Article
Genetics & Heredity
Kheloud M. Alhamoudi, Balgees Alghamdi, Abeer Aljomaiah, Meshael Alswailem, Hindi Al-Hindi, Ali S. Alzahrani
Summary: A young girl with 46,XY DSD was found to have a unique novel mutation in the NR5A1 gene, resulting in severe gonadal dysgenesis and deficiency of testosterone and anti-Mullerian hormone secretion. Despite the atrophied testes and lack of breast development, the patient identified as female and responded well to estrogen/progesterone therapy, showing excellent breast development and normal cyclical menses. This case demonstrates the importance of a genetic mutation in explaining the clinical phenotype of DSD.
FRONTIERS IN GENETICS
(2022)
Article
Medicine, General & Internal
Benedicte Sudrie-Arnaud, Sarah Snanoudj, Ivana Dabaj, Helene Dranguet, Lenaig Abily-Donval, Axel Lebas, Myriam Vezain, Benedicte Heron, Isabelle Marie, Marc Duval-Arnould, Stephane Marret, Abdellah Tebani, Soumeya Bekri
Summary: Diagnosis of lysosomal disorders can be challenging due to their clinical heterogeneity and overlapping phenotypes. A newly developed capture-based NGS panel allows for efficient detection of genetic variations associated with LDs, potentially improving diagnostic speed and accuracy. This advanced sequencing approach, combined with bioinformatics analyses, offers a cost-effective method for identifying causative variants in lysosomal disorders.
Article
Endocrinology & Metabolism
Khouloud Rjiba, Soumaya Mougou-Zerelli, Imen hadj Hamida, Ghada Saad, Bochra Khadija, Afef Jelloul, Wafa Slimani, Yosra Hasni, Sarra Dimassi, Hela Ben Khelifa, Amira Sallem, Molka Kammoun, Hamza Hadj Abdallah, Moez Gribaa, Joelle Bignon-Topalovic, Sami Chelly, Hedi Khairi, Mohamed Bibi, Maha Kacem, Ali Saad, Anu Bashamboo, Kenneth McElreavey
Summary: This study investigated the genetic causes of 46,XY DSD in 165 Tunisian patients. Cytogenetic abnormalities accounted for 30.9% of the cases, and pathogenic variants were identified through candidate gene sequencing and whole-exome sequencing. The overall genetic diagnosis rate of 46,XY DSD was 41.2%.
REPRODUCTIVE BIOLOGY AND ENDOCRINOLOGY
(2023)
Review
Medicine, General & Internal
Syahzuwan Hassan, Rosnah Bahar, Muhammad Farid Johan, Ezzeddin Kamil Mohamed Hashim, Wan Zaidah Abdullah, Ezalia Esa, Faidatul Syazlin Abdul Hamid, Zefarina Zulkafli
Summary: Thalassemia is a highly heterogeneous disease with over a thousand recorded mutation types worldwide. Conventional PCR-based DNA analysis for thalassemia diagnosis is time-consuming and resource-intensive due to phenotype variability, disease complexity, and test limitations. Advanced molecular techniques such as next-generation sequencing (NGS) and third-generation sequencing (TGS) offer more suitable and valuable options for DNA analysis of thalassemia. The continuous improvement of sequencing methods and bioinformatics tools, particularly for identifying copy number variations and homologous genes, will lead to more accurate thalassemia detection.
Article
Immunology
Lauren M. Walker, Andrea R. Shiakolas, Rohit Venkat, Zhaojing Ariel Liu, Steven Wall, Nagarajan Raju, Kelsey A. Pilewski, Ian Setliff, Amyn A. Murji, Rebecca Gillespie, Nigel A. Makoah, Masaru Kanekiyo, Mark Connors, Lynn Morris, Ivelin S. Georgiev
Summary: The development of novel technologies for discovering human monoclonal antibodies has been extremely valuable in combating infectious diseases. LIBRA-seq with epitope mapping is a next-generation sequencing technology that can determine residue-level epitopes for thousands of single B cells simultaneously, making it an efficient tool for high-throughput identification of antibodies against specific antigen epitopes.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Microbiology
Ying Bai, Lynn M. Osikowicz, Andrias Hojgaard, Rebecca J. Eisen
Summary: In this study, a quadruplex PCR amplicon sequencing assay using next-generation sequencing technology was developed to accurately and rapidly detect and differentiate Bartonella species. The assay demonstrated high specificity and accuracy in differentiating Bartonella species in various tissue types.
