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Method: Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis
- Adrian Viehweger,
- Sebastian Krautwurst,
- Kevin Lamkiewicz,
- Ramakanth Madhugiri,
- John Ziebuhr,
- Martin Hölzer,
- and Manja Marz
Genome Res. September 2019 29: 1545-1554; Published in Advance August 22, 2019, doi:10.1101/gr.247064.118
..., replication by viral RNA-dependent RNA polymerases leads to populations of closely related viruses, so-called “quasispecies.” Standard (short-read) sequencing technologies are ill-suited to reconstruct large numbers of full-length haplotypes of (1) RNA virus s and (2) sub-length (sg) RNAs composed...
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Method: Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing
- Lin Lyu,
- Xue Li,
- Ru Feng,
- Xin Zhou,
- Tuhin K. Guha,
- Xiaofei Yu,
- Guo Qiang Chen,
- Yufeng Yao,
- Bing Su,
- Duowu Zou,
- Michael P. Snyder,
- and Lei Chen
Genome Res. March 2023 33: 401-411; Published in Advance March 27, 2023, doi:10.1101/gr.277178.122
...sequences as well as bacteria ones. Zoonotic viruses generally have mRNA that resemble their hosts, and we can identify one such virus infection case in great spatial detail in one of the CRC patients. In both replicate windows of patient M1016, viral sequences reached as high as 3.4%. These viral sequences...
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Resource: A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
- Samia N. Naccache,
- Scot Federman,
- Narayanan Veeraraghavan,
- Matei Zaharia,
- Deanna Lee,
- Erik Samayoa,
- Jerome Bouquet,
- Alexander L. Greninger,
- Ka-Cheung Luk,
- Barryett Enge,
- Debra A. Wadford,
- Sharon L. Messenger,
- Gillian L. Genrich,
- Kristen Pellegrino,
- Gilda Grard,
- Eric Leroy,
- Bradley S. Schneider,
- Joseph N. Fair,
- Miguel A. Martínez,
- Pavel Isa,
- John A. Crump,
- Joseph L. DeRisi,
- Taylor Sittler,
- John Hackett, Jr.,
- Steve Miller,
- and Charles Y. Chiu
Genome Res. July 2014 24: 1180-1192; Published in Advance June 4, 2014, doi:10.1101/gr.171934.113
..., reads are aligned using SNAP to all nucleotide sequences in the NCBI nt collection, enabling identification of bacteria, fungi, parasites, and viruses. For pathogen discovery of divergent microorganisms, unmatched reads and contigs generated from de novo assembly are then aligned to a viral protein...
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Research: Transcriptome innovations in primates revealed by single-molecule long-read sequencing
- Luis Ferrández-Peral,
- Xiaoyu Zhan,
- Marina Alvarez-Estape,
- Cristina Chiva,
- Paula Esteller-Cucala,
- Raquel García-Pérez,
- Eva Julià,
- Esther Lizano,
- Òscar Fornas,
- Eduard Sabidó,
- Qiye Li,
- Tomàs Marquès-Bonet,
- David Juan,
- and Guojie Zhang
Genome Res. August 2022 32: 1448-1462; Published in Advance July 15, 2022, doi:10.1101/gr.276395.121
...that comprehensive studies based on long reads will further extend our knowledge on the transcriptome complexity by assessing multiple tissues from numerous species and individuals. The increasing availability of long-read transcriptomes will enable the identification of tissue-specific and cell type...
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Method: Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid
- Steve Miller,
- Samia N. Naccache,
- Erik Samayoa,
- Kevin Messacar,
- Shaun Arevalo,
- Scot Federman,
- Doug Stryke,
- Elizabeth Pham,
- Becky Fung,
- William J. Bolosky,
- Danielle Ingebrigtsen,
- Walter Lorizio,
- Sandra M. Paff,
- John A. Leake,
- Rick Pesano,
- Roberta DeBiasi,
- Samuel Dominguez,
- and Charles Y. Chiu
Genome Res. May 2019 29: 831-842; Published in Advance April 16, 2019, doi:10.1101/gr.238170.118
.... These results demonstrate the analytic performance of a laboratory-validated mNGS assay for pan-pathogen detection, to be used clinically for diagnosis of neurological infections from CSF.Metagenomic next-generation sequencing (mNGS) provides a comprehensive method by which nearly all potential pathogens—viruses...
