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Shih AJ, Jun T, Skol AD, Bao R, Huang L, Vora S, McNerney ME, Hungate EA, Le Beau MM, Larson RA, Elliott A, Lu HM, Huether R, Hernandez F, Stölzel F, Allan JM, Onel K. Inherited cancer predisposing mutations in patients with therapy-related myeloid neoplasms. Br J Haematol 2023; 200:489-493. [PMID: 36349721 DOI: 10.1111/bjh.18543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022]
Abstract
Some patients with therapy-related myeloid neoplasms (t-MN) may have unsuspected inherited cancer predisposition syndrome (CPS). We propose a set of clinical criteria to identify t-MN patients with high risk of CPS (HR-CPS). Among 225 t-MN patients with an antecedent non-myeloid malignancy, our clinical criteria identified 52 (23%) HR-CPS patients. Germline whole-exome sequencing identified pathogenic or likely pathogenic variants in 10 of 27 HR-CPS patients compared to 0 of 9 low-risk CPS patients (37% vs. 0%, p = 0.04). These simple clinical criteria identify t-MN patients most likely to benefit from genetic testing for inherited CPS.
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Affiliation(s)
- Andrew J Shih
- The Feinstein Institute for Medical Research, Northwell Health, Manhasset, New York, USA
| | - Tomi Jun
- Sema4, Stamford, Connecticut, USA
| | - Andrew D Skol
- Department of Pediatrics, The University of Chicago, Chicago, Illinois, USA
| | - Riyue Bao
- Department of Medicine, The University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Lei Huang
- Center for Research Informatics, The University of Chicago, Chicago, Illinois, USA
| | - Sapana Vora
- Department of Pediatrics, The University of Chicago, Chicago, Illinois, USA
| | - Megan E McNerney
- Department of Pediatrics, The University of Chicago, Chicago, Illinois, USA.,Department of Pathology, The University of Chicago, Chicago, Illinois, USA
| | - Eric A Hungate
- Department of Pediatrics, The University of Chicago, Chicago, Illinois, USA
| | - Michelle M Le Beau
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Richard A Larson
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | | | | | | | | | - Friedrich Stölzel
- Department of Internal Medicine I, University Hospital Carl Gustav Carus Dresden, Dresden University of Technology, Dresden, Germany
| | - James M Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Kenan Onel
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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2
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De La Vega F, Trigg L, Gaastra K, Irvine S, Selkov G, Yang Y, Choi K, Huether R. eP107: Accurate genotyping of UGT1A1 dinucleotide repeat polymorphism from targeted NGS data for the assessment of irinotecan chemotherapy adverse events. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.143] [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: 11/17/2022] Open
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3
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Fortuno C, Lee K, Olivier M, Pesaran T, Mai PL, de Andrade KC, Attardi LD, Crowley S, Evans DG, Feng BJ, Major Foreman AK, Frone MN, Huether R, James PA, McGoldrick K, Mester J, Seifert BA, Slavin TP, Witkowski L, Zhang L, Plon SE, Spurdle AB, Savage SA. Specifications of the ACMG/AMP variant interpretation guidelines for germline TP53 variants. Hum Mutat 2021; 42:223-236. [PMID: 33300245 PMCID: PMC8374922 DOI: 10.1002/humu.24152] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [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: 04/01/2020] [Revised: 11/05/2020] [Accepted: 12/07/2020] [Indexed: 12/28/2022]
Abstract
Germline pathogenic variants in TP53 are associated with Li-Fraumeni syndrome, a cancer predisposition disorder inherited in an autosomal dominant pattern associated with a high risk of malignancy, including early-onset breast cancers, sarcomas, adrenocortical carcinomas, and brain tumors. Intense cancer surveillance for individuals with TP53 germline pathogenic variants is associated with reduced cancer-related mortality. Accurate and consistent classification of germline variants across clinical and research laboratories is important to ensure appropriate cancer surveillance recommendations. Here, we describe the work performed by the Clinical Genome Resource TP53 Variant Curation Expert Panel (ClinGen TP53 VCEP) focused on specifying the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines for germline variant classification to the TP53 gene. Specifications were developed for 20 ACMG/AMP criteria, while nine were deemed not applicable. The original strength level for the 10 criteria was also adjusted due to current evidence. Use of TP53-specific guidelines and sharing of clinical data among experts and clinical laboratories led to a decrease in variants of uncertain significance from 28% to 12% compared with the original guidelines. The ClinGen TP53 VCEP recommends the use of these TP53-specific ACMG/AMP guidelines as the standard strategy for TP53 germline variant classification.
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Affiliation(s)
- Cristina Fortuno
- QIMR Berghofer Medical Research Institute, Brisbane City, Australia, AUS
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Phuong L. Mai
- Magee-Womens Hospital, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Kelvin C. de Andrade
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Laura D. Attardi
- Departments of Radiation-Oncology and Genetics, Stanford University, Stanford, CA, USA
| | - Stephanie Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | | | - Megan N. Frone
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | - Paul A. James
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | | | | | - Bryce A. Seifert
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Leora Witkowski
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA, USA
| | - Liying Zhang
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sharon E. Plon
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Amanda B. Spurdle
- QIMR Berghofer Medical Research Institute, Brisbane City, Australia, AUS
| | - Sharon A. Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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4
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Fernandes LE, Epstein CG, Bobe AM, Bell JSK, Stumpe MC, Salazar ME, Salahudeen AA, Pe Benito RA, McCarter C, Leibowitz BD, Kase M, Igartua C, Huether R, Hafez A, Beaubier N, Axelson MD, Pegram MD, Sammons SL, O'Shaughnessy JA, Palmer GA. Real-world Evidence of Diagnostic Testing and Treatment Patterns in US Patients With Breast Cancer With Implications for Treatment Biomarkers From RNA Sequencing Data. Clin Breast Cancer 2021; 21:e340-e361. [PMID: 33446413 DOI: 10.1016/j.clbc.2020.11.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/27/2020] [Accepted: 11/13/2020] [Indexed: 01/21/2023]
Abstract
OBJECTIVE/BACKGROUND We performed a retrospective analysis of longitudinal real-world data (RWD) from patients with breast cancer to replicate results from clinical studies and demonstrate the feasibility of generating real-world evidence. We also assessed the value of transcriptome profiling as a complementary tool for determining molecular subtypes. METHODS De-identified, longitudinal data were analyzed after abstraction from records of patients with breast cancer in the United States (US) structured and stored in the Tempus database. Demographics, clinical characteristics, molecular subtype, treatment history, and survival outcomes were assessed according to strict qualitative criteria. RNA sequencing and clinical data were used to predict molecular subtypes and signaling pathway enrichment. RESULTS The clinical abstraction cohort (n = 4000) mirrored the demographics and clinical characteristics of patients with breast cancer in the US, indicating feasibility for RWE generation. Among patients who were human epidermal growth factor receptor 2-positive (HER2+), 74.2% received anti-HER2 therapy, with ∼70% starting within 3 months of a positive test result. Most non-treated patients were early stage. In this RWD set, 31.7% of patients with HER2+ immunohistochemistry (IHC) had discordant fluorescence in situ hybridization results recorded. Among patients with multiple HER2 IHC results at diagnosis, 18.6% exhibited intra-test discordance. Through development of a whole-transcriptome model to predict IHC receptor status in the molecular sequenced cohort (n = 400), molecular subtypes were resolved for all patients (n = 36) with equivocal HER2 statuses from abstracted test results. Receptor-related signaling pathways were differentially enriched between clinical molecular subtypes. CONCLUSIONS RWD in the Tempus database mirrors the overall population of patients with breast cancer in the US. These results suggest that real-time, RWD analyses are feasible in a large, highly heterogeneous database. Furthermore, molecular data may aid deficiencies and discrepancies observed from breast cancer RWD.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Mark D Pegram
- Stanford Comprehensive Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Sarah L Sammons
- Department of Medicine, Duke University Medical Center, Duke University, Durham, NC
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5
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Islam SA, Huether R, Kudalkar E. Abstract 5474: Identification of novel druggable fusions enabled through the use of an automated RNA fusion prioritization pipeline. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5474] [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
Gene fusions can serve as key drivers in the development of various cancers and represent important therapeutic targets and diagnostic biomarkers. Due to high detection of candidate fusions from RNA-sequencing data, there is a recognized need to build tools that will make reasonable and automated predictions to identify clinically or biologically relevant fusion events in a tumor sample. We developed a computational pipeline which scores and prioritizes all detected fusion transcripts within a sample to determine which fusions are likely driver events in the tumor. Specifically, the pipeline implements a categorization scheme that bins all scored fusion events into Low, Medium and High Confidence levels based on threshold read support levels and a DriverScore metric, which is derived from a binary classification algorithm using specific features, such as reading frame, breakpoint region, kinase domain and transcript isoform. We systematically analyzed 3200 fusion candidates from a previously published cohort of 500 paired tumor-normal samples sequenced with the Tempus xT assay. We found that 1.7% and 20.1% of fusion candidates were categorized in the High and Medium Confidence levels, respectively, while 78.2% of fusion events were deprioritized as Low Confidence calls. Of the 35 clinically-relevant fusions, 27 (77.1%) were captured in our prioritized set (High/Medium Confidence), including National Comprehensive Cancer Network actionable gene rearrangements involving RET, STAT6 and FUS, while the remaining 8 were assigned as Low Confidence due to an out of frame fusion transcript and insufficient read support. The frequency of prioritized fusions varied by cancer type, with prostate and breast cancer having the highest frequency of prioritized fusions. In addition to well-established canonical fusions, we also sought to characterize novel fusions, identifying a subset of 21 novel prioritized fusions which were also observed in The Cancer Genome Atlas tumor samples. Within this subset, 3% of fusion candidates contained a druggable domain such as a tyrosine kinase or Ras-binding domain, signifying the potential of categorization to enable novel fusion drug target discovery. Overall, our analysis highlights the utility of using an automated prioritization tool to detect known canonical fusion drivers and explore novel fusion drug targets and biomarkers.
Citation Format: Sumaiya A. Islam, Robert Huether, Emily Kudalkar. Identification of novel druggable fusions enabled through the use of an automated RNA fusion prioritization pipeline [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5474.
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6
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Mapes BL, Bell JSK, Langer LF, Huether R, Igartua C, Sanchez-Freire V, Tell R, Borgia JA, Masood A, Salahudeen AA. Abstract 3908: Universal genetic and transcriptomic concordance metrics to validate patient-derived tumor organoid models. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3908] [Citation(s) in RCA: 1] [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
Background
Patient derived tumor organoids (TOs) are emerging as potential models to elucidate mechanisms of tumor biology and therapeutic response. Here, we establish pan-cancer metrics for validation of genetic and transcriptomic recapitulation, and concordance of an organoid to its native tumor.
Methods/Results
We sequenced 50 tumor/TO pairs from 12 cancer types using the Tempus xT DNAseq panel and transcriptome RNAseq platforms. Concordance metrics between tumors and TOs were derived for genomic variants called by the DNA xT platform and comparative ratios were calculated for all detected somatic variants. Across all sequenced pairs, somatic variant detection concordance between any mutation identified in primary tissues and tumor organoids resulted in a mean value of 88.1%. Somatic primary tumor variant recapitulation, the percent of somatic variants identified in the primary tumors that were also detected in the TO, averaged 96.3%.
In addition to genetic concordance, DNAseq can identify and track clonal and subclonal diversity from source material to TO. In particular, we observed that >90% of source tumor/TO pairs harbor variants with allelic fractions <40% in both the sequenced TO and primary tumor tissue, suggesting intra-tumor heterogeneity in subclonal cell populations is maintained.
TOs and primary tumor transcriptomic profiles were compared by dimensionality reduction approaches (i.e. Uniform Manifold Approximation and Projection (UMAP), and Principal Components Analysis (PCA)) as well as differential expression analysis between cancer types. Overall, TOs recapitulated expected transcriptional programs of their tumor type as evidenced by UMAP and PCA as well as upregulation of defining pathways, such as estrogen receptor pathways in breast cancer TOs (ssGSEA p-values ranging from 0.004 to 5 × 10−5 for 5 gene ontology estrogen response pathways when compared to non-breast cancer TOs).
Conclusion
Determining genomic and transcriptomic concordance of TOs to source tumors is essential to confirm the validity of a given patient derived model. Our approach establishes metrics through key genomic features identified from routine next-generation sequencing data and can be extended beyond model validation to tracking clonal evolution over time in the presence or absence of therapeutic selection pressures. Our metrics may also serve as a critical quality control step if TOs are utilized in the clinical setting for personalized medicine.
Citation Format: Brandon L. Mapes, Joshua SK Bell, Lee F. Langer, Robert Huether, Catherine Igartua, Veronica Sanchez-Freire, Robert Tell, Jeffrey A. Borgia, Ashiq Masood, Ameen A. Salahudeen. Universal genetic and transcriptomic concordance metrics to validate patient-derived tumor organoid models [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3908.
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7
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Carvill GL, Helbig KL, Myers CT, Scala M, Huether R, Lewis S, Kruer TN, Guida BS, Bakhtiari S, Sebe J, Tang S, Stickney H, Oktay SU, Bhandiwad AA, Ramsey K, Narayanan V, Feyma T, Rohena LO, Accogli A, Severino M, Hollingsworth G, Gill D, Depienne C, Nava C, Sadleir LG, Caruso PA, Lin AE, Jansen FE, Koeleman B, Brilstra E, Willemsen MH, Kleefstra T, Sa J, Mathieu ML, Perrin L, Lesca G, Striano P, Casari G, Scheffer IE, Raible D, Sattlegger E, Capra V, Padilla-Lopez S, Mefford HC, Kruer MC. Damaging de novo missense variants in EEF1A2 lead to a developmental and degenerative epileptic-dyskinetic encephalopathy. Hum Mutat 2020; 41:1263-1279. [PMID: 32196822 DOI: 10.1002/humu.24015] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/14/2020] [Accepted: 03/13/2020] [Indexed: 11/08/2022]
Abstract
Heterozygous de novo variants in the eukaryotic elongation factor EEF1A2 have previously been described in association with intellectual disability and epilepsy but never functionally validated. Here we report 14 new individuals with heterozygous EEF1A2 variants. We functionally validate multiple variants as protein-damaging using heterologous expression and complementation analysis. Our findings allow us to confirm multiple variants as pathogenic and broaden the phenotypic spectrum to include dystonia/choreoathetosis, and in some cases a degenerative course with cerebral and cerebellar atrophy. Pathogenic variants appear to act via a haploinsufficiency mechanism, disrupting both the protein synthesis and integrated stress response functions of EEF1A2. Our studies provide evidence that EEF1A2 is highly intolerant to variation and that de novo pathogenic variants lead to an epileptic-dyskinetic encephalopathy with both neurodevelopmental and neurodegenerative features. Developmental features may be driven by impaired synaptic protein synthesis during early brain development while progressive symptoms may be linked to an impaired ability to handle cytotoxic stressors.
