7 results on '"Danecek, Petr"'
Search Results
2. Dissecting the contribution of common variants to risk of rare neurodevelopmental conditions
- Author
-
Huang, Qin Qin, primary, Wigdor, Emilie M, additional, Campbell, Patrick, additional, Malawsky, Daniel S, additional, Samocha, Kaitlin E, additional, Chundru, V Kartik, additional, Danecek, Petr, additional, Lindsay, Sarah, additional, Marchant, Thomas, additional, Musa, Mahmoud Koko, additional, Amanat, Sana, additional, Bonifanti, Davide, additional, Sheridan, Eamonn, additional, Radford, Elizabeth J, additional, Barrett, Jeffrey C, additional, Wright, Caroline F, additional, Firth, Helen V, additional, Warrier, Varun, additional, Young, Alexander Strudwick, additional, Hurles, Matthew, additional, and Martin, Hilary C, additional
- Published
- 2024
- Full Text
- View/download PDF
3. De novo variants in the RNU4-2snRNA cause a frequent neurodevelopmental syndrome
- Author
-
Chen, Yuyang, Dawes, Ruebena, Kim, Hyung Chul, Ljungdahl, Alicia, Stenton, Sarah L., Walker, Susan, Lord, Jenny, Lemire, Gabrielle, Martin-Geary, Alexandra C., Ganesh, Vijay S., Ma, Jialan, Ellingford, Jamie M., Delage, Erwan, D’Souza, Elston N., Dong, Shan, Adams, David R., Allan, Kirsten, Bakshi, Madhura, Baldwin, Erin E., Berger, Seth I., Bernstein, Jonathan A., Bhatnagar, Ishita, Blair, Ed, Brown, Natasha J., Burrage, Lindsay C., Chapman, Kimberly, Coman, David J., Compton, Alison G., Cunningham, Chloe A., D’Souza, Precilla, Danecek, Petr, Délot, Emmanuèle C., Dias, Kerith-Rae, Elias, Ellen R., Elmslie, Frances, Evans, Care-Anne, Ewans, Lisa, Ezell, Kimberly, Fraser, Jamie L., Gallacher, Lyndon, Genetti, Casie A., Goriely, Anne, Grant, Christina L., Haack, Tobias, Higgs, Jenny E., Hinch, Anjali G., Hurles, Matthew E., Kuechler, Alma, Lachlan, Katherine L., Lalani, Seema R., Lecoquierre, François, Leitão, Elsa, Fevre, Anna Le, Leventer, Richard J., Liebelt, Jan E., Lindsay, Sarah, Lockhart, Paul J., Ma, Alan S., Macnamara, Ellen F., Mansour, Sahar, Maurer, Taylor M., Mendez, Hector R., Metcalfe, Kay, Montgomery, Stephen B., Moosajee, Mariya, Nassogne, Marie-Cécile, Neumann, Serena, O’Donoghue, Michael, O’Leary, Melanie, Palmer, Elizabeth E., Pattani, Nikhil, Phillips, John, Pitsava, Georgia, Pysar, Ryan, Rehm, Heidi L., Reuter, Chloe M., Revencu, Nicole, Riess, Angelika, Rius, Rocio, Rodan, Lance, Roscioli, Tony, Rosenfeld, Jill A., Sachdev, Rani, Shaw-Smith, Charles J., Simons, Cas, Sisodiya, Sanjay M., Snell, Penny, St Clair, Laura, Stark, Zornitza, Stewart, Helen S., Tan, Tiong Yang, Tan, Natalie B., Temple, Suzanna E. L., Thorburn, David R., Tifft, Cynthia J., Uebergang, Eloise, VanNoy, Grace E., Vasudevan, Pradeep, Vilain, Eric, Viskochil, David H., Wedd, Laura, Wheeler, Matthew T., White, Susan M., Wojcik, Monica, Wolfe, Lynne A., Wolfenson, Zoe, Wright, Caroline F., Xiao, Changrui, Zocche, David, Rubenstein, John L., Markenscoff-Papadimitriou, Eirene, Fica, Sebastian M., Baralle, Diana, Depienne, Christel, MacArthur, Daniel G., Howson, Joanna M. M., Sanders, Stephan J., O’Donnell-Luria, Anne, and Whiffin, Nicola
- Abstract
Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes1. Large genome-sequenced cohorts are improving our ability to discover new diagnoses in the non-coding genome. Here we identify the non-coding RNA RNU4-2as a syndromic NDD gene. RNU4-2encodes the U4 small nuclear RNA (snRNA), which is a critical component of the U4/U6.U5 tri-snRNP complex of the major spliceosome2. We identify an 18 base pair region of RNU4-2mapping to two structural elements in the U4/U6 snRNA duplex (the T-loop and stem III) that is severely depleted of variation in the general population, but in which we identify heterozygous variants in 115 individuals with NDD. Most individuals (77.4%) have the same highly recurrent single base insertion (n.64_65insT). In 54 individuals in whom it could be determined, the de novo variants were all on the maternal allele. We demonstrate that RNU4-2is highly expressed in the developing human brain, in contrast to RNU4-1and other U4 homologues. Using RNA sequencing, we show how 5′ splice-site use is systematically disrupted in individuals with RNU4-2variants, consistent with the known role of this region during spliceosome activation. Finally, we estimate that variants in this 18 base pair region explain 0.4% of individuals with NDD. This work underscores the importance of non-coding genes in rare disorders and will provide a diagnosis to thousands of individuals with NDD worldwide.
