Article
Endocrinology & Metabolism
Vincenza Precone, Rossella Cannarella, Stefano Paolacci, Gian Maria Busetto, Tommaso Beccari, Liborio Stuppia, Gerolamo Tonini, Alessandra Zulian, Giuseppe Marceddu, Aldo E. Calogero, Matteo Bertelli
Summary: This study utilized a next-generation sequencing gene panel to identify potential gene variants in idiopathic male infertile patients. The findings suggest that searching for pre-diagnostic genes may help in pinpointing the cause of idiopathic male infertility.
FRONTIERS IN ENDOCRINOLOGY
(2021)
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
Andrology
Rossella Cannarella, Rosita A. Condorelli, Stefano Paolacci, Federica Barbagallo, Giulia Guerri, Matteo Bertelli, Sandro La Vignera, Aldo E. Calogero
Summary: This study identified rare variants in NR5A1 and TEX11 genes with a pathogenic role in patients with idiopathic oligozoospermia or NOA. Multiple new variants were discovered, with potential pathogenic implications that warrant further study. NGS technology, utilizing a custom-made gene panel, holds promise in increasing diagnostic rates for these patients.
ASIAN JOURNAL OF ANDROLOGY
(2021)
Review
Biochemistry & Molecular Biology
Natsuko Aida, Akiko Saito, Toshifumi Azuma
Summary: The development of next-generation sequencing (NGS) has greatly improved the speed and capacity of genetic analysis, expanding its applications to include genome, epigenome, metagenome, and transcriptome analyses. Bone tissue, as a crucial unit supporting the body, is susceptible to genetic diseases. The relationship between age-related bone fragility and genetic factors has recently gained attention.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Fisheries
Yongyu Huang, Lili Zhang, Hui Ge, Guodong Wang, Shiyu Huang, Zhangwu Yang
Summary: This study aimed to call SNPs from the transcriptomes of rapid-growing and slow-growing individuals, and assess the reliability of SNPs using DNA pool sequencing. High-quality SNPs have an accuracy of 72.22%, while low-quality SNPs only achieved 52.94% accuracy, enriching data for population genetics studies and potential SNP marker development in Penaeus vannamei.
Article
Biochemistry & Molecular Biology
Lei Zhao, Rasmus Nielsen, Thorfinn Sand Korneliussen
Summary: Commonly used methods for inferring phylogenies are not well-suited for handling challenges associated with noisy, diploid sequencing data. To address this problem, we introduce two new probabilistic approaches, distAngsd-geno and distAngsd-nuc, that account for uncertainty in genotype calling and are specifically designed for next-generation sequencing data.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Valerio Benedetti, Rosalia Canzoneri, Andrea Perrelli, Carlo Arduino, Andrea Zonta, Alfredo Brusco, Saverio Francesco Retta
Summary: Cerebral Cavernous Malformation (CCM) is a genetic cerebrovascular disease that can cause seizures, neurological deficits, and fatal intracerebral hemorrhage. It is associated with loss-of-function mutations in three genes and may have additional genetic modifiers. A study in Italy identified pathogenic variants in CCM genes in 29% of CCM cases, as well as variants in other genes related to oxidative stress and inflammation.
Article
Biology
Jesse Farek, Daniel Hughes, William Salerno, Yiming Zhu, Aishwarya Pisupati, Adam Mansfield, Olga Krasheninina, Adam C. English, Ginger Metcalf, Eric Boerwinkle, Donna M. Muzny, Richard Gibbs, Ziad Khan, Fritz J. Sedlazeck
Summary: xAtlas is a fast, lightweight, and accurate method for calling SNVs and small indels, with rapid runtimes, support for various file formats, and retraining capabilities.
Article
Cell Biology
Sheng-Nan Chang, Jien-Jiun Chen, Jo-Hsuan Wu, Yao-Te Chung, Jin-Wun Chen, Chu-Hsuan Chiu, Chia-Ju Liu, Meng-Tsun Liu, Yi-Cheng Chang, Chin Li, Jou-Wei Lin, Juey-Jen Hwang, Wen-Pin Lien
Summary: The study identified specific exosomal miRNAs that may serve as biomarkers for coronary artery disease (CAD).
