Multiomics characterization of breast angiosarcoma from an Asian cohort reveals enrichment for angiogenesis signaling pathway and tumor-infiltrating macrophages by Tun Kiat Ko, Zexi Guo, Bavani Kannan, Boon Yee Lim, Jing Yi Lee, Zhimei Li, Elizabeth Chun Yong Lee, Bin Tean Teh, Bin Tean Teh, Jason Yongsheng Chan, Jason Yongsheng Chan, Jason Yongsheng Chan

“…However, unlike head and neck angiosarcoma (AS-HN), AS-B disease characteristics in Asia remain unclear.MethodsWe examined clinical patterns of angiosarcoma patients (n = 176) seen in an Asiantertiary cancer center from 1999 to 2021, and specifically investigated the molecular and immune features of AS-B in comparison to AS-HN. Data from whole genome sequencing (WGS), NanoString gene expression profiling and 10x Genomics Visium spatial transcriptomics were analyzed.ResultsMajority of cases were AS-HN (n = 104; 59.1%), while AS-B (n = 16, all females) accounted for 9.1% of the cases. …”
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Serial Paediatrics Omics Tracking in Myalgic Encephalomyelitis (SPOT-ME): protocol paper for a multidisciplinary, observational study of clinical and biological markers of paediatr... by Adam Scheinberg, Natalie Thomas, Katherine Huang, Paul R Gooley, Elisha K Josev, Tracey Chau, Darcy Tantanis, Sarah J Knight, Christopher W Armstrong

“…ME/CFS patients aged 12–19 years and controls will donate biosamples of urine, blood, and peripheral blood mononuclear cells for an in-depth omics profiling analysis (whole-genome sequencing, metabolomics and quantitative proteomics) while being assessed by gold-standard clinical and neuropsychological measures. …”
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Genomic patterns of strain-specific genetic structure, linkage, and selection across fall armyworm populations by Ashley E. Tessnow, Rodney N. Nagoshi, Robert L. Meagher, Todd M. Gilligan, Ben M. Sadd, Yves Carrière, Holly N. Davis, Shelby J. Fleischer, Kelly Richers, John C. Palumbo, Patrick Porter, Jose Carlos Verle Rodrigues, Gregory A. Sword

“…Here, we used whole genome sequencing population genomics to unravel novel patterns of population structure, linkage, and selection across the genome of a notorious agricultural pest, the fall armyworm. …”
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Gut microbial 3α‐hydroxysteroid dehydrogenase promotes depression in males via degrading testosterone by Di Li, Jingru Cheng, Wei Zhang, Pengfei Cheng, Yuan He, Jinghan Jia, Chao Wang, Zhongchun Liu, Zhou Sun, Jinxi Wang

“…We found that A. koreensis administration in mice led to reduced serum testosterone levels and depression‐like behaviors, which were improved by antibiotic treatment. Using whole genome sequencing, the gene mediating testosterone degradation in A. koreensis was identified and annotated as 3α‐hydroxysteroid dehydrogenase (3α‐HSD). …”
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Adaptive evolution of stress response genes in parasites aligns with host niche diversity by Armando J. Cruz-Laufer, Maarten P. M. Vanhove, Lutz Bachmann, Maxwell Barson, Hassan Bassirou, Arnold R. Bitja Nyom, Mare Geraerts, Christoph Hahn, Tine Huyse, Gyrhaiss Kapepula Kasembele, Samuel Njom, Philipp Resl, Karen Smeets, Nikol Kmentová

“…We comparatively investigated antioxidant, heat shock, osmoregulatory, and behaviour-related genes (foraging) in two model parasitic flatworm lineages with contrasting ecological diversity, Cichlidogyrus and Kapentagyrus (Platyhelminthes: Monopisthocotyla), through whole-genome sequencing of 11 species followed by in silico exon bait capture as well as phylogenetic and codon analyses. …”
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Profiling of pathogenic variants in Japanese patients with sarcoglycanopathy by Rui Shimazaki, Yoshihiko Saito, Tomonari Awaya, Narihiro Minami, Ryo Kurosawa, Motoyasu Hosokawa, Hiroaki Ohara, Shinichiro Hayashi, Akihide Takeuchi, Masatoshi Hagiwara, Yukiko K. Hayashi, Satoru Noguchi, Ichizo Nishino

