Article
Pharmacology & Pharmacy
Samuel D. Chorlton, Gordon Ritchie, Tanya Lawson, Elizabeth McLachlan, Marc G. Romney, Nancy Matic, Christopher F. Lowe
Summary: A next-generation sequencing (NGS) assay was developed for CMV antiviral drug resistance (AVDR) testing, which using MinION technology detected additional mutations compared to traditional Sanger sequencing. Through the application of an online bioinformatics pipeline, barriers associated with MinION and NGS in clinical laboratories were eliminated.
ANTIVIRAL RESEARCH
(2021)
Article
Biochemical Research Methods
Jie Huang, Stefano Pallotti, Qianling Zhou, Marcus Kleber, Xiaomeng Xin, Daniel A. King, Valerio Napolioni
Summary: The development of PERHAPS allows for direct calling of haplotypes from short-read, paired-end NGS data with high reliability. By applying this method, the study successfully extracted haplotype data related to APOE polymorphism and identified the rare APOE(*)1 haplotype in the African population.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Kang Huang, Wenkai Li, Bing Yang, Dan Wang, Shujun He, Yujia Shen, Jincuo Ao, Yuhang Li, Yunxia Cui, Yuchen Kong, Wei Li, Nianlong Li, Derek W. Dunn, Baoguo Li
Summary: Polyploid plants are important for studying evolution, molecular ecology, and agriculture. However, their unique genetic inheritance requires specific software for population genetic analysis.
MOLECULAR ECOLOGY RESOURCES
(2022)
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)
Article
Immunology
Ferhat Guzel, Micol Romano, Erdi Keles, David Piskin, Seza Ozen, Hakan Poyrazoglu, Ozgur Kasapcopur, Erkan Demirkaya
Summary: This study describes the development and validation of an NGS-based multiplex array for targeted sequencing of nine genes associated with common AIDs, offering a cost-effective, comprehensive, and informative screening tool compared to other methods.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Forestry
Tomas Byrne, Niall Farrelly, Colin Kelleher, Trevor R. Hodkinson, Stephen L. Byrne, Susanne Barth
Summary: Picea sitchensis, or Sitka spruce, is a forestry species of interest both for conservation and as a productive crop. This study analyzed the genetic diversity and differentiation of this species across its native range using genotyping-by-sequencing. The results showed low levels of genetic differentiation across the broader environmental gradient, but island effects were observed on geographically distant populations. The findings provide valuable information for breeders and researchers in terms of breeding programs, scientific studies, and climate change adaptation.
Review
Pharmacology & Pharmacy
Xiangjun Ji, Baitang Ning, Jinghua Liu, Ruth Roberts, Larry Lesko, Weida Tong, Zhichao Liu, Tieliu Shi
Summary: Pharmacogenomics plays essential roles in optimizing drug responses and avoiding adverse events. Population-specific therapeutic interventions and genotyping can improve clinical outcomes, highlighting the importance of precision medicine strategies. Challenges and regulatory efforts still exist in advancing this field further.
DRUG DISCOVERY TODAY
(2021)
Article
Urology & Nephrology
Jose Lazaro-Guevara, Julio Fierro-Morales, A. Hunter Wright, River Gunville, Christopher Simeone, Scott G. Frodsham, Melissa H. Pezzolesi, Courtney A. Zaffino, Laith Al-Rabadi, Nirupama Ramkumar, Marcus G. Pezzolesi
Summary: This study investigated the genetic basis of nondiabetic kidney disease (NDKD) and diabetic kidney disease (DKD) through targeted NGS, finding rare diagnostic variants consistent with clinical diagnoses in 19% of NDKD patients and in 22% of DKD patients. Additionally, genetic variants suggestive of NDKD were detected in 3% of diabetic patients. These findings suggest that rare variants in kidney disease-related genes may contribute to the pathogenesis of DKD and NDKD in patients with diabetes.
AMERICAN JOURNAL OF NEPHROLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Kaja Wasik, Tomaz Berisa, Joseph K. Pickrell, Jeremiah H. Li, Dana J. Fraser, Karen King, Charles Cox
Summary: The study found that low-pass sequencing to a depth above 0.4x coverage achieves higher power for association studies in pharmacogenetics compared to genotyping arrays.
Article
Clinical Neurology
Jakub Scaber, Alexander G. Thompson, Lucy Farrimond, Emily Feneberg, Malcolm Proudfoot, Lynn Ossher, Martin R. Turner, Kevin Talbot
Summary: This study demonstrates that expanding genetic testing to all patients diagnosed with ALS can enhance recruitment potential for clinical trials, but also has significant resource implications for genetic counseling.
EUROPEAN JOURNAL OF NEUROLOGY
(2023)
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
Medicine, Legal
Hirak Ranjan Dash, Eduardo Avila, Soumya Ranjan Jena, Kamlesh Kaitholia, Radhika Agarwal, Clarice Sampaio Alho, Ankit Srivastava, Anil Kumar Singh
Summary: The emergence of next-generation sequencing technology has led to the exploration of SNP markers as an alternative to traditional capillary electrophoresis-based STR typing, offering advantages such as low mutation rates and short amplicons. To achieve a sufficient level of discrimination, a higher number of SNPs need to be characterized simultaneously, highlighting the usefulness of NGS technology. Analysis of 124 SNPs in the central Indian population demonstrated the potential utility of SNP markers for forensic applications.
INTERNATIONAL JOURNAL OF LEGAL MEDICINE
(2022)
Article
Medical Laboratory Technology
Bennett Oh Vic Shum, Carel Jacobus Pretorius, Letitia Min Fen Sng, Ilya Henner, Paulette Barahona, Emre Basar, Jim McGill, Urs Wilgen, Anna Zournazi, Lilian Downie, Natalie Taylor, Liam Cheney, Sylvania Wu, Natalie Angela Twine, Denis Carolin Bauer, Gerald Francis Watts, Akash Navilebasappa, Kishore Rajagopal Kumar, Jacobus Petrus Johannes Ungerer, Glenn Bennett
Summary: The study found that newborn screening can be expanded using targeted gene sequencing (TGS), which is a feasible and cost-effective method. The TGS assay had a high sensitivity (>99%) and specificity (100%) with a turnaround time of 7 to 10 days and a maximum batch size of 1536 samples. This approach can increase the number of conditions screened and improve the effectiveness of newborn screening programs.
CLINICAL CHEMISTRY
(2023)
Article
Oncology
Karoline Andersen, Kasper Holm, Mette Tranberg, Cecilie Lebech Pedersen, Sara Bonlokke, Torben Steiniche, Berit Andersen, Magnus Stougaard
Summary: This study demonstrates the use of a targeted HPV next generation sequencing (NGS) panel for cervical cancer screening. The targeted panel shows similar sensitivity and specificity to commercial HPV assays, but also provides additional advantages such as specific detection of all relevant HPV types and identification of viral integration and variants.
Article
Pathology
J. Lippert, S. Bonlokke, A. Utke, B. R. Knudsen, B. S. Sorensen, T. Steiniche, M. Stougaard
Summary: The study demonstrates that targeted NGS is effective in detecting and genotyping HPV in both FFPE biopsies and plasma samples. This method provides early diagnosis and prognosis for cervical cancer progression, enhancing recovery and survival potential for patients.
EXPERIMENTAL AND MOLECULAR PATHOLOGY
(2021)