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Saldivar JS, Harris J, Ayash E, Hong M, Tandon P, Sinha S, Hebron PM, Houghton EE, Thorne K, Goodman LJ, Li C, Marfatia TR, Anderson J, Morra M, Lyle J, Bartha G, Chen R. Analytic validation of NeXT Dx™, a comprehensive genomic profiling assay. Oncotarget 2023; 14:789-806. [PMID: 37646774 PMCID: PMC10467627 DOI: 10.18632/oncotarget.28490] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/19/2023] [Indexed: 09/01/2023] Open
Abstract
We describe the analytic validation of NeXT Dx, a comprehensive genomic profiling assay to aid therapy and clinical trial selection for patients diagnosed with solid tumor cancers. Proprietary methods were utilized to perform whole exome and whole transcriptome sequencing for detection of single nucleotide variants (SNVs), insertions/deletions (indels), copy number alterations (CNAs), and gene fusions, and determination of tumor mutation burden and microsatellite instability. Variant calling is enhanced by sequencing a patient-specific normal sample from, for example, a blood specimen. This provides highly accurate somatic variant calls as well as the incidental reporting of pathogenic and likely pathogenic germline alterations. Fusion detection via RNA sequencing provides more extensive and accurate fusion calling compared to DNA-based tests. NeXT Dx features the proprietary Accuracy and Content Enhanced technology, developed to optimize sequencing and provide more uniform coverage across the exome. The exome was validated at a median sequencing depth of >500x. While variants from 401 cancer-associated genes are currently reported from the assay, the exome/transcriptome assay is broadly validated to enable reporting of additional variants as they become clinically relevant. NeXT Dx demonstrated analytic sensitivities as follows: SNVs (99.4%), indels (98.2%), CNAs (98.0%), and fusions (95.8%). The overall analytic specificity was >99.0%.
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Affiliation(s)
| | - Jason Harris
- Personalis, Inc., Fremont, CA 94555, USA
- These authors contributed equally to this work
| | - Erin Ayash
- Personalis, Inc., Fremont, CA 94555, USA
| | | | | | | | | | | | | | | | - Conan Li
- Personalis, Inc., Fremont, CA 94555, USA
| | | | | | | | - John Lyle
- Personalis, Inc., Fremont, CA 94555, USA
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Vilov S, Heinig M. DeepSom: a CNN-based approach to somatic variant calling in WGS samples without a matched normal. Bioinformatics 2023; 39:6986966. [PMID: 36637201 PMCID: PMC9843587 DOI: 10.1093/bioinformatics/btac828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/19/2022] [Accepted: 01/12/2023] [Indexed: 01/14/2023] Open
Abstract
MOTIVATION Somatic mutations are usually called by analyzing the DNA sequence of a tumor sample in conjunction with a matched normal. However, a matched normal is not always available, for instance, in retrospective analysis or diagnostic settings. For such cases, tumor-only somatic variant calling tools need to be designed. Previously proposed approaches demonstrate inferior performance on whole-genome sequencing (WGS) samples. RESULTS We present the convolutional neural network-based approach called DeepSom for detecting somatic single nucleotide polymorphism and short insertion and deletion variants in tumor WGS samples without a matched normal. We validate DeepSom by reporting its performance on five different cancer datasets. We also demonstrate that on WGS samples DeepSom outperforms previously proposed methods for tumor-only somatic variant calling. AVAILABILITY AND IMPLEMENTATION DeepSom is available as a GitHub repository at https://github.com/heiniglab/DeepSom. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sergey Vilov
- Institute of Computational Biology, Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), 85764 Neuherberg, Germany
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3
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Cai Y, Chen R, Gao S, Li W, Liu Y, Su G, Song M, Jiang M, Jiang C, Zhang X. Artificial intelligence applied in neoantigen identification facilitates personalized cancer immunotherapy. Front Oncol 2023; 12:1054231. [PMID: 36698417 PMCID: PMC9868469 DOI: 10.3389/fonc.2022.1054231] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/16/2022] [Indexed: 01/10/2023] Open
Abstract
The field of cancer neoantigen investigation has developed swiftly in the past decade. Predicting novel and true neoantigens derived from large multi-omics data became difficult but critical challenges. The rise of Artificial Intelligence (AI) or Machine Learning (ML) in biomedicine application has brought benefits to strengthen the current computational pipeline for neoantigen prediction. ML algorithms offer powerful tools to recognize the multidimensional nature of the omics data and therefore extract the key neoantigen features enabling a successful discovery of new neoantigens. The present review aims to outline the significant technology progress of machine learning approaches, especially the newly deep learning tools and pipelines, that were recently applied in neoantigen prediction. In this review article, we summarize the current state-of-the-art tools developed to predict neoantigens. The standard workflow includes calling genetic variants in paired tumor and blood samples, and rating the binding affinity between mutated peptide, MHC (I and II) and T cell receptor (TCR), followed by characterizing the immunogenicity of tumor epitopes. More specifically, we highlight the outstanding feature extraction tools and multi-layer neural network architectures in typical ML models. It is noted that more integrated neoantigen-predicting pipelines are constructed with hybrid or combined ML algorithms instead of conventional machine learning models. In addition, the trends and challenges in further optimizing and integrating the existing pipelines are discussed.