FRONTIERS IN MICROBIOLOGY
(2023)
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
Muhammad Tahir, Muhammad Sardaraz, Zahid Mehmood, Muhammad Saud Khan
Summary: This paper proposed an efficient error estimation computational model ESREEM to assess error rates in NGS data. The model is based on a probabilistic error model integrated with Hidden Markov Model, and experimental results show that it efficiently estimates errors compared to state-of-the-art algorithms.
CURRENT BIOINFORMATICS
(2021)
Article
Urology & Nephrology
Vuthy Ea, Anne Bergougnoux, Pascal Philibert, Nadege Servant-Fauconnet, Alice Faure, Jean Breaud, Laura Gaspari, Charles Sultan, Francoise Paris, Nicolas Kalfa
Summary: The study evaluated the clinical utility of NGS for patients with hypospadias and found that even mild cases can benefit from advanced sequencing techniques. Some variants of unknown significance (VUSs) were identified, but most cases remain unexplained.
Article
Genetics & Heredity
Simona Mellone, Chiara Puricelli, Denise Vurchio, Sara Ronzani, Simone Favini, Arianna Maruzzi, Cinzia Peruzzi, Amanda Papa, Alice Spano, Fabio Sirchia, Giorgia Mandrile, Alessandra Pelle, Paolo Rasmini, Fabiana Vercellino, Andrea Zonta, Ivana Rabbone, Umberto Dianzani, Maurizio Viri, Mara Giordano
Summary: This study evaluated the clinical performance of a targeted next-generation sequencing gene panel as a second-tier test in undiagnosed patients with neurodevelopmental disorders (NDDs). The results showed that the panel significantly increased the diagnostic yield in different types of NDDs, particularly in females, Autism Spectrum Disorders (ASD), and Epilepsy patients.
FRONTIERS IN GENETICS
(2022)
Review
Genetics & Heredity
Ziga I. Remec, Katarina Trebusak Podkrajsek, Barbka Repic Lampret, Jernej Kovac, Urh Groselj, Tine Tesovnik, Tadej Battelino, Marusa Debeljak
Summary: Newborn screening was introduced in the 1960s, and has expanded over time with the advancement of technology, particularly high-throughput sequencing. Genomic sequencing is now widely used in clinical applications, including newborn screening, but has also raised various concerns and challenges.
FRONTIERS IN GENETICS
(2021)
Article
Physiology
Agnes Bloch-Zupan, Tristan Rey, Alexandra Jimenez-Armijo, Marzena Kawczynski, Naji Kharouf, Muriel de La Dure-Molla, Emmanuelle Noirrit, Magali Hernandez, Clara Joseph-Beaudin, Serena Lopez, Corinne Tardieu, Beatrice Thivichon-Prince, Tatjana Dostalova, Milan Macek Jr, Mustapha El Alloussi, Leila Qebibo, Supawich Morkmued, Patimaporn Pungchanchaikul, Blanca Urzua Orellana, Marie-Cecile Maniere, Benedicte Gerard, Isaac Maximiliano Bugueno, Virginie Laugel-Haushalter
Summary: In this study, next-generation sequencing was used to analyze a cohort of Amelogenesis imperfecta (AI) patients, revealing more than 70 genes associated with AI. The findings showed that 73% of the cases were non-syndromic AI and 27% were syndromic AI. The genetic diagnosis provided important insights for the diagnosis and treatment of AI. This study demonstrated the potential of next-generation sequencing in AI research and provided new insights into the classification and treatment of AI.
FRONTIERS IN PHYSIOLOGY
(2023)
Article
Genetics & Heredity
T. Imizcoz, C. Prieto-Matos, R. Manrique-Huarte, D. Calavia, A. Huarte, P. C. Pruneda, G. R. Ordonez, E. Canada-Higueras, A. Patino-Garcia, G. Alkorta-Aranburu, M. Manrique Rodriguez
Summary: An early etiological diagnosis of hearing loss positively impacts children's quality of life. Next-Generation Sequencing (NGS)-based gene panel testing has been proven to reduce the time between onset and diagnosis. In this study, sequencing of nuclear and mitochondrial genes in Spanish individuals with hearing loss revealed a genetic diagnosis in 34% of cases. Different inheritance patterns, rare gene variants, and pathogenic copy number variants were identified.
