Pub Date : 2024-11-08DOI: 10.1038/s41588-024-02002-3
The standardized naming of gene variants in both databases and publications is crucial to ensure their discoverability and clinical application. Efforts are underway in conjunction with the Human Genome Organization (HUGO) to develop a field standard for variant reporting through the use of validation software prior to publication.
{"title":"Improving reporting standards for genetic variants","authors":"","doi":"10.1038/s41588-024-02002-3","DOIUrl":"10.1038/s41588-024-02002-3","url":null,"abstract":"The standardized naming of gene variants in both databases and publications is crucial to ensure their discoverability and clinical application. Efforts are underway in conjunction with the Human Genome Organization (HUGO) to develop a field standard for variant reporting through the use of validation software prior to publication.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2283-2283"},"PeriodicalIF":31.7,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-02002-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142596169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-08DOI: 10.1038/s41588-024-02008-x
Chiara Anania
{"title":"Single-cell 3D multi-omics during human brain development","authors":"Chiara Anania","doi":"10.1038/s41588-024-02008-x","DOIUrl":"10.1038/s41588-024-02008-x","url":null,"abstract":"","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2296-2296"},"PeriodicalIF":31.7,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142596149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-05DOI: 10.1038/s41588-024-01957-7
Yuanyuan Zhang, Zhiquan Yang, Yizhou He, Dongxu Liu, Yueying Liu, Congyuan Liang, Meili Xie, Yupeng Jia, Qinglin Ke, Yongming Zhou, Xiaohui Cheng, Junyan Huang, Lijiang Liu, Yang Xiang, Harsh Raman, Daniel J. Kliebenstein, Shengyi Liu, Qing-Yong Yang
Although individual genomic structural variants (SVs) are known to influence gene expression and trait variation, the extent and scale of SV impact across a species remain unknown. In the present study, we constructed a reference library of 334,461 SVs from genome assemblies of 16 representative morphotypes of neopolyploid Brassica napus accessions and detected 258,865 SVs in 2,105 resequenced genomes. Coupling with 5 tissue population transcriptomes, we uncovered 285,976 SV-expression quantitative trait loci (eQTLs) that associate with altered expression of 73,580 genes. We developed a pipeline for the high-throughput joint analyses of SV-genome-wide association studies (SV-GWASs) and transcriptome-wide association studies of phenomic data, eQTLs and eQTL-GWAS colocalization, and identified 726 SV–gene expression–trait variation associations, some of which were verified by transgenics. The pervasive SV impact on how SV reshapes trait variation was demonstrated with the glucosinolate biosynthesis and transport pathway. The study highlighting the impact of genome-wide and species-scale SVs provides a powerful methodological strategy and valuable resources for studying evolution, gene discovery and breeding. Multiomics joint analyses based on a structural variant (SV) map from 16 genome assemblies and 2,105 resequenced accession genomes shed light on the regulatory effect of SVs on gene expression and trait variation in Brassica napus.
{"title":"Structural variation reshapes population gene expression and trait variation in 2,105 Brassica napus accessions","authors":"Yuanyuan Zhang, Zhiquan Yang, Yizhou He, Dongxu Liu, Yueying Liu, Congyuan Liang, Meili Xie, Yupeng Jia, Qinglin Ke, Yongming Zhou, Xiaohui Cheng, Junyan Huang, Lijiang Liu, Yang Xiang, Harsh Raman, Daniel J. Kliebenstein, Shengyi Liu, Qing-Yong Yang","doi":"10.1038/s41588-024-01957-7","DOIUrl":"10.1038/s41588-024-01957-7","url":null,"abstract":"Although individual genomic structural variants (SVs) are known to influence gene expression and trait variation, the extent and scale of SV impact across a species remain unknown. In the present study, we constructed a reference library of 334,461 SVs from genome