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Pitt JJ, Riester M, Zheng Y, Yoshimatsu TF, Sanni A, Oluwasola O, Veloso A, Labrot E, Wang S, Odetunde A, Ademola A, Okedere B, Mahan S, Leary R, Macomber M, Ajani M, Johnson RS, Fitzgerald D, Grundstad AJ, Tuteja JH, Khramtsova G, Zhang J, Sveen E, Hwang B, Clayton W, Nkwodimmah C, Famooto B, Obasi E, Aderoju V, Oludara M, Omodele F, Akinyele O, Adeoye A, Ogundiran T, Babalola C, MacIsaac K, Popoola A, Morrissey MP, Chen LS, Wang J, Olopade CO, Falusi AG, Winckler W, Haase K, Van Loo P, Obafunwa J, Papoutsakis D, Ojengbede O, Weber B, Ibrahim N, White KP, Huo D, Olopade OI, Barretina J. Author Correction: Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features. Nat Commun 2019; 10:288. [PMID: 30643118 PMCID: PMC6331546 DOI: 10.1038/s41467-018-07886-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The original version of this Article contained an error in the author affiliations. The affiliation of Kevin P. White with Tempus Labs, Inc. Chicago, IL, USA was inadvertently omitted. This has now been corrected in both the PDF and HTML versions of the Article.
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Affiliation(s)
- Jason J Pitt
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA.,Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - Markus Riester
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Toshio F Yoshimatsu
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Ayodele Sanni
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | | | - Artur Veloso
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Emma Labrot
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Shengfeng Wang
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing 100191, China
| | - Abayomi Odetunde
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Adeyinka Ademola
- Department of Surgery, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Babajide Okedere
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Scott Mahan
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Rebecca Leary
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Maura Macomber
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Mustapha Ajani
- Department of Pathology, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Ryan S Johnson
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Dominic Fitzgerald
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - A Jason Grundstad
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Jigyasa H Tuteja
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Galina Khramtsova
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Jing Zhang
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Elisabeth Sveen
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Bryce Hwang
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Wendy Clayton
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | | | - Bisola Famooto
- Department of Surgery, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Esther Obasi
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Victor Aderoju
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Mobolaji Oludara
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Folusho Omodele
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Odunayo Akinyele
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Adewunmi Adeoye
- Department of Pathology, University of Ibadan, Ibadan, Oyo, Nigeria
| | | | - Chinedum Babalola
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria.,Department of Pharmaceutical Chemistry, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Kenzie MacIsaac
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Abiodun Popoola
- Oncology Unit, Department of Radiology, Lagos State University, Ikeja, Lagos, Nigeria
| | | | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Jiebiao Wang
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Christopher O Olopade
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Adeyinka G Falusi
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Wendy Winckler
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Kerstin Haase
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Peter Van Loo
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Department of Human Genetics, University of Leuven, Oude Markt 13, Leuven 3000, Belgium
| | - John Obafunwa
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | | | - Oladosu Ojengbede
- Centre for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Barbara Weber
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Nasiru Ibrahim
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Kevin P White
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA. .,Tempus Labs, Inc., Chicago, IL, USA.
| | - Dezheng Huo
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA. .,Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA.
| | - Olufunmilayo I Olopade
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA. .,Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.
| | - Jordi Barretina
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA. .,Girona Biomedical Research Institute (IDIBGI), 17007, Girona 17007, Spain.