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Affiliation(s)
- Gemma L Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University, Chicago, Illinois
| | - Katherine L Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Candace T Myers
- Division of Genetic Medicine, Department of Pediatrics, Seattle, Washington
| | - Marcello Scala
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genoa, Italy
| | - Robert Huether
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, California
| | - Sara Lewis
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Tyler N Kruer
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Brandon S Guida
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Joy Sebe
- Department of Biology, University of Washington, Seattle, Washington.,Department of Biological Structure, University of Washington, Seattle, Washington
| | - Sha Tang
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, California
| | - Heather Stickney
- Department of Biological Structure, University of Washington, Seattle, Washington
| | - Sehribani Ulusoy Oktay
- Department of Biology, University of Washington, Seattle, Washington.,Department of Biological Structure, University of Washington, Seattle, Washington
| | - Ashwin A Bhandiwad
- Department of Biological Structure, University of Washington, Seattle, Washington
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona
| | - Timothy Feyma
- Department of Neurology, Gillette Children's Specialty Healthcare, St. Paul, Minnesota
| | - Luis O Rohena
- Department of Pediatrics, Division of Genetics, San Antonio Military Medical Center, San Antonio, Texas.,Department of Pediatrics, Long School of Medicine, University of Texas, San Antonio, Texas
| | - Andrea Accogli
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genoa, Italy.,Medical Genetics Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Mariasavina Severino
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy
| | - Georgina Hollingsworth
- Departments of Medicine and Paediatrics, University of Melbourne and Austin Health Royal Children's Hospital, Melbourne, Australia
| | - Deepak Gill
- Ty Nelson Department of Neurology, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Christel Depienne
- INSERM UMR 975, Institut du Cerveau et de la Moelle Epinière, Hôpital Pitié-Salpêtrière, Paris, France
| | - Caroline Nava
- INSERM UMR 975, Institut du Cerveau et de la Moelle Epinière, Hôpital Pitié-Salpêtrière, Paris, France
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington South, New Zealand
| | - Paul A Caruso
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Angela E Lin
- Medical Genetics, Department of Pediatrics, MassGeneral Hospital for Children, Harvard Medical School, Boston, Massachusetts
| | - Floor E Jansen
- Department of Pediatric Neurology, University Medical Center, Utrecht, The Netherlands
| | - Bobby Koeleman
- Department of Pediatric Neurology, University Medical Center, Utrecht, The Netherlands
| | - Eva Brilstra
- Department of Genetics, Utrecht University, Utrecht, The Netherlands
| | - Marjolein H Willemsen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joaquim Sa
- Serviço de Genética Médica, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Marie-Laure Mathieu
- Neuropaediatrics Department, Femme Mère Enfant Hospital, Lyon, France.,Claude Bernard Lyon 1 University, Lyon, France
| | - Laurine Perrin
- Department of Paediatric Physical Medicine and Rehabilitation, CHU Saint-Etienne, Hôpital Bellevue, Saint-Étienne, France
| | - Gaetan Lesca
- CRNL Inserm U1028-CNRS UMR5292-Claude Bernard University Lyon 1, Lyon, France.,Department of Medical Genetics, Lyon University Hospital, Lyon, France
| | - Pasquale Striano
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genoa, Italy
| | - Giorgio Casari
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genoa, Italy
| | - Ingrid E Scheffer
- Departments of Medicine and Paediatrics, University of Melbourne and Austin Health Royal Children's Hospital, Melbourne, Australia
| | - David Raible
- Department of Biology, University of Washington, Seattle, Washington.,Department of Biological Structure, University of Washington, Seattle, Washington
| | - Evelyn Sattlegger
- School of Natural & Computational Sciences, Massey University, Auckland, New Zealand
| | - Valeria Capra
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy
| | - Sergio Padilla-Lopez
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, Seattle, Washington
| | - Michael C Kruer
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
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8
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Chamberlin A, Huether R, Machado AZ, Groden M, Liu HM, Upadhyay K, O V, Gomes NL, Lerario AM, Nishi MY, Costa EMF, Mendonca B, Domenice S, Velasco J, Loke J, Ostrer H. Mutations in MAP3K1 that cause 46,XY disorders of sex development disrupt distinct structural domains in the protein. Hum Mol Genet 2020; 28:1620-1628. [PMID: 30608580 DOI: 10.1093/hmg/ddz002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/19/2018] [Accepted: 12/31/2018] [Indexed: 02/07/2023] Open
Abstract
Missense mutations in the gene, MAP3K1, are a common cause of 46,XY gonadal dysgenesis, accounting for 15-20% of cases [Ostrer, 2014, Disorders of sex development (DSDs): an update. J. Clin. Endocrinol. Metab., 99, 1503-1509]. Functional studies demonstrated that all of these mutations cause a protein gain-of-function that alters co-factor binding and increases phosphorylation of the downstream MAP kinase pathway targets, MAPK11, MAP3K and MAPK1. This dysregulation of the MAP kinase pathway results in increased CTNNB1, increased expression of WNT4 and FOXL2 and decreased expression of SRY and SOX9. Unique and recurrent pathogenic mutations cluster in three semi-contiguous domains outside the kinase region of the protein, a newly identified N-terminal domain that shares homology with the Guanine Exchange Factor (residues Met164 to Glu231), a Plant HomeoDomain (residues Met442 to Trp495) and an ARMadillo repeat domain (residues Met566 to Glu862). Despite the presence of the mutation clusters and clinical data, there exists a dearth of mechanistic insights behind the development imbalance. In this paper, we use structural modeling and functional data of these mutations to understand alterations of the MAP3K1 protein and the effects on protein folding, binding and downstream target phosphorylation. We show that these mutations have differential effects on protein binding depending on the domains in which they occur. These mutations increase the binding of the RHOA, MAP3K4 and FRAT1 proteins and generally decrease the binding of RAC1. Thus, pathologies in MAP3K1 disrupt the balance between the pro-kinase activities of the RHOA and MAP3K4 binding partners and the inhibitory activity of RAC1.
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Affiliation(s)
| | | | - Aline Z Machado
- Division of Endocrinology, Hormone and Molecular Genetics Laboratory (LIM), Hospital das Clinicas, University of Sao Paulo Medical School, Avenida Dr. Eneas de C Aguiar, andar Bloco, São Paulo, SP, Brazil
| | - Michael Groden
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Kinnari Upadhyay
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Vivian O
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nathalia L Gomes
- Division of Endocrinology, Hormone and Molecular Genetics Laboratory (LIM), Hospital das Clinicas, University of Sao Paulo Medical School, Avenida Dr. Eneas de C Aguiar, andar Bloco, São Paulo, SP, Brazil
| | - Antonio M Lerario
- Division of Metabolism, Endocrinology and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Mirian Y Nishi
- Division of Endocrinology, Hormone and Molecular Genetics Laboratory (LIM), Hospital das Clinicas, University of Sao Paulo Medical School, Avenida Dr. Eneas de C Aguiar, andar Bloco, São Paulo, SP, Brazil
| | - Elaine M F Costa
- Division of Endocrinology, Hormone and Molecular Genetics Laboratory (LIM), Hospital das Clinicas, University of Sao Paulo Medical School, Avenida Dr. Eneas de C Aguiar, andar Bloco, São Paulo, SP, Brazil
| | - Berenice Mendonca
- Division of Endocrinology, Hormone and Molecular Genetics Laboratory (LIM), Hospital das Clinicas, University of Sao Paulo Medical School, Avenida Dr. Eneas de C Aguiar, andar Bloco, São Paulo, SP, Brazil
| | - Sorahia Domenice
- Division of Endocrinology, Hormone and Molecular Genetics Laboratory (LIM), Hospital das Clinicas, University of Sao Paulo Medical School, Avenida Dr. Eneas de C Aguiar, andar Bloco, São Paulo, SP, Brazil
| | | | - Johnny Loke
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Harry Ostrer
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
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9
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Parikh K, Huether R, White K, Hoskinson D, Beaubier N, Dong H, Adjei AA, Mansfield AS. Tumor Mutational Burden From Tumor-Only Sequencing Compared With Germline Subtraction From Paired Tumor and Normal Specimens. JAMA Netw Open 2020; 3:e200202. [PMID: 32108894 PMCID: PMC7049088 DOI: 10.1001/jamanetworkopen.2020.0202] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
IMPORTANCE Tumor mutation burden (TMB) is an emerging factor associated with survival with immunotherapy. When tumor-normal pairs are available, TMB is determined by calculating the difference between somatic and germline sequences. In the case of commonly used tumor-only sequencing, additional steps are needed to estimate the somatic alterations. Computational tools have been developed to determine germline contribution based on sample copy state, purity estimates, and occurrence of the variant in population databases; however, there is potential for sampling bias in population data sets. OBJECTIVE To investigate whether tumor-only filtering approaches overestimate TMB. DESIGN, SETTING, AND PARTICIPANTS This was a retrospective cohort study of 50 tumor samples from 10 different tumor types. A 595-gene panel test was used to assess TMB by adding all missense, indels, and frameshift variants with an allelic fraction of at least 5% and coverage of at least 100× within each tumor. Tumor-only TMB was evaluated against the criterion standard of matched germline-subtracted TMB at 3 levels. Level 1 removed all the tumor-only variants with allelic fraction of at least 1% in the Exome Aggregation Consortium database (with the Cancer Genome Atlas cohort removed). Level 2 removed all variants observed in population databases, simulating a naive approach of removing germline variation. Level 3 used an internal tumor-only pipeline for calculating TMB. These specimens were processed with a commercially available panel, and results were analyzed at the Mayo Clinic. Data were analyzed between December 1, 2018, and May 28, 2019. MAIN OUTCOMES AND MEASURES Tumor mutation burden per megabase (Mb) as determined by 3 levels of filtering and germline subtraction. RESULTS There were significantly higher estimates of TMB with level 1 (median [range] mutations per Mb, 28.8 [17.5-67.1]), level 2 (median [range] mutations per Mb, 20.8 [10.4-30.8]), and level 3 (median [range] mutations per Mb, 3.8 [0.8-12.1]) tumor-only filtering approaches than those determined by germline subtraction (median [range] mutations per Mb, 1.7 [0.4-9.2]). There were no strong associations between TMB estimates and tumor-germline TMB for level 1 filtering (r = 0.008; 95% CI, -0.004 to 0.020), level 2 filtering (r = 0.018; 95% CI, 0.003 to 0.033), or level 3 filtering (r = 0.54; 95% CI, 0.36 to 0.68). CONCLUSIONS AND RELEVANCE The findings of this study indicate that tumor-only approaches that filter variants in population databases can overestimate TMB compared with germline subtraction methods. Despite improved association with more stringent filtering approaches, these falsely elevated estimates may result in the inappropriate categorization of tumor specimens and negatively affect clinical trial results and patient outcomes.
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Affiliation(s)
- Kaushal Parikh
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota
- Division of Medical Oncology, John Theurer Cancer Center, Hackensack, New Jersey
| | | | | | | | | | - Haidong Dong
- Department of Urology, Department of Immunology, Mayo Clinic, Rochester, Minnesota
| | - Alex A. Adjei
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota
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10
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Mester JL, Ghosh R, Pesaran T, Huether R, Karam R, Hruska KS, Costa HA, Lachlan K, Ngeow J, Barnholtz-Sloan J, Sesock K, Hernandez F, Zhang L, Milko L, Plon SE, Hegde M, Eng C. Gene-specific criteria for PTEN variant curation: Recommendations from the ClinGen PTEN Expert Panel. Hum Mutat 2019; 39:1581-1592. [PMID: 30311380 PMCID: PMC6329583 DOI: 10.1002/humu.23636] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/27/2018] [Accepted: 08/28/2018] [Indexed: 01/07/2023]
Abstract
The ClinGen PTEN Expert Panel was organized by the ClinGen Hereditary Cancer Clinical Domain Working Group to assemble clinicians, researchers, and molecular diagnosticians with PTEN expertise to develop specifications to the 2015 ACMG/AMP Sequence Variant Interpretation Guidelines for PTEN variant interpretation. We describe finalized PTEN-specific variant classification criteria and outcomes from pilot testing of 42 variants with benign/likely benign (BEN/LBEN), pathogenic/likely pathogenic (PATH/LPATH), uncertain significance (VUS), and conflicting (CONF) ClinVar assertions. Utilizing these rules, classifications concordant with ClinVar assertions were achieved for 14/15 (93.3%) BEN/LBEN and 16/16 (100%) PATH/LPATH ClinVar consensus variants for an overall concordance of 96.8% (30/31). The variant where agreement was not reached was a synonymous variant near a splice donor with noncanonical sequence for which in silico models cannot predict the native site. Applying these rules to six VUS and five CONF variants, adding shared internal laboratory data enabled one VUS to be classified as LBEN and two CONF variants to be as classified as PATH and LPATH. This study highlights the benefit of gene-specific criteria and the value of sharing internal laboratory data for variant interpretation. Our PTEN-specific criteria and expertly reviewed assertions should prove helpful for laboratories and others curating PTEN variants.
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Affiliation(s)
| | | | | | | | | | | | - Helio A Costa
- Stanford University School of Medicine, Stanford, California
| | - Katherine Lachlan
- Wessex Clinical Genetics Service, University Hospitals Southampton, Southampton, UK.,Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Jill Barnholtz-Sloan
- Case Comprehensive Cancer Center, Cleveland, Ohio.,Case Western Reserve University School of Medicine, Cleveland, Ohio
| | | | | | - Liying Zhang
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laura Milko
- University of North Carolina, Chapel Hill, North Carolina
| | | | - Madhuri Hegde
- Emory University, Atlanta, Georgia.,PerkinElmer Genetics, Pittsburgh, Pennsylvania
| | - Charis Eng
- Case Comprehensive Cancer Center, Cleveland, Ohio.,Case Western Reserve University School of Medicine, Cleveland, Ohio.,Cleveland Clinic Genomic Medicine Institute, Cleveland, Ohio
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11
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Parikh K, Huether R, White K, Hoskinson D, Dong H, Adjei AA, Mansfield AS. Overestimation of tumor mutational burden (TMB) using algorithms compared to germline subtraction. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.2621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2621 Background: TMB is an emerging predictor of survival with immunotherapy. TMB is determined by taking the difference between somatic and germline datasets when tumor-normal pairs are available. In the case of commonly utilized tumor-only sequencing, additional steps are needed to estimate the somatic alterations. Computational tools have been developed that determine germline contribution based on sample copy state, purity estimates and occurrence of the variant in population databases. Given the potential bias of population datasets, we hypothesized that tumor-only filtering approaches may overestimate the actual TMB. Methods: We assessed the TMB from 50 tumors in 10 diseases including all missense, indels, and frameshift variants with an allelic fraction (AF) ≥5% and Coverage ≥100X within the tumor. Tumor-only TMB was evaluated against the gold standard of matched germline subtracted TMB at three levels. Level 1 removed all the tumor-only variants with AF in the non-TCGA ExAC database ≥1%. Level 2 removed all variants observed in population databases simulating a naive approach of removing germline variation. Level 3 used an internal tumor-only pipeline for calculating TMB. Results: There were significantly higher estimates of TMB with Level 1, Level 2 and Level 3 tumor-only filtering approaches than that determined by germline subtraction, resulting in significant bias. Whereas there was no correlation between TMB estimates and tumor-germline TMB for Level 1 filtering, there were improvements in correlations for Level 2 and Level 3. Conclusions: The tumor-only approaches that filter variants in population databases overestimate TMB compared to that determined by germline subtraction. Despite improved correlations with more stringent filtering approaches, these falsely elevated estimates may result in the inappropriate categorization of tumor specimens and negatively impact clinical trial results and patient outcomes. [Table: see text]
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12
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Beaubier N, Tell R, Lau D, Parsons JR, Bush S, Perera J, Sorrells S, Baker T, Chang A, Michuda J, Iguartua C, MacNeil S, Shah K, Ellis P, Yeatts K, Mahon B, Taxter T, Bontrager M, Khan A, Huether R, Lefkofsky E, White KP. Clinical validation of the tempus xT next-generation targeted oncology sequencing assay. Oncotarget 2019; 10:2384-2396. [PMID: 31040929 PMCID: PMC6481324 DOI: 10.18632/oncotarget.26797] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 02/03/2019] [Indexed: 12/13/2022] Open
Abstract
We developed and clinically validated a hybrid capture next generation sequencing assay to detect somatic alterations and microsatellite instability in solid tumors and hematologic malignancies. This targeted oncology assay utilizes tumor-normal matched samples for highly accurate somatic alteration calling and whole transcriptome RNA sequencing for unbiased identification of gene fusion events. The assay was validated with a combination of clinical specimens and cell lines, and recorded a sensitivity of 99.1% for single nucleotide variants, 98.1% for indels, 99.9% for gene rearrangements, 98.4% for copy number variations, and 99.9% for microsatellite instability detection. This assay presents a wide array of data for clinical management and clinical trial enrollment while conserving limited tissue.
