Article
Biotechnology & Applied Microbiology
Pourya Davoudi, Duy Ngoc Do, Bruce Rathgeber, Stefanie M. Colombo, Mehdi Sargolzaei, Graham Plastow, Zhiquan Wang, Karim Karimi, Guoyu Hu, Shafagh Valipour, Younes Miar
Summary: This study presents the first genome-wide CNV analysis of American mink, using whole-genome sequence data from 100 individuals. The results suggest potential links between CNVs and mink behavior, fur quality, and immune response.
Article
Genetics & Heredity
Karim Karimi, Duy Ngoc Do, Mehdi Sargolzaei, Younes Miar
Summary: The study demonstrates the importance of understanding the genetic structure of American mink for the development of genomic breeding strategies. Significant genetic variation was observed among color-types, with admixture analysis suggesting three ancestral populations as the most suitable. The density of 120,000 and 24,000 SNPs was identified as adequate for genomic evaluation accuracy in CCFAR and Millbank Fur Farm populations, respectively.
Article
Biotechnology & Applied Microbiology
Zhe Xu, Si Cheng, Xin Qiu, Xiaoqi Wang, Qiuwen Hu, Yanfeng Shi, Yang Liu, Jinxi Lin, Jichao Tian, Yongfei Peng, Yong Jiang, Yadong Yang, Jianwei Ye, Yilong Wang, Xia Meng, Zixiao Li, Hao Li, Yongjun Wang
Summary: This study constructed an optimized pipeline and identified applicable fingerprint panels to address the sample tagging problem in whole genome bisulfite sequencing (WGBS) data. By using autosome-wide A/T polymorphic single nucleotide variants (SNVs), a fingerprint panel was designed and genotypes were called from the WGBS data. The capability to tag WGBS data was validated and the lower boundary for the number of fingerprint genetic variants needed for correct sample tagging was determined.
Article
Biochemistry & Molecular Biology
Xavier Vekemans, Vincent Castric, Helen Hipperson, Niels A. Muller, Helena Westerdahl, Quentin Cronk
Summary: Whole-genome sequencing of non-model organisms is now widely accessible, allowing for the investigation of high biological interest genomic regions, such as the major histocompatibility complex (MHC), sex-determining regions (SDRs), and the plant self-incompatibility locus (S-locus). Advances in bioinformatics and technology have enabled new approaches to studying these highly polymorphic regions, with techniques such as mapping short-read sequences against multiple alternative references and long-read sequencing facilitating assembly and resequencing. Additional technical improvements, such as nanopore adaptive sequencing and pangenome-based bioinformatic tools, have the potential to further expand knowledge of challenging genomic regions.
Article
Biochemistry & Molecular Biology
Ying Ni, Xudong Liu, Zemenu Mengistie Simeneh, Mengsu Yang, Runsheng Li
Summary: This study evaluates the application of the recently released R10.4 flow cell from Oxford Nanopore Technologies in human cancer genomics and epigenomic research. The results show that R10.4 performs better than R9.4.1 in terms of read accuracy, variant detection, methylation calling, and genome recovery rate. In addition, the study proposes a promising method for high-yield single-cell whole-genome amplification sequencing and provides a possible solution for filtering false positive sites using R10.4 data.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Review
Biodiversity Conservation
Israel Aguilar-Ordonez, Josue Guzman-Linares, Judith Ballesteros-Villascan, Fernanda Miron-Toruno, Alejandra Perez-Gonzalez, Jose Garcia-Lopez, Fabricio Cruz-Lopez, Enrique Morett
Summary: Indigenous people from the American continent are underrepresented in genomic studies, with limited data availability and a focus on ancient samples. There is a need for greater involvement of the home countries in indigenous genomic research.