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Pitt JJ, Riester M, Zheng Y, Yoshimatsu TF, Sanni A, Oluwasola O, Veloso A, Labrot E, Wang S, Odetunde A, Ademola A, Okedere B, Mahan S, Leary R, Macomber M, Ajani M, Johnson RS, Fitzgerald D, Grundstad AJ, Tuteja JH, Khramtsova G, Zhang J, Sveen E, Hwang B, Clayton W, Nkwodimmah C, Famooto B, Obasi E, Aderoju V, Oludara M, Omodele F, Akinyele O, Adeoye A, Ogundiran T, Babalola C, MacIsaac K, Popoola A, Morrissey MP, Chen LS, Wang J, Olopade CO, Falusi AG, Winckler W, Haase K, Van Loo P, Obafunwa J, Papoutsakis D, Ojengbede O, Weber B, Ibrahim N, White KP, Huo D, Olopade OI, Barretina J. Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features. Nat Commun 2018; 9:4181. [PMID: 30327465 PMCID: PMC6191428 DOI: 10.1038/s41467-018-06616-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 09/13/2018] [Indexed: 02/08/2023] Open
Abstract
Racial/ethnic disparities in breast cancer mortality continue to widen but genomic studies rarely interrogate breast cancer in diverse populations. Through genome, exome, and RNA sequencing, we examined the molecular features of breast cancers using 194 patients from Nigeria and 1037 patients from The Cancer Genome Atlas (TCGA). Relative to Black and White cohorts in TCGA, Nigerian HR + /HER2 - tumors are characterized by increased homologous recombination deficiency signature, pervasive TP53 mutations, and greater structural variation-indicating aggressive biology. GATA3 mutations are also more frequent in Nigerians regardless of subtype. Higher proportions of APOBEC-mediated substitutions strongly associate with PIK3CA and CDH1 mutations, which are underrepresented in Nigerians and Blacks. PLK2, KDM6A, and B2M are also identified as previously unreported significantly mutated genes in breast cancer. This dataset provides novel insights into potential molecular mechanisms underlying outcome disparities and lay a foundation for deployment of precision therapeutics in underserved populations.
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Affiliation(s)
- Jason J Pitt
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA.,Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Markus Riester
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Toshio F Yoshimatsu
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Ayodele Sanni
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | | | - Artur Veloso
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Emma Labrot
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Shengfeng Wang
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, 100191, China
| | - Abayomi Odetunde
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Adeyinka Ademola
- Department of Surgery, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Babajide Okedere
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Scott Mahan
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Rebecca Leary
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Maura Macomber
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Mustapha Ajani
- Department of Pathology, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Ryan S Johnson
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Dominic Fitzgerald
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - A Jason Grundstad
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Jigyasa H Tuteja
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Galina Khramtsova
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Jing Zhang
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Elisabeth Sveen
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Bryce Hwang
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Wendy Clayton
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | | | - Bisola Famooto
- Department of Surgery, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Esther Obasi
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Victor Aderoju
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Mobolaji Oludara
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Folusho Omodele
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Odunayo Akinyele
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Adewunmi Adeoye
- Department of Pathology, University of Ibadan, Ibadan, Oyo, Nigeria
| | | | - Chinedum Babalola
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria.,Department of Pharmaceutical Chemistry, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Kenzie MacIsaac
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Abiodun Popoola
- Oncology Unit, Department of Radiology, Lagos State University, Ikeja, Lagos, Nigeria
| | | | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Jiebiao Wang
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Christopher O Olopade
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Adeyinka G Falusi
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Wendy Winckler
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Kerstin Haase
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Peter Van Loo
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Human Genetics, University of Leuven, Oude Markt 13, Leuven, 3000, Belgium
| | - John Obafunwa
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | | | - Oladosu Ojengbede
- Centre for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Barbara Weber
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Nasiru Ibrahim
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Kevin P White
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA. .,Tempus Labs Inc., Chicago, IL, USA.
| | - Dezheng Huo
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA. .,Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA.
| | - Olufunmilayo I Olopade
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA. .,Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
| | - Jordi Barretina
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA. .,Girona Biomedical Research Institute (IDIBGI), Girona, 17007, Spain.
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3
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Ma L, Zhao B, Chen K, Thomas A, Tuteja JH, He X, He C, White KP. Evolution of transcript modification by N6-methyladenosine in primates. Genome Res 2017; 27:385-392. [PMID: 28052920 PMCID: PMC5340966 DOI: 10.1101/gr.212563.116] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 12/19/2016] [Indexed: 11/24/2022]
Abstract
Phenotypic differences within populations and between closely related species are often driven by variation and evolution of gene expression. However, most analyses have focused on the effects of genomic variation at cis-regulatory elements such as promoters and enhancers that control transcriptional activity, and little is understood about the influence of post-transcriptional processes on transcript evolution. Post-transcriptional modification of RNA by N6-methyladenosine (m6A) has been shown to be widespread throughout the transcriptome, and this reversible mark can affect transcript stability and translation dynamics. Here we analyze m6A mRNA modifications in lymphoblastoid cell lines (LCLs) from human, chimpanzee and rhesus, and we identify patterns of m6A evolution among species. We find that m6A evolution occurs in parallel with evolution of consensus RNA sequence motifs known to be associated with the enzymatic complexes that regulate m6A dynamics, and expression evolution of m6A-modified genes occurs in parallel with m6A evolution.