assemblies of 16 representative morphotypes of neopolyploid Brassica napus accessions and detected 258,865 SVs in 2,105 resequenced genomes. Coupling with 5 tissue population transcriptomes, we uncovered 285,976 SV-expression quantitative trait loci (eQTLs) that associate with altered expression of 73,580 genes. We developed a pipeline for the high-throughput joint analyses of SV-genome-wide association studies (SV-GWASs) and transcriptome-wide association studies of phenomic data, eQTLs and eQTL-GWAS colocalization, and identified 726 SV–gene expression–trait variation associations, some of which were verified by transgenics. The pervasive SV impact on how SV reshapes trait variation was demonstrated with the glucosinolate biosynthesis and transport pathway. The study highlighting the impact of genome-wide and species-scale SVs provides a powerful methodological strategy and valuable resources for studying evolution, gene discovery and breeding. Multiomics joint analyses based on a structural variant (SV) map from 16 genome assemblies and 2,105 resequenced accession genomes shed light on the regulatory effect of SVs on gene expression and trait variation in Brassica napus.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2538-2550"},"PeriodicalIF":31.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-01957-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142580333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-05DOI: 10.1038/s41588-024-02017-w
Tanya J. Major, Riku Takei, Hirotaka Matsuo, Megan P. Leask, Nicholas A. Sumpter, Ruth K. Topless, Yuya Shirai, Wei Wang, Murray J. Cadzow, Amanda J. Phipps-Green, Zhiqiang Li, Aichang Ji, Marilyn E. Merriman, Emily Morice, Eric E. Kelley, Wen-Hua Wei, Sally P. A. McCormick, Matthew J. Bixley, Richard J. Reynolds, Kenneth G. Saag, Tayaza Fadason, Evgenia Golovina, Justin M. O’Sullivan, Lisa K. Stamp, Nicola Dalbeth, Abhishek Abhishek, Michael Doherty, Edward Roddy, Lennart T. H. Jacobsson, Meliha C. Kapetanovic, Olle Melander, Mariano Andrés, Fernando Pérez-Ruiz, Rosa J. Torres, Timothy Radstake, Timothy L. Jansen, Matthijs Janssen, Leo A. B. Joosten, Ruiqi Liu, Orsolya I. Gaal, Tania O. Crişan, Simona Rednic, Fina Kurreeman, Tom W. J. Huizinga, René Toes, Frédéric Lioté, Pascal Richette, Thomas Bardin, Hang Korng Ea, Tristan Pascart, Geraldine M. McCarthy, Laura Helbert, Blanka Stibůrková, Anne-K. Tausche, Till Uhlig, Véronique Vitart, Thibaud S. Boutin, Caroline Hayward, Philip L. Riches, Stuart H. Ralston, Archie Campbell, Thomas M. MacDonald, FAST Study Group, Akiyoshi Nakayama, Tappei Takada, Masahiro Nakatochi, Seiko Shimizu, Yusuke Kawamura, Yu Toyoda, Hirofumi Nakaoka, Ken Yamamoto, Keitaro Matsuo, Nariyoshi Shinomiya, Kimiyoshi Ichida, Japan Gout Genomics Consortium, Chaeyoung Lee, Asia Pacific Gout Consortium, Linda A. Bradbury, Matthew A. Brown, Philip C. Robinson, Russell R. C. Buchanan, Catherine L. Hill, Susan Lester, Malcolm D. Smith, Maureen Rischmueller, Hyon K. Choi, Eli A. Stahl, Jeff N. Miner, Daniel H. Solomon, Jing Cui, Kathleen M. Giacomini, Deanna J. Brackman, Eric M. Jorgenson, GlobalGout Genetics Consortium, Hongbo Liu, Katalin Susztak, 23andMe Research Team, Suyash Shringarpure, Alexander So, Yukinori Okada, Changgui Li, Yongyong Shi, Tony R. Merriman
{"title":"Publisher Correction: A genome-wide association analysis reveals new pathogenic pathways in gout","authors":"Tanya J. Major, Riku Takei, Hirotaka Matsuo, Megan P. Leask, Nicholas A. Sumpter, Ruth K. Topless, Yuya Shirai, Wei Wang, Murray J. Cadzow, Amanda J. Phipps-Green, Zhiqiang Li, Aichang Ji, Marilyn E. Merriman, Emily Morice, Eric E. Kelley, Wen-Hua Wei, Sally P. A. McCormick, Matthew J. Bixley, Richard J. Reynolds, Kenneth G. Saag, Tayaza Fadason, Evgenia Golovina, Justin M. O’Sullivan, Lisa K. Stamp, Nicola Dalbeth, Abhishek Abhishek, Michael Doherty, Edward Roddy, Lennart T. H. Jacobsson, Meliha C. Kapetanovic, Olle Melander, Mariano Andrés, Fernando Pérez-Ruiz, Rosa J. Torres, Timothy Radstake, Timothy L. Jansen, Matthijs Janssen, Leo A. B. Joosten, Ruiqi Liu, Orsolya