Article
Biochemical Research Methods
Angelo Fortunato, Diego Mallo, Shawn M. Rupp, Lorraine M. King, Timothy Hardman, Joseph Y. Lo, Allison Hall, Jeffrey R. Marks, E. Shelley Hwang, Carlo C. Maley
Summary: A new bioinformatic pipeline was developed to accurately identify somatic single nucleotide variants (SNVs) from archival FFPE samples of breast cancers, resulting in a significant improvement in SNV detection compared to existing tools. The method demonstrated increased accuracy and efficiency in detecting mutations, particularly in comparing different stages of breast cancer.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Oncology
Lorraine Dalens, Julie Niogret, Coureche Guillaume Kaderbhai, Romain Boidot
Summary: This study compared the value of whole exome sequencing (WES) and smaller gene panels in the diagnosis and management of non-small-cell lung cancer (NSCLC). The results showed that WES detected more mutations, but had lower efficiency for common mutations. Therefore, smaller targeted panels may be preferred for the initial diagnosis of metastatic NSCLC.
FRONTIERS IN ONCOLOGY
(2022)
Article
Health Care Sciences & Services
JaeMoon Shin, Junbeom Jeon, Dawoon Jung, Kiyong Kim, Yun Joong Kim, Dong-Hoon Jeong, JeeHee Yoon
Summary: Precision medicine has been transformed by the development of high-throughput next-generation sequencing technology and bioinformatic analysis tools. These advancements have led to the identification of genetic variations associated with diseases and phenotypes at both the population and individual levels. However, it remains challenging to develop user-friendly programs for clinical physicians lacking bioinformatics skills to diagnose diseases using genomic data. To address this, a user-friendly Phenotype to Genotype Variation program (PhenGenVar) was developed, allowing for flexible filtering and browsing of disease and phenotype-associated gene variants. The program was successfully tested using whole-genome sequencing data, demonstrating its potential for disease diagnosis. PhenGenVar is freely accessible on the website.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Kevin Yauy, Charles Van Goethem, Henri Pegeot, David Baux, Thomas Guignard, Corinne Theze, Olivier Ardouin, Anne-Francoise Roux, Michel Koenig, Anne Bergougnoux, Mireille Cossee
Summary: The transition from targeted sequencing to exome or genome sequencing in clinical contexts lacks clear recommendations or methodology. This study developed a method for evaluating the performance of exome sequencing strategies based on specific sequencing metrics. The study compared different exome kits and a targeted sequencing method, finding significant differences in coverage and PCR duplicates. This study is important for assisting molecular diagnostic laboratories in adopting and evaluating exome sequencing kits in a diagnostic context.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Iolanda Veneruso, Annaluisa Ranieri, Noemi Falcone, Lorella Tripodi, Carmela Scarano, Ilaria La Monica, Lucio Pastore, Barbara Lombardo, Valeria D'Argenio
Summary: Expanded carrier screening (ECS) is a comprehensive genetic analysis to determine an individual's carrier status, which is increasingly used due to advancements in technology. This case report highlights the usefulness of ECS in the context of autism spectrum disorder and identifies potential genetic risk factors. However, concerns regarding incidental findings and interpretation of results need to be addressed before ECS can be widely implemented.
Review
Endocrinology & Metabolism
Arianna Maiorana, Francesca Romana Lepri, Antonio Novelli, Carlo Dionisi-Vici
Summary: A large number of inborn errors of metabolism, involving various biochemical pathways, can cause hypoglycemia. New generation sequencing technology has enabled extensive molecular testing, leading to rapid diagnosis and specific therapies. Understanding the biochemical and clinical phenotypes is crucial for guiding molecular analysis and interpreting genetic results. Multidisciplinary collaboration is essential for translating research findings into clinical practice.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Editorial Material
Cell Biology
Julie Di Cristofaro, Philippe Gouret, Jacques Chiaroni, Laurent Abi-Rached, Julien Paganini
Summary: 11 novel HLA alleles were isolated in the 1000 Genomes Project using PolyPheMe software.