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Affiliation(s)
- Lijia Ma
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois 60637, USA.,Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Boxuan Zhao
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.,Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Kai Chen
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.,Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Amber Thomas
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois 60637, USA.,Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jigyasa H Tuteja
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois 60637, USA.,Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Xin He
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.,Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Kevin P White
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois 60637, USA.,Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA.,Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois 60637, USA.,Tempus Health, Incorporated, Chicago, Illinois 60654, USA
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4
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Kadri S, Long BC, Mujacic I, Zhen CJ, Wurst MN, Sharma S, McDonald N, Niu N, Benhamed S, Tuteja JH, Seiwert TY, White KP, McNerney ME, Fitzpatrick C, Wang YL, Furtado LV, Segal JP. Clinical Validation of a Next-Generation Sequencing Genomic Oncology Panel via Cross-Platform Benchmarking against Established Amplicon Sequencing Assays. J Mol Diagn 2016; 19:43-56. [PMID: 27836695 DOI: 10.1016/j.jmoldx.2016.07.012] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/10/2016] [Accepted: 07/19/2016] [Indexed: 10/20/2022] Open
Abstract
Next-generation sequencing (NGS) genomic oncology profiling assays have emerged as key drivers of personalized cancer care and translational research. However, validation of these assays to meet strict clinical standards has been historically problematic because of both significant assay complexity and a scarcity of optimal validation samples. Herein, we present the clinical validation of 76 genes from a novel 1212-gene large-scale hybrid capture cancer sequencing assay (University of Chicago Medicine OncoPlus) using full-data comparisons against multiple clinical NGS amplicon-based assays to yield dramatic increases in per-sample data comparison efficiency compared with previously published validations. Using a sample set of 104 normal, solid tumor, and hematopoietic malignancy specimens, head-to-head NGS data analyses allowed for 6.8 million individual clinical base call comparisons, including 2729 previously confirmed variants, with 100% sensitivity and specificity. University of Chicago Medicine OncoPlus showed excellent performance for detection of single-nucleotide variants, insertions/deletions up to 52 bp, and FLT3 internal tandem duplications of up to 102 bp or larger. Highly concordant copy number variant and ALK/RET/ROS1 gene fusion detection were also observed. In addition to underlining the efficiency of NGS validation via full-data benchmarking against existing clinical NGS assays, this study also highlights the degree of performance similarity between hybrid capture and amplicon assays that is attainable with the application of strict quality control parameters and optimized computational analytics.
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Affiliation(s)
- Sabah Kadri
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Bradley C Long
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Ibro Mujacic
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Chao J Zhen
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Michelle N Wurst
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Shruti Sharma
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Nadia McDonald
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Nifang Niu
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Sonia Benhamed
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Jigyasa H Tuteja
- Department of Pathology, the Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois
| | - Tanguy Y Seiwert
- Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Kevin P White
- Department of Pathology, the Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois
| | - Megan E McNerney
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Carrie Fitzpatrick
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Y Lynn Wang
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Larissa V Furtado
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Jeremy P Segal
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois.