- Published
- 2024
- Full Text
- View/download PDF
4. A panoramic view of the virosphere in three wastewater treatment plants by integrating viral‐like particle‐concentrated and traditional non‐concentrated metagenomic approaches.
- Author
-
Zhang, Jiayu, Tang, Aixi, Jin, Tao, Sun, Deshou, Guo, Fangliang, Lei, Huaxin, Lin, Lin, Shu, Wensheng, Yu, Pingfeng, Li, Xiaoyan, and Li, Bing
- Subjects
SEWAGE disposal plants ,CARBON cycle ,METAGENOMICS ,WASTEWATER treatment ,BACTERIOPHAGES - Abstract
Wastewater biotreatment systems harbor a rich diversity of microorganisms, and the effectiveness of biotreatment systems largely depends on the activity of these microorganisms. Specifically, viruses play a crucial role in altering microbial behavior and metabolic processes throughout their infection phases, an aspect that has recently attracted considerable interest. Two metagenomic approaches, viral‐like particle‐concentrated (VPC, representing free viral‐like particles) and non‐concentrated (NC, representing the cellular fraction), were employed to assess their efficacy in revealing virome characteristics, including taxonomy, diversity, host interactions, lifestyle, dynamics, and functional genes across processing units of three wastewater treatment plants (WWTPs). Our findings indicate that each approach offers unique insights into the viral community and functional composition. Their combined use proved effective in elucidating WWTP viromes. We identified nearly 50,000 viral contigs, with Cressdnaviricota and Uroviricota being the predominant phyla in the VPC and NC fractions, respectively. Notably, two pathogenic viral families, Asfarviridae and Adenoviridae, were commonly found in these WWTPs. We also observed significant differences in the viromes of WWTPs processing different types of wastewater. Additionally, various phage‐derived auxiliary metabolic genes (AMGs) were active at the RNA level, contributing to the metabolism of the microbial community, particularly in carbon, sulfur, and phosphorus cycling. Moreover, we identified 29 virus‐carried antibiotic resistance genes (ARGs) with potential for host transfer, highlighting the role of viruses in spreading ARGs in the environment. Overall, this study provides a detailed and integrated view of the virosphere in three WWTPs through the application of VPC and NC metagenomic approaches. Our findings enhance the understanding of viral communities, offering valuable insights for optimizing the operation and regulation of wastewater treatment systems. Highlights: This study comprehensively compared viral‐like particle‐concentrated (VPC) and non‐concentrated (NC) metagenomic approaches in virome investigation, highlighting their respective efficacies in detecting different viral communities and functional elements in wastewater treatment plants (WWTPs).Eukaryotic viruses belonging to Cressdnaviricota were the most prevalent in VPC metagenomes, while bacterial viruses belonging to Uroviricota were the most abundant in NC metagenomes.Diverse phage‐born auxiliary metabolic genes (AMGs) were discovered in the virome of WWTPs, and a large array of AMGs involved in biogeochemical cycles like carbon, sulfur, and phosphorus cycling showed transcriptional activation in wastewater treatment systems.A tiny proportion (less than 0.08% of viral operational taxonomic units) of viruses was discovered to harbor antibiotic resistance genes (ARGs) (29 phage‐born ARGs) only in the cellular fraction, and phage‐born ARG types primarily included macrolide–lincosamide–streptogramin, tetracycline, and aminoglycoside resistance. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