I. Gaal, Tania O. Crişan, Simona Rednic, Fina Kurreeman, Tom W. J. Huizinga, René Toes, Frédéric Lioté, Pascal Richette, Thomas Bardin, Hang Korng Ea, Tristan Pascart, Geraldine M. McCarthy, Laura Helbert, Blanka Stibůrková, Anne-K. Tausche, Till Uhlig, Véronique Vitart, Thibaud S. Boutin, Caroline Hayward, Philip L. Riches, Stuart H. Ralston, Archie Campbell, Thomas M. MacDonald, FAST Study Group, Akiyoshi Nakayama, Tappei Takada, Masahiro Nakatochi, Seiko Shimizu, Yusuke Kawamura, Yu Toyoda, Hirofumi Nakaoka, Ken Yamamoto, Keitaro Matsuo, Nariyoshi Shinomiya, Kimiyoshi Ichida, Japan Gout Genomics Consortium, Chaeyoung Lee, Asia Pacific Gout Consortium, Linda A. Bradbury, Matthew A. Brown, Philip C. Robinson, Russell R. C. Buchanan, Catherine L. Hill, Susan Lester, Malcolm D. Smith, Maureen Rischmueller, Hyon K. Choi, Eli A. Stahl, Jeff N. Miner, Daniel H. Solomon, Jing Cui, Kathleen M. Giacomini, Deanna J. Brackman, Eric M. Jorgenson, GlobalGout Genetics Consortium, Hongbo Liu, Katalin Susztak, 23andMe Research Team, Suyash Shringarpure, Alexander So, Yukinori Okada, Changgui Li, Yongyong Shi, Tony R. Merriman","doi":"10.1038/s41588-024-02017-w","DOIUrl":"10.1038/s41588-024-02017-w","url":null,"abstract":"","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2577-2577"},"PeriodicalIF":31.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-02017-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142580519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-29DOI: 10.1038/s41588-024-02001-4
Peter J. Freeman, John F. Wagstaff, Ivo F. A. C. Fokkema, Garry R. Cutting, Heidi L. Rehm, Angela C. Davies, Johan T. den Dunnen, Liam J. Gretton, Raymond Dalgleish
{"title":"Author Correction: Standardizing variant naming in literature with VariantValidator to increase diagnostic rates","authors":"Peter J. Freeman, John F. Wagstaff, Ivo F. A. C. Fokkema, Garry R. Cutting, Heidi L. Rehm, Angela C. Davies, Johan T. den Dunnen, Liam J. Gretton, Raymond Dalgleish","doi":"10.1038/s41588-024-02001-4","DOIUrl":"10.1038/s41588-024-02001-4","url":null,"abstract":"","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2574-2574"},"PeriodicalIF":31.7,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-02001-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142536905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-29DOI: 10.1038/s41588-024-01964-8
Jianying Li, Zhenping Liu, Chunyuan You, Zhengyang Qi, Jiaqi You, Corrinne E. Grover, Yuexuan Long, Xianhui Huang, Sifan Lu, Yuejin Wang, Sainan Zhang, Yawen Wang, Ruizhe Bai, Mengke Zhang, Shuangxia Jin, Xinhui Nie, Jonathan F. Wendel, Xianlong Zhang, Maojun Wang
Polyploidy is an important driving force in speciation and evolution; however, the genomic basis for parallel selection of a particular trait between polyploids and ancestral diploids remains unexplored. Here we construct graph-based pan-genomes for diploid (A2) and allotetraploid (AD1) cotton species, enabled by an assembly of 50 genomes of genetically diverse accessions. We delineate a mosaic genome map of tetraploid cultivars that illustrates genomic contributions from semi-wild forms into modern cultivars. Pan-genome comparisons identify syntenic and hyper-divergent regions of continued variation between diploid and tetraploid cottons, and suggest an ongoing process of sequence evolution potentially linked to the contrasting genome size change in two subgenomes. We highlight 43% of genetic regulatory relationships for gene expression in diploid encompassing sequence divergence after polyploidy, and specifically characterize six underexplored convergent genetic loci contributing to parallel selection of fiber quality. This study offers a framework for pan-genomic dissection of genetic regulatory components underlying parallel selection of desirable traits in organisms. High-quality assemblies of 15 diploid and 35 allotetraploid cotton accessions are analyzed in graph-based pan-genomes, providing insights into genome dynamics and regulatory control of fiber transcriptomes under varying ploidy and selection pressures.