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Affiliation(s)
| | | | - Denise Lau
- Tempus Labs Inc., Chicago, IL 60654, USA
| | | | | | | | | | | | - Alan Chang
- Tempus Labs Inc., Chicago, IL 60654, USA
| | | | | | | | | | | | | | | | | | | | - Aly Khan
- Tempus Labs Inc., Chicago, IL 60654, USA
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13
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Sadaps M, Funchain P, Heald B, Huether R, Pitt J, White K, Khorana AA, Sohal D. A multi-institutional study assessing prevalence of deleterious germline mutations in pancreatic cancer. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.4_suppl.280] [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: 11/20/2022] Open
Abstract
280 Background: Pancreatic cancer is being increasingly associated with germline implications. Some large single-center studies have reported results ranging from 3.9% to 19.8% of patients found to have germline variants [Shindo, JCO 2017; Lowery, JNCI 2018]. Due to this wide range, we aim to further delineate prevalence of deleterious germline mutations in pancreatic cancer using a multi-institutional data set. We also aim to analyze predictive factors such as mutant allele frequency (MAF, in %) in germline versus somatic calls. Methods: We sequenced 23 genes in DNA prepared from clinical tissue and blood specimens submitted to Tempus Labs. Germline variants and somatic variants were processed separately. Germline variants were determined to be deleterious through the sum effect of a combination of in silico predictors, population databases, and internal evaluations. Tumor-normal comparisons were used to define somatic versus germline, and MAFs were calculated for each. Results: A total of 234 patient samples from 17 institutions were analyzed. Of these, 12 (5.1%) had predicted deleterious germline variants involving 8 different genes: BRCA1 (n = 3), CHEK2 (n = 3), ATM (n = 1), MLH1 (n = 1), MUTYH (n = 1), PALB2 (n = 1), SMAD4 (n = 1), TP53 (n = 1). For most somatic alterations, the MAFs were found to be greater than the germline deleterious alterations, with the latter approaching ~50% in most cases (Table). Conclusions: This multi-institutional study identifies 5% of patients with pancreatic cancer to have deleterious germline alterations. Somatic variant testing, particularly when paired with germline, can be used as a screening method for genetic counseling referrals, especially with MAF analyses of paired tumor-normal samples. [Table: see text]
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14
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Lu HM, Li S, Black MH, Lee S, Hoiness R, Wu S, Mu W, Huether R, Chen J, Sridhar S, Tian Y, McFarland R, Dolinsky J, Tippin Davis B, Mexal S, Dunlop C, Elliott A. Association of Breast and Ovarian Cancers With Predisposition Genes Identified by Large-Scale Sequencing. JAMA Oncol 2019; 5:51-57. [PMID: 30128536 PMCID: PMC6439764 DOI: 10.1001/jamaoncol.2018.2956] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/04/2018] [Indexed: 12/21/2022]
Abstract
Importance Since the discovery of BRCA1 and BRCA2, multiple high- and moderate-penetrance genes have been reported as risk factors for hereditary breast cancer, ovarian cancer, or both; however, it is unclear whether these findings represent the complete genetic landscape of these cancers. Systematic investigation of the genetic contributions to breast and ovarian cancers is needed to confirm these findings and explore potentially new associations. Objective To confirm reported and identify additional predisposition genes for breast or ovarian cancer. Design, Setting, and Participants In this sample of 11 416 patients with clinical features of breast cancer, ovarian cancer, or both who were referred for genetic testing from 1200 hospitals and clinics across the United States and of 3988 controls who were referred for genetic testing for noncancer conditions between 2014 and 2015, whole-exome sequencing was conducted and gene-phenotype associations were examined. Case-control analyses using the Genome Aggregation Database as a set of reference controls were also conducted. Main Outcomes and Measures Breast cancer risk associated with pathogenic variants among 625 cancer predisposition genes; association of identified predisposition breast or ovarian cancer genes with the breast cancer subtypes invasive ductal, invasive lobular, hormone receptor-positive, hormone receptor-negative, and male, and with early-onset disease. Results Of 9639 patients with breast cancer, 3960 (41.1%) were early-onset cases (≤45 years at diagnosis) and 123 (1.3%) were male, with men having an older age at diagnosis than women (mean [SD] age, 61.8 [12.8] vs 48.6 [11.4] years). Of 2051 women with ovarian cancer, 445 (21.7%) received a diagnosis at 45 years or younger. Enrichment of pathogenic variants were identified in 4 non-BRCA genes associated with breast cancer risk: ATM (odds ratio [OR], 2.97; 95% CI, 1.67-5.68), CHEK2 (OR, 2.19; 95% CI, 1.40-3.56), PALB2 (OR, 5.53; 95% CI, 2.24-17.65), and MSH6 (OR, 2.59; 95% CI, 1.35-5.44). Increased risk for ovarian cancer was associated with 4 genes: MSH6 (OR, 4.16; 95% CI, 1.95-9.47), RAD51C (OR, not estimable; false-discovery rate-corrected P = .004), TP53 (OR, 18.50; 95% CI, 2.56-808.10), and ATM (OR, 2.85; 95% CI, 1.30-6.32). Neither the MRN complex genes nor CDKN2A was associated with increased breast or ovarian cancer risk. The findings also do not support previously reported breast cancer associations with the ovarian cancer susceptibility genes BRIP1, RAD51C, and RAD51D, or mismatch repair genes MSH2 and PMS2. Conclusions and Relevance The results of this large-scale exome sequencing of patients and controls shed light on both well-established and controversial non-BRCA predisposition gene associations with breast or ovarian cancer reported to date and may implicate additional breast or ovarian cancer susceptibility gene candidates involved in DNA repair and genomic maintenance.
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Affiliation(s)
| | - Shuwei Li
- Ambry Genetics, Aliso Viejo, California
| | | | - Shela Lee
- Ambry Genetics, Aliso Viejo, California
- Now with Simcere Pharmaceutical, Jiangsu, China
| | | | - Sitao Wu
- Ambry Genetics, Aliso Viejo, California
| | - Wenbo Mu
- Ambry Genetics, Aliso Viejo, California
| | - Robert Huether
- Ambry Genetics, Aliso Viejo, California
- Tempus, Chicago, Illinois
| | | | - Srijani Sridhar
- Ambry Genetics, Aliso Viejo, California
- Intellia Therapeutics, Cambridge, Massachusetts
| | - Yuan Tian
- Ambry Genetics, Aliso Viejo, California
| | - Rachel McFarland
- Ambry Genetics, Aliso Viejo, California
- Department of Epidemiology, School of Medicine,
University of California, Irvine
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15
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Beaubier N, Tell R, Huether R, Bontrager M, Bush S, Parsons J, Shah K, Baker T, Selkov G, Taxter T, Thomas A, Bettis S, Khan A, Lau D, Lee C, Barber M, Cieslik M, Frankenberger C, Franzen A, Weiner A, Palmer G, Lonigro R, Robinson D, Wu YM, Cao X, Lefkofsky E, Chinnaiyan A, White KP. Clinical validation of the Tempus xO assay. Oncotarget 2018; 9:25826-25832. [PMID: 29899824 PMCID: PMC5995233 DOI: 10.18632/oncotarget.25381] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 03/21/2018] [Indexed: 01/01/2023] Open
Abstract
We have developed a clinically validated NGS assay that includes tumor, germline and RNA sequencing. We apply this assay to clinical specimens and cell lines, and we demonstrate a clinical sensitivity of 98.4% and positive predictive value of 100% for the clinically actionable variants measured by the assay. We also demonstrate highly accurate copy number measurements and gene rearrangement identification.
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Affiliation(s)
| | - Robert Tell
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | | | | | | | | | - Kaanan Shah
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Tim Baker
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Gene Selkov
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Tim Taxter
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | | | - Sam Bettis
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Aly Khan
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Denise Lau
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | | | | | - Marcin Cieslik
- Department of Pathology and Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Amy Franzen
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Ali Weiner
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Gary Palmer
- Tempus Labs, Inc., Chicago, Illinois 60654, USA
| | - Robert Lonigro
- Department of Pathology and Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Dan Robinson
- Department of Pathology and Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Yi-Mi Wu
- Department of Pathology and Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xuhong Cao
- Department of Pathology and Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Arul Chinnaiyan
- Department of Pathology and Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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16
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Powis Z, Petrik I, Cohen J, Escolar D, Burton J, van Ravenswaaij-Arts C, Sival D, Stegmann A, Kleefstra T, Pfundt R, Chikarmane R, Begtrup A, Huether R, Tang S, Shinde D. De novo variants in KLF7
are a potential novel cause of developmental delay/intellectual disability, neuromuscular and psychiatric symptoms. Clin Genet 2018; 93:1030-1038. [DOI: 10.1111/cge.13198] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Z. Powis
- Ambry Genetics; Aliso Viejo California
| | - I. Petrik
- Ambry Genetics; Aliso Viejo California
| | - J.S. Cohen
- Kennedy Krieger Institute; Baltimore Maryland
| | - D. Escolar
- Kennedy Krieger Institute; Baltimore Maryland
| | - J. Burton
- University of Illinois College of Medicine at Peoria; Peoria Illinois
| | - C.M.A. van Ravenswaaij-Arts
- Department of Genetics; University of Groningen, University Medical Center Groningen; Groningen The Netherlands
| | - D.A. Sival
- Department of Neurology; University of Groningen, University Medical Center Groningen; Groningen The Netherlands
| | - A.P.A. Stegmann
- Clinical Genetics; Maastricht University Medical Center; Maastricht The Netherlands
- Department of Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | - T. Kleefstra
- Clinical Genetics; Maastricht University Medical Center; Maastricht The Netherlands
| | - R. Pfundt
- Clinical Genetics; Maastricht University Medical Center; Maastricht The Netherlands
| | | | | | | | - S. Tang
- Ambry Genetics; Aliso Viejo California
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17
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Powis Z, Farwell Hagman K, Mroske C, McWalter K, Cohen J, Colombo R, Serretti A, Fatemi A, David K, Reynolds J, Immken L, Nagakura H, Cunniff C, Payne K, Barbaro-Dieber T, Gripp K, Baker L, Stamper T, Aleck K, Jordan E, Hersh J, Burton J, Wentzensen I, Guillen Sacoto M, Willaert R, Cho M, Petrik I, Huether R, Tang S. Expansion and further delineation of the SETD5
phenotype leading to global developmental delay, variable dysmorphic features, and reduced penetrance. Clin Genet 2018; 93:752-761. [DOI: 10.1111/cge.13132] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/30/2017] [Accepted: 09/04/2017] [Indexed: 01/23/2023]
Affiliation(s)
- Z. Powis
- Division of Emerging Genetics Medicine; Ambry Genetics; Aliso Viejo California
| | | | - C. Mroske
- Division of Clinical Genomics; Ambry Genetics; Aliso Viejo California
| | | | - J.S. Cohen
- Division of Neurogenetics, Hugo W. Moser Research Institute; Kennedy Krieger Institute; Baltimore Maryland
| | - R. Colombo
- Faculty of Medicine, Institute of Clinical Biochemistry; Catholic University and Policlinico Agostino Gemelli; Rome Italy
- Center for the Study of Rare Hereditary Disease; Niguarda Ca’ Granda Metropolitan Hospital; Milan Italy
| | - A. Serretti
- Department of Biomedical and NeuroMotor Sciences; University of Bologna; Bologna Italy
| | - A. Fatemi
- Division of Neurogenetics, Hugo W. Moser Research Institute; Kennedy Krieger Institute; Baltimore Maryland
- Department of Neurology and Pediatrics; The Johns Hopkins Hospital; Baltimore Maryland
| | - K.L. David
- Department of Medicine, Division of Genetics, New York Methodist Hospital; Brooklyn New York
| | - J. Reynolds
- Department of Medical Genetics, Shodair Children's Hospital; Helena Montana
| | - L. Immken
- Department of Genetics Specially for Children Genetics; Austin Texas
| | - H. Nagakura
- Department of Genetics Specially for Children Genetics; Austin Texas
| | - C.M. Cunniff
- Department of Pediatrics, Weill Cornell Medicine; New York New York
| | - K. Payne
- Child Neurology; Riley Hospital for Children; Indianapolis Indiana
| | - T. Barbaro-Dieber
- Department of Genetics, Cook Children's Medical Center; Fort Worth Texas
| | - K.W. Gripp
- Department of Genetics, Cook Children's Medical Center; Fort Worth Texas
| | - L. Baker
- Division of Medical Genetics; A.I. duPont Hospital for Children; Wilmington Delaware
| | - T. Stamper
- Department of Pediatrics, Section on Medical Genetics; Wake Forest Baptist Medical Center; Winston-Salem North Carolina
| | - K.A. Aleck
- Department of Genetics and Metabolism, Phoenix Children's Hospital; Phoenix Arizona
| | - E.S. Jordan
- Weisskopf Center, University of Louisville Clinical Genetics Unit; Louisville Kentucky
| | - J.H. Hersh
- Weisskopf Center, University of Louisville Clinical Genetics Unit; Louisville Kentucky
| | - J. Burton
- Department of Genetics, University of Illinois College of Medicine at Peoria; Peoria Illinois
| | | | | | | | | | - I. Petrik
- Division of Clinical Genomics; Ambry Genetics; Aliso Viejo California
| | - R. Huether
- Division of Clinical Genomics; Ambry Genetics; Aliso Viejo California
| | - S. Tang
- Division of Clinical Genomics; Ambry Genetics; Aliso Viejo California
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18
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Couch FJ, Shimelis H, Hu C, Hart SN, Polley EC, Na J, Hallberg E, Moore R, Thomas A, Lilyquist J, Feng B, McFarland R, Pesaran T, Huether R, LaDuca H, Chao EC, Goldgar DE, Dolinsky JS. Associations Between Cancer Predisposition Testing Panel Genes and Breast Cancer. JAMA Oncol 2017; 3:1190-1196. [PMID: 28418444 PMCID: PMC5599323 DOI: 10.1001/jamaoncol.2017.0424] [Citation(s) in RCA: 404] [Impact Index Per Article: 57.7] [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: 12/13/2022]
Abstract
IMPORTANCE Germline pathogenic variants in BRCA1 and BRCA2 predispose to an increased lifetime risk of breast cancer. However, the relevance of germline variants in other genes from multigene hereditary cancer testing panels is not well defined. OBJECTIVE To determine the risks of breast cancer associated with germline variants in cancer predisposition genes. DESIGN, SETTING, AND PARTICIPANTS A study population of 65 057 patients with breast cancer receiving germline genetic testing of cancer predisposition genes with hereditary cancer multigene panels. Associations between pathogenic variants in non-BRCA1 and non-BRCA2 predisposition genes and breast cancer risk were estimated in a case-control analysis of patients with breast cancer and Exome Aggregation Consortium reference controls. The women underwent testing between March 15, 2012, and June 30, 2016. MAIN OUTCOMES AND MEASURES Breast cancer risk conferred by pathogenic variants in non-BRCA1 and non-BRCA2 predisposition genes. RESULTS The mean (SD) age at diagnosis for the 65 057 women included in the analysis was 48.5 (11.1) years. The frequency of pathogenic variants in 21 panel genes identified in 41 611 consecutively tested white women with breast cancer was estimated at 10.2%. After exclusion of BRCA1, BRCA2, and syndromic breast cancer genes (CDH1, PTEN, and TP53), observed pathogenic variants in 5 of 16 genes were associated with high or moderately increased risks of breast cancer: ATM (OR, 2.78; 95% CI, 2.22-3.62), BARD1 (OR, 2.16; 95% CI, 1.31-3.63), CHEK2 (OR, 1.48; 95% CI, 1.31-1.67), PALB2 (OR, 7.46; 95% CI, 5.12-11.19), and RAD51D (OR, 3.07; 95% CI, 1.21-7.88). Conversely, variants in the BRIP1 and RAD51C ovarian cancer risk genes; the MRE11A, RAD50, and NBN MRN complex genes; the MLH1 and PMS2 mismatch repair genes; and NF1 were not associated with increased risks of breast cancer. CONCLUSIONS AND RELEVANCE This study establishes several panel genes as high- and moderate-risk breast cancer genes and provides estimates of breast cancer risk associated with pathogenic variants in these genes among individuals qualifying for clinical genetic testing.