Article
Oncology
Xiaonan Wu, Jun Zhao, Ling Yang, Xin Nie, Zheng Wang, Ping Zhang, Chao Li, Xueqing Hu, Min Tang, Yuting Yi, Xinhua Du, Xuefeng Xia, Yanfang Guan, Zicheng Yu, Wenguang Gu, Xiangming Quan, Lin Li, Hong Shi
Summary: This study reveals the differences in somatic genetic mutations and tumor mutation burden between young and aged lung adenocarcinoma (LUAD) patients, which may provide directions for targeted therapy and advantages of immunotherapy for the elderly in the future.
Review
Biochemistry & Molecular Biology
Esmat Karimi, Fatemeh Mahmoudian, Saul O. Lugo Reyes, Umair Ahmed Bargir, Manisha Madkaikar, Hasibe Artac, Araz Sabzevari, Na Lu, Gholamreza Azizi, Hassan Abolhassani
Summary: Patients with inborn errors of immunity (IEI) exhibit diverse clinical and immunological phenotypes, emphasizing the importance of accurate molecular diagnosis. Next generation sequencing has facilitated genetic examinations for rare inherited disorders, allowing a suitable molecular diagnosis for IEI patients. An efficient stepwise approach to molecular diagnosis of inborn errors of immunity has been suggested in light of current findings in the field.
MOLECULAR IMMUNOLOGY
(2021)
Article
Genetics & Heredity
Sharon A. Savage, Kristine Jones, Kedest Teshome, Adriana Lori, Lisa J. McReynolds, Marena R. Niewisch
Summary: This study identified a limitation of Next-generation sequencing (NGS) in sequencing through homopolymers. Additionally, a polymorphic site in the WRAP53 gene was reported, and it was recommended that all variants in regions of the genome with homopolymers be validated by Sanger sequencing before clinical action.
Review
Urology & Nephrology
Jiahui Zhang, Changming Zhang, Erzhi Gao, Qing Zhou
Summary: Recent advances in genomics have revealed the complexity of Mendelian disorders, highlighting allelic heterogeneity, locus heterogeneity, reduced penetrance, variable expressivity, modifier genes, and/or environmental factors. Precision medicine in clinical nephrology can improve the clinical diagnostic rate and treatment efficiency of kidney diseases, requiring nephrologists to have a good understanding of genetics.
Article
Biochemistry & Molecular Biology
Che-Hsiung Wu, Kang-Yung Peng, Daw-Yang Hwang, Yen-Hung Lin, Vin-Cent Wu, Jeff S. Chueh
Summary: This study identified somatic mutations in adrenal tissues of patients with unilateral primary aldosteronism (uPA) using a customized and targeted next-generation sequencing (cNGS) approach. The presence of mutations in aldosterone-driver genes was associated with better clinical outcomes after adrenalectomy, suggesting that the identification of such mutations may help predict success rates in uPA patients.