Article
Biochemistry & Molecular Biology
Lucas Andre Cavalcanti Brandao, Ronald Rodrigues de Moura, Angelo Valerio Marzano, Chiara Moltrasio, Paola Maura Tricarico, Sergio Crovella
Summary: Unravelling the molecular basis of multifactorial disorders requires new genomic analysis tools that focus on disrupted pathways rather than associated gene variants, as association studies have limitations in understanding the interactions between disease-causing variants. In this study, Variant Enrichment Analysis (VEA) was developed and applied to identify novel pathways altered in patients with complex autoinflammatory skin disorders.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell & Tissue Engineering
Terry Lappin
Summary: The 7th International Forum on Stem Cells in Tianjin, China, covered a wide range of topics from basic biology to translational research, focusing on hematopoietic stem cells and other minor stem cell populations. Held virtually due to the COVID pandemic, the meeting provided a platform for global investigators to exchange ideas. Professor Cheng, the organizer, has a strong background in hematopoietic stem cell research and a commitment to advancing the field through collaboration and training.
STEM CELLS TRANSLATIONAL MEDICINE
(2021)
Review
Medicine, General & Internal
Daniele Guadagnolo, Gioia Mastromoro, Francesca Di Palma, Antonio Pizzuti, Enrica Marchionni
Summary: The introduction of Next Generation Sequencing technologies has significantly impacted prenatal diagnosis, with Prenatal Exome Sequencing being increasingly used in fetuses with structural anomalies and negative chromosomal analysis. The diagnostic yield of pES varies widely, with differences in sample sizes and inclusion criteria influencing its efficiency. While pES has a pivotal role in prenatal diagnosis, there is a need for more homogeneity in access criteria and consensus on clinical management to achieve widespread use in the future.
Article
Biotechnology & Applied Microbiology
Vera Belova, Anna Shmitko, Anna Pavlova, Robert Afasizhev, Valery Cheranev, Anastasia Tabanakova, Natalya Ponikarovskaya, Denis Rebrikov, Dmitriy Korostin
Summary: This study compared the newly released Agilent SureSelect Human All Exon v8 probe set with the previous v7 set, finding that the v8 probe set can more accurately call SNVs and indels on the same target regions, indicating better data quality.
Article
Health Care Sciences & Services
Giulio Maltoni, Roberto Franceschi, Valeria Di Natale, Randa Al-Qaisi, Valentina Greco, Roberto Bertorelli, Veronica De Sanctis, Alessandro Quattrone, Vilma Mantovani, Vittoria Cauvin, Stefano Zucchini
Summary: This study utilized an NGS panel to diagnose pediatric patients suspected of having MODY-X, and identified rare subtypes of MODY in 6 out of 28 patients. The availability of the NGS panel for MD was determined to be crucial in accurately identifying different forms of MODY.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Article
Genetics & Heredity
Ege Ulgen, Ozge Can, Kaya Bilguvar, Cemaliye Akyerli Boylu, Sirin Kilicturgay Yuksel, Ayca Ersen Danyeli, O. Ugur Sezerman, M. Cengiz Yakicier, M. Necmettin Pamir, Koray Ozduman
Summary: In the clinical setting, a comprehensive workflow for analyzing individual genomics data was created for identifying genomic alterations in brain tumors. The workflow efficiently yielded clinically relevant results in a concise manner.
BMC MEDICAL GENOMICS
(2021)
Review
Genetics & Heredity
Maria Juliana Ballesta-Martinez, Virginia Perez-Fernandez, Vanesa Lopez-Gonzalez, Maria Jose Sanchez-Soler, Ana Teresa Serrano-Anton, Lidia Isolina Rodriguez-Pena, Maria Barreda-Sanchez, Lluis Armengol-Dulcet, Encarna Guillen-Navarro
Summary: Intellectual disability (ID) affects 1-3% of the population, with approximately 30-50% of cases having a genetic cause. Next-generation sequencing has provided high diagnostic potential for ID patients. This study evaluated the diagnostic yield and economic impact of clinical exome sequencing in 188 ID patients, highlighting a significant diagnostic yield (34%) and reduced costs and time to diagnosis. The findings support the early implementation of clinical exome sequencing in the diagnostic workup of ID patients in clinical practice.
ORPHANET JOURNAL OF RARE DISEASES
(2023)
Article
Genetics & Heredity
Stefania Martone, Autilia Tommasina Buonagura, Roberta Marra, Barbara Eleni Rosato, Federica Del Giudice, Ferdinando Bonfiglio, Mario Capasso, Achille Iolascon, Immacolata Andolfo, Roberta Russo
Summary: Next-generation sequencing-based genetic testing provides an opportunity to identify and manage medically actionable disorders, such as cancer predisposition, cardiac disorders, and familial hypercholesterolemia. Active search for causative variants in genes associated with these conditions can support early surveillance and treatment decisions for individuals and families, as well as aid in reproductive choices.
FRONTIERS IN GENETICS
(2022)