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Affiliation(s)
- Yu Cai
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Rui Chen
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Shenghan Gao
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Wenqing Li
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Yuru Liu
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Guodong Su
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Mingming Song
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Mengju Jiang
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Chao Jiang
- Department of Neurology, The Second Affiliated Hospital of Xi’an Medical University, Xi’an, Shaanxi, China,*Correspondence: Chao Jiang, ; Xi Zhang,
| | - Xi Zhang
- School of Medicine, Northwest University, Xi’an, Shaanxi, China,*Correspondence: Chao Jiang, ; Xi Zhang,
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4
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McLaughlin RT, Asthana M, Di Meo M, Ceccarelli M, Jacob HJ, Masica DL. Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning. NPJ Precis Oncol 2023; 7:4. [PMID: 36611079 PMCID: PMC9825621 DOI: 10.1038/s41698-022-00340-1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 12/12/2022] [Indexed: 01/08/2023] Open
Abstract
Accurately identifying somatic mutations is essential for precision oncology and crucial for calculating tumor-mutational burden (TMB), an important predictor of response to immunotherapy. For tumor-only variant calling (i.e., when the cancer biopsy but not the patient's normal tissue sample is sequenced), accurately distinguishing somatic mutations from germline variants is a challenging problem that, when unaddressed, results in unreliable, biased, and inflated TMB estimates. Here, we apply machine learning to the task of somatic vs germline classification in tumor-only solid tumor samples using TabNet, XGBoost, and LightGBM, three machine-learning models for tabular data. We constructed a training set for supervised classification using features derived exclusively from tumor-only variant calling and drawing somatic and germline truth labels from an independent pipeline using the patient-matched normal samples. All three trained models achieved state-of-the-art performance on two holdout test datasets: a TCGA dataset including sarcoma, breast adenocarcinoma, and endometrial carcinoma samples (AUC > 94%), and a metastatic melanoma dataset (AUC > 85%). Concordance between matched-normal and tumor-only TMB improves from R2 = 0.006 to 0.71-0.76 with the addition of a machine-learning classifier, with LightGBM performing best. Notably, these machine-learning models generalize across cancer subtypes and capture kits with a call rate of 100%. We reproduce the recent finding that tumor-only TMB estimates for Black patients are extremely inflated relative to that of white patients due to the racial biases of germline databases. We show that our approach with XGBoost and LightGBM eliminates this significant racial bias in tumor-only variant calling.
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Affiliation(s)
| | - Maansi Asthana
- Agricultural and Biological Engineering at Purdue University, West Lafayette, IN, USA
| | - Marc Di Meo
- Johns Hopkins University, Baltimore, MD, USA
| | - Michele Ceccarelli
- Department of Electrical Engineering and Information Technology, University of Naples "Federico II", Naples, Italy
- Biogem, Instituto di Biologia e Genetica Molecolare, Ariano Irpino, Italy
| | | | - David L Masica
- Genomics Research Center, AbbVie, Redwood City, CA, USA.
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Arora K, Tran TN, Kemel Y, Mehine M, Liu YL, Nandakumar S, Smith SA, Brannon AR, Ostrovnaya I, Stopsack KH, Razavi P, Safonov A, Rizvi HA, Hellmann MD, Vijai J, Reynolds TC, Fagin JA, Carrot-Zhang J, Offit K, Solit DB, Ladanyi M, Schultz N, Zehir A, Brown CL, Stadler ZK, Chakravarty D, Bandlamudi C, Berger MF. Genetic Ancestry Correlates with Somatic Differences in a Real-World Clinical Cancer Sequencing Cohort. Cancer Discov 2022; 12:2552-2565. [PMID: 36048199 PMCID: PMC9633436 DOI: 10.1158/2159-8290.cd-22-0312] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/12/2022] [Accepted: 08/29/2022] [Indexed: 01/12/2023]
Abstract
Accurate ancestry inference is critical for identifying genetic contributors of cancer disparities among populations. Although methods to infer genetic ancestry have historically relied upon genome-wide markers, the adaptation to targeted clinical sequencing panels presents an opportunity to incorporate ancestry inference into routine diagnostic workflows. We show that global ancestral contributions and admixture of continental populations can be quantitatively inferred using markers captured by the MSK-IMPACT clinical panel. In a pan-cancer cohort of 45,157 patients, we observed differences by ancestry in the frequency of somatic alterations, recapitulating known associations and revealing novel associations. Despite the comparable overall prevalence of driver alterations by ancestry group, the proportion of patients with clinically actionable alterations was lower for African (30%) compared with European (33%) ancestry. Although this result is largely explained by population-specific cancer subtype differences, it reveals an inequity in the degree to which different populations are served by existing precision oncology interventions. SIGNIFICANCE We performed a comprehensive analysis of ancestral associations with somatic mutations in a real-world pan-cancer cohort, including >5,000 non-European individuals. Using an FDA-authorized tumor sequencing panel and an FDA-recognized oncology knowledge base, we detected differences in the prevalence of clinically actionable alterations, potentially contributing to health care disparities affecting underrepresented populations. This article is highlighted in the In This Issue feature, p. 2483.