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
Genetics & Heredity
Kenneth D. Mandl, Tracy Glauser, Ian D. Krantz, Paul Avillach, Anna Bartels, Alan H. Beggs, Sawona Biswas, Florence T. Bourgeois, Jeremy Corsmo, Andrew Dauber, Batsal Devkota, Gary R. Fleisher, Allison P. Heath, Ingo Helbig, Joel N. Hirschhorn, Judson Kilbourn, Sek Won Kong, Susan Kornetsky, Joseph A. Majzoub, Keith Marsolo, Lisa J. Martin, Jeremy Nix, Amy Schwarzhoff, Jason Stedman, Arnold Strauss, Kristen L. Sund, Deanne M. Taylor, Peter S. White, Eric Marsh, Adda Grimberg, Colin Hawkes, Darlene Barkman, Erin M. Borglund, Ramkrishna Chakrabarty, Alka Chandel, Anil Kumar Degala, Thomas DeSain, Philip Dexheimer, Parth Divekar, Alyssa Ellis, Mike Furgason, Christopher Geehan, Andrew Joseph Guidetti, Alba Gutierrez, Barbara Hallinan, Becca Harper, Niloofar Jalali, Jaspreet Khanna, Christopher Kirby, Gabor Korodi, Michal Kouril, Amy Kratchman, Ranjay Kumar, Guillaume Labilloy, In-Hee Lee, Bria Morgan, James Morgan, Louis J. Muglia, Aleksandr Nikitin, Mike Pistone, Anna Poduri, Andrew Rupert, Kristen Safier, Piotr Sliz, Gelvina Stevenson, Joseph St Gemeiii, Vidhu Thaker, Simone Temporal, Prakash Velayutham, Julie Wijesooriya, Bryan Wolf, Andrew Wooten, Alan Yen, Yu Zhang
GENETICS IN MEDICINE
(2020)
Correction
Genetics & Heredity
Kenneth D. Mandl, Tracy Glauser, Ian D. Krantz, Paul Avillach, Anna Bartels, Alan H. Beggs, Sawona Biswas, Florence T. Bourgeois, Jeremy Corsmo, Andrew Dauber, Batsal Devkota, Gary R. Fleisher, Allison P. Heath, Ingo Helbig, Joel N. Hirschhorn, Judson Kilbourn, Sek Won Kong, Susan Kornetsky, Joseph A. Majzoub, Keith Marsolo, Lisa J. Martin, Jeremy Nix, Amy Schwarzhoff, Jason Stedman, Arnold Strauss, Kristen L. Sund, Deanne M. Taylor, Peter S. White, Eric Marsh, Adda Grimberg, Colin Hawkes
GENETICS IN MEDICINE
(2020)
Letter
Oncology
Mukta Asnani, Katharina E. Hayer, Ammar S. Naqvi, Sisi Zheng, Scarlett Y. Yang, Derek Oldridge, Fadia Ibrahim, Manolis Maragkakis, Matthew R. Gazzara, Kathryn L. Black, Asen Bagashev, Deanne Taylor, Zissimos Mourelatos, Stephan A. Grupp, David Barrett, John M. Maris, Elena Sotillo, Yoseph Barash, Andrei Thomas-Tikhonenko
Correction
Oncology
Colleen T. Harrington, Elena Sotillo, Aude Robert, Katharina E. Hayer, Agata M. Bogusz, James Psathas, Duonan Yu, Deanne Taylor, Chi V. Dang, Peter S. Klein, Michael D. Hogarty, Birgit Geoerger, Wafik S. El-Deiry, Joelle Wiels, Andrei Thomas-Tikhonenko
Article
Pediatrics
Scott M. Gordon, Lakshmi Srinivasan, Deanne M. Taylor, Stephen R. Master, Marissa A. Tremoglie, Adriana Hankeova, Dustin D. Flannery, Soraya Abbasi, Julie C. Fitzgerald, Mary C. Harris
PEDIATRIC RESEARCH
(2020)
Correction
Multidisciplinary Sciences
Afshin Beheshti, Kaushik Chakravarty, Homer Fogle, Hossein Fazelinia, Willian A. da Silveira, Valery Boyko, San-Huei Lai Polo, Amanda M. Saravia-Butler, Gary Hardiman, Deanne Taylor, Jonathan M. Galazka, Sylvain V. Costes
SCIENTIFIC REPORTS
(2020)
Article
Oncology
J. Tyson McDonald, Robert Stainforth, Jack Miller, Thomas Cahill, Willian A. Silveira, Komal S. Rathi, Gary Hardiman, Deanne Taylor, Sylvain Costes, Vinita Chauhan, Robert Meller, Afshin Beheshti
Editorial Material
Biochemical Research Methods
Judit Kumuthini, Michael Chimenti, Sven Nahnsen, Alexander Peltzer, Rebone Meraba, Ross McFadyen, Gordon Wells, Deanne Taylor, Mark Maienschein-Cline, Jian-Liang Li, Jyothi Thimmapuram, Radha Murthy-Karuturi, Lyndon Zass
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Multidisciplinary Sciences
Anshuman Sewda, A. J. Agopian, Elizabeth Goldmuntz, Hakon Hakonarson, Bernice E. Morrow, Fadi Musfee, Deanne Taylor, Laura E. Mitchell
Article
Genetics & Heredity
Fadi Musfee, A. J. Agopian, Elizabeth Goldmuntz, Hakon Hakonarson, Bernice E. Morrow, Deanne M. Taylor, Martin Tristani-Firouzi, W. Scott Watkins, Mark Yandell, Laura E. Mitchell
Summary: Research shows an association between cytoskeletal genes and conotruncal heart defects (CHDs), suggesting that common variants may increase the risk of CHDs.