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5
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Zabala G, Campos E, Varala KK, Bloomfield S, Jones SI, Win H, Tuteja JH, Calla B, Clough SJ, Hudson M, Vodkin LO. Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max. BMC Plant Biol 2012; 12:177. [PMID: 23031057 PMCID: PMC3534067 DOI: 10.1186/1471-2229-12-177] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 09/22/2012] [Indexed: 05/21/2023]
Abstract
BACKGROUND Small non-coding RNAs (smRNAs) are known to have major roles in gene regulation in eukaryotes. In plants, knowledge of the biogenesis and mechanisms of action of smRNA classes including microRNAs (miRNAs), short interfering RNAs (siRNAs), and trans-acting siRNAs (tasiRNAs) has been gained mostly through studies with Arabidopsis. In recent years, high throughput sequencing of smRNA populations has enabled extension of knowledge from model systems to plants with larger, more complex genomes. Soybean (Glycine max) now has many genomics resources available including a complete genome sequence and predicted gene models. Relatively little is known, however, about the full complement of its endogenous smRNAs populations and the silenced genes. RESULTS Using Illumina sequencing and computational analysis, we characterized eight smRNA populations from multiple tissues and organs of soybean including developing seed and vegetative tissues. A total of 41 million raw sequence reads collapsed into 135,055 unique reads were mapped to the soybean genome and its predicted cDNA gene models. Bioinformatic analyses were used to distinguish miRNAs and siRNAs and to determine their genomic origins and potential target genes. In addition, we identified two soybean TAS3 gene homologs, the miRNAs that putatively guide cleavage of their transcripts, and the derived tasiRNAs that could target soybean genes annotated as auxin response factors. Tissue-differential expression based on the flux of normalized miRNA and siRNA abundances in the eight smRNA libraries was evident, some of which was confirmed by smRNA blotting. Our global view of these smRNA populations also revealed that the size classes of smRNAs varied amongst different tissues, with the developing seed and seed coat having greater numbers of unique smRNAs of the 24-nt class compared to the vegetative tissues of germinating seedlings. The 24-nt class is known to be derived from repetitive elements including transposons. Detailed analysis of the size classes associated with ribosomal RNAs and transposable element families showed greater diversity of smRNAs in the 22- and 24-nt size classes. CONCLUSIONS The flux of endogenous smRNAs within multiple stages and tissues of seed development was contrasted with vegetative tissues of soybean, one of the dominant sources of protein and oil in world markets. The smRNAs varied in size class, complexity of origins, and possible targets. Sequencing revealed tissue-preferential expression for certain smRNAs and expression differences among closely related miRNA family members.
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MESH Headings
- Base Pairing/genetics
- Base Sequence
- Computational Biology
- DNA Transposable Elements/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Plant
- Genes, Plant/genetics
- Molecular Sequence Data
- Nucleic Acid Conformation
- Organ Specificity/genetics
- Plant Proteins/chemistry
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Ribosomal/genetics
- RNA, Small Interfering/genetics
- RNA, Small Untranslated/chemistry
- RNA, Small Untranslated/genetics
- Retroelements/genetics
- Seeds/genetics
- Sequence Alignment
- Sequence Analysis, RNA
- Glycine max/genetics
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Affiliation(s)
- Gracia Zabala
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Edhilvia Campos
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Kranthi K Varala
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Sean Bloomfield
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Sarah I Jones
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Hlaing Win
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Jigyasa H Tuteja
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Bernarda Calla
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Steven J Clough
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Matthew Hudson
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Lila O Vodkin
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
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Tuteja JH, Zabala G, Varala K, Hudson M, Vodkin LO. Endogenous, tissue-specific short interfering RNAs silence the chalcone synthase gene family in glycine max seed coats. Plant Cell 2009; 21:3063-77. [PMID: 19820189 PMCID: PMC2782299 DOI: 10.1105/tpc.109.069856] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Revised: 09/03/2009] [Accepted: 09/16/2009] [Indexed: 05/18/2023]
Abstract
Two dominant alleles of the I locus in Glycine max silence nine chalcone synthase (CHS) genes to inhibit function of the flavonoid pathway in the seed coat. We describe here the intricacies of this naturally occurring silencing mechanism based on results from small RNA gel blots and high-throughput sequencing of small RNA populations. The two dominant alleles of the I locus encompass a 27-kb region containing two perfectly repeated and inverted clusters of three chalcone synthase genes (CHS1, CHS3, and CHS4). This structure silences the expression of all CHS genes, including CHS7 and CHS8, located on other chromosomes. The CHS short interfering RNAs (siRNAs) sequenced support a mechanism by which RNAs transcribed from the CHS inverted repeat form aberrant double-stranded RNAs that become substrates for dicer-like ribonuclease. The resulting primary siRNAs become guides that target the mRNAs of the nonlinked, highly expressed CHS7 and CHS8 genes, followed by subsequent amplification of CHS7 and CHS8 secondary siRNAs by RNA-dependent RNA polymerase. Most remarkably, this silencing mechanism occurs only in one tissue, the seed coat, as shown by the lack of CHS siRNAs in cotyledons and vegetative tissues. Thus, production of the trigger double-stranded RNA that initiates the process occurs in a specific tissue and represents an example of naturally occurring inhibition of a metabolic pathway by siRNAs in one tissue while allowing expression of the pathway and synthesis of valuable secondary metabolites in all other organs/tissues of the plant.