{"title":"Convergence and divergence of diploid and tetraploid cotton genomes","authors":"Jianying Li, Zhenping Liu, Chunyuan You, Zhengyang Qi, Jiaqi You, Corrinne E. Grover, Yuexuan Long, Xianhui Huang, Sifan Lu, Yuejin Wang, Sainan Zhang, Yawen Wang, Ruizhe Bai, Mengke Zhang, Shuangxia Jin, Xinhui Nie, Jonathan F. Wendel, Xianlong Zhang, Maojun Wang","doi":"10.1038/s41588-024-01964-8","DOIUrl":"10.1038/s41588-024-01964-8","url":null,"abstract":"Polyploidy is an important driving force in speciation and evolution; however, the genomic basis for parallel selection of a particular trait between polyploids and ancestral diploids remains unexplored. Here we construct graph-based pan-genomes for diploid (A2) and allotetraploid (AD1) cotton species, enabled by an assembly of 50 genomes of genetically diverse accessions. We delineate a mosaic genome map of tetraploid cultivars that illustrates genomic contributions from semi-wild forms into modern cultivars. Pan-genome comparisons identify syntenic and hyper-divergent regions of continued variation between diploid and tetraploid cottons, and suggest an ongoing process of sequence evolution potentially linked to the contrasting genome size change in two subgenomes. We highlight 43% of genetic regulatory relationships for gene expression in diploid encompassing sequence divergence after polyploidy, and specifically characterize six underexplored convergent genetic loci contributing to parallel selection of fiber quality. This study offers a framework for pan-genomic dissection of genetic regulatory components underlying parallel selection of desirable traits in organisms. High-quality assemblies of 15 diploid and 35 allotetraploid cotton accessions are analyzed in graph-based pan-genomes, providing insights into genome dynamics and regulatory control of fiber transcriptomes under varying ploidy and selection pressures.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2562-2573"},"PeriodicalIF":31.7,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142536626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-29DOI: 10.1038/s41588-024-01966-6
Erna V. Ivarsdottir, Julius Gudmundsson, Vinicius Tragante, Gardar Sveinbjornsson, Snaedis Kristmundsdottir, Simon N. Stacey, Gisli H. Halldorsson, Magnus I. Magnusson, Asmundur Oddsson, G. Bragi Walters, Asgeir Sigurdsson, Saedis Saevarsdottir, Doruk Beyter, Gudmar Thorleifsson, Bjarni V. Halldorsson, Pall Melsted, Hreinn Stefansson, Ingileif Jonsdottir, Erik Sørensen, Ole B. Pedersen, Christian Erikstrup, Martin Bøgsted, Mette Pøhl, Andreas Røder, Hein Vincent Stroomberg, Ismail Gögenur, Jens Hillingsø, Stig E. Bojesen, Ulrik Lassen, Estrid Høgdall, Henrik Ullum, Søren Brunak, Sisse R. Ostrowski, DBDS Genomic Consortium, Ida Elken Sonderby, Oleksandr Frei, Srdjan Djurovic, Alexandra Havdahl, Pal Moller, Mev Dominguez-Valentin, Jan Haavik, Ole A. Andreassen, Eivind Hovig, Bjarni A. Agnarsson, Rafn Hilmarsson, Oskar Th. Johannsson, Trausti Valdimarsson, Steinn Jonsson, Pall H. Moller, Jon H. Olafsson, Bardur Sigurgeirsson, Jon G. Jonasson, Geir Tryggvason, Hilma Holm, Patrick Sulem, Thorunn Rafnar, Daniel F. Gudbjartsson, Kari Stefansson
Discovery of cancer risk variants in the sequence of the germline genome can shed light on carcinogenesis. Here we describe gene burden association analyses, aggregating rare missense and loss of function variants, at 22 cancer sites, including 130,991 cancer cases and 733,486 controls from Iceland, Norway and the United Kingdom. We identified four genes associated with increased cancer risk; the pro-apoptotic BIK for prostate cancer, the autophagy involved ATG12 for colorectal cancer, TG for thyroid cancer and CMTR2 for both lung cancer and cutaneous melanoma. Further, we found genes with rare variants that associate with decreased risk of cancer; AURKB for any cancer, irrespective of site, and PPP1R15A for breast cancer, suggesting that inhibition of PPP1R15A may be a preventive strategy for breast cancer. Our findings pinpoint several new cancer risk genes and emphasize autophagy, apoptosis and cell stress response as a focus point for developing new therapeutics. Burden testing in three large European ancestry cohorts identifies new risk genes for a number of common cancer types, including pan-cancer protective variants in AURKB and breast cancer protective variants in PPP1R15A.