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Affiliation(s)
- Kanika Arora
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thinh Ngoc. Tran
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yelena Kemel
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Miika Mehine
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying L. Liu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Subhiksha Nandakumar
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shaleigh A Smith
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A. Rose Brannon
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Konrad H. Stopsack
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anton Safonov
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hira A. Rizvi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew D. Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph Vijai
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thomas C. Reynolds
- Office of Health Equity, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James A. Fagin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jian Carrot-Zhang
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth Offit
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B. Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carol L. Brown
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Office of Health Equity, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zsofia K. Stadler
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Debyani Chakravarty
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chaitanya Bandlamudi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F. Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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6
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Postel MD, Culver JO, Ricker C, Craig DW. Transcriptome analysis provides critical answers to the "variants of uncertain significance" conundrum. Hum Mutat 2022; 43:1590-1608. [PMID: 35510381 PMCID: PMC9560997 DOI: 10.1002/humu.24394] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/16/2022] [Accepted: 04/26/2022] [Indexed: 12/30/2022]
Abstract
While whole-genome and exome sequencing have transformed our collective understanding of genetics' role in disease pathogenesis, there are certain conditions and populations for whom DNA-level data fails to identify the underlying genetic etiology. Specifically, patients of non-White race and non-European ancestry are disproportionately affected by "variants of unknown/uncertain significance" (VUS), limiting the scope of precision medicine for minority patients and perpetuating health disparities. VUS often include deep intronic and splicing variants which are difficult to interpret from DNA data alone. RNA analysis can illuminate the consequences of VUS, thereby allowing for their reclassification as pathogenic versus benign. Here we review the critical role transcriptome analysis plays in clarifying VUS in both neoplastic and non-neoplastic diseases.
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Affiliation(s)
- Mackenzie D. Postel
- Department of Translational GenomicsUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Julie O. Culver
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Charité Ricker
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - David W. Craig
- Department of Translational GenomicsUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
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7
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Gerami P, Benton S, Zhao J, Zhang B, Lampley N, Roth A, Boutko A, Olivares S, Busam KJ. PRAME Expression Correlates With Genomic Aberration and Malignant Diagnosis of Spitzoid Melanocytic Neoplasms. Am J Dermatopathol 2022; 44:575-580. [PMID: 35503885 PMCID: PMC11010723 DOI: 10.1097/dad.0000000000002208] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
ABSTRACT Spitzoid melanocytic neoplasms are a diagnostically challenging class of lesions in dermatopathology. Recently, molecular assays and immunohistochemical markers have been explored as ancillary methods to assist in the diagnostic workup. Specifically, preferentially expressed antigen in melanoma (PRAME) immunohistochemistry is a nuclear stain commonly positive in melanomas, but not in nevi. This study investigates PRAME immunoreactivity (≥75% positive nuclear staining in tumor cells) in a set of 59 spitzoid melanocytic neoplasms with known clinical outcomes. We compared PRAME status with (1) the clinical outcomes, (2) the morphologic diagnoses, and (3) the status of TERT promoter mutation. Regarding clinical outcomes, 3 cases developed metastatic disease, of which 2 expressed diffusely positive PRAME staining. Of the 56 cases that did not show evidence of metastasis, 6 expressed diffusely positive PRAME staining. Morphologically, diffusely positive PRAME staining was seen in 7 of 21 cases (33.3%) diagnosed as melanoma and only 1 benign tumor 1 of 38 (2.6%). There were 4 of 8 cases with a TERT promoter mutation which were diffusely PRAME-positive compared with 4 of 51 cases without TERT promoter mutation ( P = 0.001). Our results show a statistically significant correlation between PRAME expression and the diagnosis, outcome, and TERT promoter mutation status of atypical spitzoid melanocytic neoplasms, suggesting immunohistochemistry for PRAME can help support a suspected diagnosis. However, because of occasional false-positive and negative test results, correlation with the clinical and histologic findings as well as results from other tests is needed for the interpretation of diagnostically challenging spitzoid melanocytic neoplasms.
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Affiliation(s)
- Pedram Gerami
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Sarah Benton
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Jeffrey Zhao
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Bin Zhang
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Nathaniel Lampley
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Andrew Roth
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Anastasiya Boutko
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Shantel Olivares
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Klaus J Busam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
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8
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Hercules SM, Liu X, Bassey-Archibong BBI, Skeete DHA, Smith Connell S, Daramola A, Banjo AA, Ebughe G, Agan T, Ekanem IO, Udosen J, Obiorah C, Ojule AC, Misauno MA, Dauda AM, Egbujo EC, Hercules JC, Ansari A, Brain I, MacColl C, Xu Y, Jin Y, Chang S, Carpten JD, Bédard A, Pond GR, Blenman KRM, Manojlovic Z, Daniel JM. Analysis of the genomic landscapes of Barbadian and Nigerian women with triple negative breast cancer. Cancer Causes Control 2022; 33:831-841. [PMID: 35384527 PMCID: PMC9085672 DOI: 10.1007/s10552-022-01574-x] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 03/12/2022] [Indexed: 11/10/2022]
Abstract
PURPOSE Triple negative breast cancer (TNBC) is an aggressive breast cancer subtype that disproportionately affects women of African ancestry (WAA) and is often associated with poor survival. Although there is a high prevalence of TNBC across West Africa and in women of the African diaspora, there has been no comprehensive genomics study to investigate the mutational profile of ancestrally related women across the Caribbean and West Africa. METHODS This multisite cross-sectional study used 31 formalin-fixed paraffin-embedded (FFPE) samples from Barbadian and Nigerian TNBC participants. High-resolution whole exome sequencing (WES) was performed on the Barbadian and Nigerian TNBC samples to identify their mutational profiles and comparisons were made to African American, European American and Asian American sequencing data obtained from The Cancer Genome Atlas (TCGA). Whole exome sequencing was conducted on tumors with an average of 382 × coverage and 4335 × coverage for pooled germline non-tumor samples. RESULTS Variants detected at high frequency in our WAA cohorts were found in the following genes NBPF12, PLIN4, TP53 and BRCA1. In the TCGA TNBC cases, these genes had a lower mutation rate, except for TP53 (32% in our cohort; 63% in TCGA-African American; 67% in TCGA-European American; 63% in TCGA-Asian). For all altered genes, there were no differences in frequency of mutations between WAA TNBC groups including the TCGA-African American cohort. For copy number variants, high frequency alterations were observed in PIK3CA, TP53, FGFR2 and HIF1AN genes. CONCLUSION This study provides novel insights into the underlying genomic alterations in WAA TNBC samples and shines light on the importance of inclusion of under-represented populations in cancer genomics and biomarker studies.
