1
|
Bick AG, Metcalf GA, Mayo KR, Lichtenstein L, Rura S, Carroll RJ, Musick A, Linder JE, Jordan IK, Nagar SD, Sharma S, Meller R, Basford M, Boerwinkle E, Cicek MS, Doheny KF, Eichler EE, Gabriel S, Gibbs RA, Glazer D, Harris PA, Jarvik GP, Philippakis A, Rehm HL, Roden DM, Thibodeau SN, Topper S, Blegen AL, Wirkus SJ, Wagner VA, Meyer JG, Cicek MS, Muzny DM, Venner E, Mawhinney MZ, Griffith SML, Hsu E, Ling H, Adams MK, Walker K, Hu J, Doddapaneni H, Kovar CL, Murugan M, Dugan S, Khan Z, Boerwinkle E, Lennon NJ, Austin-Tse C, Banks E, Gatzen M, Gupta N, Henricks E, Larsson K, McDonough S, Harrison SM, Kachulis C, Lebo MS, Neben CL, Steeves M, Zhou AY, Smith JD, Frazar CD, Davis CP, Patterson KE, Wheeler MM, McGee S, Lockwood CM, Shirts BH, Pritchard CC, Murray ML, Vasta V, Leistritz D, Richardson MA, Buchan JG, Radhakrishnan A, Krumm N, Ehmen BW, Schwartz S, Aster MMT, Cibulskis K, Haessly A, Asch R, Cremer A, Degatano K, Shergill A, Gauthier LD, Lee SK, Hatcher A, Grant GB, Brandt GR, Covarrubias M, Banks E, Able A, Green AE, Carroll RJ, Zhang J, Condon HR, Wang Y, Dillon MK, Albach CH, Baalawi W, Choi SH, Wang X, Rosenthal EA, Ramirez AH, Lim S, Nambiar S, Ozenberger B, Wise AL, Lunt C, Ginsburg GS, Denny JC. Genomic data in the All of Us Research Program. Nature 2024; 627:340-346. [PMID: 38374255 PMCID: PMC10937371 DOI: 10.1038/s41586-023-06957-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/08/2023] [Indexed: 02/21/2024]
Abstract
Comprehensively mapping the genetic basis of human disease across diverse individuals is a long-standing goal for the field of human genetics1-4. The All of Us Research Program is a longitudinal cohort study aiming to enrol a diverse group of at least one million individuals across the USA to accelerate biomedical research and improve human health5,6. Here we describe the programme's genomics data release of 245,388 clinical-grade genome sequences. This resource is unique in its diversity as 77% of participants are from communities that are historically under-represented in biomedical research and 46% are individuals from under-represented racial and ethnic minorities. All of Us identified more than 1 billion genetic variants, including more than 275 million previously unreported genetic variants, more than 3.9 million of which had coding consequences. Leveraging linkage between genomic data and the longitudinal electronic health record, we evaluated 3,724 genetic variants associated with 117 diseases and found high replication rates across both participants of European ancestry and participants of African ancestry. Summary-level data are publicly available, and individual-level data can be accessed by researchers through the All of Us Researcher Workbench using a unique data passport model with a median time from initial researcher registration to data access of 29 hours. We anticipate that this diverse dataset will advance the promise of genomic medicine for all.
Collapse
|
2
|
Venner E, Patterson K, Kalra D, Wheeler MM, Chen YJ, Kalla SE, Yuan B, Karnes JH, Walker K, Smith JD, McGee S, Radhakrishnan A, Haddad A, Empey PE, Wang Q, Lichtenstein L, Toledo D, Jarvik G, Musick A, Gibbs RA. The frequency of pathogenic variation in the All of Us cohort reveals ancestry-driven disparities. Commun Biol 2024; 7:174. [PMID: 38374434 PMCID: PMC10876563 DOI: 10.1038/s42003-023-05708-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 12/13/2023] [Indexed: 02/21/2024] Open
Abstract
Disparities in data underlying clinical genomic interpretation is an acknowledged problem, but there is a paucity of data demonstrating it. The All of Us Research Program is collecting data including whole-genome sequences, health records, and surveys for at least a million participants with diverse ancestry and access to healthcare, representing one of the largest biomedical research repositories of its kind. Here, we examine pathogenic and likely pathogenic variants that were identified in the All of Us cohort. The European ancestry subgroup showed the highest overall rate of pathogenic variation, with 2.26% of participants having a pathogenic variant. Other ancestry groups had lower rates of pathogenic variation, including 1.62% for the African ancestry group and 1.32% in the Latino/Admixed American ancestry group. Pathogenic variants were most frequently observed in genes related to Breast/Ovarian Cancer or Hypercholesterolemia. Variant frequencies in many genes were consistent with the data from the public gnomAD database, with some notable exceptions resolved using gnomAD subsets. Differences in pathogenic variant frequency observed between ancestral groups generally indicate biases of ascertainment of knowledge about those variants, but some deviations may be indicative of differences in disease prevalence. This work will allow targeted precision medicine efforts at revealed disparities.
Collapse
Affiliation(s)
- Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| | - Karynne Patterson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Divya Kalra
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Marsha M Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Yi-Ju Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Sara E Kalla
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Bo Yuan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jason H Karnes
- University of Arizona, R Ken Coit College of Pharmacy, Department of Pharmacy Practice and Science, Tucson, AZ, USA
- Vanderbilt University Medical Center, Department of Biomedical Informatics, Boston, MA, USA
| | - Kimberly Walker
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Joshua D Smith
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sean McGee
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Andrew Haddad
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Philip E Empey
- Department of Pharmacy and Therapeutics, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Qiaoyan Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Diana Toledo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gail Jarvik
- Department of Medicine (Medical Genetics), University of Washington School of Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Anjene Musick
- NIH All of Us Research Program, National Institutes of Health Office of the Director, Bethesda, MD, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
3
|
Mayo KR, Basford MA, Carroll RJ, Dillon M, Fullen H, Leung J, Master H, Rura S, Sulieman L, Kennedy N, Banks E, Bernick D, Gauchan A, Lichtenstein L, Mapes BM, Marginean K, Nyemba SL, Ramirez A, Rotundo C, Wolfe K, Xia W, Azuine RE, Cronin RM, Denny JC, Kho A, Lunt C, Malin B, Natarajan K, Wilkins CH, Xu H, Hripcsak G, Roden DM, Philippakis AA, Glazer D, Harris PA. The All of Us Data and Research Center: Creating a Secure, Scalable, and Sustainable Ecosystem for Biomedical Research. Annu Rev Biomed Data Sci 2023; 6:443-464. [PMID: 37561600 DOI: 10.1146/annurev-biodatasci-122120-104825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
The All of Us Research Program's Data and Research Center (DRC) was established to help acquire, curate, and provide access to one of the world's largest and most diverse datasets for precision medicine research. Already, over 500,000 participants are enrolled in All of Us, 80% of whom are underrepresented in biomedical research, and data are being analyzed by a community of over 2,300 researchers. The DRC created this thriving data ecosystem by collaborating with engaged participants, innovative program partners, and empowered researchers. In this review, we first describe how the DRC is organized to meet the needs of this broad group of stakeholders. We then outline guiding principles, common challenges, and innovative approaches used to build the All of Us data ecosystem. Finally, we share lessons learned to help others navigate important decisions and trade-offs in building a modern biomedical data platform.
