND GENOMICS ADVANCES
(2023)
Letter
Dermatology
Aurore Dupont, Remi Vergara, Alize Pacaud, Laure Dequidt, Caroline Dutriaux, Valentine Saunier, Charline Caumont, Marie-Laure Jullie, Alain Taieb, Fanny Morice-Picard, Lea Dousset
JOURNAL OF THE EUROPEAN ACADEMY OF DERMATOLOGY AND VENEREOLOGY
(2023)
Article
Oncology
Vincent Michaud, Angele Sequeira, Elina Mercier, Eulalie Lasseaux, Claudio Plaisant, Smail Hadj-Rabia, Sandra Whalen, Dominique Bonneau, Anne Dieux-Coeslier, Fanny Morice-Picard, Juliette Coursimault, Benoit Arveiler, Sophie Javerzat
Summary: Oculocutaneous albinism type 2 (OCA2) is a common form of albinism, representing about 30% of cases worldwide. This study focused on a subgroup of 29 patients with uncertain genetic variants in or around exon 10 of OCA2. By analyzing blood cell RNA, the researchers were able to detect excessive exon skipping and mRNA deficiency in these patients.
PIGMENT CELL & MELANOMA RESEARCH
(2023)
Article
Obstetrics & Gynecology
Manon De Vriendt, Caroline Rooryck, Frederic Coatleven, Marie Sarrau, Marie Vincienne, Perrine Prier, Sophie Naudion, Loic Sentilhes, Hanane Bouchghoul
Summary: The management of isolated increased nuchal translucency (NT) in the first trimester is not agreed upon among the Pluridisciplinary Centers for Prenatal Diagnosis (CPDPN) in France. A survey was conducted among 46 CPDPNs, showing heterogeneity in the threshold for invasive diagnosis testing depending on the center. Chromosomal Microarray Analysis (CMA) and early reference morphological ultrasound scan were not consistently performed.
GYNECOLOGIE OBSTETRIQUE FERTILITE & SENOLOGIE
(2023)
Article
Genetics & Heredity
Burcu Yaldiz, Erdi Kucuk, Juliet Hampstead, Tom Hofste, Rolph Pfundt, Jordi Corominas Galbany, Tuula Rinne, Helger G. Yntema, Alexander Hoischen, Marcel Nelen, Christian Gilissen, Solve-RD consortium
Summary: This study compared different enrichment kits and sequencing techniques in terms of their ability to cover the entire exome. The results showed that Twist exome capture had significantly better coverage and uniformity across coding regions compared to other kits. Twist performed equally well as short-read and long-read whole genome sequencing, and even at lower average coverage, there was only minimal loss in sensitivity for SNV and CNV detection.