FRONTIERS IN GENETICS
(2023)
Article
Oncology
Christian Rolfo, Alexander Drilon, David Hong, Caroline McCoach, Afshin Dowlati, Jessica J. Lin, Alessandro Russo, Alison M. Schram, Stephen Liu, Jorge J. Nieva, Timmy Nguyen, Shahrooz Eshaghian, Michael Morse, Scott Gettinger, Mohammad Mobayed, Sarah Goldberg, Emilio Araujo-Mino, Neelima Vidula, Aditya Bardia, Janakiraman Subramanian, Deepa Sashital, Thomas Stinchcombe, Lesli Kiedrowski, Kristin Price, David R. Gandara
Summary: This study retrospectively reviewed a ctDNA database in advanced stage solid tumors to identify NTRK1 fusions, and found NTRK1 fusion events in 37 patients with nine unique fusion partners. 44% of cases had tissue testing for NTRK1 fusions, and the NTRK1 fusions detected by ctDNA were confirmed in tissue in 88% of cases. This study reports for the first time that minimally-invasive plasma NGS can detect NTRK fusions with a high positive predictive value.
BRITISH JOURNAL OF CANCER
(2022)
Article
Veterinary Sciences
Rebecca P. Wilkes
Summary: Although still mainly used for research purposes, NGS has been adopted by some veterinary diagnostic laboratories. Metagenomics approaches offer the widest detection range for infectious disease diagnostics, but at a higher cost. tNGS maintains the ability to detect a broad range of pathogens at a lower cost compared to mNGS, making it a viable option for syndromic testing in veterinary diagnostic laboratories.
VETERINARY CLINICS OF NORTH AMERICA-FOOD ANIMAL PRACTICE
(2023)
Article
Cell Biology
Pierre Cauchy, Sally R. James, Joaquin Zacarias-Cabeza, Anetta Ptasinska, Maria Rosaria Imperato, Salam A. Assi, Jason Piper, Martina Canestraro, Maarten Hoogenkamp, Manoj Raghavan, Justin Loke, Susanna Akiki, Samuel J. Clokie, Stephen J. Richards, David R. Westhead, Michael J. Griffiths, Sascha Ott, Constanze Bonifer, Peter N. Cockerill
Article
Genetics & Heredity
Michael Parks, Samantha Court, Siobhan Cleary, Samuel Clokie, Julie Hewitt, Denise Williams, Trevor Cole, Fiona MacDonald, Mike Griffiths, Stephanie Allen
PRENATAL DIAGNOSIS
(2016)
Article
Biochemistry & Molecular Biology
Michael Parks, Samantha Court, Benjamin Bowns, Siobhan Cleary, Samuel Clokie, Julie Hewitt, Denise Williams, Trevor Cole, Fiona MacDonald, Mike Griffiths, Stephanie Allen
EUROPEAN JOURNAL OF HUMAN GENETICS
(2017)
Article
Genetics & Heredity
Christopher M. Watson, Nick Camm, Laura A. Crinnion, Samuel Clokie, Rachel L. Robinson, Julian Adlard, Ruth Charlton, Alexander F. Markham, Ian M. Carr, David T. Bonthron
MOLECULAR DIAGNOSIS & THERAPY
(2017)
Letter
Oncology
Ceri E. Oldreive, Philip J. Byrd, Grant S. Stewart, Alexander J. Taylor, Sana Farhat, Anna Skowronska, Edward Smith, Manoj Raghavan, Dragana Janic, Lidija Dokmanovic, Sam Clokie, Nicholas Davies, Marwan Kwok, Guy Pratt, Shankara Paneesha, Paul Moss, Tatjana Stankovic, Malcolm Taylor
LEUKEMIA & LYMPHOMA
(2019)
Article
Genetics & Heredity