Collapse
Affiliation(s)
- Kelsey R Mayo
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Melissa A Basford
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Robert J Carroll
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| | - Moira Dillon
- Verily Life Sciences, South San Francisco, California, USA
| | - Heather Fullen
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jesse Leung
- Verily Life Sciences, South San Francisco, California, USA
| | - Hiral Master
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Shimon Rura
- Verily Life Sciences, South San Francisco, California, USA
| | - Lina Sulieman
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| | - Nan Kennedy
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Eric Banks
- Data Sciences Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - David Bernick
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Asmita Gauchan
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lee Lichtenstein
- Data Sciences Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Brandy M Mapes
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kayla Marginean
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Steve L Nyemba
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| | - Andrea Ramirez
- The All of Us Research Program, National Institutes of Health, Bethesda, Maryland, USA
| | - Charissa Rotundo
- Vanderbilt University Medical Center Enterprise Cybersecurity, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Keri Wolfe
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Weiyi Xia
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| | - Romuladus E Azuine
- The All of Us Research Program, National Institutes of Health, Bethesda, Maryland, USA
| | - Robert M Cronin
- Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Joshua C Denny
- The All of Us Research Program, National Institutes of Health, Bethesda, Maryland, USA
| | - Abel Kho
- Department of Medicine and Institute for Augmented Intelligence in Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Christopher Lunt
- The All of Us Research Program, National Institutes of Health, Bethesda, Maryland, USA
| | - Bradley Malin
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| | - Karthik Natarajan
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Consuelo H Wilkins
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Hua Xu
- Section of Biomedical Informatics and Data Science, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Dan M Roden
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - David Glazer
- Verily Life Sciences, South San Francisco, California, USA
| | - Paul A Harris
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| |
Collapse
|
4
|
Shand M, Soto J, Lichtenstein L, Benjamin D, Farjoun Y, Brody Y, Maruvka Y, Blainey PC, Banks E. A validated lineage-derived somatic truth data set enables benchmarking in cancer genome analysis. Commun Biol 2020; 3:744. [PMID: 33293579 PMCID: PMC7722876 DOI: 10.1038/s42003-020-01460-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 01/02/2020] [Accepted: 11/04/2020] [Indexed: 11/30/2022] Open
Abstract
Existing cancer benchmark data sets for human sequencing data use germline variants, synthetic methods, or expensive validations, none of which are satisfactory for providing a large collection of true somatic variation across a whole genome. Here we propose a data set, Lineage derived Somatic Truth (LinST), of short somatic mutations in the HT115 colon cancer cell-line, that are validated using a known cell lineage that includes thousands of mutations and a high confidence region covering 2.7 gigabases per sample. Megan Shand et al. present Lineage derived Somatic Truth (LinST), a validated data set of somatic mutations from a colon cancer cell line with a known lineage tree structure. They show that LinST can be used to benchmark true-positive and false-positive rates in somatic variant-calling pipelines applied to cancer genomic data.
Collapse
Affiliation(s)
- Megan Shand
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Jose Soto
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | | | - Yossi Farjoun
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yehuda Brody
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yosef Maruvka
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,MGH Cancer Center and Department of Pathology, Boston, MA, USA
| | - Paul C Blainey
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,MIT Department of Biological Engineering, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
| | - Eric Banks
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| |
Collapse
|
5
|
Braun DA, Hou Y, Bakouny Z, Ficial M, Sant' Angelo M, Forman J, Ross-Macdonald P, Berger AC, Jegede OA, Elagina L, Steinharter J, Sun M, Wind-Rotolo M, Pignon JC, Cherniack AD, Lichtenstein L, Neuberg D, Catalano P, Freeman GJ, Sharpe AH, McDermott DF, Van Allen EM, Signoretti S, Wu CJ, Shukla SA, Choueiri TK. Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma. Nat Med 2020; 26:909-918. [PMID: 32472114 DOI: 10.1038/s41591-020-0839-y] [Citation(s) in RCA: 461] [Impact Index Per Article: 115.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 03/16/2020] [Indexed: 12/24/2022]
Abstract
PD-1 blockade has transformed the management of advanced clear cell renal cell carcinoma (ccRCC), but the drivers and resistors of the PD-1 response remain incompletely elucidated. Here, we analyzed 592 tumors from patients with advanced ccRCC enrolled in prospective clinical trials of treatment with PD-1 blockade by whole-exome and RNA sequencing, integrated with immunofluorescence analysis, to uncover the immunogenomic determinants of the therapeutic response. Although conventional genomic markers (such as tumor mutation burden and neoantigen load) and the degree of CD8+ T cell infiltration were not associated with clinical response, we discovered numerous chromosomal alterations associated with response or resistance to PD-1 blockade. These advanced ccRCC tumors were highly CD8+ T cell infiltrated, with only 27% having a non-infiltrated phenotype. Our analysis revealed that infiltrated tumors are depleted of favorable PBRM1 mutations and enriched for unfavorable chromosomal losses of 9p21.3, as compared with non-infiltrated tumors, demonstrating how the potential interplay of immunophenotypes with somatic alterations impacts therapeutic efficacy.
Collapse
Affiliation(s)
- David A Braun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yue Hou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ziad Bakouny
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Miriam Ficial
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Miriam Sant' Angelo
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Juliet Forman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Opeyemi A Jegede
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - John Steinharter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Maxine Sun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Jean-Christophe Pignon
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Andrew D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Donna Neuberg
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paul Catalano
- Harvard Medical School, Boston, MA, USA.,Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Arlene H Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - David F McDermott
- Harvard Medical School, Boston, MA, USA.,Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sabina Signoretti
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Sachet A Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
6
|
Lichtenstein L, Smith J, Benjamin D, Chevalier A, Cibulskis K, Lee SK, Banks E. Abstract 5108: Somatic small variant and copy number alteration calling with the Genome Analysis Toolkit. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-5108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Somatic small mutations, SNVs or Indels, and copy number alterations are the two categories of mutations with the largest impact on cancer tumors. The Broad Institute has released somatic variant calling workflows for small mutations (M2) and copy number alterations (ModelSegments) based on the Genome Analysis Toolkit (GATK). The suite of workflows can call variants in capture or whole-genome sequencing data and will include functional annotations (Funcotator), such as protein change (for small variants) and impacted gene (for all variants). Common artifacts in sequencing data, such as those arising from oxidative DNA damage, FFPE/deamination, or mapping errors, are corrected automatically. Evaluation of the workflows is standardized and repeatable, which allows tracking of performance across versions, both detection performance (e.g. sensitivity, precision), as well as runtime performance (e.g. CPU and RAM usage). A matched normal is not required for a given tumor sample, since the workflows can leverage pre-processed panels of normals (PoNs). The workflows are freely available, are portable (i.e. can be run on local, on-prem, or cloud compute), are optimized for cost reduction, and can be tuned to optimally leverage available compute.The measured sensitivity of M2 was at least 0.93 for small somatic nucleotide variants (SNVs) and 0.83 for small insertions/deletions (Indels) on DREAM1, DREAM2, and DREAM3 challenges, and on a titrated mixture of germline samples (>=100x depth, AF = 0.2). The measured precision of M2 ranged from 0.91 to 0.98 on DREAM1, DREAM2, and DREAM3 for both SNVs and Indels. The false positive rate (FPR) of M2 was between 0.03 and 0.21 FP/Mb for SNVs, and between 0.0 and 0.1 FP/Mb for indels, on twelve paired, replicate normal-normal samples. The cost of the M2 workflow is about USD$1.15 for a pair of 35x WGS matched tumor-normal samples, using Google Cloud Compute, and required about 32 hours of CPU time on a single core with 3GB RAM.
The measured sensitivity of ModelSegments was at least 0.91 for deletions and amplifications across three cohorts of TCGA whole-exome samples (Stomach adenocarcinoma N=39, Thyroid carcinoma N=50, and Lung adenocarcinoma N=60). The measured specificity for the same set of cohorts was at least 0.96 for both deletions and amplifications. All results reported here were using the corresponding SNP Array results as a truth set.
GATK MS cost was approximately USD$0.65 on a 30x WGS pair using Google Cloud Compute and required about 6 hours of CPU time with a single core. The RAM usage was varied automatically in the workflow to minimize cost, but was in the range of 2-13GB.
Citation Format: Lee Lichtenstein, Jonn Smith, David Benjamin, Aaron Chevalier, Kristian Cibulskis, Samuel K. Lee, Eric Banks. Somatic small variant and copy number alteration calling with the Genome Analysis Toolkit [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5108.
Collapse
Affiliation(s)
| | - Jonn Smith
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | | - Eric Banks
- Broad Institute of MIT and Harvard, Cambridge, MA
| |
Collapse
|
7
|
Abstract
Abstract
We propose, implement, and evaluate a novel method (GATK gCNV) for accurate discovery of rare and common copy-number variations (CNVs) from read-depth data obtained from whole genome sequencing (WGS), whole exome sequencing (WES), or custom gene panels. GATK gCNV utilizes a sophisticated Bayesian model to learn bias factors arising from sequencing and library preparation. This model accounts for ploidy of sex chromosomes and autosomal aneuploidies, treats GC bias probabilistically, and automatically determines the necessary level of model complexity in a data-driven manner. Unlike most existing read-depth methods, GATK gCNV maintains a high level of sensitivity in common CNV regions, due to a hierarchical hidden Markov model used for accurate genotyping of multi-allelic loci. Furthermore, GATK gCNV performs bias modeling and CNV discovery simultaneously and self-consistently, resulting in significantly improved sensitivity and precision. Our implementation utilizes the PyMC3/Theano framework for performing automatic differentiation variational inference (ADVI). In addition, GATK gCNV automatically scatters large tasks across multiple machines using the Cromwell/WDL framework, enabling the scalable processing of large cohorts.