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Affiliation(s)
- Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Hermela Shimelis
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Chunling Hu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Steven N Hart
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Eric C Polley
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Jie Na
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Emily Hallberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Raymond Moore
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Abigail Thomas
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jenna Lilyquist
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Bingjian Feng
- Huntsman Cancer Institute, Department of Dermatology, University of Utah, Salt Lake City
| | - Rachel McFarland
- Department of Clinical Diagnostics, Ambry Genetics Inc, Aliso Viejo, California
| | - Tina Pesaran
- Department of Clinical Diagnostics, Ambry Genetics Inc, Aliso Viejo, California
| | - Robert Huether
- Department of Clinical Diagnostics, Ambry Genetics Inc, Aliso Viejo, California
| | - Holly LaDuca
- Department of Clinical Diagnostics, Ambry Genetics Inc, Aliso Viejo, California
| | - Elizabeth C Chao
- Department of Clinical Diagnostics, Ambry Genetics Inc, Aliso Viejo, California
- Now, Division of Genetics and Genomics, Department of Pediatrics, University of California-Irvine
| | - David E Goldgar
- Huntsman Cancer Institute, Department of Dermatology, University of Utah, Salt Lake City
| | - Jill S Dolinsky
- Department of Clinical Diagnostics, Ambry Genetics Inc, Aliso Viejo, California
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19
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von Spiczak S, Helbig KL, Shinde DN, Huether R, Pendziwiat M, Lourenço C, Nunes ME, Sarco DP, Kaplan RA, Dlugos DJ, Kirsch H, Slavotinek A, Cilio MR, Cervenka MC, Cohen JS, McClellan R, Fatemi A, Yuen A, Sagawa Y, Littlejohn R, McLean SD, Hernandez-Hernandez L, Maher B, Møller RS, Palmer E, Lawson JA, Campbell CA, Joshi CN, Kolbe DL, Hollingsworth G, Neubauer BA, Muhle H, Stephani U, Scheffer IE, Pena SDJ, Sisodiya SM, Helbig I. DNM1 encephalopathy: A new disease of vesicle fission. Neurology 2017; 89:385-394. [PMID: 28667181 PMCID: PMC5574673 DOI: 10.1212/wnl.0000000000004152] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [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: 12/22/2016] [Accepted: 04/26/2017] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To evaluate the phenotypic spectrum caused by mutations in dynamin 1 (DNM1), encoding the presynaptic protein DNM1, and to investigate possible genotype-phenotype correlations and predicted functional consequences based on structural modeling. METHODS We reviewed phenotypic data of 21 patients (7 previously published) with DNM1 mutations. We compared mutation data to known functional data and undertook biomolecular modeling to assess the effect of the mutations on protein function. RESULTS We identified 19 patients with de novo mutations in DNM1 and a sibling pair who had an inherited mutation from a mosaic parent. Seven patients (33.3%) carried the recurrent p.Arg237Trp mutation. A common phenotype emerged that included severe to profound intellectual disability and muscular hypotonia in all patients and an epilepsy characterized by infantile spasms in 16 of 21 patients, frequently evolving into Lennox-Gastaut syndrome. Two patients had profound global developmental delay without seizures. In addition, we describe a single patient with normal development before the onset of a catastrophic epilepsy, consistent with febrile infection-related epilepsy syndrome at 4 years. All mutations cluster within the GTPase or middle domains, and structural modeling and existing functional data suggest a dominant-negative effect on DMN1 function. CONCLUSIONS The phenotypic spectrum of DNM1-related encephalopathy is relatively homogeneous, in contrast to many other genetic epilepsies. Up to one-third of patients carry the recurrent p.Arg237Trp variant, which is now one of the most common recurrent variants in epileptic encephalopathies identified to date. Given the predicted dominant-negative mechanism of this mutation, this variant presents a prime target for therapeutic intervention.
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Affiliation(s)
| | | | | | - Robert Huether
- Author affiliations are provided at the end of the article
| | | | | | - Mark E Nunes
- Author affiliations are provided at the end of the article
| | - Dean P Sarco
- Author affiliations are provided at the end of the article
| | | | | | - Heidi Kirsch
- Author affiliations are provided at the end of the article
| | | | - Maria R Cilio
- Author affiliations are provided at the end of the article
| | | | - Julie S Cohen
- Author affiliations are provided at the end of the article
| | | | - Ali Fatemi
- Author affiliations are provided at the end of the article
| | - Amy Yuen
- Author affiliations are provided at the end of the article
| | - Yoshimi Sagawa
- Author affiliations are provided at the end of the article
| | | | - Scott D McLean
- Author affiliations are provided at the end of the article
| | | | - Bridget Maher
- Author affiliations are provided at the end of the article
| | - Rikke S Møller
- Author affiliations are provided at the end of the article
| | | | - John A Lawson
- Author affiliations are provided at the end of the article
| | | | | | - Diana L Kolbe
- Author affiliations are provided at the end of the article
| | | | | | - Hiltrud Muhle
- Author affiliations are provided at the end of the article
| | | | | | | | | | - Ingo Helbig
- Author affiliations are provided at the end of the article.
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20
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Couch FJ, Hu C, Lilyquist J, Shimelis H, Akinhanmi M, Na J, Polley EC, Hart SN, McFarland R, LaDuca H, Huether R, Goldgar DE, Dolinsky JS. Abstract S2-01: Breast cancer risks associated with mutations in cancer predisposition genes identified by clinical genetic testing of 60,000 breast cancer patients. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-s2-01] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Clinical genetic testing panels are broadly used to gather information about cancer predisposition in individuals with personal and/or family history of breast cancer. However, the involvement of several of the genes on clinical testing panels in predisposition to breast cancer, such as MRE11A and RAD50, has recently come into question. In addition, accurate risk estimates for breast and other cancer are not well defined for the majority of genes on testing panels. We studied 60,000 women diagnosed with breast cancer who were tested for germline cancer predisposing mutations using hereditary cancer gene panels. Information on personal and family cancer history, age of diagnosis, and ethnicity of patients was obtained from test requisition forms. Greater than 90% met National Comprehensive Cancer Network HBOC testing criteria. To estimate gene-specific risks for breast cancer, case-control analyses were performed comparing the frequencies of pathogenic mutations from Caucasian cancer cases with frequencies from Caucasian, non-Finnish, non-TCGA controls from the Exome Aggregation Consortium (ExAC) database. Mutations were detected in 9% of breast cancer patients. Twelve genes displayed a significant association (p<0.05) with breast cancer. Nine of these genes, including ATM, RAD51D, NF1, and MSH6, were associated with moderate risk (RR>2.0) of breast cancer and three genes (BRCA1, BRCA2, PALB2) were associated with high risk (RR>5.0) of breast cancer. Cumulative age-dependent risk models were developed for each gene. This large clinical testing dataset of 60,000 women with breast cancer provides useful data for many predisposition genes previously lacking risk estimates, and should prove useful for clinical risk management of patients with inherited mutations in these genes.
Citation Format: Couch FJ, Hu C, Lilyquist J, Shimelis H, Akinhanmi M, Na J, Polley EC, Hart SN, McFarland R, LaDuca H, Huether R, Goldgar DE, Dolinsky JS. Breast cancer risks associated with mutations in cancer predisposition genes identified by clinical genetic testing of 60,000 breast cancer patients [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr S2-01.
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Affiliation(s)
- FJ Couch
- Mayo Clinic, Rochester, MN; Ambry Genetics, Aliso Viejo, CA; University of Utah, Salt Lake, UT
| | - C Hu
- Mayo Clinic, Rochester, MN; Ambry Genetics, Aliso Viejo, CA; University of Utah, Salt Lake, UT
| | - J Lilyquist
- Mayo Clinic, Rochester, MN; Ambry Genetics, Aliso Viejo, CA; University of Utah, Salt Lake, UT
| | - H Shimelis
- Mayo Clinic, Rochester, MN; Ambry Genetics, Aliso Viejo, CA; University of Utah, Salt Lake, UT
| | - M Akinhanmi
- Mayo Clinic, Rochester, MN; Ambry Genetics, Aliso Viejo, CA; University of Utah, Salt Lake, UT
| | - J Na
- Mayo Clinic, Rochester, MN; Ambry Genetics, Aliso Viejo, CA; University of Utah, Salt Lake, UT
| | - EC Polley
- Mayo Clinic, Rochester, MN; Ambry Genetics, Aliso Viejo, CA; University of Utah, Salt Lake, UT
| | - SN Hart
- Mayo Clinic, Rochester, MN; Ambry Genetics, Aliso Viejo, CA; University of Utah, Salt Lake, UT
| | - R McFarland
- Mayo Clinic, Rochester, MN; Ambry Genetics, Aliso Viejo, CA; University of Utah, Salt Lake, UT
| | - H LaDuca
- Mayo Clinic, Rochester, MN; Ambry Genetics, Aliso Viejo, CA; University of Utah, Salt Lake, UT
| | - R Huether
- Mayo Clinic, Rochester, MN; Ambry Genetics, Aliso Viejo, CA; University of Utah, Salt Lake, UT
| | - DE Goldgar
- Mayo Clinic, Rochester, MN; Ambry Genetics, Aliso Viejo, CA; University of Utah, Salt Lake, UT
| | - JS Dolinsky
- Mayo Clinic, Rochester, MN; Ambry Genetics, Aliso Viejo, CA; University of Utah, Salt Lake, UT
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21
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Pesaran T, Karam R, Huether R, Li S, Farber-Katz S, Chamberlin A, Chong H, LaDuca H, Elliott A. Beyond DNA: An Integrated and Functional Approach for Classifying Germline Variants in Breast Cancer Genes. Int J Breast Cancer 2016; 2016:2469523. [PMID: 27822389 PMCID: PMC5086358 DOI: 10.1155/2016/2469523] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [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: 06/04/2016] [Revised: 09/04/2016] [Accepted: 09/19/2016] [Indexed: 11/17/2022] Open
Abstract
Genetic testing for hereditary breast cancer is an integral part of individualized care in the new era of precision medicine. The accuracy of an assay is reliant on not only the technology and bioinformatics analysis utilized but also the experience and infrastructure required to correctly classify genetic variants as disease-causing. Interpreting the clinical significance of germline variants identified by hereditary cancer testing is complex and has a significant impact on the management of patients who are at increased cancer risk. In this review we give an overview of our clinical laboratory's integrated approach to variant assessment. We discuss some of the nuances that should be considered in the assessment of genomic variants. In addition, we highlight lines of evidence such as functional assays and structural analysis that can be useful in the assessment of rare and complex variants.
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Affiliation(s)
- T. Pesaran
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - R. Karam
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - R. Huether
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - S. Li
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - S. Farber-Katz
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - A. Chamberlin
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - H. Chong
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - H. LaDuca
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - A. Elliott
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
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22
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Cohen JS, Srivastava S, Farwell Hagman KD, Shinde DN, Huether R, Darcy D, Wallerstein R, Houge G, Berland S, Monaghan KG, Poretti A, Wilson AL, Chung WK, Fatemi A. Further evidence that de novo missense and truncating variants in ZBTB18 cause intellectual disability with variable features. Clin Genet 2016; 91:697-707. [PMID: 27598823 DOI: 10.1111/cge.12861] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/12/2016] [Accepted: 09/01/2016] [Indexed: 01/21/2023]
Abstract
Identification of rare genetic variants in patients with intellectual disability (ID) has been greatly accelerated by advances in next generation sequencing technologies. However, due to small numbers of patients, the complete phenotypic spectrum associated with pathogenic variants in single genes is still emerging. Among these genes is ZBTB18 (ZNF238), which is deleted in patients with 1q43q44 microdeletions who typically present with ID, microcephaly, corpus callosum (CC) abnormalities, and seizures. Here we provide additional evidence for haploinsufficiency or dysfunction of the ZBTB18 gene as the cause of ID in five unrelated patients with variable syndromic features who underwent whole exome sequencing revealing separate de novo pathogenic or likely pathogenic variants in ZBTB18 (two missense alterations and three truncating alterations). The neuroimaging findings in our cohort (CC hypoplasia seen in 4/4 of our patients who underwent MRI) lend further support for ZBTB18 as a critical gene for CC abnormalities. A similar phenotype of microcephaly, CC agenesis, and cerebellar vermis hypoplasia has been reported in mice with central nervous system-specific knockout of Zbtb18. Our five patients, in addition to the previously described cases of de novo ZBTB18 variants, add to knowledge about the phenotypic spectrum associated with ZBTB18 haploinsufficiency/dysfunction.
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Affiliation(s)
- J S Cohen
- Division of Neurogenetics, Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD, USA
| | - S Srivastava
- Division of Neurogenetics, Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD, USA.,Department of Neurology, The Johns Hopkins Hospital, Baltimore, MD, USA.,Department of Pediatrics, The Johns Hopkins Hospital, Baltimore, MD, USA
| | | | - D N Shinde
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | - R Huether
- Department of Bioinformatics, Ambry Genetics, Aliso Viejo, CA, USA
| | - D Darcy
- Silicon Valley Genetics Center, Santa Clara Valley Medical Center, San Jose, CA, USA
| | - R Wallerstein
- Hawaii Community Genetics, Kapiolani Medical Center for Women and Children, Honolulu, HI, USA
| | - G Houge
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.,Department of Medical Genetics, St. Olav Hospital, Trondheim, Norway
| | - S Berland
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.,Department of Medical Genetics, St. Olav Hospital, Trondheim, Norway
| | | | - A Poretti
- Section of Pediatric Neuroradiology, Division of Pediatric Radiology, Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins Hospital, Baltimore, MD, USA
| | - A L Wilson
- Department of Clinical Genetics, New York Presbyterian Hospital, New York, NY, USA
| | - W K Chung
- Department of Pediatrics, Columbia University, New York, NY, USA.,Department of Medicine, Columbia University, New York, NY, USA
| | - A Fatemi
- Division of Neurogenetics, Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD, USA.,Department of Neurology, The Johns Hopkins Hospital, Baltimore, MD, USA.,Department of Pediatrics, The Johns Hopkins Hospital, Baltimore, MD, USA
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23
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Helbig KL, Hedrich UBS, Shinde DN, Krey I, Teichmann AC, Hentschel J, Schubert J, Chamberlin AC, Huether R, Lu HM, Alcaraz WA, Tang S, Jungbluth C, Dugan SL, Vainionpää L, Karle KN, Synofzik M, Schöls L, Schüle R, Lehesjoki AE, Helbig I, Lerche H, Lemke JR. A recurrent mutation in KCNA2 as a novel cause of hereditary spastic paraplegia and ataxia. Ann Neurol 2016; 80. [PMID: 27543892 PMCID: PMC5129488 DOI: 10.1002/ana.24762] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [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: 04/19/2016] [Revised: 08/02/2016] [Accepted: 08/14/2016] [Indexed: 01/30/2023]
Abstract
The hereditary spastic paraplegias (HSPs) are heterogeneous neurodegenerative disorders with over 50 known causative genes. We identified a recurrent mutation in KCNA2 (c.881G>A, p.R294H), encoding the voltage-gated K(+) -channel, KV 1.2, in two unrelated families with HSP, intellectual disability (ID), and ataxia. Follow-up analysis of > 2,000 patients with various neurological phenotypes identified a de novo p.R294H mutation in a proband with ataxia and ID. Two-electrode voltage-clamp recordings of Xenopus laevis oocytes expressing mutant KV 1.2 channels showed loss of function with a dominant-negative effect. Our findings highlight the phenotypic spectrum of a recurrent KCNA2 mutation, implicating ion channel dysfunction as a novel HSP disease mechanism. Ann Neurol 2016.