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Affiliation(s)
- Shawn M. Hercules
- grid.25073.330000 0004 1936 8227Department of Biology, McMaster University, Hamilton, ON Canada
- African Caribbean Cancer Consortium, Philadelphia, PA USA
| | - Xiyu Liu
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | | | - Desiree H. A. Skeete
- African Caribbean Cancer Consortium, Philadelphia, PA USA
- grid.412886.10000 0004 0592 769XFaculty of Medical Sciences, University of the West Indies at Cave Hill, Bridgetown, Barbados
- grid.415521.60000 0004 0570 5165Department of Pathology, Queen Elizabeth Hospital, Bridgetown, Barbados
| | - Suzanne Smith Connell
- grid.412886.10000 0004 0592 769XFaculty of Medical Sciences, University of the West Indies at Cave Hill, Bridgetown, Barbados
- grid.415521.60000 0004 0570 5165Department of Radiation Oncology, Queen Elizabeth Hospital, Bridgetown, Barbados
- Present Address: Cancer Specialists Inc, Bridgetown, Barbados
| | - Adetola Daramola
- grid.411283.d0000 0000 8668 7085Department of Anatomic and Molecular Pathology, Lagos University Teaching Hospital, Lagos, Nigeria
| | - Adekunbiola A. Banjo
- grid.411283.d0000 0000 8668 7085Department of Anatomic and Molecular Pathology, Lagos University Teaching Hospital, Lagos, Nigeria
| | - Godwin Ebughe
- grid.413097.80000 0001 0291 6387Department of Pathology, University of Calabar Teaching Hospital, Calabar, Nigeria
| | - Thomas Agan
- grid.413097.80000 0001 0291 6387Department of Obstetrics & Gynaecology, College of Medical Sciences, University of Calabar Teaching Hospital, Calabar, Nigeria
| | - Ima-Obong Ekanem
- grid.413097.80000 0001 0291 6387Department of Pathology, College of Medical Sciences, University of Calabar Teaching Hospital, Calabar, Nigeria
| | - Joe Udosen
- grid.413097.80000 0001 0291 6387Division of General and Breast Surgery, University of Calabar Teaching Hospital, Calabar, Nigeria
| | - Christopher Obiorah
- grid.412738.bDepartment of Anatomical Pathology, University of Port Harcourt Teaching Hospital, Port Harcourt, Nigeria
| | - Aaron C. Ojule
- grid.412738.bDepartment of Chemical Pathology, University of Port Harcourt Teaching Hospital, Port Harcourt, Nigeria
| | - Michael A. Misauno
- grid.411946.f0000 0004 1783 4052Department of Surgery, Jos University Teaching Hospital, Jos, Nigeria
| | - Ayuba M. Dauda
- grid.411946.f0000 0004 1783 4052Department of Pathology, Jos University Teaching Hospital, Jos, Nigeria
| | | | - Jevon C. Hercules
- grid.12916.3d0000 0001 2322 4996Department of Mathematics, University of the West Indies at Mona, Kingston, Jamaica
- grid.12955.3a0000 0001 2264 7233Present Address: Wang Yanan Institute for Studies in Economics, Xiamen University, Xiamen, China
| | - Amna Ansari
- grid.25073.330000 0004 1936 8227Department of Biology, McMaster University, Hamilton, ON Canada
| | - Ian Brain
- grid.25073.330000 0004 1936 8227Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON Canada
| | - Christine MacColl
- grid.25073.330000 0004 1936 8227Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON Canada
| | - Yili Xu
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Yuxin Jin
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Sharon Chang
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - John D. Carpten
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - André Bédard
- grid.25073.330000 0004 1936 8227Department of Biology, McMaster University, Hamilton, ON Canada
| | - Greg R. Pond
- grid.25073.330000 0004 1936 8227Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON Canada
- grid.25073.330000 0004 1936 8227Department of Oncology, McMaster University, Hamilton, ON Canada
| | - Kim R. M. Blenman
- grid.433818.5Department of Internal Medicine, Section of Medical Oncology, Yale Cancer Center, School of Medicine, New Haven, CT USA
- grid.47100.320000000419368710Department of Computer Science, School of Engineering and Applied Science, Yale University, New Haven, CT USA
| | - Zarko Manojlovic
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Juliet M. Daniel
- grid.25073.330000 0004 1936 8227Department of Biology, McMaster University, Hamilton, ON Canada
- African Caribbean Cancer Consortium, Philadelphia, PA USA
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9
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Borden ES, Buetow KH, Wilson MA, Hastings KT. Cancer Neoantigens: Challenges and Future Directions for Prediction, Prioritization, and Validation. Front Oncol 2022; 12:836821. [PMID: 35311072 PMCID: PMC8929516 DOI: 10.3389/fonc.2022.836821] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 12/15/2021] [Accepted: 02/07/2022] [Indexed: 12/16/2022] Open
Abstract
Prioritization of immunogenic neoantigens is key to enhancing cancer immunotherapy through the development of personalized vaccines, adoptive T cell therapy, and the prediction of response to immune checkpoint inhibition. Neoantigens are tumor-specific proteins that allow the immune system to recognize and destroy a tumor. Cancer immunotherapies, such as personalized cancer vaccines, adoptive T cell therapy, and immune checkpoint inhibition, rely on an understanding of the patient-specific neoantigen profile in order to guide personalized therapeutic strategies. Genomic approaches to predicting and prioritizing immunogenic neoantigens are rapidly expanding, raising new opportunities to advance these tools and enhance their clinical relevance. Predicting neoantigens requires acquisition of high-quality samples and sequencing data, followed by variant calling and variant annotation. Subsequently, prioritizing which of these neoantigens may elicit a tumor-specific immune response requires application and integration of tools to predict the expression, processing, binding, and recognition potentials of the neoantigen. Finally, improvement of the computational tools is held in constant tension with the availability of datasets with validated immunogenic neoantigens. The goal of this review article is to summarize the current knowledge and limitations in neoantigen prediction, prioritization, and validation and propose future directions that will improve personalized cancer treatment.