We use GATK gCNV to compute copy-number transmission and de novo rates in a cohort of WES trios and observe consistency with observed population metrics. Furthermore, we benchmark GATK gCNV for sensitivity, precision, and reproducibility of both rare and common CNV calls. Using a cohort of WES blood normal samples from The Cancer Genome Atlas (TCGA), we show that GATK gCNV calls are in remarkable concordance with Genome STRiP calls on matched WGS data and gCNV substantially outperforms XHMM and CODEX. We also validate GATK gCNV calls on WGS data against calls made using PacBio long reads.
Citation Format: Mehrtash Babadi, Samuel K. Lee, Andrey Smirnov, Lee Lichtenstein, Laura D. Gauthier, Daniel P. Howrigan, Timothy Poterba. Precise common and rare germline CNV calling with GATK [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2287.
Collapse
|
8
|
Chevalier A, Lichtenstein L, Smirnov A, Lee SK, Babidi M, Benjamin DI, Ruano-Rubio V. Abstract 3581: GATK ACNV: allelic copy-number variation discovery from SNPs and coverage data. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The presence of somatic copy-number alterations in tumor genomes can be used to predict both patient sensitivity to treatments as well as outcomes. The inclusion of allelic data improves statistical power to detect copy-number events and allows for discovery of copy-neutral events. We present GATK ACNV, an allelic copy-number variation method built on the Genome Analysis Toolkit. ACNV is a tool for detecting somatic copy-number activity from whole exome and whole genome sequencing data by segmenting the genome into regions of constant copy number and estimating copy ratio and minor-allele fraction in those regions.
ACNV uses a novel probabilistic model to account for reference bias (optionally using a panel of normals), which improves the estimation of minor-allele fraction. We combine this with the coverage model from GATK CNV by segmenting with a unified hidden Markov model, improving the statistical power to detect copy-number variation.
We validate ACNV using a purity series of the cell line HCC1143 and cancer samples from The Cancer Genome Atlas. Our results show that ACNV is able to discover regions of somatic copy-number activity accurately and with high resolution in both whole exome and whole genome sequencing data.
Citation Format: Aaron Chevalier, Lee Lichtenstein, Andrey Smirnov, Samuel K. Lee, Mehrtash Babidi, David I. Benjamin, Valentin Ruano-Rubio. GATK ACNV: allelic copy-number variation discovery from SNPs and coverage data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3581. doi:10.1158/1538-7445.AM2017-3581
Collapse
|
9
|
Brat DJ, Verhaak RGW, Aldape KD, Yung WKA, Salama SR, Cooper LAD, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, Akbani R, Huse JT, Ciriello G, Poisson LM, Barnholtz-Sloan JS, Berger MS, Brennan C, Colen RR, Colman H, Flanders AE, Giannini C, Grifford M, Iavarone A, Jain R, Joseph I, Kim J, Kasaian K, Mikkelsen T, Murray BA, O'Neill BP, Pachter L, Parsons DW, Sougnez C, Sulman EP, Vandenberg SR, Van Meir EG, von Deimling A, Zhang H, Crain D, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton T, Sherman M, Yena P, Black A, Bowen J, Dicostanzo K, Gastier-Foster J, Leraas KM, Lichtenberg TM, Pierson CR, Ramirez NC, Taylor C, Weaver S, Wise L, Zmuda E, Davidsen T, Demchok JA, Eley G, Ferguson ML, Hutter CM, Mills Shaw KR, Ozenberger BA, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Ayala B, Baboud J, Chudamani S, Jensen MA, Liu J, Pihl T, Raman R, Wan Y, Wu Y, Ally A, Auman JT, Balasundaram M, Balu S, Baylin SB, Beroukhim R, Bootwalla MS, Bowlby R, Bristow CA, Brooks D, Butterfield Y, Carlsen R, Carter S, Chin L, Chu A, Chuah E, Cibulskis K, Clarke A, Coetzee SG, Dhalla N, Fennell T, Fisher S, Gabriel S, Getz G, Gibbs R, Guin R, Hadjipanayis A, Hayes DN, Hinoue T, Hoadley K, Holt RA, Hoyle AP, Jefferys SR, Jones S, Jones CD, Kucherlapati R, Lai PH, Lander E, Lee S, Lichtenstein L, Ma Y, Maglinte DT, Mahadeshwar HS, Marra MA, Mayo M, Meng S, Meyerson ML, Mieczkowski PA, Moore RA, Mose LE, Mungall AJ, Pantazi A, Parfenov M, Park PJ, Parker JS, Perou CM, Protopopov A, Ren X, Roach J, Sabedot TS, Schein J, Schumacher SE, Seidman JG, Seth S, Shen H, Simons JV, Sipahimalani P, Soloway MG, Song X, Sun H, Tabak B, Tam A, Tan D, Tang J, Thiessen N, Triche T, Van Den Berg DJ, Veluvolu U, Waring S, Weisenberger DJ, Wilkerson MD, Wong T, Wu J, Xi L, Xu AW, Yang L, Zack TI, Zhang J, Aksoy BA, Arachchi H, Benz C, Bernard B, Carlin D, Cho J, DiCara D, Frazer S, Fuller GN, Gao J, Gehlenborg N, Haussler D, Heiman DI, Iype L, Jacobsen A, Ju Z, Katzman S, Kim H, Knijnenburg T, Kreisberg RB, Lawrence MS, Lee W, Leinonen K, Lin P, Ling S, Liu W, Liu Y, Liu Y, Lu Y, Mills G, Ng S, Noble MS, Paull E, Rao A, Reynolds S, Saksena G, Sanborn Z, Sander C, Schultz N, Senbabaoglu Y, Shen R, Shmulevich I, Sinha R, Stuart J, Sumer SO, Sun Y, Tasman N, Taylor BS, Voet D, Weinhold N, Weinstein JN, Yang D, Yoshihara K, Zheng S, Zhang W, Zou L, Abel T, Sadeghi S, Cohen ML, Eschbacher J, Hattab EM, Raghunathan A, Schniederjan MJ, Aziz D, Barnett G, Barrett W, Bigner DD, Boice L, Brewer C, Calatozzolo C, Campos B, Carlotti CG, Chan TA, Cuppini L, Curley E, Cuzzubbo S, Devine K, DiMeco F, Duell R, Elder JB, Fehrenbach A, Finocchiaro G, Friedman W, Fulop J, Gardner J, Hermes B, Herold-Mende C, Jungk C, Kendler A, Lehman NL, Lipp E, Liu O, Mandt R, McGraw M, Mclendon R, McPherson C, Neder L, Nguyen P, Noss A, Nunziata R, Ostrom QT, Palmer C, Perin A, Pollo B, Potapov A, Potapova O, Rathmell WK, Rotin D, Scarpace L, Schilero C, Senecal K, Shimmel K, Shurkhay V, Sifri S, Singh R, Sloan AE, Smolenski K, Staugaitis SM, Steele R, Thorne L, Tirapelli DPC, Unterberg A, Vallurupalli M, Wang Y, Warnick R, Williams F, Wolinsky Y, Bell S, Rosenberg M, Stewart C, Huang F, Grimsby JL, Radenbaugh AJ, Zhang J. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med 2015; 372:2481-98. [PMID: 26061751 PMCID: PMC4530011 DOI: 10.1056/nejmoa1402121] [Citation(s) in RCA: 2125] [Impact Index Per Article: 236.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Diffuse low-grade and intermediate-grade gliomas (which together make up the lower-grade gliomas, World Health Organization grades II and III) have highly variable clinical behavior that is not adequately predicted on the basis of histologic class. Some are indolent; others quickly progress to glioblastoma. The uncertainty is compounded by interobserver variability in histologic diagnosis. Mutations in IDH, TP53, and ATRX and codeletion of chromosome arms 1p and 19q (1p/19q codeletion) have been implicated as clinically relevant markers of lower-grade gliomas. METHODS We performed genomewide analyses of 293 lower-grade gliomas from adults, incorporating exome sequence, DNA copy number, DNA methylation, messenger RNA expression, microRNA expression, and targeted protein expression. These data were integrated and tested for correlation with clinical outcomes. RESULTS Unsupervised clustering of mutations and data from RNA, DNA-copy-number, and DNA-methylation platforms uncovered concordant classification of three robust, nonoverlapping, prognostically significant subtypes of lower-grade glioma that were captured more accurately by IDH, 1p/19q, and TP53 status than by histologic class. Patients who had lower-grade gliomas with an IDH mutation and 1p/19q codeletion had the most favorable clinical outcomes. Their gliomas harbored mutations in CIC, FUBP1, NOTCH1, and the TERT promoter. Nearly all lower-grade gliomas with IDH mutations and no 1p/19q codeletion had mutations in TP53 (94%) and ATRX inactivation (86%). The large majority of lower-grade gliomas without an IDH mutation had genomic aberrations and clinical behavior strikingly similar to those found in primary glioblastoma. CONCLUSIONS The integration of genomewide data from multiple platforms delineated three molecular classes of lower-grade gliomas that were more concordant with IDH, 1p/19q, and TP53 status than with histologic class. Lower-grade gliomas with an IDH mutation either had 1p/19q codeletion or carried a TP53 mutation. Most lower-grade gliomas without an IDH mutation were molecularly and clinically similar to glioblastoma. (Funded by the National Institutes of Health.).