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Affiliation(s)
| | - Ulrike B S Hedrich
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | | | - Ilona Krey
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | | | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Julian Schubert
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | | | - Robert Huether
- Department of Bioinformatics, Ambry Genetics, Aliso Viejo, CA
| | - Hsiao-Mei Lu
- Department of Bioinformatics, Ambry Genetics, Aliso Viejo, CA
| | - Wendy A Alcaraz
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA
| | - Sha Tang
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA
| | - Chelsy Jungbluth
- Department of Medical Genetics, Children's Hospitals and Clinics of Minnesota, Minneapolis, MN
| | - Sarah L Dugan
- Department of Medical Genetics, Children's Hospitals and Clinics of Minnesota, Minneapolis, MN.,Division of Medical Genetics, University of Utah, Salt Lake City, UT
| | - Leena Vainionpää
- Department of Pediatrics and Adolescence, Oulu University Hospital, PEDEGO Research Unit, University of Oulu, Oulu, Finland
| | - Kathrin N Karle
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.,Department of Psychiatry and Psychotherapy, University of Tübingen, Tübingen, Germany
| | - Matthis Synofzik
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Ludger Schöls
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Rebecca Schüle
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Anna-Elina Lehesjoki
- Folkhälsan Institute of Genetics, Helsinki, Finland; Research Programs Unit, Molecular Neurology and Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Ingo Helbig
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Christian-Albrechts-University, Kiel, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany.
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24
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Farwell Hagman KD, Shinde DN, Mroske C, Smith E, Radtke K, Shahmirzadi L, El-Khechen D, Powis Z, Chao EC, Alcaraz WA, Helbig KL, Sajan SA, Rossi M, Lu HM, Huether R, Li S, Wu S, Nuñes ME, Tang S. Candidate-gene criteria for clinical reporting: diagnostic exome sequencing identifies altered candidate genes among 8% of patients with undiagnosed diseases. Genet Med 2016; 19:224-235. [PMID: 27513193 PMCID: PMC5303763 DOI: 10.1038/gim.2016.95] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [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: 01/28/2016] [Accepted: 05/25/2016] [Indexed: 02/07/2023] Open
Abstract
Purpose: Diagnostic exome sequencing (DES) is now a commonly ordered test for individuals with undiagnosed genetic disorders. In addition to providing a diagnosis for characterized diseases, exome sequencing has the capacity to uncover novel candidate genes for disease. Methods: Family-based DES included analysis of both characterized and novel genetic etiologies. To evaluate candidate genes for disease in the clinical setting, we developed a systematic, rule-based classification schema. Results: Testing identified a candidate gene among 7.7% (72/934) of patients referred for DES; 37 (4.0%) and 35 (3.7%) of the genes received evidence scores of “candidate” and “suspected candidate,” respectively. A total of 71 independent candidate genes were reported among the 72 patients, and 38% (27/71) were subsequently corroborated in the peer-reviewed literature. This rate of corroboration increased to 51.9% (27/52) among patients whose gene was reported at least 12 months previously. Conclusions: Herein, we provide transparent, comprehensive, and standardized scoring criteria for the clinical reporting of candidate genes. These results demonstrate that DES is an integral tool for genetic diagnosis, especially for elucidating the molecular basis for both characterized and novel candidate genetic etiologies. Gene discoveries also advance the understanding of normal human biology and more common diseases. Genet Med19 2, 224–235.
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Affiliation(s)
| | - Deepali N Shinde
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Cameron Mroske
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Erica Smith
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Kelly Radtke
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Layla Shahmirzadi
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Dima El-Khechen
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Zöe Powis
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Elizabeth C Chao
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA.,Division of Genetics and Genomics, Department of Pediatrics, University of California, Irvine, Irvine, California, USA
| | - Wendy A Alcaraz
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Katherine L Helbig
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Samin A Sajan
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Mari Rossi
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Hsiao-Mei Lu
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Robert Huether
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Shuwei Li
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Sitao Wu
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Mark E Nuñes
- Department of Genetics, Kaiser Permanente, San Diego, California, USA
| | - Sha Tang
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
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25
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Couch FJ, Goldgar DE, Hart SN, Hallberg E, Moore R, Meeks H, Huether R, LaDuca H, Chao E, Dolinsky J. Abstract 2597: Breast and ovarian cancer risks associated with cancer predisposition gene mutations identified by multigene panel testing. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2597] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Multigene panel testing (MGPT) for hereditary cancer is increasing in popularity in the USA. Many panels include genes identified as hereditary breast and/or ovarian cancer (HBOC) genes despite limited data regarding the precise cancer risks associated with mutations in these genes. Here we report on results from BreastNext and OvaNext panel testing of 20 genes (ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MLH1, MRE11A, MSH2, MSH6, NBN, NF1, PALB2, PMS2, PTEN, RAD50, RAD51C, RAD51D, TP53) in a cohort of 15,083 individuals. The majority of individuals were from high-risk breast and/or ovarian (Br/Ov) cancer families, with 92.4% of all probands meeting National Comprehensive Cancer Network HBOC testing criteria. Pathogenic mutations were identified in 9.4% of the overall cohort.
To estimate gene-specific breast and ovarian cancer risks, case-control analyses were performed comparing the frequencies of pathogenic mutations from Caucasian breast or ovarian cancer cases from BreastNext and OvaNext with frequencies from Caucasian, non-Finnish, non-TCGA controls from the Exome Aggregation Consortium (ExAC) database. Mutations in the well studied ATM and CHEK2 genes were associated with moderate risks (OR>2) of breast cancer and mutations in PALB2 were associated with high-risks (OR>5) of breast cancer, consistent with previous reports. In addition, the study suggested that pathogenic mutations in MSH6, RAD51D, CDH1, and NF1 are associated with moderate to high risks of breast cancer. In contrast, RAD51C, RAD51D, and BRIP1 mutations were associated with high risks of ovarian cancer, PALB2 mutations were associated with moderate risks, but ATM and CHEK2 mutations were not associated with increased ovarian cancer risk. In addition, modeling of missense mutations in the predisposition genes using in silico prediction algorithms suggested that missense mutations in CDH1, CHEK2, MSH2, and MSH6 are associated with moderate risks of breast cancer and missense mutations in RAD51C increase risks of ovarian cancer. This large breast and ovarian cancer case-control analysis provides useful data for many predisposition genes previously lacking risk estimates, and should prove useful for clinical risk management of patients after clinical panel testing.
Citation Format: Fergus J. Couch, David E. Goldgar, Steven N. Hart, Emily Hallberg, Raymond Moore, Huong Meeks, Robert Huether, Holly LaDuca, Elizabeth Chao, Jill Dolinsky. Breast and ovarian cancer risks associated with cancer predisposition gene mutations identified by multigene panel testing. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2597.
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26
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Couch FJ, Akinhanmi M, Shimelis H, Hallberg EJ, Hu C, Hart S, Moore R, Meeks H, Huether R, Laduca H, Chao E, Goldgar D, Dolinsky JS. Risks of triple negative breast cancer associated with cancer predisposition gene mutations. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.1513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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27
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Mroske C, Rasmussen K, Shinde DN, Huether R, Powis Z, Lu HM, Baxter RM, McPherson E, Tang S. Germline activating MTOR mutation arising through gonadal mosaicism in two brothers with megalencephaly and neurodevelopmental abnormalities. BMC Med Genet 2015; 16:102. [PMID: 26542245 PMCID: PMC4635597 DOI: 10.1186/s12881-015-0240-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/03/2015] [Indexed: 01/06/2023]
Abstract
Background In humans, Mammalian Target of Rapamycin (MTOR) encodes a 300 kDa serine/ threonine protein kinase that is ubiquitously expressed, particularly at high levels in brain. MTOR functions as an integrator of multiple cellular processes, and in so doing either directly or indirectly regulates the phosphorylation of at least 800 proteins. While somatic MTOR mutations have been recognized in tumors for many years, and more recently in hemimegalencephaly, germline MTOR mutations have rarely been described. Case presentation We report the successful application of family-trio Diagnostic Exome Sequencing (DES) to identify the underlying molecular etiology in two brothers with multiple neurological and developmental lesions, and for whom previous testing was non-diagnostic. The affected brothers, who were 6 and 23 years of age at the time of DES, presented symptoms including but not limited to mild Autism Spectrum Disorder (ASD), megalencephaly, gross motor skill delay, cryptorchidism and bilateral iris coloboma. Importantly, we determined that each affected brother harbored the MTOR missense alteration p.E1799K (c.5395G>A). This exact variant has been previously identified in multiple independent human somatic cancer samples and has been shown to result in increased MTOR activation. Further, recent independent reports describe two unrelated families in whom p.E1799K co-segregated with megalencephaly and intellectual disability (ID); in both cases, p.E1799K was shown to have originated due to germline mosaicism. In the case of the family reported herein, the absence of p.E1799K in genomic DNA extracted from the blood of either parent suggests that this alteration most likely arose due to gonadal mosaicism. Further, the p.E1799K variant exerts its effect by a gain-of-function (GOF), autosomal dominant mechanism. Conclusion Herein, we describe the use of DES to uncover an activating MTOR missense alteration of gonadal mosaic origin that is likely to be the causative mutation in two brothers who present multiple neurological and developmental abnormalities. Our report brings the total number of families who harbor MTOR p.E1799K in association with megalencephaly and ID to three. In each case, evidence suggests that p.E1799K arose in the affected individuals due to gonadal mosaicism. Thus, MTOR p.E1799K can now be classified as a pathogenic GOF mutation that causes megalencephaly and cognitive impairment in humans. Electronic supplementary material The online version of this article (doi:10.1186/s12881-015-0240-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cameron Mroske
- Ambry Genetics Corporation, Aliso Viejo, CA, 92656, USA.
| | | | | | - Robert Huether
- Ambry Genetics Corporation, Aliso Viejo, CA, 92656, USA.
| | - Zoe Powis
- Ambry Genetics Corporation, Aliso Viejo, CA, 92656, USA.
| | - Hsiao-Mei Lu
- Ambry Genetics Corporation, Aliso Viejo, CA, 92656, USA.
| | - Ruth M Baxter
- Ambry Genetics Corporation, Aliso Viejo, CA, 92656, USA.
| | | | - Sha Tang
- Ambry Genetics Corporation, Aliso Viejo, CA, 92656, USA.
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28
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Hernandez F, Huether R, Carter L, Johnston T, Thompson J, Gossage JR, Chao E, Elliott AM. Mutations in RASA1 and GDF2 identified in patients with clinical features of hereditary hemorrhagic telangiectasia. Hum Genome Var 2015; 2:15040. [PMID: 27081547 PMCID: PMC4785548 DOI: 10.1038/hgv.2015.40] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [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: 05/27/2015] [Revised: 09/02/2015] [Accepted: 09/09/2015] [Indexed: 01/18/2023] Open
Abstract
Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant vascular disorder caused by mutations in ENG, ACVRL1 and SMAD4, which function in regulating the transforming growth factor beta and bone morphogenetic protein signaling pathways. Symptoms of HHT can be present in individuals who test negative for mutations in these three genes indicating other genes may be involved. In this study, we tested for mutations in two genes, RASA1 and GDF2, which were recently reported to be involved in vascular disorders. To determine whether RASA1 and GDF2 have phenotypic overlap with HHT and should be included in diagnostic testing, we developed a next-generation sequencing assay to detect mutations in 93 unrelated individuals who previously tested negative for mutations in ENG, ACVRL1 and SMAD4, but were clinically suspected to have HHT. Pathogenic mutations in RASA1 were identified in two samples (2.15%) and a variant of unknown significance in GDF2 was detected in one sample. All three individuals experienced epistaxis with dermal lesions described in medical records as telangiectases. These results indicate that the inclusion of RASA1 and GDF2 screening in individuals suspected to have HHT will increase the detection rate and aid clinicians in making an accurate diagnosis.
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Affiliation(s)
- Felicia Hernandez
- Department of Research and Development, Ambry Genetics , Aliso Viejo, CA, USA
| | - Robert Huether
- Department of Bioinformatics, Ambry Genetics , Aliso Viejo, CA, USA
| | - Lester Carter
- Department of Bioinformatics, Ambry Genetics , Aliso Viejo, CA, USA
| | - Tami Johnston
- Department of Clinical Genetics, Ambry Genetics , Aliso Viejo, CA, USA
| | - Jennifer Thompson
- Department of Clinical Genetics, Ambry Genetics , Aliso Viejo, CA, USA
| | - James R Gossage
- Division of Pulmonary/Critical Care, Georgia Regents University , Augusta, GA, USA
| | - Elizabeth Chao
- Department of Clinical Genetics, Ambry Genetics , Aliso Viejo, CA, USA
| | - Aaron M Elliott
- Department of Research and Development, Ambry Genetics , Aliso Viejo, CA, USA
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29
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Andersson AK, Ma J, Wang J, Chen X, Gedman AL, Dang J, Nakitandwe J, Holmfeldt L, Parker M, Easton J, Huether R, Kriwacki R, Rusch M, Wu G, Li Y, Mulder H, Raimondi S, Pounds S, Kang G, Shi L, Becksfort J, Gupta P, Payne-Turner D, Vadodaria B, Boggs K, Yergeau D, Manne J, Song G, Edmonson M, Nagahawatte P, Wei L, Cheng C, Pei D, Sutton R, Venn NC, Chetcuti A, Rush A, Catchpoole D, Heldrup J, Fioretos T, Lu C, Ding L, Pui CH, Shurtleff S, Mullighan CG, Mardis ER, Wilson RK, Gruber TA, Zhang J, Downing JR. The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias. Nat Genet 2015; 47:330-7. [PMID: 25730765 PMCID: PMC4553269 DOI: 10.1038/ng.3230] [Citation(s) in RCA: 355] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 02/02/2015] [Indexed: 12/13/2022]
Abstract
Infant acute lymphoblastic leukemia (ALL) with MLL rearrangements (MLL-R) represents a distinct leukemia with a poor prognosis. To define its mutational landscape, we performed whole genome, exome, RNA and targeted DNA sequencing on 65 infants (47 MLL-R and 18 non-MLL-R) and 20 older children (MLL-R cases) with leukemia. Our data demonstrated infant MLL-R ALL to have one of the lowest frequencies of somatic mutations of any sequenced cancer, with the predominant leukemic clone carrying a mean of 1.3 non-silent mutations. Despite the paucity of mutations, activating mutations in kinase/PI3K/RAS signaling pathways were detected in 47%. Surprisingly, however, these mutations were often sub-clonal and frequently lost at relapse. In contrast to infant cases, MLL-R leukemia in older children had more somatic mutations (a mean of 6.5/case versus 1.3/case, P=7.15×10−5) and contained frequent mutations (45%) in epigenetic regulators, a category of genes that with the exception of MLL was rarely mutated in infant MLL-R ALL.
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Affiliation(s)
- Anna K Andersson
- 1] Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. [2] Department of Clinical Genetics, Lund University, Lund, Sweden
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jianmin Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Amanda Larson Gedman
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jinjun Dang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Joy Nakitandwe
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Linda Holmfeldt
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Matthew Parker
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - John Easton
- Pediatric Cancer Genome Project Laboratory, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Robert Huether
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Richard Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yongjin Li
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Heather Mulder
- Pediatric Cancer Genome Project Laboratory, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Susana Raimondi
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Guolian Kang
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Lei Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jared Becksfort
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Pankaj Gupta
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Debbie Payne-Turner
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Bhavin Vadodaria
- Pediatric Cancer Genome Project Laboratory, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kristy Boggs
- Pediatric Cancer Genome Project Laboratory, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Donald Yergeau
- Pediatric Cancer Genome Project Laboratory, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jayanthi Manne
- Pediatric Cancer Genome Project Laboratory, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Michael Edmonson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Panduka Nagahawatte
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Lei Wei
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rosemary Sutton
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Nicola C Venn
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Albert Chetcuti
- Tumor Bank, Children's Cancer Research Unit, Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Amanda Rush
- Tumor Bank, Children's Cancer Research Unit, Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Daniel Catchpoole
- Tumor Bank, Children's Cancer Research Unit, Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Jesper Heldrup
- Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | - Thoas Fioretos
- Department of Clinical Genetics, Lund University, Lund, Sweden
| | - Charles Lu
- 1] Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA. [2] Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Li Ding
- 1] Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA. [2] Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Ching-Hon Pui
- 1] Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. [2] Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Sheila Shurtleff
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Elaine R Mardis
- 1] Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA. [2] Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Richard K Wilson
- 1] Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA. [2] Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Tanja A Gruber
- 1] Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. [2] Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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30
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Koçer ZA, Fan Y, Huether R, Obenauer J, Webby RJ, Zhang J, Webster RG, Wu G. Survival analysis of infected mice reveals pathogenic variations in the genome of avian H1N1 viruses. Sci Rep 2014; 4:7455. [PMID: 25503687 PMCID: PMC4264002 DOI: 10.1038/srep07455] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 11/24/2014] [Indexed: 11/09/2022] Open
Abstract
Most influenza pandemics have been caused by H1N1 viruses of purely or partially avian origin. Here, using Cox proportional hazard model, we attempt to identify the genetic variations in the whole genome of wild-type North American avian H1N1 influenza A viruses that are associated with their virulence in mice by residue variations, host origins of virus (Anseriformes-ducks or Charadriiformes-shorebirds), and host-residue interactions. In addition, through structural modeling, we predicted that several polymorphic sites associated with pathogenicity were located in structurally important sites, especially in the polymerase complex and NS genes. Our study introduces a new approach to identify pathogenic variations in wild-type viruses circulating in the natural reservoirs and ultimately to understand their infectious risks to humans as part of risk assessment efforts towards the emergence of future pandemic strains.
