Editorial Material
Multidisciplinary Sciences
Jeffrey M. Perkel
Summary: Specialists provide seven tips for effectively sharing data.
Article
Cardiac & Cardiovascular Systems
Domitilla Russo, Francesco Cappelli, Gianluca Di Bella, Giacomo Tini, Aldostefano Porcari, Alberto Cipriani, Marco Canepa, Marco Merlo, Roberto Licordari, Pier Filippo Vianello, Mattia Zampieri, Laura De Michieli, Riccardo Scirpa, Federico Perfetto, Gianfranco Sinagra, Camillo Autore, Claudio Rapezzi, Maria Beatrice Musumeci
Summary: This study analyzed the electrocardiographic characteristics of patients with vATTR and their correlation with clinical and echocardiographic aspects, focusing on different TTR mutations. The results showed that different TTR mutations tend to have distinctive ECG features and are associated with distinct instrumental and clinical features.
INTERNATIONAL JOURNAL OF CARDIOLOGY
(2023)
Article
Genetics & Heredity
Xudong Wang, Zhongmin Xia, Ying He, Xiaoman Zhou, Haixia Zhang, Chunliu Gao, Yunsheng Ge, Xiaofang Cai, Yulin Zhou, Qiwei Guo
Summary: This study evaluated the profile of G6PD deficiency in Xiamen, China, finding a prevalence of 1.39% and identifying 12 variants and 32 genotypes, with the six most common variants accounting for approximately 94% of the identified alleles. The use of genotyping helped confirm the presence of pathogenic G6PD variants and improve the accuracy of newborn screening, with cold-chain transportation significantly enhancing the positive predictive value (PPV).
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Bin Li, Zheng Wang, Qian Chen, Kuokuo Li, Xiaomeng Wang, Yijing Wang, Qian Zeng, Ying Han, Bin Lu, Yuwen Zhao, Rui Zhang, Li Jiang, Hongxu Pan, Tengfei Luo, Yi Zhang, Zhenghuan Fang, Xuewen Xiao, Xun Zhou, Rui Wang, Lu Zhou, Yige Wang, Zhenhua Yuan, Lu Xia, Jifeng Guo, Beisha Tang, Kun Xia, Guihu Zhao, Jinchen Li
Summary: To address the challenge of accessing detailed clinical phenotypic features of patients with genetic variants, researchers developed an online database called GPCards, which integrates genetic and clinical data to provide interpretation of genotype-phenotype correlations and prioritization of candidate functional variants. This tool accelerates the interpretation of genotype-phenotype correlations in human genetic diseases and aids researchers in making faster diagnostic and treatment decisions.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemical Research Methods
Leonid Chindelevitch, Maarten van Dongen, Heather Graz, Antonio Pedrotta, Anita Suresh, Swapna Uplekar, Elita Jauneikaite, Nicole Wheeler
Summary: The threat of antimicrobial resistance (AMR) requires sharing resistance data to ensure effective research and public health response. The combination of high-throughput sequencing data and AMR phenotypes has the potential to revolutionize diagnostics and surveillance. However, the heterogeneity in data sharing practices poses challenges for large-scale analysis. To address this, the authors propose 10 rules to enhance data interoperability and enable computational biology tools for AMR analysis.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Editorial Material
Microbiology
Taj Azarian
Summary: Population genomic analysis is a powerful tool to understand the evolutionary history and success factors of pathogens. This article demonstrates the utility of pathogen genomic data by elucidating the origin of methicillin-resistant Staphylococcus aureus ST239. The availability of representative genomic data and associated metadata is crucial for these analyses.
Article
Multidisciplinary Sciences
Mitsuru Watanabe, Yuri Nakamura, Shinya Sato, Masaaki Niino, Hikoaki Fukaura, Masami Tanaka, Hirofumi Ochi, Takashi Kanda, Yukio Takeshita, Takanori Yokota, Yoichiro Nishida, Makoto Matsui, Shigemi Nagayama, Susumu Kusunoki, Katsuichi Miyamoto, Masanori Mizuno, Izumi Kawachi, Etsuji Saji, Takashi Ohashi, Shun Shimohama, Shin Hisahara, Kazutoshi Nishiyama, Takahiro Iizuka, Yuji Nakatsuji, Tatsusada Okuno, Kazuhide Ochi, Akio Suzumura, Ken Yamamoto, Yuji Kawano, Shoji Tsuji, Makoto Hirata, Ryuichi Sakate, Tomonori Kimura, Yuko Shimizu, Akiko Nagaishi, Kazumasa Okada, Fumie Hayashi, Ayako Sakoda, Katsuhisa Masaki, Koji Shinoda, Noriko Isobe, Takuya Matsushita, Jun-ichi Kira
Summary: HLA genotypes are associated with susceptibility and protection against multiple sclerosis, influencing the clinical manifestations, but such correlations are unclear in neuromyelitis optica spectrum disorders.