Article
Multidisciplinary Sciences
Muzlifah Haniffa, Deanne Taylor, Sten Linnarsson, Bruce J. Aronow, Gary D. Bader, Roger A. Barker, Pablo G. Camara, J. Gray Camp, Alain Chedotal, Andrew Copp, Heather C. Etchevers, Paolo Giacobini, Berthold Gottgens, Guoji Guo, Ania Hupalowska, Kylie R. James, Emily Kirby, Arnold Kriegstein, Joakim Lundeberg, John C. Marioni, Kerstin B. Meyer, Kathy K. Niakan, Mats Nilsson, Bayanne Olabi, Dana Pe'er, Aviv Regev, Jennifer Rood, Orit Rozenblatt-Rosen, Rahul Satija, Sarah A. Teichmann, Barbara Treutlein, Roser Vento-Tormo, Simone Webb
Summary: The Human Developmental Cell Atlas initiative aims to create a comprehensive reference map of cells during development to understand the basis of human development, congenital and childhood disorders, as well as aging, cancer, and regenerative medicine. The initiative integrates scientists’ data on human development and uses state-of-the-art technologies to create a reference atlas across gestation.
Article
Multidisciplinary Sciences
Tianyu Cai, Agnes Gouble, Kathryn L. Black, Anna Skwarska, Ammar S. Naqvi, Deanne Taylor, Ming Zhao, Qi Yuan, Mayumi Sugita, Qi Zhang, Roman Galetto, Stephanie Filipe, Antonio Cavazos, Lina Han, Vinitha Kuruvilla, Helen Ma, Connie Weng, Chang-Gong Liu, Xiuping Liu, Sergej Konoplev, Jun Gu, Guilin Tang, Xiaoping Su, Gheath Al-Atrash, Stefan Ciurea, Sattva S. Neelapu, Andrew A. Lane, Hagop Kantarjian, Monica L. Guzman, Naveen Pemmaraju, Julianne Smith, Andrei Thomas-Tikhonenko, Marina Konopleva
Summary: This study demonstrates that UCART123 has selective anti-tumor activity against CD123-positive BPDCN cells, and exhibits strong efficacy in vitro and in mouse models.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Min Heui Ha, Man S. S. Kim, Hyun-Ju An, Min-Ji Sung, Yu Ho Lee, Dong-Ho Yang, Sang Hyun Jung, Jihyun Baek, Yueun Choi, Deanne M. Taylor, Yuanchao Zhang, So-Young Lee, Hye Yun Jeong
Summary: Mitochondrial dysfunction is a key factor in the aging process of chronic kidney disease, particularly through the cGAS-STING pathway. PINK1 deficiency contributes to kidney fibrosis, injury, and cellular senescence, and activates the cGAS-STING pathway. Mitochondrial metabolic dysregulation caused by PINK1 deficiency is associated with renal aging.
Article
Biochemical Research Methods
Komal S. Rathi, Sherjeel Arif, Mateusz Koptyra, Ammar S. Naqvi, Deanne M. Taylor, Phillip B. Storm, Adam C. Resnick, Jo Lynne Rokita, Pichai Raman
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Medicine, Research & Experimental
Sara Gonzales, Lisa O'Keefe, Karen Gutzman, Guillaume Viger, Annie B. Wescott, Bailey Farrow, Allison P. Heath, Meen Chul Kim, Deanne Taylor, Robin Champieux, Po-Yin Yen, Kristi Holmes
JOURNAL OF CLINICAL AND TRANSLATIONAL SCIENCE
(2020)