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Affiliation(s)
- Elizabeth S Borden
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, United States.,Department of Research and Internal Medicine (Dermatology), Phoenix Veterans Affairs Health Care System, Phoenix, AZ, United States
| | - Kenneth H Buetow
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
| | - Karen Taraszka Hastings
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, United States.,Department of Research and Internal Medicine (Dermatology), Phoenix Veterans Affairs Health Care System, Phoenix, AZ, United States
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10
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Benton S, Zhao J, Zhang B, Bahrami A, Barnhill RL, Busam K, Cerroni L, Cook MG, de la Fouchardière A, Elder DE, Johansson I, Landman G, Lazar A, LeBoit P, Lowe L, Massi D, Duncan LM, Messina J, Mihic-Probst D, Mihm MC Jr, Piepkorn MW, Schmidt B, Scolyer RA, Shea CR, Tetzlaff MT, Tron VA, Xu X, Yeh I, Yun SJ, Zembowicz A, Gerami P. Impact of Next-generation Sequencing on Interobserver Agreement and Diagnosis of Spitzoid Neoplasms. Am J Surg Pathol 2021; 45:1597-605. [PMID: 34757982 DOI: 10.1097/PAS.0000000000001753] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Atypical Spitzoid melanocytic tumors are diagnostically challenging. Many studies have suggested various genomic markers to improve classification and prognostication. We aimed to assess whether next-generation sequencing studies using the Tempus xO assay assessing mutations in 1711 cancer-related genes and performing whole transcriptome mRNA sequencing for structural alterations could improve diagnostic agreement and accuracy in assessing neoplasms with Spitzoid histologic features. Twenty expert pathologists were asked to review 70 consultation level cases with Spitzoid features, once with limited clinical information and again with additional genomic information. There was an improvement in overall agreement with additional genomic information. Most significantly, there was increase in agreement of the diagnosis of conventional melanoma from moderate (κ=0.470, SE=0.0105) to substantial (κ=0.645, SE=0.0143) as measured by an average Cohen κ. Clinical follow-up was available in all 70 cases which substantiated that the improved agreement was clinically significant. Among 3 patients with distant metastatic disease, there was a highly significant increase in diagnostic recognition of the cases as conventional melanoma with genomics (P<0.005). In one case, none of 20 pathologists recognized a tumor with BRAF and TERT promoter mutations associated with fatal outcome as a conventional melanoma when only limited clinical information was provided, whereas 60% of pathologists correctly diagnosed this case when genomic information was also available. There was also a significant improvement in agreement of which lesions should be classified in the Spitz category/WHO Pathway from an average Cohen κ of 0.360 (SE=0.00921) to 0.607 (SE=0.0232) with genomics.
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11
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Little P, Jo H, Hoyle A, Mazul A, Zhao X, Salazar AH, Farquhar D, Sheth S, Masood M, Hayward MC, Parker JS, Hoadley KA, Zevallos J, Hayes DN. UNMASC: tumor-only variant calling with unmatched normal controls. NAR Cancer 2021; 3:zcab040. [PMID: 34632388 PMCID: PMC8494212 DOI: 10.1093/narcan/zcab040] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 09/07/2021] [Accepted: 10/04/2021] [Indexed: 12/11/2022] Open
Abstract
Despite years of progress, mutation detection in cancer samples continues to require significant manual review as a final step. Expert review is particularly challenging in cases where tumors are sequenced without matched normal control DNA. Attempts have been made to call somatic point mutations without a matched normal sample by removing well-known germline variants, utilizing unmatched normal controls, and constructing decision rules to classify sequencing errors and private germline variants. With budgetary constraints related to computational and sequencing costs, finding the appropriate number of controls is a crucial step to identifying somatic variants. Our approach utilizes public databases for canonical somatic variants as well as germline variants and leverages information gathered about nearby positions in the normal controls. Drawing from our cohort of targeted capture panel sequencing of tumor and normal samples with varying tumortypes and demographics, these served as a benchmark for our tumor-only variant calling pipeline to observe the relationship between our ability to correctly classify variants against a number of unmatched normals. With our benchmarked samples, approximately ten normal controls were needed to maintain 94% sensitivity, 99% specificity and 76% positive predictive value, far outperforming comparable methods. Our approach, called UNMASC, also serves as a supplement to traditional tumor with matched normal variant calling workflows and can potentially extend to other concerns arising from analyzing next generation sequencing data.