SCIENTIFIC REPORTS
(2021)
Review
Genetics & Heredity
Lili Yang, Xiaoli Shu, Shujiong Mao, Yi Wang, Xiaonan Du, Chaochun Zou
Summary: Angelman syndrome is a rare neurodevelopmental disease caused by the loss of function of the maternal copy of UBE3A. It is characterized by developmental delay, intellectual disability, lack of speech, and ataxia. Different genetic types may show different phenotypes, and understanding genotype-phenotype correlations can lead to individualized treatment options.
Article
Genetics & Heredity
Ruiji Guo, Xia Fang, Hailei Mao, Bin Sun, Jiateng Zhou, Yu An, Bin Wang
Summary: Synpolydactyly (SPD) is a hereditary congenital limb malformation caused by mutations in the HOXD13 gene. Research has shown that different mutations in HOXD13 are associated with the severity and symptoms of SPD, providing insights for clinical diagnosis and genetic counseling.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Mark J. Margres, Rhett M. Rautsaw, Jason L. Strickland, Andrew J. Mason, Tristan D. Schramer, Erich P. Hofmann, Erin Stiers, Schyler A. Ellsworth, Gunnar S. Nystrom, Michael P. Hogan, Daniel A. Bartlett, Timothy J. Colston, David M. Gilbert, Darin R. Rokyta, Christopher L. Parkinson
Summary: The researchers sequenced the genome of the Tiger Rattlesnake and found that the simple venom phenotype is contributed to by gene loss, chromatin accessibility, and methylation levels. They provided the most complete characterization of the venom gene-regulatory network to date and identified key mechanisms mediating phenotypic variation across a polygenic regulatory network.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Genetics & Heredity
Laurien Vaes, Daisy Rymen, David Cassiman, Anna Ligezka, Nele Vanhoutvin, Dulce Quelhas, Eva Morava, Peter Witters
Summary: PMM2-CDG is a rare disease that affects the glycosylation of proteins, leading to impaired functionality. A retrospective cohort study on 26 PMM2-CDG patients revealed different pathogenic variants of the genotype can impact disease severity differently. Variants involving specific domains can result in a less severe or worse clinical course, offering insights into the phenotypic prognosis of PMM2-CDG.
Article
Genetics & Heredity
Zhiyuan Chen, Andrew S. Azman, Xinhua Chen, Junyi Zou, Yuyang Tian, Ruijia Sun, Xiangyanyu Xu, Yani Wu, Wanying Lu, Shijia Ge, Zeyao Zhao, Juan Yang, Daniel T. Leung, Daryl B. Domman, Hongjie Yu
Summary: This study analyzed global SARS-CoV-2 genomic surveillance and genomic data, finding significant variations in surveillance and sequencing capabilities among different countries. It also identified heterogeneity in sequencing percentage, sequencing technologies, turnaround time, and completeness of released metadata across regions and income groups. Moreover, it revealed a lack of proactive sharing of sequences related to variant of concerns (VOCs) in public repositories by some countries. Urgent actions are required to enhance timely and full sharing of sequences, standardize metadata files, and support countries with limited sequencing and bioinformatics capacity.
Article
Health Care Sciences & Services
Fruzsina Molnar-Gabor, Michael J. S. Beauvais, Alexander Bernier, Maria Pilar Nicolas Jimenez, Mikel Recuero, Bartha Maria Knoppers
Summary: This viewpoint emphasizes the importance of establishing data spaces for genomic research that separate from surveillance measures to protect fundamental rights. Despite the existence of data protection regulations for research purposes, international data transfers face significant barriers. The European Health Data Space initiative presents an opportunity for EU's contribution to international genomic research, but further changes to the EU's regulation on the secondary use of health data are necessary.
JOURNAL OF MEDICAL INTERNET RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Zbigniew J. Krol, Paula Dobosz, Antonina Slubowska, Magdalena Mroczek
Summary: Initially, exome sequencing was expected to uncover the genetic basis of most heritable diseases. However, attention has shifted to the non-coding sequences that make up 98% of the genome and have important regulatory functions. The release of whole-genome sequencing datasets, including underrepresented populations, and the recognition of the importance of local databases have further enhanced the potential of genomic databases in diagnostics, therapies, and various fields of research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Oncology
Cristina Peduto, Mariateresa Zanobio, Vincenzo Nigro, Silverio Perrotta, Giulio Piluso, Claudia Santoro
Summary: In recent years, there has been an increase in the description of genotype-phenotype correlations for neurofibromatosis type 1 (NF1), which affects the clinical follow-up of patients, especially children. The use of molecular diagnosis, facilitated by next generation sequencing technology, allows for early confirmation of clinical diagnosis, even in cases with atypical presentation or overlapping conditions. This article reviews the main clinical characteristics and complications of NF1, particularly in children, and discusses the genotype-phenotype associations that impact genetic counseling and prognosis. Molecular diagnosis is crucial for confirming clinical diagnoses, especially with recently revised diagnostic criteria, and for early identification of genotypes associated with specific phenotypes.