5. SeqKit2: A Swiss army knife for sequence and alignment processing.
- Author
-
Shen, Wei, Sipos, Botond, and Zhao, Liuyang
- Subjects
SEQUENCE alignment ,NUCLEOTIDE sequencing ,SEQUENCE analysis ,KNIVES - Abstract
In the era of ubiquitous high‐throughput sequencing studies, there is a growing need for analysis tools that are not just performant but also comprehensive and user‐friendly enough to cater to both novice and advanced users. This article introduces SeqKit2, the next iteration of the widely used sequence analysis tool SeqKit, featuring expanded functionality, performance optimizations, and support for additional compression methods. Retaining a pragmatic subcommand architecture, SeqKit2 represents substantial enhancement through the inclusion of 19 additional subcommands, expanding its overall repertoire to a total of 38 in eight categories. The new subcommands add functionality such as amplicon processing and robust, error‐tolerant parsing of sequence records. In addition, three subcommands designed for real‐time analysis are added for periodic monitoring of properties of FASTQ and Binary Alignment/Map alignment records and real‐time streaming from multiple sequence files. The performance of SeqKit2 is benchmarked against the old version of SeqKit, Bioawk, Seqtk, and SeqFu tools. SeqKit2 consistently outperforms its predecessor, albeit with marginally higher memory usage, while maintaining competitive runtimes against other tools. With its broad functionality, proven usability, and ongoing development driven by user feedback, we hope that bioinformaticians will find SeqKit2 useful as a "Swiss army knife" of sequence and alignment processing—equally adept at facilitating ad hoc analyses and seamlessly integrating into larger pipelines. Highlights: SeqKit2 expands its capabilities, doubling the number of subcommands from 19 to 38, and adding support for three more compression file formats.SeqKit2 outperforms its predecessor and maintains competitive with other tools.SeqKit2 improves user‐friendliness with new features, like, autocompletion, progress bars, and enhanced error handling. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
6. Black rice diet alleviates colorectal cancer development through modulating tryptophan metabolism and activating AHR pathway.