“…Genetic analyses were performed using a combination of targeted resequencing with a hereditary muscle disease panel, whole genome sequencing, multiplex ligation-dependent probe amplification, and long-read sequencing. …”
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Multidrug-Resistant Salmonella enterica Serovar Rissen Clusters Detected in Azores Archipelago, Portugal by Leonor Silveira, Miguel Pinto, Joana Isidro, Ângela Pista, Patrícia Themudo, Luís Vieira, Jorge Machado, João Paulo Gomes

“…In the present study, we analyzed by whole genome sequencing (WGS) all clinical, animal, food, and environmental isolates received up to 2017 in the Portuguese Reference Laboratories. …”
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Auditory Phenotype of a Novel Missense Variant in the CEACAM16 Gene in a Large Russian Family With Autosomal Dominant Nonsyndromic Hearing Loss by Tatiana G. Markova, Natalia N. Alekseeva, Oxana P. Ryzhkova, Olga L. Shatokhina, Anna A. Orlova, Viktoriia V. Zabnenkova, Olga S. Groznova, Olesya V. Sagaydak, Svetlana S. Chibisova, Alexander V. Polyakov, George A. Tavartkiladze

“…Genetic testing was performed, including whole-genome sequencing for the proband’s son and Sanger sequence analysis for the proband and for all available family members. …”
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Genomic characteristics and molecular epidemiology of MRSA from medical centers in Mexico: Results from the Invifar network. by Gabriela Echaniz-Avilés, Luis Ángel Núñez-García, Eduardo Rodríguez-Noriega, Consuelo Velázquez-Acosta, Luis Esaú López-Jácome, Eduardo López-Gutiérrez, Talia Pérez-Vicelis, Cristina Torres-Báez, Ulises Garza-Ramos, Nadia Rodríguez-Medina, Juan Manuel Barajas-Magallón, Rosario Vázquez-Larios, Aldo Rafael Silva-Gamiño, Rafael Franco-Cendejas, Adolfo Gómez-Quiroz, Elvira Garza-González

“…This study aims to determine the genomic characteristics of MRSA using whole-genome sequencing (WGS) data from medical centers in Mexico and to explore the associations between antimicrobial resistance genes and virulence factors.…”
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Antimicrobial Susceptibility of <i>Glaesserella parasuis</i> to Macrolides and Characterization of <i>erm</i>(T)-Carrying Mobile Elements on Chromosome by Peng Zhang, Changmin Li, Shuna Shang, Ting Huang, Junqi Liu, Qianwen Ge, Xiaoping Liao, Liangxing Fang, Yang Yu

“…Erythromycin-resistant isolates were sequenced using whole-genome sequencing. Further analysis of these sequences revealed the genetic basis of macrolide resistance in <i>G. parasuis</i>. …”
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Targeted detection of sequence variants in cell-free DNA from cerebrospinal fluid in pediatric central nervous system tumors by Katrina O’Halloran, Katrina O’Halloran, Erin E. Crotty, Eirini Christodoulou, Sarah E. Leary, Alexandra Miller, Alexandra Miller, Vera A. Paulson, Christina M. Lockwood, Ashley S. Margol, Ashley S. Margol, Jaclyn A. Biegel, Jaclyn A. Biegel

“…In contrast to broad lower-depth sequencing, commonly referred to as low pass whole genome sequencing (WGS), targeted platforms with a higher depth of coverage have also been established. …”
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Understanding the clinical and molecular epidemiological characteristics of carbapenem-resistant Acinetobacter baumannii infections within intensive care units of three teaching ho... by Pengyu Zhang, Jingchen Hao, Yafen Zhang, Junfeng Su, Guozhuang Sun, Jun Xie, Jian Hu, Guocai Li

“…Genome characteristics of isolates were investigated by whole genome sequencing. Multilocus sequence typing and phylogenetic trees were used to assess the genetic similarity of isolates. …”
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Microbial keratitis in Southern Malawi: a microbiological pilot study by Timothy Neal, Dean Everett, Stephen B Kaye, Alistair Darby, Moira Gandiwa, Shaffi Mdala, Caroline E Corless, Rose Herbert, Nicholas A V Beare, Tobi F Somerville, Thokozani Zungu, Malcolm J Horsburgh, Petros C Kayange

“…We investigated the feasibility of using a novel corneal impression membrane (CIM) for obtaining and processing samples by culture, PCR and whole-genome sequencing (WGS) in patients presenting with suspected MK in Malawi.Methods and analysis Samples were collected from patients presenting with suspected MK using a 12 mm diameter polytetrafluoroethylene CIM disc. …”
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Cultivation and molecular characterization of complete genome sequences of M. pneumoniae isolated in Russia by Matsvay A.D., Bezrukov V.M., Nikolaeva P.A., Stetsenko I.F., Nurmukanova V.A., Dikaya G.S., Gordukova M.A., Galeeva E.V., Shipulin G.A.