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Affiliation(s)
- Zeynep A Koçer
- Department of Infectious Diseases, Division of Virology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - Robert Huether
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - John Obenauer
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - Richard J Webby
- Department of Infectious Diseases, Division of Virology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - Robert G Webster
- Department of Infectious Diseases, Division of Virology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
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31
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Diaz AK, Wu G, Paugh BS, Li Y, Zhu X, Rankin S, Qu C, Chen X, Zhang J, Easton J, Edmonson M, Lu C, Nagahawatte P, Hedlund E, Rusch M, Pounds S, Lin T, Onar-Thomas A, Huether R, Kriwacki R, Parker M, Gupta P, Becksfort J, Wei L, Mulder HL, Boggs K, Vadodaria B, Yergeau D, Ochoa K, Fulton RS, Fulton LS, Jones C, Broniscer A, Wetmore C, Gajjar A, Ding L, Mardis ER, Wilson RK, Downing JR, Ellison DW, Zhang J, Baker SJ. Abstract PR03: The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma. Cancer Res 2014. [DOI: 10.1158/1538-7445.pedcan-pr03] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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
Pediatric high-grade glioma (HGG) remains a tremendous clinical challenge, with a two-year survival of less than 20%. We analyzed 127 pediatric HGGs, including diffuse intrinsic pontine gliomas (DIPGs) and non-brainstem HGGs (NBS-HGGs) by whole-genome, whole-exome, and/or transcriptome sequencing. Somatic mutations in the bone morphogenetic protein (BMP) receptor ACVR1 occurred in 32% of DIPG, a finding exclusive to brainstem HGG. Structural variants generating fusion genes were found in 47% of pediatric HGG, with recurrent fusions involving the neurotrophin receptor genes NTRK1, 2, or 3 in 40% of infant NBS-HGGs and 5% of pediatric HGG overall. Multiple mutations targeted pathways involving histone modification or chromatin remodeling, cell cycle regulation and receptor tyrosine kinase/RAS/PI3K signaling, in both DIPG and NBS-HGGs at frequencies of greater than 39% in the entire cohort. The HGG mutation burden ranged from 2 non-silent mutations in an infant HGG to more than a million mutations in a tumor associated with germline mismatch repair deficiency. From these findings, we have established novel tumor models to better understand this devastating disease. This work provides new insight into the genetic events driving pediatric HGG tumorigenesis.
This abstract is also presented as Poster B14.
Citation Format: Alexander K. Diaz, Gang Wu, Barbara S. Paugh, Yongjin Li, Xiaoyan Zhu, Sherri Rankin, Chunxu Qu, Xiang Chen, Junyuan Zhang, John Easton, Michael Edmonson, Charles Lu, Panduka Nagahawatte, Erin Hedlund, Michael Rusch, Stanley Pounds, Tong Lin, Arzu Onar-Thomas, Robert Huether, Richard Kriwacki, Matthew Parker, Pankaj Gupta, Jared Becksfort, Lei Wei, Heather L. Mulder, Kristy Boggs, Bhavin Vadodaria, Donald Yergeau, Kerri Ochoa, Robert S. Fulton, Lucinda S. Fulton, Chris Jones, Alberto Broniscer, Cynthia Wetmore, Amar Gajjar, Li Ding, Elaine R. Mardis, Richard K. Wilson, James R. Downing, David W. Ellison, Jinghui Zhang, Suzanne J. Baker, For the St Jude Children's Research Hospital – Washington University Pediatric Cancer Genome Project. The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr PR03.
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Affiliation(s)
| | - Gang Wu
- 1St. Jude Children's Research Hospital, Memphis, TN,
| | | | - Yongjin Li
- 1St. Jude Children's Research Hospital, Memphis, TN,
| | - Xiaoyan Zhu
- 1St. Jude Children's Research Hospital, Memphis, TN,
| | - Sherri Rankin
- 1St. Jude Children's Research Hospital, Memphis, TN,
| | - Chunxu Qu
- 1St. Jude Children's Research Hospital, Memphis, TN,
| | - Xiang Chen
- 1St. Jude Children's Research Hospital, Memphis, TN,
| | - Junyuan Zhang
- 1St. Jude Children's Research Hospital, Memphis, TN,
| | - John Easton
- 1St. Jude Children's Research Hospital, Memphis, TN,
| | | | | | | | - Erin Hedlund
- 1St. Jude Children's Research Hospital, Memphis, TN,
| | - Michael Rusch
- 1St. Jude Children's Research Hospital, Memphis, TN,
| | | | - Tong Lin
- 1St. Jude Children's Research Hospital, Memphis, TN,
| | | | | | | | | | - Pankaj Gupta
- 1St. Jude Children's Research Hospital, Memphis, TN,
| | | | - Lei Wei
- 3Roswell Park Cancer Institute, Buffalo, NY,
| | | | - Kristy Boggs
- 1St. Jude Children's Research Hospital, Memphis, TN,
| | | | | | | | | | | | - Chris Jones
- 4Institute for Cancer Research, London, United Kingdom
| | | | | | - Amar Gajjar
- 1St. Jude Children's Research Hospital, Memphis, TN,
| | - Li Ding
- 2Washington University, St. Louis, MO,
| | | | | | | | | | - Jinghui Zhang
- 1St. Jude Children's Research Hospital, Memphis, TN,
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32
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Chan HM, Jaffe JD, Wang Y, Zhang J, Huether R, Kryukov GV, Bhang HEC, Taylor JE, Hu M, Englund NP, Yan F, Wang Z, McDonald ER, Wei L, Ma J, Easton J, Yu Z, deBeaumount R, Gibaja V, Venkatesan K, Schlegel R, Sellers WR, Keen N, Liu J, Caponigro G, Barretina J, Cooke VG, Mullighan C, Carr SA, Downing JR, Garraway LA, Stegmeier F. Abstract 2930: Global chromatin profiling reveals NSD2 mutation in pediatric ALL. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-2930] [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
Epigenetic dysregulation is an emerging hallmark of cancers. We developed a high-information-content mass spectrometry approach to profile global histone modifications in human cancers. When applied to 115 lines of the Cancer Cell Line Encyclopedia1, this approach identified distinct molecular chromatin signatures. One signature was characterized by increased H3K36 dimethylation, exhibited by several lines harboring NSD2 translocations. A novel NSD2 p.E1099K variant was identified in non-translocated acute lymphoblastic leukemia (ALL) lines sharing this signature. Ectopic expression of the variant induced a chromatin signature characteristic of NSD2 hyperactivation and promoted transformation. NSD2 knockdown selectively inhibited the proliferation of NSD2-mutant lines and impaired the in vivo growth of an NSD2-mutant ALL xenograft. Sequencing analysis of >1000 pediatric cancer genomes identified the NSD2 p.E1099K mutation in 14% of t(12;21)[ETV6-RUNX1]-containing ALLs. These findings identify NSD2 as a potential therapeutic target for pediatric ALL and provide a general framework for the functional annotation of cancer epigenomes.
1.
Barretina,J. et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603-607 (2012).
Citation Format: Ho Man Chan, Jacob D. Jaffe, Yan Wang, Jinghui Zhang, Robert Huether, Gregory V. Kryukov, Hyo-eun C. Bhang, Jordan E. Taylor, Min Hu, Nathan P. Englund, Feng Yan, Zhaofu Wang, E Robert McDonald III, Lei Wei, Jing Ma, John Easton, Zhengtian Yu, Rosalie deBeaumount, Veronica Gibaja, Kavitha Venkatesan, Robert Schlegel, William R. Sellers, Nicholas Keen, Jun Liu, Giordano Caponigro, Jordi Barretina, Vesselina G. Cooke, Charles Mullighan, Steven A. Carr, James R. Downing, Levi A. Garraway, Frank Stegmeier. Global chromatin profiling reveals NSD2 mutation in pediatric ALL. [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 2930. doi:10.1158/1538-7445.AM2014-2930
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Affiliation(s)
- Ho Man Chan
- 1Novartis Insts. for BioMedical Research, Cambridge, MA
| | | | - Yan Wang
- 3Genomic Institute of the Novartis Research Foundation, San Diego, CA
| | | | | | | | | | | | - Min Hu
- 5Novartis Insts. for BioMedical Research, Shanghai, China
| | - Nathan P. Englund
- 3Genomic Institute of the Novartis Research Foundation, San Diego, CA
| | - Feng Yan
- 3Genomic Institute of the Novartis Research Foundation, San Diego, CA
| | - Zhaofu Wang
- 5Novartis Insts. for BioMedical Research, Shanghai, China
| | | | - Lei Wei
- 4St. Jude Children's Research Hospital, Memphis, TN
| | - Jing Ma
- 4St. Jude Children's Research Hospital, Memphis, TN
| | - John Easton
- 4St. Jude Children's Research Hospital, Memphis, TN
| | - Zhengtian Yu
- 5Novartis Insts. for BioMedical Research, Shanghai, China
| | | | | | | | | | | | - Nicholas Keen
- 1Novartis Insts. for BioMedical Research, Cambridge, MA
| | - Jun Liu
- 3Genomic Institute of the Novartis Research Foundation, San Diego, CA
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33
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Gilbertson R, Parker M, Mohankumar KM, Punchihewa C, Weinlich R, Dalton JD, Li Y, Lee R, Tatevossian RG, Phoenix TN, Thiruvenkatam R, White E, Tang B, Orisme W, Gupta K, Rusch M, Chen X, Li Y, Nagahawhatta P, Hedlund E, Finkelstein D, Wu G, Shurtleff S, Easton J, Boggs K, Yergeau D, Vadodaria B, Mulder HL, Becksford J, Gupta P, Huether R, Ma J, Song G, Gajjar A, Merchant T, Boop F, Smith AA, Ding L, Lu C, Ochoa K, Zhao D, Fulton RS, Fulton LL, Mardis ER, Wilson RK, Downing JR, Green DR, Zhang J, Ellison DW, Gilbertson RJ. C11ORF95-RELA FUSIONS DRIVE ONCOGENIC NF-KB SIGNALING IN EPENDYMOMA. Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou206.57] [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: 11/12/2022] Open
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34
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Huether R, Dong L, Chen X, Wu G, Parker M, Wei L, Ma J, Edmonson MN, Hedlund EK, Rusch MC, Shurtleff SA, Mulder HL, Boggs K, Vadordaria B, Cheng J, Yergeau D, Song G, Becksfort J, Lemmon G, Weber C, Cai Z, Dang J, Walsh M, Gedman AL, Faber Z, Easton J, Gruber T, Kriwacki RW, Partridge JF, Ding L, Wilson RK, Mardis ER, Mullighan CG, Gilbertson RJ, Baker SJ, Zambetti G, Ellison DW, Zhang J, Downing JR. The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes. Nat Commun 2014; 5:3630. [PMID: 24710217 DOI: 10.1038/ncomms4630] [Citation(s) in RCA: 288] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 03/12/2014] [Indexed: 02/07/2023] Open
Abstract
Studies of paediatric cancers have shown a high frequency of mutation across epigenetic regulators. Here we sequence 633 genes, encoding the majority of known epigenetic regulatory proteins, in over 1,000 paediatric tumours to define the landscape of somatic mutations in epigenetic regulators in paediatric cancer. Our results demonstrate a marked variation in the frequency of gene mutations across 21 different paediatric cancer subtypes, with the highest frequency of mutations detected in high-grade gliomas, T-lineage acute lymphoblastic leukaemia and medulloblastoma, and a paucity of mutations in low-grade glioma and retinoblastoma. The most frequently mutated genes are H3F3A, PHF6, ATRX, KDM6A, SMARCA4, ASXL2, CREBBP, EZH2, MLL2, USP7, ASXL1, NSD2, SETD2, SMC1A and ZMYM3. We identify novel loss-of-function mutations in the ubiquitin-specific processing protease 7 (USP7) in paediatric leukaemia, which result in decreased deubiquitination activity. Collectively, our results help to define the landscape of mutations in epigenetic regulatory genes in paediatric cancer and yield a valuable new database for investigating the role of epigenetic dysregulations in cancer.
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Affiliation(s)
- Robert Huether
- 1] Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA [2]
| | - Li Dong
- 1] Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA [2]
| | - Xiang Chen
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Gang Wu
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Matthew Parker
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Lei Wei
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jing Ma
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Michael N Edmonson
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Erin K Hedlund
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Michael C Rusch
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Sheila A Shurtleff
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Heather L Mulder
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Kristy Boggs
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Bhavin Vadordaria
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jinjun Cheng
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Donald Yergeau
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Guangchun Song
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jared Becksfort
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Gordon Lemmon
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Catherine Weber
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Zhongling Cai
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jinjun Dang
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Michael Walsh
- Department of Oncology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Amanda L Gedman
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Zachary Faber
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - John Easton
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Tanja Gruber
- 1] Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA [2] Department of Oncology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Janet F Partridge
- Department of Biochemistry, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Li Ding
- 1] The Genome Institute, Washington University School of Medicine, St Louis, Missouri 63108, USA [2] Department of Genetics, Washington University School of Medicine, 4444 Forest Park Ave, St Louis, Missouri 63108, USA [3] Siteman Cancer Center, Washington University, St Louis, Missouri 63108, USA
| | - Richard K Wilson
- 1] The Genome Institute, Washington University School of Medicine, St Louis, Missouri 63108, USA [2] Department of Genetics, Washington University School of Medicine, 4444 Forest Park Ave, St Louis, Missouri 63108, USA [3] Siteman Cancer Center, Washington University, St Louis, Missouri 63108, USA
| | - Elaine R Mardis
- 1] The Genome Institute, Washington University School of Medicine, St Louis, Missouri 63108, USA [2] Department of Genetics, Washington University School of Medicine, 4444 Forest Park Ave, St Louis, Missouri 63108, USA [3] Siteman Cancer Center, Washington University, St Louis, Missouri 63108, USA
| | - Charles G Mullighan
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Richard J Gilbertson
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Gerard Zambetti
- Department of Biochemistry, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - David W Ellison
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - James R Downing
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
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35
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Wu G, Diaz AK, Paugh BS, Rankin SL, Ju B, Li Y, Zhu X, Qu C, Chen X, Zhang J, Easton J, Edmonson M, Ma X, Lu C, Nagahawatte P, Hedlund E, Rusch M, Pounds S, Lin T, Onar-Thomas A, Huether R, Kriwacki R, Parker M, Gupta P, Becksfort J, Wei L, Mulder HL, Boggs K, Vadodaria B, Yergeau D, Russell JC, Ochoa K, Fulton RS, Fulton LL, Jones C, Boop FA, Broniscer A, Wetmore C, Gajjar A, Ding L, Mardis ER, Wilson RK, Taylor MR, Downing JR, Ellison DW, Zhang J, Baker SJ. The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma. Nat Genet 2014; 46:444-450. [PMID: 24705251 PMCID: PMC4056452 DOI: 10.1038/ng.2938] [Citation(s) in RCA: 743] [Impact Index Per Article: 74.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 03/06/2014] [Indexed: 12/12/2022]
Abstract
Pediatric high-grade glioma (HGG) is a devastating disease with a two-year survival of less than 20%1. We analyzed 127 pediatric HGGs, including diffuse intrinsic pontine gliomas (DIPGs) and non-brainstem HGGs (NBS-HGGs) by whole genome, whole exome, and/or transcriptome sequencing. We identified recurrent somatic mutations in ACVR1 exclusively in DIPG (32%), in addition to the previously reported frequent somatic mutations in histone H3, TP53 and ATRX in both DIPG and NBS-HGGs2-5. Structural variants generating fusion genes were found in 47% of DIPGs and NBS-HGGs, with recurrent fusions involving the neurotrophin receptor genes NTRK1, 2, or 3 in 40% of NBS-HGGs in infants. Mutations targeting receptor tyrosine kinase/RAS/PI3K signaling, histone modification or chromatin remodeling, and cell cycle regulation were found in 68%, 73% and 59%, respectively, of pediatric HGGs, including DIPGs and NBS-HGGs. This comprehensive analysis provides insights into the unique and shared pathways driving pediatric HGG within and outside the brainstem.