Collapse
|
10
|
Ramos AH, Lichtenstein L, Gupta M, Lawrence MS, Pugh TJ, Saksena G, Meyerson M, Getz G. Oncotator: cancer variant annotation tool. Hum Mutat 2015; 36:E2423-9. [PMID: 25703262 DOI: 10.1002/humu.22771] [Citation(s) in RCA: 382] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 02/06/2015] [Indexed: 01/10/2023]
Abstract
Oncotator is a tool for annotating genomic point mutations and short nucleotide insertions/deletions (indels) with variant- and gene-centric information relevant to cancer researchers. This information is drawn from 14 different publicly available resources that have been pooled and indexed, and we provide an extensible framework to add additional data sources. Annotations linked to variants range from basic information, such as gene names and functional classification (e.g. missense), to cancer-specific data from resources such as the Catalogue of Somatic Mutations in Cancer (COSMIC), the Cancer Gene Census, and The Cancer Genome Atlas (TCGA). For local use, Oncotator is freely available as a python module hosted on Github (https://github.com/broadinstitute/oncotator). Furthermore, Oncotator is also available as a web service and web application at http://www.broadinstitute.org/oncotator/.
Collapse
Affiliation(s)
- Alex H Ramos
- Cancer Program, Broad Institute, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Ojesina AI, Murray B, Bjorge L, Woie K, Krakstad C, Lichtenstein L, Pedamallu CS, Taylor-Weiner A, Freeman SS, Cherniack AD, Lawrence MS, Cibulskis K, Carter SL, Walline H, Carey TE, Vintermyr OK, Bertelsen B, Crum CP, Getz G, Meyerson M, Salvesen HB. Abstract 4692: Relationships between somatic genomic alterations, tumor stage and progression-free survival in cervical cancer. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-4692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background:
Cervical cancer is a major public health problem worldwide. We have recently identified novel significantly recurrent somatic mutations in HLA-B, ERBB2 and MAPK1 in cervical squamous cell carcinomas. However, the significance of somatic mutations and copy number alterations for clinical phenotype in cervical cancer is not well understood. This study seeks to identify relationships between somatic genomic alterations, epidemiological exposures, tumor stage (FIGO) and progression-free survival in cervical carcinomas.
Methods:
Cervical tumors were surgically resected or biopsied from 100 Norwegian women with tumor stages I - IV. Patients were subsequently followed for 0-109 months (mean=25 months). Whole exome sequencing (WES) was performed on DNA extracted from tumors and corresponding normal blood. Somatic single nucleotide variants and small insertion/deletions were identified by the MuTect and Indelocator algorithms respectively. The ABSOLUTE algorithm was used to classify mutations as clonal or subclonal. Somatic copy number (CN) data were derived from WES data using the CapSeg algorithm, and significantly recurrent CN alterations were identified by GISTIC2.0 analysis (q<0.25). HPV typing was done by the multiplex fluorescent f-HPV DNA and MassARRAY assays. The log-rank test was used to compare survival curves.
Results:
Non-localized tumors (FIGO stages ≥ II) were associated with focal amplification of the FGFR2 gene on chromosomal cytoband 10q26 (GISTIC q = 0.18531). Indeed, 6 of 8 (75%) tumors with FGFR2 amplification were non-localized, in contrast to 16 of 92 (17%) tumors without FGFR2 amplification (p = 0.001). In addition, patients with somatic ERBB2 mutations and/or amplifications (p = 0.04), somatic TP53 mutations and/or deletions (p = 0.04), or infection with multiple HPV types (p = 0.02) had poorer prognosis (progression-free survival). We also observed a trend for higher frequency of subclonal driver events in patients with poorer survival (p = 0.07).
Conclusion:
We have identified novel relationships between somatic genomic alterations, tumor stage and patient prognosis in cervical cancer. Our data suggest a potential for exploring FGFR2 inhibition in non-localized cervical carcinomas with FGFR2 alterations in a clinical trial context.
Citation Format: Akinyemi I. Ojesina, Bradley Murray, Line Bjorge, Kathrine Woie, Camilla Krakstad, Lee Lichtenstein, Chandra Sekhar Pedamallu, Amaro Taylor-Weiner, Samuel S. Freeman, Andrew D. Cherniack, Michael S. Lawrence, Kristian Cibulskis, Scott L. Carter, Heather Walline, Thomas E. Carey, Olav K. Vintermyr, Bjorn Bertelsen, Christopher P. Crum, Gad Getz, Matthew Meyerson, Helga B. Salvesen. Relationships between somatic genomic alterations, tumor stage and progression-free survival in cervical cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4692. doi:10.1158/1538-7445.AM2014-4692
Collapse
Affiliation(s)
| | | | - Line Bjorge
- 3Haukeland University Hospital/University of Bergen, Bergen, Norway
| | - Kathrine Woie
- 3Haukeland University Hospital/University of Bergen, Bergen, Norway
| | - Camilla Krakstad
- 3Haukeland University Hospital/University of Bergen, Bergen, Norway
| | | | | | | | | | | | | | | | | | | | | | | | - Bjorn Bertelsen
- 3Haukeland University Hospital/University of Bergen, Bergen, Norway
| | | | - Gad Getz
- 6Broad Institute/Massachusetts General Hospital, Cambridge, MA
| | | | | |
Collapse
|
12
|
Ojesina AI, Lichtenstein L, Freeman SS, Pedamallu CS, Imaz-Rosshandler I, Pugh TJ, Cherniack AD, Ambrogio L, Cibulskis K, Bertelsen B, Romero-Cordoba S, Treviño V, Vazquez-Santillan K, Guadarrama AS, Wright AA, Rosenberg MW, Duke F, Kaplan B, Wang R, Nickerson E, Walline HM, Lawrence MS, Stewart C, Carter SL, McKenna A, Rodriguez-Sanchez IP, Espinosa-Castilla M, Woie K, Bjorge L, Wik E, Halle MK, Hoivik EA, Krakstad C, Gabiño NB, Gómez-Macías GS, Valdez-Chapa LD, Garza-Rodríguez ML, Maytorena G, Vazquez J, Rodea C, Cravioto A, Cortes ML, Greulich H, Crum CP, Neuberg DS, Hidalgo-Miranda A, Escareno CR, Akslen LA, Carey TE, Vintermyr OK, Gabriel SB, Barrera-Saldaña HA, Melendez-Zajgla J, Getz G, Salvesen HB, Meyerson M. Landscape of genomic alterations in cervical carcinomas. Nature 2013; 506:371-5. [PMID: 24390348 DOI: 10.1038/nature12881] [Citation(s) in RCA: 599] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 11/13/2013] [Indexed: 12/14/2022]
Abstract
Cervical cancer is responsible for 10-15% of cancer-related deaths in women worldwide. The aetiological role of infection with high-risk human papilloma viruses (HPVs) in cervical carcinomas is well established. Previous studies have also implicated somatic mutations in PIK3CA, PTEN, TP53, STK11 and KRAS as well as several copy-number alterations in the pathogenesis of cervical carcinomas. Here we report whole-exome sequencing analysis of 115 cervical carcinoma-normal paired samples, transcriptome sequencing of 79 cases and whole-genome sequencing of 14 tumour-normal pairs. Previously unknown somatic mutations in 79 primary squamous cell carcinomas include recurrent E322K substitutions in the MAPK1 gene (8%), inactivating mutations in the HLA-B gene (9%), and mutations in EP300 (16%), FBXW7 (15%), NFE2L2 (4%), TP53 (5%) and ERBB2 (6%). We also observe somatic ELF3 (13%) and CBFB (8%) mutations in 24 adenocarcinomas. Squamous cell carcinomas have higher frequencies of somatic nucleotide substitutions occurring at cytosines preceded by thymines (Tp*C sites) than adenocarcinomas. Gene expression levels at HPV integration sites were statistically significantly higher in tumours with HPV integration compared with expression of the same genes in tumours without viral integration at the same site. These data demonstrate several recurrent genomic alterations in cervical carcinomas that suggest new strategies to combat this disease.