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Affiliation(s)
| | | | | | | | - Lila O. Vodkin
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801S
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Clough SJ, Tuteja JH, Li M, Marek LF, Shoemaker RC, Vodkin LO. Features of a 103-kb gene-rich region in soybean include an inverted perfect repeat cluster of CHS genes comprising the I locus. Genome 2004; 47:819-31. [PMID: 15499396 DOI: 10.1139/g04-049] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The I locus in soybean (Glycine max) corresponds to a region of chalcone synthase (CHS) gene duplications affecting seed pigmentation. We sequenced and annotated BAC clone 104J7, which harbors a dominant i(i) allele from Glycine max 'Williams 82', to gain insight into the genetic structure of this multigenic region in addition to examining its flanking regions. The 103-kb BAC encompasses a gene-rich region with 11 putatively expressed genes. In addition to six copies of CHS, these genes include: a geranylgeranyltransferase type II beta subunit (E.C.2.5.1.60), a beta-galactosidase, a putative spermine and (or) spermidine synthase (E.C.2.5.1.16), and an unknown expressed gene. Strikingly, sequencing data revealed that the 10.91-kb CHS1, CHS3, CHS4 cluster is present as a perfect inverted repeat separated by 5.87 kb. Contiguous arrangement of CHS paralogs could lead to folding into multiple secondary structures, hypothesized to induce deletions that have previously been shown to effect CHS expression. BAC104J7 also contains several gene fragments representing a cation/hydrogen exchanger, a 40S ribosomal protein, a CBL-interacting protein kinase, and the amino terminus of a subtilisin. Chimeric ESTs were identified that may represent read-through transcription from a flanking truncated gene into a CHS cluster, generating aberrant CHS RNA molecules that could play a role in CHS gene silencing.
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Affiliation(s)
- Steven J Clough
- USDA-ARS and the Department of Crop Science, University of Illinois, Urbana, IL 61801, USA
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Tuteja JH, Clough SJ, Chan WC, Vodkin LO. Tissue-specific gene silencing mediated by a naturally occurring chalcone synthase gene cluster in Glycine max. Plant Cell 2004; 16:819-35. [PMID: 15064367 PMCID: PMC412859 DOI: 10.1105/tpc.021352] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2004] [Accepted: 02/10/2004] [Indexed: 05/18/2023]
Abstract
Chalcone synthase, a key regulatory enzyme in the flavonoid pathway, constitutes an eight-member gene family in Glycine max (soybean). Three of the chalcone synthase (CHS) gene family members are arranged as inverted repeats in a 10-kb region, corresponding to the I locus (inhibitor). Spontaneous mutations of a dominant allele (I or i(i)) to a recessive allele (i) have been shown to delete promoter sequences, paradoxically increasing total CHS transcript levels and resulting in black seed coats. However, it is not known which of the gene family members contribute toward pigmentation and how this locus affects CHS expression in other tissues. We investigated the unusual nature of the I locus using four pairs of isogenic lines differing with respect to alleles of the I locus. RNA gel blots using a generic open reading frame CHS probe detected similar CHS transcript levels in stems, roots, leaves, young pods, and cotyledons of the yellow and black isolines but not in the seed coats, which is consistent with the dominant I and i(i) alleles mediating CHS gene silencing in a tissue-specific manner. Using real-time RT-PCR, a variable pattern of expression of CHS genes in different tissues was demonstrated. However, increase in pigmentation in the black seed coats was associated with release of the silencing effect specifically on CHS7/CHS8, which occurred at all stages of seed coat development. These expression changes were linked to structural changes taking place at the I locus, shown to encompass a much wider region of at least 27 kb, comprising two identical 10.91-kb stretches of CHS gene duplications. The suppressive effect of this 27-kb I locus in a specific tissue of the G. max plant represents a unique endogenous gene silencing mechanism.
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Affiliation(s)
- Jigyasa H Tuteja
- Program in Physiological and Molecular Plant Biology, University of Illinois, Urbana 61801, USA
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