Article
Genetics & Heredity
Katerina S. Kucera, Beth Lincoln Boyea, Brooke Migliore, Sarah Nelson Potter, Veronica R. Robles, Oksana Kutsa, Heidi Cope, Katherine C. Okoniewski, Anne Wheeler, Catherine W. Rehder, Edward C. Smith, Holly L. Peay
Summary: Screening for elevated CK-MM levels in dried blood spots is a feasible method to identify newborns with DMD. Including specific cutoffs, repeat testing, and genetic sequencing can improve the accuracy and sensitivity of screening.
GENETICS IN MEDICINE
(2024)
Article
Genetics & Heredity
Madeline Currey, Ilana Solomon, Sarah Mcgraw, Jenny Shen, Francisco Munoz, Ernesto Sosa, Vanessa Puello-Lozano, Sam Wing, Lisa Lopez, Michelle Afkhami, Janine Lobello, Szabolcs Szelinger, Stacy W. Gray
Summary: This study conducted qualitative interviews with cancer patients and providers to identify gaps in clinical care and propose care delivery solutions for the return of secondary germline findings. The responses of patients varied depending on the amount of pre-test counseling they received, and providers identified insufficient clinic time as a major barrier to pretest education. Online support tools and standardized pre-test education models were favored by providers. There were differing perspectives on how pre-test education should be integrated into clinical workflows, but agreement on the inclusion of differences between somatic and germline testing, likelihood of medically actionable findings, and the possibility of being referred to a genetics provider.
GENETICS IN MEDICINE
(2024)
Article
Genetics & Heredity
Kiely N. James, Shimul Chowdhury, Yan Ding, Sergey Batalov, Kelly Watkins, Yong Hyun Kwon, Lucitia Van Der Kraan, Katarzyna Ellsworth, Stephen F. Kingsmore, Lucia Guidugli
Summary: This study used genome sequencing to detect a wide range of copy-number variants (CNVs) and other non-single nucleotide variant/indel variant types. These genetic alterations accounted for 15.8% of reported variants, with deletions being the most common type. The study also found that additional genetic tests were ordered in some cases, but failed to report the variants detected by genome sequencing.
GENETICS IN MEDICINE
(2024)
Article
Genetics & Heredity
Asem Berkalieva, Nicole R. Kelly, Ashley Fisher, Samuel F. Hohmann, Monisha Sebastin, Miranda Di Biase, Katherine E. Bonini, Priya Marathe, Jacqueline A. Odgis, Sabrina A. Suckiel, Michelle A. Ramos, Rosamond Rhodes, Noura S. Abul-Husn, John M. Greally, Carol R. Horowitz, Melissa P. Wasserstein, Eimear E. Kenny, Bruce D. Gelb, Bart S. Ferket
Summary: The study aims to understand the effects of returning diagnostic sequencing results on clinical actions and economic outcomes for pediatric patients with suspected genetic disorders. The results showed that patients with positive findings were more likely to receive specialist consultation, but there were no significant increases in overall physician services and costs. More large-scale studies are needed to confirm these findings.
GENETICS IN MEDICINE
(2024)
Article
Genetics & Heredity
Kirstine Stochholm, Camilla Holmgard, Shanlee M. Davis, Claus H. Gravholt, Agnethe Berglund
Summary: This study assessed the incidence, prevalence, and age at diagnosis of individuals with 45,X/46,XY mosaicism and described the associated mortality pattern. The study found an increasing incidence of 45,X/46,XY mosaicism in males and a stable incidence in females. Males were diagnosed at an older age than females. Additionally, 45,X/46,XY mosaicism was associated with increased all-cause mortality.
GENETICS IN MEDICINE
(2024)
Article
Genetics & Heredity
Yunjia Chen, Ender Karaca, Nathaniel H. Robin, Dana Goodloe, Ali Al-Beshri, S. Joy Dean, Anna C. E. Hurst, Andrew J. Carroll, Fady M. Mikhail
Summary: This study confirms the association between DLG2 intragenic deletions and neurodevelopmental disorders, supports the haploinsufficiency of the DLG2 gene, and suggests a potential association between these deletions and congenital anomalies and dysmorphism.
GENETICS IN MEDICINE
(2024)