Collapse
Affiliation(s)
- Akinyemi I Ojesina
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA [3]
| | - Lee Lichtenstein
- 1] The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA [2]
| | - Samuel S Freeman
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Chandra Sekhar Pedamallu
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | | | - Trevor J Pugh
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Lauren Ambrogio
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Kristian Cibulskis
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Bjørn Bertelsen
- Department of Pathology, Haukeland University Hospital, N5021 Bergen, Norway
| | | | | | | | | | - Alexi A Wright
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Mara W Rosenberg
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Fujiko Duke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Bethany Kaplan
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Rui Wang
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Elizabeth Nickerson
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Heather M Walline
- Cancer Biology Program, Program in the Biomedical Sciences, Rackham Graduate School, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Michael S Lawrence
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Chip Stewart
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Scott L Carter
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Aaron McKenna
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Iram P Rodriguez-Sanchez
- Facultad de Medicina y Hospital Universitario 'Dr. José Eluterio González' de la Universidad Autónoma de Nuevo León, Monterrey, Nuevo León 64460, México
| | | | - Kathrine Woie
- Department of Obstetrics and Gynecology, Haukeland University Hospital, N5021 Bergen, Norway
| | - Line Bjorge
- 1] Department of Obstetrics and Gynecology, Haukeland University Hospital, N5021 Bergen, Norway [2] Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, N5020 Bergen, Norway
| | - Elisabeth Wik
- 1] Department of Obstetrics and Gynecology, Haukeland University Hospital, N5021 Bergen, Norway [2] Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, N5020 Bergen, Norway
| | - Mari K Halle
- 1] Department of Obstetrics and Gynecology, Haukeland University Hospital, N5021 Bergen, Norway [2] Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, N5020 Bergen, Norway
| | - Erling A Hoivik
- 1] Department of Obstetrics and Gynecology, Haukeland University Hospital, N5021 Bergen, Norway [2] Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, N5020 Bergen, Norway
| | - Camilla Krakstad
- 1] Department of Obstetrics and Gynecology, Haukeland University Hospital, N5021 Bergen, Norway [2] Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, N5020 Bergen, Norway
| | | | - Gabriela Sofia Gómez-Macías
- Facultad de Medicina y Hospital Universitario 'Dr. José Eluterio González' de la Universidad Autónoma de Nuevo León, Monterrey, Nuevo León 64460, México
| | - Lezmes D Valdez-Chapa
- Facultad de Medicina y Hospital Universitario 'Dr. José Eluterio González' de la Universidad Autónoma de Nuevo León, Monterrey, Nuevo León 64460, México
| | - María Lourdes Garza-Rodríguez
- Facultad de Medicina y Hospital Universitario 'Dr. José Eluterio González' de la Universidad Autónoma de Nuevo León, Monterrey, Nuevo León 64460, México
| | | | - Jorge Vazquez
- Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico
| | - Carlos Rodea
- Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico
| | - Adrian Cravioto
- Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico
| | - Maria L Cortes
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Heidi Greulich
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA [3] Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Christopher P Crum
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Donna S Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | | | - Claudia Rangel Escareno
- 1] Instituto Nacional de Medicina Genomica, Mexico City 14610, Mexico [2] Claremont Graduate University, Claremont, California 91711, USA
| | - Lars A Akslen
- 1] Department of Pathology, Haukeland University Hospital, N5021 Bergen, Norway [2] Centre for Cancer Biomarkers, Department of Clinical Medicine, University of Bergen, N5020 Bergen, Norway
| | - Thomas E Carey
- Head and Neck Oncology Program and Department of Otolaryngology, University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan 38109, USA
| | - Olav K Vintermyr
- 1] Department of Pathology, Haukeland University Hospital, N5021 Bergen, Norway [2] Centre for Cancer Biomarkers, Department of Clinical Medicine, University of Bergen, N5020 Bergen, Norway
| | - Stacey B Gabriel
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Hugo A Barrera-Saldaña
- Facultad de Medicina y Hospital Universitario 'Dr. José Eluterio González' de la Universidad Autónoma de Nuevo León, Monterrey, Nuevo León 64460, México
| | | | - Gad Getz
- 1] The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA [2] Massachusetts General Hospital Cancer Center and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Helga B Salvesen
- 1] Department of Obstetrics and Gynecology, Haukeland University Hospital, N5021 Bergen, Norway [2] Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, N5020 Bergen, Norway [3]
| | - Matthew Meyerson
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA [3] Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA [4]
| |
Collapse
|
13
|
Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortés ML, Auclair D, Saksena G, Voet D, Noble M, DiCara D, Lin P, Lichtenstein L, Heiman DI, Fennell T, Imielinski M, Hernandez B, Hodis E, Baca S, Dulak AM, Lohr J, Landau DA, Wu CJ, Melendez-Zajgla J, Hidalgo-Miranda A, Koren A, McCarroll SA, Mora J, Crompton B, Onofrio R, Parkin M, Winckler W, Ardlie K, Gabriel SB, Roberts CWM, Biegel JA, Stegmaier K, Bass AJ, Garraway LA, Meyerson M, Golub TR, Gordenin DA, Sunyaev S, Lander ES, Getz G. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 2013. [PMID: 23770567 DOI: 10.1038/nature12213.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Major international projects are underway that are aimed at creating a comprehensive catalogue of all the genes responsible for the initiation and progression of cancer. These studies involve the sequencing of matched tumour-normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false-positive findings that overshadow true driver events. We show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumour-normal pairs and discover extraordinary variation in mutation frequency and spectrum within cancer types, which sheds light on mutational processes and disease aetiology, and in mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and enable the identification of genes truly associated with cancer.
Collapse
Affiliation(s)
| | - Petar Stojanov
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Paz Polak
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Gregory V Kryukov
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Brigham and Women's Hospital, Boston, MA, 02115, USA
| | | | | | - Scott L Carter
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Chip Stewart
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Craig H Mermel
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Steven A Roberts
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC 27709, USA
| | - Adam Kiezun
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Peter S Hammerman
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Aaron McKenna
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Genome Sciences, University of Washington, Seattle, WA 98195
| | - Yotam Drier
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Massachusetts General Hospital, Boston, MA, 02114, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.,Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Lihua Zou
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Alex H Ramos
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Trevor J Pugh
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Nicolas Stransky
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Elena Helman
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jaegil Kim
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Carrie Sougnez
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Lauren Ambrogio
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | | | - Erica Shefler
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Maria L Cortés
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Daniel Auclair
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Gordon Saksena
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Douglas Voet
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Michael Noble
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Daniel DiCara
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Pei Lin
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Lee Lichtenstein
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - David I Heiman
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Timothy Fennell
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Marcin Imielinski
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Bryan Hernandez
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Eran Hodis
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sylvan Baca
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Austin M Dulak
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jens Lohr
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Dan-Avi Landau
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Yale Cancer Center, Department of Hematology, New Haven, CT
| | - Catherine J Wu
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | | | | | - Amnon Koren
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Steven A McCarroll
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Jaume Mora
- Department of Pediatric Oncology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Brian Crompton
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Boston Children's Hospital, Boston, MA, 02115, USA
| | - Robert Onofrio
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Melissa Parkin
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Wendy Winckler
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Kristin Ardlie
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Stacey B Gabriel
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Charles W M Roberts
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Boston Children's Hospital, Boston, MA, 02115, USA
| | | | - Kimberly Stegmaier
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Boston Children's Hospital, Boston, MA, 02115, USA
| | - Adam J Bass
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Levi A Garraway
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Matthew Meyerson
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Todd R Golub
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Dmitry A Gordenin
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC 27709, USA
| | - Shamil Sunyaev
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Eric S Lander
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Massachusetts General Hospital, Boston, MA, 02114, USA
| |
Collapse
|
14
|
Stojanov P, Carter SL, Rosshandler II, Sivachenko A, Salido Guadarrama A, Vazquez K, Cordoba SR, Cibulskis K, Sougnez C, Voet D, Saksena G, Lichtenstein L, Zou L, Frazer S, Stewart C, Beroukhim R, Meyerson M, Lawrence MS, Getz G. Abstract 5135: Analysis of formalin-fixed paraffin-embedded (FFPE) samples. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-5135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The availability of large numbers of formalin-fixed, paraffin-embedded (FFPE) tumor DNA samples, together with accurate and specific clinical annotations, can be a great resource for in-depth analysis of correlations of somatic and germline DNA alterations with clinical outcome. However, the effects of this tissue preservation technique on next-generation DNA sequencing technologies and downstream analyses are still being investigated. Furthermore, usually the archives of such FFPE samples do not include matched normal tissue, which complicates the process of identifying somatic alterations. We are in the process of analyzing lung adenocarcinoma, colorectal and prostate patient datasets, which contain both an FFPE and a fresh-frozen tumor together with a matched blood normal sample. The availability of both a frozen and an FFPE tumor sample enables us to compare the detected somatic point mutations and indels, taking into account the fact that these pairs are produced from different aliquots of DNA. This analysis includes calculating the power to detect variants in the FFPE sample given that they have been observed in the fresh frozen tumor, as well as the validation rate of clonal SNVs between the two samples. We are also developing a method for classification of SNVs as germline or somatic without a paired normal sample by taking advantage of the fact that most tumor samples contain a substantial fraction of normal cells. Because stromal contamination has a different effect on the allelic fraction of somatic vs. germline SNVs, we can apply algorithms to estimate tumor purity and absolute somatic copy numbers in order to distinguish the two types of events. We present preliminary results from these analyses.