Article
Genetics & Heredity
Santiago G. Medina-Munoz, Diego Ortega-Del Vecchyo, Luis Pablo Cruz-Hervert, Leticia Ferreyra-Reyes, Lourdes Garcia-Garcia, Andres Moreno-Estrada, Aaron P. Ragsdale
Summary: This study used high-coverage whole-genome data and existing genomes from Latin America to infer the complex evolutionary history of Latin American populations. The models developed in this study provide a more accurate prediction of genetic variation in admixed populations and can be a valuable resource for future studies.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Public, Environmental & Occupational Health
A. Muyldermans, F. Crombe, P. Bosmans, F. Cools, D. Pierard, I Wybo
Summary: Analysis of a Serratia marcescens outbreak in an NICU from 2018-2019 revealed that replacing siphons and weekly decontamination with acetic acid were key infection control measures. Whole-genome sequencing (WGS) enabled faster recognition and accurate mapping of the outbreak, facilitating the implementation of control measures. Additionally, WGS provided valuable insights into the spread of antibiotic resistance and virulence genes.
JOURNAL OF HOSPITAL INFECTION
(2021)
Article
Multidisciplinary Sciences
Brigitte Glanzmann, Tracey Jooste, Samira Ghoor, Richard Gordon, Rizwana Mia, Jun Mao, Hao Li, Patrick Charls, Craig Douman, Maritha J. Kotze, Armand V. Peeters, Glaudina Loots, Monika Esser, Caroline T. Tiemessen, Robert J. Wilkinson, Johan Louw, Glenda Gray, Robin M. Warren, Marlo Moeller, Craig Kinnear
Summary: The emergence of next generation sequencing has had a significant impact on genomic research, enabling South African researchers to access high quality data comparable to international standards at the South African Medical Research Council's Genomics Centre. This has enhanced the capacity of African researchers to sequence whole genomes and analyze data locally.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
Hisashi Udagawa, Hiroyuki Ichida, Takanori Takeuchi, Tomoko Abe, Yoshimitsu Takakura
Summary: In this study, a whole-exome sequencing (WES) procedure was developed in tobacco to characterize EMS-induced mutations in a test population, revealing a high number of single nucleotide variants. The amount of mutations detected by WES was 93.5% of those detected by whole-genome sequencing, while requiring significantly less sequencing data, making it a cost-effective tool for high-throughput mutation identification in tobacco.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biology
Michael D. Linderman, Crystal Paudyal, Musab Shakeel, William Kelley, Ali Bashir, Bruce D. Gelb
Summary: The study introduces a new machine-learning based approach, NPSV, for accurately genotyping known structural variants, overcoming limitations and biases present in traditional methods. NPSV demonstrates high accuracy and robustness across different datasets and samples.
Article
Microbiology
Roan Pijnacker, Maaike van den Beld, Kim van der Zwaluw, Anjo Verbruggen, Claudia Coipan, Alejandra Hernandez Segura, Lapo Mughini-Gras, Eelco Franz, Thijs Bosch
Summary: This study compared MLVA and WGS-based core-genome Multilocus Sequence Typing (cgMLST) as typing tools for S. Enteritidis isolates. The results showed a higher discriminatory power of WGS-based cgMLST over MLVA, but a poor concordance between both typing methods regarding clustering of S. Enteritidis isolates.
MICROBIOLOGY SPECTRUM
(2022)
Article
Clinical Neurology
Ryan L. Davis, Kishore R. Kumar, Eloise C. Watson, Carolyn M. Sue
Summary: We strongly agree that alpha-methylacyl-CoA racemase (AMACR) deficiency should be considered in patients with combinations of stroke-like episodes, seizures, encephalopathy, and retinal pigmentary changes. Our study and other case reports highlight the importance of a comprehensive sequencing approach to identify mitochondrial disease phenocopies. Such phenocopies include individuals with causative AMACR variants, as well as those from other studies and projects.