Salam A. Assi, Maria Rosaria Imperato, Daniel J. L. Coleman, Anna Pickin, Sandeep Potluri, Anetta Ptasinska, Paulynn Suyin Chin, Helen Blair, Pierre Cauchy, Sally R. James, Joaquin Zacarias-Cabeza, L. Niall Gilding, Andrew Beggs, Sam Clokie, Justin C. Loke, Phil Jenkin, Ash Uddin, Ruud Delwel, Stephen J. Richards, Manoj Raghavan, Michael J. Griffiths, Olaf Heidenreich, Peter N. Cockerill, Constanze Bonifer
Review
Ophthalmology
Amy Gerrish, Edward Stone, Samuel Clokie, John R. Ainsworth, Helen Jenkinson, Maureen McCalla, Carol Hitchcott, Isabel Colmenero, Stephanie Allen, Manoj Parulekar, Trevor Cole
BRITISH JOURNAL OF OPHTHALMOLOGY
(2019)
Article
Genetics & Heredity
Richard J. Holt, Rodrigo M. Young, Berta Crespo, Fabiola Ceroni, Cynthia J. Curry, Emanuele Bellacchio, Dorine A. Bax, Andrea Ciolfi, Marleen Simon, Christina R. Fagerberg, Ellen van Binsbergen, Alessandro De Luca, Luigi Memo, William B. Dobyns, Alaa Afif Mohammed, Samuel J. H. Clokie, Celia Zazo Seco, Yong-Hui Jiang, Kristina P. Sorensen, Helle Andersen, Jennifer Sullivan, Zoe Powis, Anna Chassevent, Constance Smith-Hicks, Slave Petrovski, Thalia Antoniadi, Vandana Shashi, Bruce D. Gelb, Stephen W. Wilson, Dianne Gerrelli, Marco Tartaglia, Nicolas Chassaing, Patrick Calvas, Nicola K. Ragge
AMERICAN JOURNAL OF HUMAN GENETICS
(2019)
Article
Pathology
Elizabeth Young, Benjamin Bowns, Amy Gerrish, Michael Parks, Samantha Court, Samuel Clokie, Chipo Mashayamombe-Wolfgarten, Julie Hewitt, Denise Williams, Trevor Cole, Stephanie Allen
JOURNAL OF MOLECULAR DIAGNOSTICS
(2020)
Article
Endocrinology & Metabolism
Eric Chang, Cong Fu, Steven L. Coon, Shahar Alon, Marjan Bozinoski, Matthew Breymaier, Diego M. Bustos, Samuel J. Clokie, Yoav Gothilf, Caroline Esnault, P. Michael Iuvone, Christopher E. Mason, Margaret J. Ochocinska, Adi Tovin, Charles Wang, Pinxian Xu, Jinhan Zhu, Ryan Dale, David C. Klein
JOURNAL OF PINEAL RESEARCH
(2020)
Article
Oncology
Hannah J. Gleneadie, Amy H. Baker, Nikolaos Batis, Jennifer Bryant, Yao Jiang, Samuel J. H. Clokie, Hisham Mehanna, Paloma Garcia, Deena M. A. Gendoo, Sally Roberts, Megan Burley, Alfredo A. Molinolo, J. Silvio Gutkind, Ben A. Scheven, Paul R. Cooper, Joanna L. Parish, Farhat L. Khanim, Malgorzata Wiench
Summary: DAC upregulates the COX-2-PGE-2 pathway in cancer cells, providing survival potential, which is offset by the addition of paracetamol. Paracetamol supplementation leads to glutathione depletion and accumulation of ROS/superoxide, restricting tumor growth.
Article
Medicine, General & Internal
Amy Gerrish, Benjamin Bowns, Chipo Mashayamombe-Wolfgarten, Elizabeth Young, Samantha Court, Joshua Bott, Maureen McCalla, Simon Ramsden, Michael Parks, David Goudie, Sue Carless, Samuel Clokie, Trevor Cole, Stephanie Allen
JOURNAL OF CLINICAL MEDICINE
(2020)
Article
Endocrinology & Metabolism
Youn Hee Jee, Jinhee Wang, Shanna Yue, Melissa Jennings, Samuel J. Clokie, Ola Nilsson, Julian C. Lui, Jeffrey Baron
Article
Genetics & Heredity
Lauren M. Watson, Elizabeth Bamber, Ricardo Parolin Schnekenberg, Jonathan Williams, Conceicao Bettencourt, Jennifer Lickiss, Katherine Fawcett, Samuel Clokie, Yvonne Wallis, Penny Clouston, David Sims, Henry Houlden, Esther B. E. Becker, Andrea H. Nemeth
AMERICAN JOURNAL OF HUMAN GENETICS
(2017)