Citation Format: Petar Stojanov, Scott L. Carter, Ivan Imaz Rosshandler, Andrey Sivachenko, Alberto Salido Guadarrama, Karla Vazquez, Sandra Romero Cordoba, Kristian Cibulskis, Carrie Sougnez, Douglas Voet, Gordon Saksena, Lee Lichtenstein, Lihua Zou, Scott Frazer, Chip Stewart, Rameen Beroukhim, Matthew Meyerson, Michael S. Lawrence, Gad Getz. Analysis of formalin-fixed paraffin-embedded (FFPE) samples. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5135. doi:10.1158/1538-7445.AM2013-5135
Collapse
|
15
|
Ojesina AI, Lichtenstein L, Ambrogio L, Cibulskis K, Freeman S, Pedamallu CS, Bertelsen B, Imaz I, Vazquez K, Salido Guadarrama A, Treviño V, Romero-Cordoba S, Duke F, Kaplan B, Rodriguez I, Espinosa Castilla M, Woie K, Bjorge L, Wik E, Halle MK, Høivik E, Krakstad C, Gómez Macías G, de Lourdes Garza Rodríguez M, Vazquez J, Rodea C, Cravioto A, Cortes ML, Greulich H, Crum CP, Akslen L, Barrera Saldaña H, Melendez-Zajgla J, Getz G, Salvesen HB, Meyerson ML. Abstract 4604: Landscape of human and viral genomic alterations in cervical carcinomas. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-4604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Cervical cancer is a major public health problem worldwide. The etiological role of human papilloma virus (HPV) infections in cervical cancer is well established. However, HPV infection is insufficient to account for the development of cervical cancers because only 2 % of women infected with HPV eventually develop invasive carcinomas. We have therefore initiated a large scale sequencing effort to provide comprehensive data on the global landscape of genomic aberrations and HPV variants that contribute to cervical cancer. Methods: We have carried out comprehensive whole exome sequencing analyses on 120 tumor-normal paired samples from Mexico and Norway. We also carried out transcriptome and whole genome sequencing analyses on a subset of the patients (81 and 14 individuals respectively). Results: The aggregate mutation rate across the dataset was 3.8 per megabase (Mb), with the most common mutations being C to T/G in the Tp*C dinucleotide context, at a rate of 15 mutations per Mb. In all, 18,037 mutations were found across the entire dataset, including 11,536 missense, 984 nonsense, 4691 silent, 231 splice site, 32 translation start site mutations, as well 443 deletions and 142 insertions. MutSig analyses to identify genes that were mutated at statistically significant frequencies across our dataset revealed 11 genes to be recurrently mutated with a false discovery rate of q<0.1 after correction for multiple hypothesis testing (and RNASeq-based evidence of robust gene expression). The most significantly mutated genes encode for members of the PIK3CA/PTEN and RAS/RAF/MAPK signaling pathways, as well as the major histocompatibility complex (MHC). We have also uncovered novel patterns of HPV transcript abundance and sites of recurrent HPV integration in cell cycle related genes. In addition, our whole genome sequencing data suggests that HPV-negative p53-mutant tumors harbor high frequencies of genomic rearrangements. Conclusion: The comprehensive catalogue of genomic alterations provided by this project reveals potential novel therapeutic targets in cervical carcinomas. Our data also sets the stage for improving diagnostic and preventive strategies, especially in resource-limited settings with the highest incidence of cervical cancer.
Citation Format: Akinyemi I. Ojesina, Lee Lichtenstein, Lauren Ambrogio, Kristian Cibulskis, Samuel Freeman, Chandra Sekhar Pedamallu, Bjørn Bertelsen, Ivan Imaz, Karla Vazquez, Alberto Salido Guadarrama, Victor Treviño, Sandra Romero-Cordoba, Fujiko Duke, Bethany Kaplan, Iram Rodriguez, Magali Espinosa Castilla, Katherine Woie, Line Bjorge, Elisabeth Wik, Mari K. Halle, Erling Høivik, Camilla Krakstad, Gabriela Gómez Macías, María de Lourdes Garza Rodríguez, Jorge Vazquez, Carlos Rodea, Adrian Cravioto, Maria L. Cortes, Heidi Greulich, Christopher P. Crum, Lars Akslen, Hugo Barrera Saldaña, Jorge Melendez-Zajgla, Gad Getz, Helga B. Salvesen, Matthew L. Meyerson. Landscape of human and viral genomic alterations in cervical carcinomas. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4604. doi:10.1158/1538-7445.AM2013-4604
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Ivan Imaz
- 4Instituto Nacional de Medicina Genomica, Mexico City, Mexico
| | - Karla Vazquez
- 4Instituto Nacional de Medicina Genomica, Mexico City, Mexico
| | | | - Victor Treviño
- 5Instituto Tecnológico y de Estudios Superiores, Monterrey, Mexico
| | | | | | | | - Iram Rodriguez
- 7Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | | | | | - Line Bjorge
- 3Haukeland University Hospital, Bergen, Norway
| | | | | | | | | | | | | | | | - Carlos Rodea
- 9Centro Medico Nacional SXXI, Mexico City, Mexico
| | | | | | - Heidi Greulich
- 1Dana-Farber Cancer Institute/Broad Institute, Cambridge, MA
| | | | - Lars Akslen
- 3Haukeland University Hospital, Bergen, Norway
| | | | | | | | | | | |
Collapse
|
16
|
Costello M, Pugh TJ, Fennell TJ, Stewart C, Lichtenstein L, Meldrim JC, Fostel JL, Friedrich DC, Perrin D, Dionne D, Kim S, Gabriel SB, Lander ES, Fisher S, Getz G. Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation. Nucleic Acids Res 2013; 41:e67. [PMID: 23303777 PMCID: PMC3616734 DOI: 10.1093/nar/gks1443] [Citation(s) in RCA: 330] [Impact Index Per Article: 30.0] [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] [Indexed: 11/20/2022] Open
Abstract
As researchers begin probing deep coverage sequencing data for increasingly rare mutations and subclonal events, the fidelity of next generation sequencing (NGS) laboratory methods will become increasingly critical. Although error rates for sequencing and polymerase chain reaction (PCR) are well documented, the effects that DNA extraction and other library preparation steps could have on downstream sequence integrity have not been thoroughly evaluated. Here, we describe the discovery of novel C > A/G > T transversion artifacts found at low allelic fractions in targeted capture data. Characteristics such as sequencer read orientation and presence in both tumor and normal samples strongly indicated a non-biological mechanism. We identified the source as oxidation of DNA during acoustic shearing in samples containing reactive contaminants from the extraction process. We show generation of 8-oxoguanine (8-oxoG) lesions during DNA shearing, present analysis tools to detect oxidation in sequencing data and suggest methods to reduce DNA oxidation through the introduction of antioxidants. Further, informatics methods are presented to confidently filter these artifacts from sequencing data sets. Though only seen in a low percentage of reads in affected samples, such artifacts could have profoundly deleterious effects on the ability to confidently call rare mutations, and eliminating other possible sources of artifacts should become a priority for the research community.