Article
Infectious Diseases
Mohamed Amine Skhairia, Naira Dekhil, Besma Mhenni, Saloua Ben Fradj, Helmi Mardassi
Summary: The study identified two main clonal complexes within the L4.3/LAM sublineage in Tunisia, with TUN4.3_CC1 being the dominant group. TUN4.3_CC1 demonstrated higher genetic diversity and stability, suggesting a more ancient origin.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Health Care Sciences & Services
Makenzie Beaman, Kimberley Fisher, Marie McDonald, Queenie K. G. Tan, David Jackson, Benjamin T. Cocanougher, Andrew P. Landstrom, Charlotte A. Hobbs, Michael Cotten, Jennifer L. Cohen
Summary: Rapid genome sequencing is crucial for providing targeted care to critically ill infants. A pilot study involving eight neonates showed a diagnostic rate of 37.5% using rapid whole genome sequencing alone, and 50% for the cohort overall. The diagnoses led to changes in management and identification of affected relatives. Challenges with sample collection were also discussed. The study also established a research protocol pipeline for cases where a diagnosis was not reached by rapid genome sequencing or other clinical testing. The benefits, limitations, challenges, and potential for incorporating rapid whole genome sequencing into routine clinical evaluation in the neonatal period were described.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Article
Neurosciences
Laura Stertz, Jessica Di Re, Guangsheng Pei, Gabriel R. Fries, Emily Mendez, Shenglan Li, Laura Smith-Callahan, Henriette Raventos, Jerricho Tipo, Rohan Cherukuru, Zhongming Zhao, Ying Liu, Peilin Jia, Fernanda Laezza, Consuelo Walss-Bass
Summary: This study utilized human-induced pluripotent stem cells (hiPSCs) derived from schizophrenia (SCZ) patients in the isolated population of the Central Valley of Costa Rica for RNA-sequencing analysis, identifying differentially expressed genes enriched in the phosphoinositide 3-kinase/glycogen synthase kinase 3 (PI3K/GSK3) signaling pathway, and suggesting disruption of the PI3K/GSK3 signaling pathway as a potential risk factor for SCZ.
NEUROPSYCHOPHARMACOLOGY
(2021)
Article
Pharmacology & Pharmacy
Gabriela Chavarria-Soley, Fernanda Francis-Cartin, Fabiola Jimenez-Gonzalez, Alejandro Avila-Aguirre, Maria Jose Castro-Gomez, Lauren Robarts, Anna Middleton, Henriette Raventos
Summary: Most people in Costa Rica are willing to donate their medical and genetic information for research, with higher willingness for nonprofit research and medical professionals compared to for-profit researchers. The main concerns regarding donation of genetic data relate to possible discrimination by health/life insurance companies and employers, according to the first study on attitudes toward genetic data donation in Costa Rica.
PERSONALIZED MEDICINE
(2021)
Article
Neurosciences
Emma E. M. Knowles, Juan M. Peralta, Laura Almasy, Vishwajit Nimgaonkar, Francis J. McMahon, Andrew M. McIntosh, Pippa Thomson, Samuel R. Mathias, Ruben C. Gur, Joanne E. Curran, Henriette Raventos, Javier Contreras, Assen Jablensky, Johanna Badcock, John Blangero, Raquel E. Gur, David C. Glahn
Summary: The study found significant genetic overlap between psychotic disorders and cognitive measures, while the genetic overlap between bipolar disorder and cognition is specific to different ascertainment strategies and ethnicities. Patients with affective disorders show enhanced performance in working and face memory.
BIOLOGICAL PSYCHIATRY
(2021)
Article
Clinical Neurology
Carolina Coto-Vilchez, Jose J. Martinez-Magana, Lara Mora-Villalobos, Daniel Valerio, Alma D. Genis-Mendoza, Jeremy M. Silverman, Humberto Nicolini, Henriette Raventos, Gabriela Chavarria-Soley
Summary: In this study, differential methylated regions (DMRs) in the genomes of cognitively healthy individuals and individuals with LOAD were identified. The study revealed 11 DMRs that contain genes involved in various biological processes. The findings suggest that PM20D1 may play a role in protection against AD. Additionally, the study found that genotypes influence the methylation levels of PM20D1.