{"title":"Gene-based burden tests of rare germline variants identify six cancer susceptibility genes","authors":"Erna V. Ivarsdottir, Julius Gudmundsson, Vinicius Tragante, Gardar Sveinbjornsson, Snaedis Kristmundsdottir, Simon N. Stacey, Gisli H. Halldorsson, Magnus I. Magnusson, Asmundur Oddsson, G. Bragi Walters, Asgeir Sigurdsson, Saedis Saevarsdottir, Doruk Beyter, Gudmar Thorleifsson, Bjarni V. Halldorsson, Pall Melsted, Hreinn Stefansson, Ingileif Jonsdottir, Erik Sørensen, Ole B. Pedersen, Christian Erikstrup, Martin Bøgsted, Mette Pøhl, Andreas Røder, Hein Vincent Stroomberg, Ismail Gögenur, Jens Hillingsø, Stig E. Bojesen, Ulrik Lassen, Estrid Høgdall, Henrik Ullum, Søren Brunak, Sisse R. Ostrowski, DBDS Genomic Consortium, Ida Elken Sonderby, Oleksandr Frei, Srdjan Djurovic, Alexandra Havdahl, Pal Moller, Mev Dominguez-Valentin, Jan Haavik, Ole A. Andreassen, Eivind Hovig, Bjarni A. Agnarsson, Rafn Hilmarsson, Oskar Th. Johannsson, Trausti Valdimarsson, Steinn Jonsson, Pall H. Moller, Jon H. Olafsson, Bardur Sigurgeirsson, Jon G. Jonasson, Geir Tryggvason, Hilma Holm, Patrick Sulem, Thorunn Rafnar, Daniel F. Gudbjartsson, Kari Stefansson","doi":"10.1038/s41588-024-01966-6","DOIUrl":"10.1038/s41588-024-01966-6","url":null,"abstract":"Discovery of cancer risk variants in the sequence of the germline genome can shed light on carcinogenesis. Here we describe gene burden association analyses, aggregating rare missense and loss of function variants, at 22 cancer sites, including 130,991 cancer cases and 733,486 controls from Iceland, Norway and the United Kingdom. We identified four genes associated with increased cancer risk; the pro-apoptotic BIK for prostate cancer, the autophagy involved ATG12 for colorectal cancer, TG for thyroid cancer and CMTR2 for both lung cancer and cutaneous melanoma. Further, we found genes with rare variants that associate with decreased risk of cancer; AURKB for any cancer, irrespective of site, and PPP1R15A for breast cancer, suggesting that inhibition of PPP1R15A may be a preventive strategy for breast cancer. Our findings pinpoint several new cancer risk genes and emphasize autophagy, apoptosis and cell stress response as a focus point for developing new therapeutics. Burden testing in three large European ancestry cohorts identifies new risk genes for a number of common cancer types, including pan-cancer protective variants in AURKB and breast cancer protective variants in PPP1R15A.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2422-2433"},"PeriodicalIF":31.7,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142536566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-28DOI: 10.1038/s41588-024-01969-3
Cerise Tang, Venise Jan Castillon, Michele Waters, Chris Fong, Tricia Park, Sonia Boscenco, Susie Kim, Kelly Pekala, Jian Carrot-Zhang, A. Ari Hakimi, Nikolaus Schultz, Irina Ostrovnaya, Alexander Gusev, Justin Jee, Ed Reznik
Obesity is a risk factor for cancer, but whether obesity is linked to specific genomic subtypes of cancer is unknown. We examined the relationship between obesity and tumor genotype in two clinicogenomic corpora. Obesity was associated with specific driver mutations in lung adenocarcinoma, endometrial carcinoma and cancers of unknown primaries, independent of clinical covariates, demographic factors and genetic ancestry. Obesity is therefore a driver of etiological heterogeneity in some cancers. Analysis of pan-cancer clinical genomic sequencing finds that body mass index associates with driver mutations in certain cancer types, including most prominently lung adenocarcinoma. Obesity may thus influence tumor genetics.
{"title":"Obesity-dependent selection of driver mutations in cancer","authors":"Cerise Tang, Venise Jan Castillon, Michele Waters, Chris Fong, Tricia Park, Sonia Boscenco, Susie Kim, Kelly Pekala, Jian Carrot-Zhang, A. Ari Hakimi, Nikolaus Schultz, Irina Ostrovnaya, Alexander Gusev, Justin Jee, Ed Reznik","doi":"10.1038/s41588-024-01969-3","DOIUrl":"10.1038/s41588-024-01969-3","url":null,"abstract":"Obesity is a risk factor for cancer, but whether obesity is linked to specific genomic subtypes of cancer is unknown. We examined the relationship between obesity and tumor genotype in two clinicogenomic corpora. Obesity was associated with specific driver mutations in lung adenocarcinoma, endometrial carcinoma and cancers of unknown primaries, independent of clinical covariates, demographic factors and genetic ancestry. Obesity is therefore a driver of etiological heterogeneity in some cancers. Analysis of pan-cancer clinical genomic sequencing finds that body mass index associates with driver mutations in certain cancer types, including most prominently lung adenocarcinoma. Obesity may thus influence tumor genetics.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2318-2321"},"PeriodicalIF":31.7,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-01969-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142519260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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