Collapse
Affiliation(s)
- Maura Costello
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Hodis E, Watson I, Theurillat JP, Zou L, Place C, Nickerson E, Auclair D, Cibulskis K, Sivachenko A, Kryukov G, Stransky N, Ramos AH, Voet D, Lawrence MS, Stojanov P, Saksena G, McKenna A, Carter SL, Pugh T, Noble M, Lin P, Lichtenstein L, Zupko R, Sougnez C, Guiducci C, Onofrio RC, Ambrogio L, Fennell T, Chong K, Winckler W, Ardlie K, Lander ES, Golub T, Meyerson M, Gabriel SB, Getz G, Wagner S, Schadendorf D, Hoon DSB, Chin L, Garraway LA. Abstract 5056: A glimpse into the somatic mutation landscape of melanoma through exome sequencing of 121 tumor-normal pairs. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-5056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Melanoma is an aggressive skin cancer of melanocytic origin characterized by high metastatic potential and mutation rate. Affording a survey of the wide breadth of genomic lesions found in melanoma, we present here an analysis of the somatic mutations discovered in the sequenced exomes of 121 melanoma tumor-normal pairs. We identify frequent genomic alterations both in genes previously implicated in melanoma (BRAF, NRAS, TP53, CDKN2A, PTEN) as well as in several genes whose role in melanoma tumorigenesis has not yet been established and thus are of particular interest. To do so we implement a novel method to increase the identification of genes that are significantly recurrently mutated in melanoma in the setting of its exceptionally high mutation rate. A preponderance of C>T transitions (∼85%) in the observed mutational profile reflects a history of DNA damage due to UV radiation, though the majority of somatic mutations in known melanoma genes are not C>T events. Our study broadens understanding of the genomic lesions involved in melanoma tumorigenesis, and we expect our analysis approach to inform future genomic studies of cancer lineages with similarly high mutation rates.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5056. doi:1538-7445.AM2012-5056
Collapse
Affiliation(s)
- Eran Hodis
- 1The Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | - Lihua Zou
- 1The Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | | | | | | | | - Alex H. Ramos
- 1The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Douglas Voet
- 1The Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | - Aaron McKenna
- 1The Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Trevor Pugh
- 1The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Michael Noble
- 1The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Pei Lin
- 1The Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Robert Zupko
- 1The Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | | | | | | | | | | | | - Todd Golub
- 1The Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | - Gad Getz
- 1The Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | | | |
Collapse
|
18
|
Löffler D, Uhlrich JJ, Baron M, Yang B, Yu X, Lichtenstein L, Heinke L, Büchner C, Heyde M, Shaikhutdinov S, Freund HJ, Włodarczyk R, Sierka M, Sauer J. Growth and structure of crystalline silica sheet on Ru(0001). Phys Rev Lett 2010; 105:146104. [PMID: 21230849 DOI: 10.1103/physrevlett.105.146104] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 08/23/2010] [Indexed: 05/30/2023]
Abstract
Thin SiO₂ films were grown on a Ru(0001) single crystal and studied by photoelectron spectroscopy, infrared spectroscopy and scanning probe microscopy. The experimental results in combination with density functional theory calculations provide compelling evidence for the formation of crystalline, double-layer sheet silica weakly bound to a metal substrate.
Collapse
Affiliation(s)
- D Löffler
- Department of Chemical Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Girousse A, Tavernier G, Tiraby C, Lichtenstein L, Iacovoni JS, Mairal A, Villarroya F, Langin D. Transcription of the human uncoupling protein 3 gene is governed by a complex interplay between the promoter and intronic sequences. Diabetologia 2009; 52:1638-46. [PMID: 19468707 DOI: 10.1007/s00125-009-1385-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Accepted: 04/17/2009] [Indexed: 11/24/2022]
Abstract
AIMS/HYPOTHESIS Uncoupling protein (UCP) 3 is an inner mitochondrial membrane transporter mainly produced in skeletal muscle in humans. UCP3 plays a role in fatty acid metabolism and energy homeostasis and modulates insulin sensitivity. In humans, UCP3 content is higher in fast-twitch glycolytic muscle than in slow-twitch oxidative muscle and is dysregulated in type 2 diabetes. Here, we studied the molecular mechanisms determining human UCP3 levels in skeletal muscle and their regulation by fasting in transgenic mice. METHODS We produced a series of transgenic lines with constructs bearing different putative regulatory regions of the human UCP3 gene, including promoter and intron sequences. UCP3 mRNA and reporter gene expression and activity were measured in different skeletal muscles and tissues. RESULTS The profile of expression and the response to fasting and thyroid hormone of human UCP3 mRNA in transgenic mice with 16 kb of the human UCP3 gene were similar to that of the endogenous human gene. Various parts of the UCP3 promoter did not confer expression in transgenic lines. Inclusion of intron 1 resulted in an expression profile in skeletal muscle that was identical to that of human UCP3 mRNA. Further dissection of intron 1 revealed that distinct regions were involved in skeletal muscle expression, distribution among fibre types and response to fasting. CONCLUSIONS/INTERPRETATION The control of human UCP3 transcription in skeletal muscle is not solely conferred by the promoter, but depends on several cis-acting elements in intron 1, suggesting a complex interplay between the promoter and intronic sequences.
Collapse
Affiliation(s)
- A Girousse
- Inserm U858, Institut de Médecine Moléculaire de Rangueil, Laboratoire de recherches sur les obésités, Equipe 4, 31432 Toulouse Cedex 4, France
| | | | | | | | | | | | | | | |
Collapse
|
20
|
Abstract
Virtual environments (VEs) allow safe, repeatable, and controlled evaluations of obstacle avoidance and navigation performance of people with visual impairments using visual aids. Proper simulation of mobility in a VE requires an interface, which allows subjects to set their walking pace. Using conventional treadmills, the subject can change their walking speed by pushing the tread with their feet, while leveraging handrails or ropes (self-propelled mode). We developed a feedback-controlled locomotion interface that allows the VE workstation to control the speed of the treadmill, based on the position of the user. The position and speed information is also used to implement automated safety measures, so that the treadmill can be halted in case of erratic behavior. We compared the feedback-controlled mode to the self-propelled mode by using speed-matching tasks (follow a moving object or match the speed of an independently moving scene) to measure the efficacy of each mode in maintaining constant subject position, subject control of the treadmill, and subject pulse rates. Additionally, we measured the perception of speed in the VE on each mode. The feedback-controlled mode required less physical exertion than self-propelled. The average position of subjects on the feedback-controlled treadmill was always within a centimeter of the desired position. There was a smaller standard deviation in subject position when using the self-propelled mode than when using the feedback-controlled mode, but the difference averaged less than six centimeters across all subjects walking at a constant speed. Although all subjects underestimated the speed of an independently moving scene at higher speeds, their estimates were more accurate when using the feedback-controlled treadmill than the self-propelled.
Collapse
|
21
|
|
22
|
Baroody FM, Ford S, Proud D, Kagey-Sobotka A, Lichtenstein L, Naclerio RM. Relationship between histamine and physiological changes during the early response to nasal antigen provocation. J Appl Physiol (1985) 1999; 86:659-68. [PMID: 9931205 DOI: 10.1152/jappl.1999.86.2.659] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
To investigate the temporal relationships of mediator release and physiological changes during the early response to allergen, we challenged allergic individuals intranasally with antigen and followed their responses. This was done by using small filter paper disks to challenge one nostril and collect secretions from both the challenged and the contralateral nostril, thus enabling us to evaluate the nasonasal reflex. There was a significant increase in sneezing after allergen challenge that peaked within 2 min and returned to baseline. The weights of nasal secretions as well as nasal symptoms increased immediately and remained significantly elevated for 20 min in both nostrils. Nasal airway resistance increased slowly, reaching its peak at approximately 6 min after challenge on the ipsilateral side, but it did not change on the contralateral side. Histamine levels peaked 30 s after removal of the allergen disk on the side of challenge, whereas albumin levels peaked after those of histamine. Lactoferrin paralleled the increase in secretion weights and occurred in both nostrils. Increasing doses of antigen produced dose-dependent increases in all parameters, whereas control challenges produced no response. These studies describe a human model for the evaluation of the allergic response that is capable of simultaneously measuring mediator release and the physiological response, including the nasonasal reflex. This model should prove useful in studying the mechanism of allergic rhinitis in humans.