“…Using biological material from patients with confirmed mycoplasma infection, cultures of M. pneumoniae were obtained, for which whole-genome sequencing was carried out, followed by assembly and annotation of the pathogen genome. …”
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Study protocol for COVID-19 breakthrough infections and vaccine-induced immune response among a cohort of healthcare workers, Bangladesh. by Md Zakiul Hassan, Ahamed Khairul Basher, Mohammed Ziaur Rahman, Taufiqur Rahman Bhuiyan, Fahmida Chowdhury, Md Kamal Hossain, Aninda Rahman, Md Nazmul Islam, Lindsey M Duca, Susan Cornelia Kaydos-Daniels, Benjamin A Dahl, Firdausi Qadri, Nancy Ortiz

“…We will also perform Whole Genome Sequencing on a subset of SARS-CoV-2 positive samples with low CT values (Ct ≤ 30) to identify emerging SARS-CoV-2 variants. …”
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The Mla pathway promotes Vibrio cholerae re-expansion from stationary phase by Deborah R. Leitner, Franz G. Zingl, Alexander A. Morano, Hailong Zhang, Matthew K. Waldor

“…By monitoring the abundances of genomically barcoded libraries of WT and ∆mlaE strains, we observed that a few barcodes dominated the mutant culture at 96 h, suggesting that the similarity of the population sizes at this time was caused by expansion of a subpopulation containing a mutation that suppressed the defect of ∆mlaE. Whole genome sequencing revealed that mlaE suppressors inactivated flagellar biosynthesis. …”
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Antimicrobial resistance, virulence gene profiles, and molecular epidemiology of enterococcal isolates from patients with urinary tract infections in Shanghai, China by Weiyi Wu, Shuzhen Xiao, Lizhong Han, Qiong Wu

“…However, five strains of linezolid-resistant E. faecalis were identified, all of which were confirmed to be optrA-positive through whole-genome sequencing (WGS), with ST300 being reported as the first instance of this ST type in China. …”
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The Presence of Two Distinct Lineages of the Foot-And-Mouth Disease Virus Type A in Russia in 2013–2014 Has Significant Implications for the Epidemiology of the Virus in the Region... by Victor V. Nikiforov, Sergey A. Noskov, Alexander V. Sprygin, Mohammad Abed Alhussen, Anastasia S. Krylova, Taisia V. Erofeeva, Svetlana N. Fomina, Svetlana R. Kremenchugskaya, Fedor I. Korennoy, Maxim V. Patrushev, Ilya A. Chvala, Tamara K. Mayorova, Stepan V. Toshchakov

“…In this study, we investigated the FMDV strains circulating in Russia during the 2013–2014 period in geographically distant regions utilizing whole genome sequencing followed by maximum-likelihood phylogenetic reconstruction of whole genome and VP1 gene sequences. …”
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Draft genome sequence of a co-harbouring blaNDM-5 and mcr-1.1 Escherichia coli phylogroup A isolate associated with patient colonisation in Ireland by Anna Tumeo, Francesca McDonagh, Aneta Kovarova, Kate Ryan, Christina Clarke, Georgios Miliotis

“…Antibiotic susceptibility testing was performed using the Sensititre-EUMDRXXF plate. Whole-genome-sequencing was conducted with NextSeq1000, and genomic analysis identified antibiotic-resistance-genes (ARGs) and virulence-factors (VFs). …”
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Identification and Characterization of a Cryptic Genomic Deletion-Insertion in EYA1 Associated with Branchio-Otic Syndrome by Hao Zheng, Jun Xu, Yu Wang, Yun Lin, Qingqiang Hu, Xing Li, Jiusheng Chu, Changling Sun, Yongchuan Chai, Xiuhong Pang

“…Real-time PCR at multiple regions of EYA1 confirmed the existence of this genomic deletion and extended its 5′ boundary beyond the 5′-UTR. Whole genome sequencing subsequently located the 5′ and 3′ breakpoints to 19268 bp upstream to the ATG initiation codon and 3180 bp downstream to exon 5. …”
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