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Method: Accurate estimation of pathway activity in single cells for clustering and differential analysis
- Daniel Davis,
- Avishai Wizel,
- and Yotam Drier
Genome Res. June 2024 34: 925-936; Published in Advance July 9, 2024, doi:10.1101/gr.278431.123
...with findings reported in previous studies in many cases, but SiPSiC also reveals the differential activity of novel pathways, enabling us to suggest new mechanisms underlying the pathophysiology of these diseases and demonstrating SiPSiC's high accuracy and sensitivity in detecting biological function...
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Resource: The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation
- Zhengcao Li,
- Xiaohong Liu,
- Chen Wang,
- Zhenyang Li,
- Bo Jiang,
- Ruifeng Zhang,
- Lu Tong,
- Youping Qu,
- Sheng He,
- Haifan Chen,
- Yafei Mao,
- Qingnan Li,
- Torsten Pook,
- Yu Wu,
- Yanjun Zan,
- Hui Zhang,
- Lu Li,
- Keying Wen,
- and Yaosheng Chen
Genome Res. October 2023 33: 1833-1847; Published in Advance November 1, 2023, doi:10.1101/gr.277638.122
...dispensable genes showed close associations with adaptation. For instance, several novel swine leukocyte antigen (SLA) genes discovered in nonreference sequences potentially participate in immune responses to productive and respiratory syndrome virus (PRRSV) infection. We delineated previously unidentified...
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Research: Plasma cell-free RNA characteristics in COVID-19 patients
- Yanqun Wang,
- Jie Li,
- Lu Zhang,
- Hai-Xi Sun,
- Zhaoyong Zhang,
- Jinjin Xu,
- Yonghao Xu,
- Yu Lin,
- Airu Zhu,
- Yuxue Luo,
- Haibo Zhou,
- Yan Wu,
- Shanwen Lin,
- Yuzhe Sun,
- Fei Xiao,
- Ruiying Chen,
- Liyan Wen,
- Wei Chen,
- Fang Li,
- Rijing Ou,
- Yanjun Zhang,
- Tingyou Kuo,
- Yuming Li,
- Lingguo Li,
- Jing Sun,
- Kun Sun,
- Zhen Zhuang,
- Haorong Lu,
- Zhao Chen,
- Guoqiang Mai,
- Jianfen Zhuo,
- Puyi Qian,
- Jiayu Chen,
- Huanming Yang,
- Jian Wang,
- Xun Xu,
- Nanshan Zhong,
- Jingxian Zhao,
- Junhua Li,
- Jincun Zhao,
- and Xin Jin
Genome Res. February 2022 32: 228-241; Published in Advance January 21, 2022, doi:10.1101/gr.276175.121
...respiratory viruses is still lacking. Follow-up studies need to be conducted to explore the impact of treatment on cfRNA profile and the cfRNA characterization among different viral infections.As a noninvasive approach, plasma cfRNA provides a good resource for COVID-19 research (Fig. 5), including potential...
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Method: Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling
- Stephanie M. Zimmerman,
- Robin Fropf,
- Bridget R. Kulasekara,
- Maddy Griswold,
- Oliver Appelbe,
- Arya Bahrami,
- Rich Boykin,
- Derek L. Buhr,
- Kit Fuhrman,
- Margaret L. Hoang,
- Quoc Huynh,
- Lesley Isgur,
- Andrew Klock,
- Alecksandr Kutchma,
- Alexa E. Lasley,
- Yan Liang,
- Jill McKay-Fleisch,
- Jeffrey S. Nelson,
- Karen Nguyen,
- Erin Piazza,
- Aric Rininger,
- Daniel R. Zollinger,
- Michael Rhodes,
- and Joseph M. Beechem
Genome Res. October 2022 32: 1892-1905; Published in Advance September 13, 2022, doi:10.1101/gr.276206.121
...Illumina sequencing workflows. The probe identification barcodes were designed to have a minimum Hamming distance of ≥2 between barcodes.We designed 18,815 human and 20,175 mouse probes targeting >99.5% of annotated protein-coding genes in human and >98.2% in mouse (Supplemental Table S1). To reduce...
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