Collapse
Affiliation(s)
- F M Baroody
- Section of Otolaryngology-Head and Neck Surgery, Pritzker School of Medicine, University of Chicago, Chicago, Illinois 60637, USA.
| | | | | | | | | | | |
Collapse
|
23
|
Silber G, Proud D, Warner J, Naclerio R, Kagey-Sobotka A, Lichtenstein L, Eggleston P. In vivo release of inflammatory mediators by hyperosmolar solutions. Am Rev Respir Dis 1988; 137:606-12. [PMID: 2449834 DOI: 10.1164/ajrccm/137.3.606] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Hyperosmolar environments induce histamine release from mast cells and basophils in vitro. To assess whether the same stimulus induces mediator release in vivo, 15 healthy human volunteers underwent nasal challenges with instilled solutions of differing osmolalities: lactated Ringer's solution (257 +/- 3 mOsm/kg), isosmolar mannitol (277 +/- 6 mOsm/kg), and hyperosmolar mannitol (869 +/- 8 mOsm/kg). The effect of these challenges on the volume, osmolality, and inflammatory mediator content of subsequent 5-ml isosmolar lavages was determined. The volumes of lavages returned after hyperosmolar challenges were significantly greater than those after isosmolar challenges (5.5 +/- 0.2 ml versus 4.2 +/- 0.1 ml; p less than 0.01) and these lavage solutions had higher osmolalities. Even when corrected for increased volumes, the lavages after hyperosmolar challenges contained significantly higher quantities of inflammatory mediators such as histamine (29.0 versus 10.1 ng; p less than 0.01), TAME-esterase activity (32.7 versus 11.1 cpm x 10(-3); p less than 0.01), and immunoreactive leukotrienes (9.9 versus 3.4 ng; p less than 0.01). The changes in mediators were dose dependent in that incremental increase in challenge osmolality were associated with incremental increases in histamine release. Therefore, when exposed to hyperosmolar stimuli in vivo, the nasal respiratory airway releases inflammatory mediators and fluid rapidly shifts into the airway lumen. It has been suggested that the mediator release observed on breathing cold and dry air is due to increased osmolality of airway secretions; the present data confirm that osmotic variations at the airway surface can provide an adequate stimulus for cell activation.
Collapse
Affiliation(s)
- G Silber
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | | | | | | | | | | | | |
Collapse
|
24
|
Togias A, Proud D, Kagey-Sobotka A, Norman P, Lichtenstein L, Naclerio R. The effect of a topical tricyclic antihistamine on the response of the nasal mucosa to challenge with cold, dry air and histamine. J Allergy Clin Immunol 1987; 79:599-604. [PMID: 3558996 DOI: 10.1016/s0091-6749(87)80155-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We have previously demonstrated that azatadine, a tricyclic antihistamine, known also to inhibit mediator release from mast cells and basophils in vitro, inhibits the early release of histamine and other mediators after nasal challenge with antigen. In this article, we studied the effect of azatadine on preventing the release of histamine after nasal challenge with cold, dry air (CDA) and its effect on antagonizing nasal challenge with histamine. With histamine challenge, azatadine inhibited symptoms (sneezing, nasal congestion, and rhinorrhea) and the increase in the level of albumin in nasal secretions (p less than 0.01 all). With challenge with CDA, the drug had no effect on either symptoms or histamine and N-tosyl-L-arginine methyl ester-esterase release. Although the patterns of mediator release after CDA and after the early reaction to antigen are similar, the pharmacologic control differs, suggesting different mechanisms of induction of histamine release from mast cells.
Collapse
|
25
|
Naclerio R, Proud D, Peters S, Sobotka AK, Lichtenstein L, Norman P. The role of inflammatory mediators in allergic rhinitis. Ear Nose Throat J 1986; 65:206-12. [PMID: 3459645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
|
26
|
Rosenberg G, Adkinson N, Kagey-Sobotka A, Lichtenstein L, Mardiney M, Norman P, Van Metre T. Reactions on ragweed immunotherapy. J Allergy Clin Immunol 1982. [DOI: 10.1016/s0091-6749(62)80372-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
27
|
|
28
|
King T, Sobotka A, Alagon A, Kochoumian L, Lichtenstein L. Corrections - Protein Allergens of White-Faced Hornet, and Yellow Hornet, and Yellow Jacket Venom. Biochemistry 1979. [DOI: 10.1021/bi00586a607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
29
|
Adams GK, Lichtenstein L. In vitro studies of antigen-induced bronchospasm: effect of antihistamine and SRS-A antagonist on response of sensitized guinea pig and human airways to antigen. J Immunol 1979; 122:555-62. [PMID: 84027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Exposure of sensitized guinea pig tracheal rings or human bronchial strips to specific antigen in vitro resulted in a rapidly developing, prolonged contraction that was resistant to washing. Treatment of the tissue with diphenhydramine, a histamine H1 antagonist, before antigen delayed the onset and decreased the amplitude of the initial phase of the contraction but did not reduce the duration. Diphenhydramine treatment after development of the contraction did not relax the airway tissue. Antigen-induced histamine release from guinea pig trachea and from human bronchus was complete within the initial 15% of the duration of the contraction. Treatment of sensitized airway tissue with FPL 55712, a SRS-A antagonist, before antigen selectively inhibited the prolonged phase of the response. FPL 55712 administration after the development of antigen-induced contraction resulted in relaxation. These data suggest that both histamine and SRS-A are involved in the response of sensitized guinea pig and human airway tissue to antigen, with histamine mediating the early phase of the contraction and SRS-A primarily mediating the protracted phase.
Collapse
|
30
|
|
31
|
Glynn JJ, Lichtenstein L. Osteoid-osteoma with multicentric nidus. A report of two cases. J Bone Joint Surg Am 1973; 55:855-8. [PMID: 4283763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
32
|
|
33
|
Gordan GS, Lichtenstein L, Roof BS. Metabolic bone diseases associated with malignancy. Isr J Med Sci 1971; 7:499-501. [PMID: 5567531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
34
|
Lichtenstein L, Jaffe HL. Ewing's Sarcoma of Bone. Am J Pathol 1947; 23:43-77. [PMID: 19970919 PMCID: PMC1934208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
|
35
|
Lichtenstein L, Fox LJ. Necrotizing Arterial Lesions Resembling Those of Periarteritis Nodosa and Focal Visceral Necrosis Following Administration of Sulfathiazole: Report of a Case. Am J Pathol 1946; 22:665-677. [PMID: 19970886 PMCID: PMC1934238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
|
36
|
Lichtenstein L, Jaffe HL. Chondrosarcoma of Bone. Am J Pathol 1943; 19:553-589. [PMID: 19970709 PMCID: PMC2033092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
|
37
|
Jaffe HL, Lichtenstein L. Benign Chondroblastoma of Bone: A Reinterpretation of the So-Called Calcifying or Chondromatous Giant Cell Tumor. Am J Pathol 1942; 18:969-991. [PMID: 19970672 PMCID: PMC2032980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
|
38
|
Jaffe HL, Lichtenstein L. Non-osteogenic fibroma of bone. Am J Pathol 1942; 18:205-221. [PMID: 19970624 PMCID: PMC2032933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
|
39
|
Lichtenstein L. A Quick Treatment of Scabies. West J Med 1942. [DOI: 10.1136/bmj.1.4226.24-b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
40
|
Lichtenstein L, Jeffe HL. Eosinophilic granuloma of bone: With report of a case. Am J Pathol 1940; 16:595-604.3. [PMID: 19970524 PMCID: PMC1965122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
|
41
|
Lichtenstein L. Pathological changes following therapeutic hyperthermia: Report of a Case. Am J Pathol 1939; 15:363-376.5. [PMID: 19970454 PMCID: PMC1965003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
|
42
|
|
43
|
D'Aunoy R, von Haam E, Lichtenstein L. The Virus of Lymphogranuloma Inguinale. Am J Pathol 1935; 11:737-752.7. [PMID: 19970230 PMCID: PMC1910985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
|
44
|
Lichtenstein L. Papillary Cystadenocarcinoma of Pancreas: Case Report, with Notes on Classification of Malignant Cystic Tumors of Pancreas. ACTA ACUST UNITED AC 1934. [DOI: 10.1158/ajc.1934.542] [Citation(s) in RCA: 43] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
45
|
|
46
|
|