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Affiliation(s)
- Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Alexander K Diaz
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105.,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163
| | - Barbara S Paugh
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Sherri L Rankin
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Bensheng Ju
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Yongjin Li
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Xiaoyan Zhu
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Chunxu Qu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Junyuan Zhang
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - John Easton
- Department of Pediatric Cancer Genome Project, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Michael Edmonson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Charles Lu
- The Genome Institute, Washington University, 633108
| | - Panduka Nagahawatte
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Erin Hedlund
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Tong Lin
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Arzu Onar-Thomas
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Robert Huether
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Richard Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Matthew Parker
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Pankaj Gupta
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Jared Becksfort
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Lei Wei
- Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY 14263
| | - Heather L Mulder
- Department of Pediatric Cancer Genome Project, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Kristy Boggs
- Department of Pediatric Cancer Genome Project, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Bhavin Vadodaria
- Department of Pediatric Cancer Genome Project, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Donald Yergeau
- Department of Pediatric Cancer Genome Project, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Jake C Russell
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Kerri Ochoa
- The Genome Institute, Washington University, 633108
| | | | | | - Chris Jones
- Division of Molecular Pathology, Institute for Cancer Research, London, UK SM2 5NG.,Division of Cancer Therapeutics, Institute for Cancer Research, London, UK SM2 5NG
| | - Frederick A Boop
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Alberto Broniscer
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Cynthia Wetmore
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Amar Gajjar
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Li Ding
- The Genome Institute, Washington University, 633108
| | | | | | - Michael R Taylor
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105.,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163
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36
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Zhang J, Wu G, Miller CP, Tatevossian RG, Dalton JD, Tang B, Orisme W, Punchihewa C, Parker M, Qaddoumi I, Boop FA, Lu C, Kandoth C, Ding L, Lee R, Huether R, Chen X, Hedlund E, Nagahawatte P, Rusch M, Boggs K, Cheng J, Becksfort J, Ma J, Song G, Li Y, Wei L, Wang J, Shurtleff S, Easton J, Zhao D, Fulton RS, Fulton LL, Dooling DJ, Vadodaria B, Mulder HL, Tang C, Ochoa K, Mullighan CG, Gajjar A, Kriwacki R, Sheer D, Gilbertson RJ, Mardis ER, Wilson RK, Downing JR, Baker SJ, Ellison DW. Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas. Nat Genet 2013; 45:602-12. [PMID: 23583981 PMCID: PMC3727232 DOI: 10.1038/ng.2611] [Citation(s) in RCA: 579] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 03/21/2013] [Indexed: 12/28/2022]
Abstract
The most common pediatric brain tumors are low-grade gliomas (LGGs). We used whole-genome sequencing to identify multiple new genetic alterations involving BRAF, RAF1, FGFR1, MYB, MYBL1 and genes with histone-related functions, including H3F3A and ATRX, in 39 LGGs and low-grade glioneuronal tumors (LGGNTs). Only a single non-silent somatic alteration was detected in 24 of 39 (62%) tumors. Intragenic duplications of the portion of FGFR1 encoding the tyrosine kinase domain (TKD) and rearrangements of MYB were recurrent and mutually exclusive in 53% of grade II diffuse LGGs. Transplantation of Trp53-null neonatal astrocytes expressing FGFR1 with the duplication involving the TKD into the brains of nude mice generated high-grade astrocytomas with short latency and 100% penetrance. FGFR1 with the duplication induced FGFR1 autophosphorylation and upregulation of the MAPK/ERK and PI3K pathways, which could be blocked by specific inhibitors. Focusing on the therapeutically challenging diffuse LGGs, our study of 151 tumors has discovered genetic alterations and potential therapeutic targets across the entire range of pediatric LGGs and LGGNTs.
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Affiliation(s)
- Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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37
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Holmfeldt L, Wei L, Diaz-Flores E, Walsh M, Zhang J, Ding L, Payne-Turner D, Churchman M, Andersson A, Chen SC, McCastlain K, Becksfort J, Ma J, Wu G, Patel SN, Heatley SL, Phillips LA, Song G, Easton J, Parker M, Chen X, Rusch M, Boggs K, Vadodaria B, Hedlund E, Drenberg C, Baker S, Pei D, Cheng C, Huether R, Lu C, Fulton RS, Fulton LL, Tabib Y, Dooling DJ, Ochoa K, Minden M, Lewis ID, To LB, Marlton P, Roberts AW, Raca G, Stock W, Neale G, Drexler HG, Dickins RA, Ellison DW, Shurtleff SA, Pui CH, Ribeiro RC, Devidas M, Carroll AJ, Heerema NA, Wood B, Borowitz MJ, Gastier-Foster JM, Raimondi SC, Mardis ER, Wilson RK, Downing JR, Hunger SP, Loh ML, Mullighan CG. The genomic landscape of hypodiploid acute lymphoblastic leukemia. Nat Genet 2013; 45:242-52. [PMID: 23334668 DOI: 10.1038/ng.2532] [Citation(s) in RCA: 477] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 12/21/2012] [Indexed: 12/17/2022]
Abstract
The genetic basis of hypodiploid acute lymphoblastic leukemia (ALL), a subtype of ALL characterized by aneuploidy and poor outcome, is unknown. Genomic profiling of 124 hypodiploid ALL cases, including whole-genome and exome sequencing of 40 cases, identified two subtypes that differ in the severity of aneuploidy, transcriptional profiles and submicroscopic genetic alterations. Near-haploid ALL with 24-31 chromosomes harbor alterations targeting receptor tyrosine kinase signaling and Ras signaling (71%) and the lymphoid transcription factor gene IKZF3 (encoding AIOLOS; 13%). In contrast, low-hypodiploid ALL with 32-39 chromosomes are characterized by alterations in TP53 (91.2%) that are commonly present in nontumor cells, IKZF2 (encoding HELIOS; 53%) and RB1 (41%). Both near-haploid and low-hypodiploid leukemic cells show activation of Ras-signaling and phosphoinositide 3-kinase (PI3K)-signaling pathways and are sensitive to PI3K inhibitors, indicating that these drugs should be explored as a new therapeutic strategy for this aggressive form of leukemia.
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Affiliation(s)
- Linda Holmfeldt
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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38
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Robinson G, Parker M, Kranenburg TA, Lu C, Chen X, Ding L, Phoenix TN, Hedlund E, Wei L, Zhu X, Chalhoub N, Baker SJ, Huether R, Kriwacki R, Curley N, Thiruvenkatam R, Wang J, Wu G, Rusch M, Hong X, Becksfort J, Gupta P, Ma J, Easton J, Vadodaria B, Onar-Thomas A, Lin T, Li S, Pounds S, Paugh S, Zhao D, Kawauchi D, Roussel MF, Finkelstein D, Ellison DW, Lau CC, Bouffet E, Hassall T, Gururangan S, Cohn R, Fulton RS, Fulton LL, Dooling DJ, Ochoa K, Gajjar A, Mardis ER, Wilson RK, Downing JR, Zhang J, Gilbertson RJ. Novel mutations target distinct subgroups of medulloblastoma. Nature 2012; 488:43-8. [PMID: 22722829 PMCID: PMC3412905 DOI: 10.1038/nature11213] [Citation(s) in RCA: 642] [Impact Index Per Article: 53.5] [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: 01/13/2012] [Accepted: 05/02/2012] [Indexed: 12/22/2022]
Abstract
Medulloblastoma is a malignant childhood brain tumour comprising four discrete subgroups. Here, to identify mutations that drive medulloblastoma, we sequenced the entire genomes of 37 tumours and matched normal blood. One-hundred and thirty-six genes harbouring somatic mutations in this discovery set were sequenced in an additional 56 medulloblastomas. Recurrent mutations were detected in 41 genes not yet implicated in medulloblastoma; several target distinct components of the epigenetic machinery in different disease subgroups, such as regulators of H3K27 and H3K4 trimethylation in subgroups 3 and 4 (for example, KDM6A and ZMYM3), and CTNNB1-associated chromatin re-modellers in WNT-subgroup tumours (for example, SMARCA4 and CREBBP). Modelling of mutations in mouse lower rhombic lip progenitors that generate WNT-subgroup tumours identified genes that maintain this cell lineage (DDX3X), as well as mutated genes that initiate (CDH1) or cooperate (PIK3CA) in tumorigenesis. These data provide important new insights into the pathogenesis of medulloblastoma subgroups and highlight targets for therapeutic development.
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Affiliation(s)
- Giles Robinson
- St Jude Children's Research Hospital, Washington University Pediatric Cancer Genome Project, Memphis, Tennessee 38105, USA
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39
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Li KKW, Pang JCS, Ng HK, Massimino M, Gandola L, Biassoni V, Spreafico F, Schiavello E, Poggi G, Casanova M, Pecori E, De Pava MV, Ferrari A, Meazza C, Terenziani M, Polastri D, Luksch R, Podda M, Modena P, Antonelli M, Giangaspero F, Ahmed S, Zaghloul MS, Mousa AG, Eldebawy E, Elbeltagy M, Awaad M, Massimino M, Gandola L, Biassoni V, Antonelli M, Schiavello E, Buttarelli F, Spreafico F, Collini P, Pollo B, Patriarca C, Giangaspero F, MacDonald T, Liu J, Munson J, Park J, Wang K, Fei B, Bellamkonda R, Arbiser J, Gomi A, Yamaguchi T, Mashiko T, Oguro K, Somasundaram A, Neuberg R, Grant G, Fuchs H, Driscoll T, Becher O, McLendon R, Cummings T, Gururangan S, Bourdeaut F, Grison C, Doz F, Pierron G, Delattre O, Couturier J, Cho YJ, Pugh T, Weeraratne SD, Archer T, Krummel DP, Auclair D, Cibulkis K, Lawrence M, Greulich H, McKenna A, Ramos A, Shefler E, Sivachenko A, Amani V, Pierre-Francois J, Teider N, Northcott P, Taylor M, Meyerson M, Pomeroy S, Potts C, Cline H, Rotenberry R, Guldal C, Bhatia B, Nahle Z, Kenney A, Fan YN, Pizer B, See V, Makino K, Nakamura H, Kuratsu JI, Grahlert J, Ma M, Fiaschetti G, Shalaby T, Grotzer M, Baumgartner M, Clifford S, Gustafsson G, Ellison D, Figarella-Branger D, Doz F, Rutkowski S, Lannering B, Pietsch T, Fiaschetti G, Shalaby T, Baumgartner M, Grotzer M, Fleischhack G, Siegler N, Zimmermann M, Rutkowski S, Warmuth-Metz M, Kortmann RD, Pietsch T, Faldum A, Bode U, Yoon JH, Kang HJ, Park KD, Park SH, Phi JH, Kim SK, Wang KC, Kim IH, Shin HY, Ahn HS, Faria C, Golbourn B, Smith C, Rutka J, Greene BD, Whitton A, Singh S, Scheinemann K, Hill R, Lindsey J, Howell C, Ryan S, Shiels K, Shrimpton E, Bailey S, Clifford S, Schwalbe E, Lindsey J, Williamson D, Hamilton D, Northcott P, O'Toole K, Nicholson SL, Lusher M, Gilbertson R, Hauser P, Taylor M, Taylor R, Ellison D, Bailey S, Clifford S, Kool M, Jones DTW, Jager N, Hovestadt V, Schuller U, Jabado N, Perry A, Cowdrey C, Croul S, Collins VP, Cho YJ, Pomeroy S, Eils R, Korshunov A, Lichter P, Pfister S, Northcott P, Shih D, Taylor M, Darabi A, Sanden E, Visse E, Siesjo P, Harris P, Venkataraman S, Alimova I, Birks D, Cristiano B, Donson A, Foreman N, Vibhakar R, Bertin D, Vallero S, Basso ME, Romano E, Peretta P, Morra I, Mussano A, Fagioli F, Kunkele A, De Preter K, Heukamp L, Thor T, Pajtler K, Hartmann W, Mittelbronn M, Grotzer M, Deubzer H, Speleman F, Schramm A, Eggert A, Schulte J, Bandopadhayay P, Kieran M, Manley P, Robison N, Chi S, Thor T, Mestdagh P, Vandesomple J, Fuchs H, Durner VG, de Angelis MH, Heukamp L, Kunkele A, Pajtler K, Eggert A, Schramm A, Schulte JH, Ohe N, Yano H, Nakayama N, Iwama T, Lastowska M, Perek-Polnik M, Grajkowska W, Malczyk K, Cukrowska B, Dembowska-Baginska B, Perek D, Othman RT, Storer L, Grundy R, Kerr I, Coyle B, Hulleman E, Lagerweij T, Biesmans D, Crommentuijn MHW, Cloos J, Tannous BA, Vandertop WP, Noske DP, Kaspers GJL, Wurdinger T, Bergthold G, El Kababri M, Varlet P, Dhermain F, Sainte-Rose C, Raquin MA, Valteau-Couanet D, Grill J, Dufour C, Burchill C, Hii H, Dallas P, Cole C, Endersby R, Gottardo N, Gevorgian A, Morozova E, Kazantsev I, Youhta T, Safonova S, Kozlov A, Punanov Y, Afanasyev B, Zheludkova O, Packer R, Gajjar A, Michalski J, Jakacki R, Gottardo N, Tarbell N, Vezina G, Olson J, Friedrich C, von Bueren AO, von Hoff K, Gerber NU, Benesch M, Faldum A, Pietsch T, Warmuth-Metz M, Kuehl J, Kortmann RD, Rutkowski S, Malbari F, Atlas M, Friedman G, Kelly V, Bray A, Cassady K, Markert J, Gillespie Y, Taylor R, Howman A, Brogden E, Robinson K, Jones D, Gibson M, Bujkiewicz S, Mitra D, Saran F, Michalski A, Pizer B, Jones DTW, Jager N, Kool M, Zichner T, Hutter B, Sultan M, Cho YJ, Pugh TJ, Warnatz HJ, Reifenberger G, Northcott PA, Taylor MD, Meyerson M, Pomeroy SL, Yaspo ML, Korbel JO, Korshunov A, Eils R, Pfister SM, Lichter P, Pajtler KW, Weingarten C, Thor T, Kuenkele A, Fleischhack G, Heukamp LC, Buettner R, Kirfel J, Eggert A, Schramm A, Schulte JH, Friedrich C, von Bueren AO, von Hoff K, Gerber NU, Benesch M, Kwiecien R, Pietsch T, Warmuth-Metz M, Faldum A, Kuehl J, Kortmann RD, Rutkowski S, Lupo P, Scheurer M, Martin A, Nirschl C, Polanczyk M, Cohen KJ, Pardoll DM, Drake CG, Lim M, Manoranjan B, Hallett R, Wang X, Venugopal C, McFarlane N, Sheinemann K, Hassell J, Singh S, Venugopal C, Manoranjan B, McFarlane N, Whitton A, Delaney K, Scheinemann K, Singh S, Manoranjan B, Hallett R, Venugopal C, McFarlane N, Hassell J, Scheinemann K, Dunn S, Singh S, Garcia I, Crowther AJ, Gama V, Miller CR, Deshmukh M, Gershon TR, Garcia I, Crowther AJ, Gershon TR, Gerber NU, von Hoff K, Friedrich C, von Bueren AO, Treulieb W, Benesch M, Faldum A, Pietsch T, Warmuth-Metz M, Rutkowski S, Kortmann RD, Zin A, De Bortoli M, Bonvini P, Viscardi E, Perilongo G, Rosolen A, Connolly E, Zhang C, Anderson R, Feldstein N, Stark E, Garvin J, Shing MMK, Lee V, Cheng FWT, Leung AWK, Zhu XL, Wong HT, Kam M, Li CK, Ward S, Sengupta R, Kroll K, Rubin J, Dallas P, Milech N, Longville B, Hopkins R, Vergiliana JVD, Endersby R, Gottardo N, von Bueren AO, Gerss