Meeting Abstract
Clinical Neurology
Gabriela Chavarria-Soley, Fernanda Francis-Cartin, Fabiola JImenez-Gonzalez, Juan Manuel Peralta, John Blangero, Raquel E. Gur, Laura Almasy, David Glahn, Henriette Raventos
EUROPEAN NEUROPSYCHOPHARMACOLOGY
(2021)
Meeting Abstract
Clinical Neurology
Gabriela Chavarria-Soley, Fernanda Francis-Cartin, Gabriel Macaya, Ronald Alfaro, Lauren Robarts, Anna Middleton, Henriette Raventos
EUROPEAN NEUROPSYCHOPHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Niamh Ryan, Cathal Ormond, Yi-Chieh Chang, Javier Contreras, Henriette Raventos, Michael Gill, Elizabeth Heron, Carol A. Mathews, Aiden Corvin
Summary: This study investigates the genetic variants associated with Tourette Syndrome (TS) in a Costa Rican family through whole-genome sequencing analysis. The researchers identified rare variants that were not present in controls and were linked with risk haplotypes in the family. These variants are enriched in pathways related to locomotion and signal transduction, suggesting their role in TS risk. The study highlights the importance of investigating both coding and non-coding variants in understanding the genetic basis of TS.
MOLECULAR PSYCHIATRY
(2022)
Article
Multidisciplinary Sciences
Jeffrey Lazarus, Diana Romero, Christopher J. Kopka, Salim Abdool Karim, Laith J. Abu-Raddad, Gisele Almeida, Ricardo Baptista-Leite, Joshua A. Barocas, Mauricio L. Barreto, Yaneer Bar-Yam, Quique Bassat, Carolina Batista, Morgan Bazilian, Shu-Ti Chiou, Carlos del Rio, Gregory J. Dore, George F. Gao, Lawrence O. Gostin, Margaret Hellard, Jose L. Jimenez, Gagandeep Kang, Nancy Lee, Mojca Maticic, Martin McKee, Sabin Nsanzimana, Miquel Oliu-Barton, Bary Pradelski, Oksana Pyzik, Kenneth Rabin, Sunil Raina, Sabina Faiz Rashid, Magdalena Rathe, Rocio Saenz, Sudhvir Singh, Malene Trock-Hempler, Sonia Villapol, Peiling Yap, Agnes Binagwaho, Adeeba Kamarulzaman, Ayman El-Mohandes
Summary: Despite scientific and medical advances, political, socioeconomic, and behavioral factors continue to undermine the response to the COVID-19 pandemic. A Delphi study involving a diverse panel of experts from 112 countries and territories developed a set of recommendations across various domains to address this global threat to public health.
Meeting Abstract
Medicine, General & Internal
Niamh Ryan, Cathal Ormond, Yi-Chieh Chang, Nelson Freimer, Javier Contreras, Henriette Raventos, Carol A. Mathews, Elizabeth Heron, Michael Gill, Aiden Corvin
IRISH JOURNAL OF MEDICAL SCIENCE
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
G. Chavarria-Soley, M. Francis, F. Jimenez, A. Avila, M. Castro-Gomez, H. Raventos
EUROPEAN JOURNAL OF HUMAN GENETICS
(2020)
Meeting Abstract
Neurosciences
Emma Knowles, Vishwajit Nimgaonkar, Henriette Raventos, Javier Contreras, Andrew McIntosh, Pippa Thomson, Assen Jablensky, Juan Peralta, Seth Ament, Francis McMahon, Ruben Gur, Maja Bucan, Joanne Curran, Laura Almasy, Raquel Gur, John Blangero, David Glahn
NEUROPSYCHOPHARMACOLOGY
(2019)
Meeting Abstract
Clinical Neurology
Henriette Raventos
EUROPEAN NEUROPSYCHOPHARMACOLOGY
(2019)
Meeting Abstract
Clinical Neurology
Alejandro Avila Aguirre, Carolina Coto-Vilchez, Daniela Ugalde Araya, Henriette Raventos, Javier Conteras
EUROPEAN NEUROPSYCHOPHARMACOLOGY
(2019)
Meeting Abstract
Clinical Neurology
Gabriela Chavarria-Soley, Javier Contreras, Patricia Bolanos-Palmieri, Daniela Ugalde-Araya, Alejandro Avila-Aguirre, Christopher Mairena-Acuna, Henriette Raventos
EUROPEAN NEUROPSYCHOPHARMACOLOGY
(2019)