- Author
-
Wang, Ling, Tu, Yi‐Xuan, Chen, Lu, Yu, Ke‐Chun, Wang, Hong‐Kai, Yang, Shu‐Qiao, Zhang, Yuan, Zhang, Shuai‐Jie, Song, Shuo, Xu, Hong‐Li, Yin, Zhu‐Cheng, Feng, Ming‐Qian, Yue, Jun‐Qiu, Huang, Xiang‐Hong, Tang, Tang, Wei, Shao‐Zhong, Liang, Xin‐Jun, and Chen, Zhen‐Xia
- Subjects
COLORECTAL cancer ,WESTERN diet ,ARYL hydrocarbon receptors ,CARCINOGENESIS ,TRYPTOPHAN ,DIET - Abstract
Consumption of dietary fiber and anthocyanin has been linked to a lower incidence of colorectal cancer (CRC). This study scrutinizes the potential antitumorigenic attributes of a black rice diet (BRD), abundantly rich in dietary fiber and anthocyanin. Our results demonstrate notable antitumorigenic effects in mice on BRD, indicated by a reduction in both the size and number of intestinal tumors and a consequent extension in life span, compared to control diet‐fed counterparts. Furthermore, fecal transplants from BRD‐fed mice to germ‐free mice led to a decrease in colonic cell proliferation, coupled with maintained integrity of the intestinal barrier. The BRD was associated with significant shifts in gut microbiota composition, specifically an augmentation in probiotic strains Bacteroides uniformis and Lactobacillus. Noteworthy changes in gut metabolites were also documented, including the upregulation of indole‐3‐lactic acid and indole. These metabolites have been identified to stimulate the intestinal aryl hydrocarbon receptor pathway, inhibiting CRC cell proliferation and colorectal tumorigenesis. In summary, these findings propose that a BRD may modulate the progression of intestinal tumors by fostering protective gut microbiota and metabolite profiles. The study accentuates the potential health advantages of whole‐grain foods, emphasizing the potential utility of black rice in promoting health. Highlights: The black rice diet (BRD) can slow down the development of colorectal tumors in ApcMin/+ and azoxymethane/dextran sulfate sodium (AOM/DSS) colorectal cancer (CRC) model mice.The BRD increases the abundance of intestinal probiotics, such as Bacteroides uniformis and Lactobacillus, while reducing potential intestinal pathogens.The upregulated metabolites indole and indole‐3‐lactic acid in BRD are ligands of the aryl hydrocarbon receptor (AHR) pathway, which slow down the development of CRC by activating intestinal AHR receptor gene expression.A moderate consumption of BRD is expected to become a potential strategy for the prevention and treatment of CRC by improving gut microbiota and metabolites. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
7. Duck pan‐genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution.
- Author
-
Wang, Kejun, Hua, Guoying, Li, Jingyi, Yang, Yu, Zhang, Chenxi, Yang, Lan, Hu, Xiaoyu, Scheben, Armin, Wu, Yanan, Gong, Ping, Zhang, Shuangjie, Fan, Yanfeng, Zeng, Tao, Lu, Lizhi, Gong, Yanzhang, Jiang, Ruirui, Sun, Guirong, Tian, Yadong, Kang, Xiangtao, and Hu, Haifei
- Subjects
PAN-genome ,QUANTITATIVE genetics ,MOLECULAR genetics ,PHENOTYPES ,FEATHERS ,GENE ontology - Abstract
Structural variations (SVs) are a major source of domestication and improvement traits. We present the first duck pan‐genome constructed using five genome assemblies capturing ∼40.98 Mb new sequences. This pan‐genome together with high‐depth sequencing data (∼46.5×) identified 101,041 SVs, of which substantial proportions were derived from transposable element (TE) activity. Many TE‐derived SVs anchoring in a gene body or regulatory region are linked to duck's domestication and improvement. By combining quantitative genetics with molecular experiments, we, for the first time, unraveled a 6945 bp Gypsy insertion as a functional mutation of the major gene IGF2BP1 associated with duck bodyweight. This Gypsy insertion, to our knowledge, explains the largest effect on bodyweight among avian species (27.61% of phenotypic variation). In addition, we also examined another 6634 bp Gypsy insertion in MITF intron, which triggers a novel transcript of MITF, thereby contributing to the development of white plumage. Our findings highlight the importance of using a pan‐genome as a reference in genomics studies and illuminate the impact of transposons in trait formation and livestock breeding. Highlights: We present the first duck pan‐genome constructed using five genome assemblies capturing ∼40.98 Mb new sequences absent from the reference genome.We find a significant portion of the detected structural variants were derived from transposable element (TE) activity. Many of these are located within gene bodies or regulatory regions, potentially linked to duck domestication and enhancement.We used two representative examples to show how TE insertions can lead phenotypic diversity, highlighting IGF2BP1's role in bodyweight and MITF's influence on white plumage in ducks.Notably, the Gypsy insertion in the IGF2BP1 promoter, to our knowledge, explains the largest effect on bodyweight among avian species (27.61% of phenotypic variation). [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.