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Affiliation(s)
- Paul Little
- Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Heejoon Jo
- Center for Cancer Research, University of Tennessee Health Science Center, 19 South Manassas, Memphis, TN 38163, USA
| | - Alan Hoyle
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 101 Manning Drive Chapel Hill, NC 27514, USA
| | - Angela Mazul
- Otolaryngology Head and Neck Surgery, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8115, St. Louis, MO 63110, USA
| | - Xiaobei Zhao
- Center for Cancer Research, University of Tennessee Health Science Center, 19 South Manassas, Memphis, TN 38163, USA
| | - Ashley H Salazar
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 101 Manning Drive Chapel Hill, NC 27514, USA
| | - Douglas Farquhar
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 101 Manning Drive Chapel Hill, NC 27514, USA
| | - Siddharth Sheth
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 101 Manning Drive Chapel Hill, NC 27514, USA
| | - Maheer Masood
- Otolaryngology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Michele C Hayward
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 101 Manning Drive Chapel Hill, NC 27514, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 101 Manning Drive Chapel Hill, NC 27514, USA
| | - Katherine A Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 101 Manning Drive Chapel Hill, NC 27514, USA
| | - Jose Zevallos
- Otolaryngology Head and Neck Surgery, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8115, St. Louis, MO 63110, USA
| | - D Neil Hayes
- Center for Cancer Research, University of Tennessee Health Science Center, 19 South Manassas, Memphis, TN 38163, USA
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12
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White T, Szelinger S, LoBello J, King A, Aldrich J, Garinger N, Halbert M, Richholt RF, Mastrian SD, Babb C, Ozols AA, Goodman LJ, Basu GD, Royce T. Analytic validation and clinical utilization of the comprehensive genomic profiling test, GEM ExTra ®. Oncotarget 2021; 12:726-739. [PMID: 33889297 PMCID: PMC8057276 DOI: 10.18632/oncotarget.27945] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 03/06/2021] [Accepted: 03/28/2021] [Indexed: 12/20/2022] Open
Abstract
We developed and analytically validated a comprehensive genomic profiling (CGP) assay, GEM ExTra, for patients with advanced solid tumors that uses Next Generation Sequencing (NGS) to characterize whole exomes employing a paired tumor-normal subtraction methodology. The assay detects single nucleotide variants (SNV), indels, focal copy number alterations (CNA), TERT promoter region, as well as tumor mutation burden (TMB) and microsatellite instability (MSI) status. Additionally, the assay incorporates whole transcriptome sequencing of the tumor sample that allows for the detection of gene fusions and select special transcripts, including AR-V7, EGFR vIII, EGFRvIV, and MET exon 14 skipping events. The assay has a mean target coverage of 180X for the normal (germline) and 400X for tumor DNA including enhanced probe design to facilitate the sequencing of difficult regions. Proprietary bioinformatics, paired with comprehensive clinical curation results in reporting that defines clinically actionable, FDA-approved, and clinical trial drug options for the management of the patient's cancer. GEM ExTra demonstrated analytic specificity (PPV) of > 99.9% and analytic sensitivity of 98.8%. Application of GEM ExTra to 1,435 patient samples revealed clinically actionable alterations in 83.9% of reports, including 31 (2.5%) where therapeutic recommendations were based on RNA fusion findings only.
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Affiliation(s)
- Tracey White
- Ashion Analytics, LLC, Phoenix, Arizona 85004, USA
- These authors contributed equally to this work
| | - Szabolcs Szelinger
- Ashion Analytics, LLC, Phoenix, Arizona 85004, USA
- These authors contributed equally to this work
| | | | - Amy King
- Ashion Analytics, LLC, Phoenix, Arizona 85004, USA
| | | | | | | | | | | | - Cody Babb
- Ashion Analytics, LLC, Phoenix, Arizona 85004, USA
| | | | | | | | - Thomas Royce
- Ashion Analytics, LLC, Phoenix, Arizona 85004, USA
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13
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Abstract
PURPOSE Allele-specific copy number alteration (CNA) analysis is essential to study the functional impact of single-nucleotide variants (SNVs) and the process of tumorigenesis. However, controversy over whether it can be performed with sufficient accuracy in data without matched normal profiles and a lack of open-source implementations have limited its application in clinical research and diagnosis. METHODS We benchmark allele-specific CNA analysis performance of whole-exome sequencing (WES) data against gold standard whole-genome SNP6 microarray data and against WES data sets with matched normal samples. We provide a workflow based on the open-source PureCN R/Bioconductor package in conjunction with widely used variant-calling and copy number segmentation algorithms for allele-specific CNA analysis from WES without matched normals. This workflow further classifies SNVs by somatic status and then uses this information to infer somatic mutational signatures and tumor mutational burden (TMB). RESULTS Application of our workflow to tumor-only WES data produces tumor purity and ploidy estimates that are highly concordant with estimates from SNP6 microarray data and matched normal WES data. The presence of cancer type–specific somatic mutational signatures was inferred with high accuracy. We also demonstrate high concordance of TMB between our tumor-only workflow and matched normal pipelines. CONCLUSION The proposed workflow provides, to our knowledge, the only open-source option with demonstrated high accuracy for comprehensive allele-specific CNA analysis and SNV classification of tumor-only WES. An implementation of the workflow is available on the Terra Cloud platform of the Broad Institute (Cambridge, MA).