J, Hagel C, Cai H, Remke M, Hasselblatt M, Feuerstein BG, Pernet S, Delattre O, Korshunov A, Rutkowski S, Pfister SM, Baudis M, Lee C, Fotovati A, Triscott J, Dunn S, Valdora F, Freier F, Seyler C, Brady N, Bender S, Northcott P, Kool M, Jones D, Coco S, Tonini GP, Scheurlen W, Boutros M, Taylor M, Katus H, Kulozik A, Zitron E, Korshunov A, Lichter P, Pfister S, Remke M, Shih DJH, Northcott PA, Van Meter T, Pollack IF, Van Meir E, Eberhart CG, Fan X, Dellatre O, Collins VP, Jones DTW, Clifford SC, Pfister SM, Taylor MD, Pompe R, von Bueren AO, von Hoff K, Friedrich C, Treulieb W, Lindow C, Deinlein F, Kuehl J, Rutkowski S, Gupta T, Krishnatry R, Shirsat N, Epari S, Kunder R, Kurkure P, Vora T, Moiyadi A, Jalali R, Cohen K, Perek D, Perek-Polnik M, Dembowska-Baginska B, Drogosiewicz M, Grajkowska W, Lastowska M, Chojnacka M, Filipek I, Tarasinska M, Roszkowski M, Hauser P, Jakab Z, Bognar L, Markia B, Gyorsok Z, Ottoffy G, Nagy K, Cservenyak J, Masat P, Turanyi E, Vizkeleti J, Krivan G, Kallay K, Schuler D, Garami M, Lacroix J, Schlund F, Adolph K, Leuchs B, Bender S, Hielscher T, Pfister S, Witt O, Schlehofer JR, Rommelaere J, Witt H, Leskov K, Ma N, Eberhart C, Stearns D, Dagri JN, Torkildson J, Evans A, Ashby LS, Zakotnik B, Brown RJ, Dhall G, Portnow J, Finlay JL, McCabe M, Pizer B, Marino AM, Baryawno N, Ekstrom TP, Ostman A, Johnsen JI, Robinson G, Parker M, Kranenburg T, Lu C, Pheonix T, Huether R, Easton J, Onar A, Lau C, Bouffet E, Gururangan S, Hassall T, Cohn R, Gajjar A, Ellison D, Mardis E, Wilson R, Downing J, Zhang J, Gilbertson R, Robinson G, Dalton J, O'Neill T, Yong W, Chingtagumpala M, Bouffet E, Bowers D, Kellie S, Gururangan S, Fisher P, Bendel A, Fisher M, Hassall T, Wetmore C, Broniscer A, Clifford S, Gilbertson R, Gajjar A, Ellison D, Zhukova N, Martin D, Lipman T, Castelo-Branco P, Zhang C, Fraser M, Baskin B, Ray P, Bouffet E, Alman B, Ramaswamy V, Dirks P, Clifford S, Rutkowski S, Pfister S, Bristow R, Taylor M, Malkin D, Hawkins C, Tabori U, Dhall G, Ji L, Haley K, Gardner S, Sposto R, Finlay J, Leary S, Strand A, Ditzler S, Heinicke G, Conrad L, Richards A, Pedro K, Knoblaugh S, Cole B, Olson J, Yankelevich M, Budarin M, Konski A, Mentkevich G, Stefanits H, Ebetsberger-Dachs G, Weis S, Haberler C, Milosevic J, Baryawno N, Sveinbjornsson B, Martinsson T, Grotzer M, Johnsen JI, Kogner P, Garzia L, Morrisy S, Jelveh S, Lindsay P, Hill R, Taylor M, Marks A, Zhang H, Rood B, Williamson D, Clifford S, Aurtenetxe O, Gaffar A, Lopez JI, Urberuaga A, Navajas A, O'Halloran K, Hukin J, Singhal A, Dunham C, Goddard K, Rassekh SR, Davidson TB, Fangusaro JR, Ji L, Sposto R, Gardner SL, Allen JC, Dunkel IJ, Dhall G, Finlay JL, Trivedi M, Tyagi A, Goodden J, Chumas P, O'kane R, Crimmins D, Elliott M, Picton S, Silva DS, Viana-Pereira M, Stavale JN, Malheiro S, Almeida GC, Clara C, Jones C, Reis RM, Spence T, Sin-Chan P, Picard D, Ho KC, Lu M, Huang A, Bochare S, Khatua S, Gopalakrishnan V, Chan TSY, Picard D, Pfister S, Hawkins C, Huang A, Chan TSY, Picard D, Ho KC, Huang A, Picard D, Millar S, Hawkins C, Rogers H, Kim SK, Ra YS, Fangusaro J, Toledano H, Nakamura H, Van Meter T, Pomeroy S, Ng HK, Jones C, Gajjar A, Clifford S, Pfister S, Eberhart C, Bouffet E, Grundy R, Huang A, Sengupta S, Weeraratne SD, Phallen J, Sun H, Rallapalli S, Amani V, Pierre-Francois J, Teider N, Cook J, Jensen F, Lim M, Pomeroy S, Cho YJ. MEDULLOBLASTOMA. Neuro Oncol 2012; 14:i82-i105. [PMCID: PMC3483339 DOI: 10.1093/neuonc/nos093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023] Open
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Robinson GW, Parker M, Kranenburg T, Lu C, Chen X, Ding L, Phoenix T, Huether R, Thiruvenkatam R, Wang J, Easton J, Onar-Thomas A, Gajjar AJ, Ellison DW, Mardis E, Wilson RK, Downing J, Zhang J, Gilbertson RJ. Use of whole genome sequencing to identify novel mutations in distinct subgroups of medulloblastoma. J Clin Oncol 2012. [DOI: 10.1200/jco.2012.30.15_suppl.9518] [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: 11/20/2022] Open
Abstract
9518 Background: Medulloblastoma is a malignant childhood brain tumor comprising four discrete subgroups (SHH-subgroup, WNT-subgroup, subgroup-3 and subgroup-4). The genetic alterations that drive these subgroups and that might serve as treatment targets are largely unknown. Methods: We sequenced entire genomes of 37 tumors and matched normal blood. 136 somatically mutated genes identified in this discovery cohort were sequenced in an additional 56 medulloblastomas. All tumors were classified into the 4 subgroups by expression profiling and immunohistochemistry. All mutations were validated by custom capture, 454, or Sanger sequencing. Results: Recurrent mutations were detected in 49 genes: 41 are not yet implicated in medulloblastoma. Several target distinct components of the epigenetic machinery in different disease subgroups, e.g., regulators of H3K27 and H3K4 trimethylation in subgroup-3 and 4 (e.g., KDM6A and ZMYM3), and CTNNB1-associated chromatin remodellers in WNT-subgroup tumors (e.g., SMARCA4 and CREBBP). Modelling of mutations in mouse lower rhombic lip progenitors that generate WNT-subgroup tumours, identified genes that maintain this cell lineage (DDX3X) as well as mutated genes that initiate (CDH1) or cooperate (PIK3CA) in tumourigenesis. Conclusions: We have identified several new recurrent somatic mutations that are enriched in specific subgroups of medulloblastoma. Alterations affecting subgroup-3 and 4 tumors appear to disrupt chromatin marking, most notably H3K27me3, potentially preserving a stem cell-like state in tumor cells. Mutations in WNT subgroup tumors affect binding partners of CTNNB1 that regulate WNT-response gene transcription. These data provide important new insights into the pathogenesis of medulloblastoma subgroups and highlight targets for therapeutic development.
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Affiliation(s)
| | | | | | - Charles Lu
- Washington University School of Medicine, St. Louis, MO
| | - Xiang Chen
- St. Jude Children's Research Hospital, Memphis, TN
| | - Li Ding
- The Genome Institute, Washington University School of Medicine, St. Louis, MO
| | | | | | | | - Jianmin Wang
- St. Jude Children's Research Hospital, Memphis, TN
| | - John Easton
- St. Jude Children's Research Hospital, Memphis, TN
| | | | | | | | - Elaine Mardis
- The Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Richard K. Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, MO
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Duax WL, Huether R, Dziak D. Evolution of bacterial ribosomal protein L1. Int J Bioinform Res Appl 2012; 8:99-111. [PMID: 22450273 DOI: 10.1504/ijbra.2012.045979] [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] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Search vectors composed of Gly, Ala, Arg, and Pro (GARP) residues retrieve 98% of each of the ribosomal proteins in prokaryotic species with no false hits. Different combinations of G, A, R and P and insertions differentiate each ribosomal protein from all others. Amino acids in two sequence positions separate Gram+ from Gram- bacteria. Specific residues separate proteins of cyanobacteria and chloroplasts from all other species. Structural information played an essential role in developing a GARP based technique to achieve perfect sequence alignment. It is possible to understand why GARP residues are 100% conserved in specific positions in families of proteins present in all species.
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Affiliation(s)
- William L Duax
- Department of Structural Biology, Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA.
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Xu I, Chee M, Duax WL, Huether R, Dziak D. Perfect alignment of ribosomal protein S3 in creating an evolutionary tree. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311093317] [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: 11/10/2022] Open
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Pacheco CM, Huether R, Duax WL. Substrate fingerprint and the structure of NADP+ dependent serine dehydrogenase from Saccharomyces cerevisiaecomplexed with NADP+. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311083991] [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: 11/11/2022] Open
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Duax WL, Huether R, Dziak D, McEachon C. Immutable glycine-based perfect alignment of protein families. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311096747] [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: 11/11/2022] Open
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Duax WL, Huether R, Dziak D. Finding LUCA, Buffalo High School students trace the origin of the genetic code. FASEB J 2011. [DOI: 10.1096/fasebj.25.1_supplement.576.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Duax WL, Huether R, Dziak D. Ribosomal protein structures and sequences define the prokaryotic tree of life. Acta Crystallogr A 2010. [DOI: 10.1107/s010876731009954x] [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: 11/10/2022] Open
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Huether R, Mao Q, Duax WL, Umland TC. The short-chain oxidoreductase Q9HYA2 from Pseudomonas aeruginosa PAO1 contains an atypical catalytic center. Protein Sci 2010; 19:1097-103. [PMID: 20340135 DOI: 10.1002/pro.384] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The characteristic oxidation or reduction reaction mechanisms of short-chain oxidoreductase (SCOR) enzymes involve a highly conserved Asp-Ser-Tyr-Lys catalytic tetrad. The SCOR enzyme Q9HYA2 from the pathogenic bacterium Pseudomonas aeruginosa was recognized to possess an atypical catalytic tetrad composed of Lys118-Ser146-Thr159-Arg163. Orthologs of Q9HYA2 containing the unusual catalytic tetrad along with conserved substrate and cofactor recognition residues were identified in 27 additional species, the majority of which are bacterial pathogens. However, this atypical catalytic tetrad was not represented within the Protein Data Bank. The crystal structures of unligated and NADPH-complexed Q9HYA2 were determined at 2.3 A resolution. Structural alignment to a polyketide ketoreductase (KR), a typical SCOR, demonstrated that Q9HYA2's Lys118, Ser146, and Arg163 superimposed upon the KR's catalytic Asp114, Ser144, and Lys161, respectively. However, only the backbone of Q9HYA2's Thr159 overlapped KR's catalytic Tyr157. The Thr159 hydroxyl in apo Q9HYA2 is poorly positioned for participating in catalysis. In the Q9HYA2-NADPH complex, the Thr159 side chain was modeled in two alternate rotamers, one of which is positioned to interact with other members of the tetrad and the bound cofactor. A chloride ion is bound at the position normally occupied by the catalytic tyrosine hydroxyl. The putative active site of Q9HYA2 contains a chemical moiety at each catalytically important position of a typical SCOR enzyme. This is the first observation of a SCOR protein with this alternate catalytic center that includes threonine replacing the catalytic tyrosine and an ion replacing the hydroxyl moiety of the catalytic tyrosine.
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Affiliation(s)
- Robert Huether
- Department of Structural Biology, University at Buffalo, Buffalo, New York 14203, USA
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Duax W, Huether R, Hogan D, Teysir J, Dziak D. Ribosomal protein sequence analysis reveals the order of evolution of bacterial classes, direct lineage of Cyanobacteria and Chloroplasts and that LUCA was an Actinobacteria. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.854.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- William Duax
- Structural BiologyHauptman‐Woodward InstituteBuffaloNY
| | | | - Dana Hogan
- Structural BiologyHauptman‐Woodward InstituteBuffaloNY
| | | | - David Dziak
- Structural BiologyHauptman‐Woodward InstituteBuffaloNY
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Huether R, Duax W. Correlation in species, cofactor, oligomerization and substrate specificity in short‐chain oxidoreductase enzymes. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.lb163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Robert Huether
- Structural BiologyState University of New York at BuffaloBuffaloNY
| | - William Duax
- Structural BiologyHauptman‐Woodward InstituteBuffaloNY
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Huether R, Liu ZJ, Xu H, Wang BC, Pletnev VZ, Mao Q, Duax WL, Umland TC. Sequence fingerprint and structural analysis of the SCOR enzyme A3DFK9 from Clostridium thermocellum. Proteins 2010; 78:603-13. [PMID: 19774618 DOI: 10.1002/prot.22584] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We have identified a highly conserved fingerprint of 40 residues in the TGYK subfamily of the short-chain oxidoreductase enzymes. The TGYK subfamily is defined by the presence of an N-terminal TGxxxGxG motif and a catalytic YxxxK motif. This subfamily contains more than 12,000 members, with individual members displaying unique substrate specificities. The 40 fingerprint residues are critical to catalysis, cofactor binding, protein folding, and oligomerization but are substrate independent. Their conservation provides critical insight into evolution of the folding and function of TGYK enzymes. Substrate specificity is determined by distinct combinations of residues in three flexible loops that make up the substrate-binding pocket. Here, we report the structure determinations of the TGYK enzyme A3DFK9 from Clostridium thermocellum in its apo form and with bound NAD(+) cofactor. The function of this protein is unknown, but our analysis of the substrate-binding loops putatively identifies A3DFK9 as a carbohydrate or polyalcohol metabolizing enzyme. C. thermocellum has potential commercial applications because of its ability to convert biomaterial into ethanol. A3DFK9 contains 31 of the 40 TGYK subfamily fingerprint residues. The most significant variations are the substitution of a cysteine (Cys84) for a highly conserved glycine within a characteristic VNNAG motif, and the substitution of a glycine (Gly106) for a highly conserved asparagine residue at a helical kink. Both of these variations occur at positions typically participating in the formation of a catalytically important proton transfer network. An alternate means of stabilizing this proton wire was observed in the A3DFK9 crystal structures.
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Affiliation(s)
- Robert Huether
- Department of Structural Biology, SUNY at Buffalo, Buffalo, New York 14203, USA
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