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Affiliation(s)
- Sehyun Oh
- Graduate School of Public Health and Health Policy, City University of New York, New York, NY.,Institute for Implementation Science and Population Health, City University of New York, New York, NY
| | - Ludwig Geistlinger
- Graduate School of Public Health and Health Policy, City University of New York, New York, NY.,Institute for Implementation Science and Population Health, City University of New York, New York, NY
| | - Marcel Ramos
- Graduate School of Public Health and Health Policy, City University of New York, New York, NY.,Institute for Implementation Science and Population Health, City University of New York, New York, NY
| | | | - Levi Waldron
- Graduate School of Public Health and Health Policy, City University of New York, New York, NY.,Institute for Implementation Science and Population Health, City University of New York, New York, NY
| | - Markus Riester
- Novartis Institutes for BioMedical Research, Cambridge, MA
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14
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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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15
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Berens ME, Sood A, Barnholtz-Sloan JS, Graf JF, Cho S, Kim S, Kiefer J, Byron SA, Halperin RF, Nasser S, Adkins J, Cuyugan L, Devine K, Ostrom Q, Couce M, Wolansky L, McDonough E, Schyberg S, Dinn S, Sloan AE, Prados M, Phillips JJ, Nelson SJ, Liang WS, Al-Kofahi Y, Rusu M, Zavodszky MI, Ginty F. Multiscale, multimodal analysis of tumor heterogeneity in IDH1 mutant vs wild-type diffuse gliomas. PLoS One 2019; 14:e0219724. [PMID: 31881020 PMCID: PMC6934292 DOI: 10.1371/journal.pone.0219724] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 06/27/2019] [Accepted: 11/12/2019] [Indexed: 12/31/2022] Open
Abstract
Glioma is recognized to be a highly heterogeneous CNS malignancy, whose diverse cellular composition and cellular interactions have not been well characterized. To gain new clinical- and biological-insights into the genetically-bifurcated IDH1 mutant (mt) vs wildtype (wt) forms of glioma, we integrated data from protein, genomic and MR imaging from 20 treatment-naïve glioma cases and 16 recurrent GBM cases. Multiplexed immunofluorescence (MxIF) was used to generate single cell data for 43 protein markers representing all cancer hallmarks, Genomic sequencing (exome and RNA (normal and tumor) and magnetic resonance imaging (MRI) quantitative features (protocols were T1-post, FLAIR and ADC) from whole tumor, peritumoral edema and enhancing core vs equivalent normal region were also collected from patients. Based on MxIF analysis, 85,767 cells (glioma cases) and 56,304 cells (GBM cases) were used to generate cell-level data for 24 biomarkers. K-means clustering was used to generate 7 distinct groups of cells with divergent biomarker profiles and deconvolution was used to assign RNA data into three classes. Spatial and molecular heterogeneity metrics were generated for the cell data. All features were compared between IDH mt and IDHwt patients and were finally combined to provide a holistic/integrated comparison. Protein expression by hallmark was generally lower in the IDHmt vs wt patients. Molecular and spatial heterogeneity scores for angiogenesis and cell invasion also differed between IDHmt and wt gliomas irrespective of prior treatment and tumor grade; these differences also persisted in the MR imaging features of peritumoral edema and contrast enhancement volumes. A coherent picture of enhanced angiogenesis in IDHwt tumors was derived from multiple platforms (genomic, proteomic and imaging) and scales from individual proteins to cell clusters and heterogeneity, as well as bulk tumor RNA and imaging features. Longer overall survival for IDH1mt glioma patients may reflect mutation-driven alterations in cellular, molecular, and spatial heterogeneity which manifest in discernable radiological manifestations.
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Affiliation(s)
- Michael E. Berens
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
- * E-mail: (MEB); (AS); (FG)
| | - Anup Sood
- GE Research Center, Niskayuna, NY, United States of America
- * E-mail: (MEB); (AS); (FG)
| | - Jill S. Barnholtz-Sloan
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - John F. Graf
- GE Research Center, Niskayuna, NY, United States of America
| | - Sanghee Cho
- GE Research Center, Niskayuna, NY, United States of America
| | - Seungchan Kim
- Department of Electrical and Computer Engineering, Roy G. Perry College of Engineering, Prairie View A&M University, Prairie View, TX, United States of America
| | - Jeffrey Kiefer
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Sara A. Byron
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Rebecca F. Halperin
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Sara Nasser
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Jonathan Adkins
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Lori Cuyugan
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Karen Devine
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Quinn Ostrom
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Marta Couce
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Leo Wolansky
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | | | | | - Sean Dinn
- GE Research Center, Niskayuna, NY, United States of America
| | - Andrew E. Sloan
- Department of Neurosurgery, University Hospitals-Seidman Cancer Center, Cleveland, OH, United States of America
| | - Michael Prados
- Department of Neurological Surgery, Helen Diller Cancer Center, University of California San Francisco, San Francisco, CA, United States of America
| | - Joanna J. Phillips
- Department of Neurological Surgery, Helen Diller Cancer Center, University of California San Francisco, San Francisco, CA, United States of America
| | - Sarah J. Nelson
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA, United States of America
| | - Winnie S. Liang
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | | | - Mirabela Rusu
- GE Research Center, Niskayuna, NY, United States of America
| | | | - Fiona Ginty
- GE Research Center, Niskayuna, NY, United States of America
- * E-mail: (MEB); (AS); (FG)
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16
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Bohannan ZS, Mitrofanova A. Calling Variants in the Clinic: Informed Variant Calling Decisions Based on Biological, Clinical, and Laboratory Variables. Comput Struct Biotechnol J 2019; 17:561-9. [PMID: 31049166 DOI: 10.1016/j.csbj.2019.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/12/2019] [Accepted: 04/03/2019] [Indexed: 01/10/2023] Open
Abstract
Deep sequencing genomic analysis is becoming increasingly common in clinical research and practice, enabling accurate identification of diagnostic, prognostic, and predictive determinants. Variant calling, distinguishing between true mutations and experimental errors, is a central task of genomic analysis and often requires sophisticated statistical, computational, and/or heuristic techniques. Although variant callers seek to overcome noise inherent in biological experiments, variant calling can be significantly affected by outside factors including those used to prepare, store, and analyze samples. The goal of this review is to discuss known experimental features, such as sample preparation, library preparation, and sequencing, alongside diverse biological and clinical variables, and evaluate their effect on variant caller selection and optimization.
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17
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Halperin RF, Liang WS, Kulkarni S, Tassone EE, Adkins J, Enriquez D, Tran NL, Hank NC, Newell J, Kodira C, Korn R, Berens ME, Kim S, Byron SA. Leveraging Spatial Variation in Tumor Purity for Improved Somatic Variant Calling of Archival Tumor Only Samples. Front Oncol 2019; 9:119. [PMID: 30949446 PMCID: PMC6435595 DOI: 10.3389/fonc.2019.00119] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 07/16/2018] [Accepted: 02/11/2019] [Indexed: 12/28/2022] Open
Abstract
Archival tumor samples represent a rich resource of annotated specimens for translational genomics research. However, standard variant calling approaches require a matched normal sample from the same individual, which is often not available in the retrospective setting, making it difficult to distinguish between true somatic variants and individual-specific germline variants. Archival sections often contain adjacent normal tissue, but this tissue can include infiltrating tumor cells. As existing comparative somatic variant callers are designed to exclude variants present in the normal sample, a novel approach is required to leverage adjacent normal tissue with infiltrating tumor cells for somatic variant calling. Here we present lumosVar 2.0, a software package designed to jointly analyze multiple samples from the same patient, built upon our previous single sample tumor only variant caller lumosVar 1.0. The approach assumes that the allelic fraction of somatic variants and germline variants follow different patterns as tumor content and copy number state change. lumosVar 2.0 estimates allele specific copy number and tumor sample fractions from the data, and uses a to model to determine expected allelic fractions for somatic and germline variants and to classify variants accordingly. To evaluate the utility of lumosVar 2.0 to jointly call somatic variants with tumor and adjacent normal samples, we used a glioblastoma dataset with matched high and low tumor content and germline whole exome sequencing data (for true somatic variants) available for each patient. Both sensitivity and positive predictive value were improved when analyzing the high tumor and low tumor samples jointly compared to analyzing the samples individually or in-silico pooling of the two samples. Finally, we applied this approach to a set of breast and prostate archival tumor samples for which tumor blocks containing adjacent normal tissue were available for sequencing. Joint analysis using lumosVar 2.0 detected several variants, including known cancer hotspot mutations that were not detected by standard somatic variant calling tools using the adjacent tissue as presumed normal reference. Together, these results demonstrate the utility of leveraging paired tissue samples to improve somatic variant calling when a constitutional sample is not available.
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Affiliation(s)
- Rebecca F Halperin
- Quantitative Medicine and Systems Biology Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Winnie S Liang
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Sidharth Kulkarni
- Quantitative Medicine and Systems Biology Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Erica E Tassone
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Jonathan Adkins
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Daniel Enriquez
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | | | | | - James Newell
- HonorHealth Scottsdale Shea Medical Center, Scottsdale, AZ, United States
| | - Chinnappa Kodira
- GE Global Research Center, Niskayuna, NY, United States.,PureTech Health, Boston, MA, United States
| | - Ronald Korn
- Imaging Endpoints, Scottsdale, AZ, United States.,HonorHealth Scottsdale Shea Medical Center, Scottsdale, AZ, United States
| | - Michael E Berens
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Seungchan Kim
- Prairie View A&M University, Prairie View, TX, United States
| | - Sara A Byron
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
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Pinto JA, Saravia CH, Flores C, Araujo JM, Martínez D, Schwarz LJ, Casas A, Bravo L, Zavaleta J, Chuima B, Alvarado H, Fujita R, Gómez HL. Precision medicine for locally advanced breast cancer: frontiers and challenges in Latin America. Ecancermedicalscience 2019; 13:896. [PMID: 30792813 PMCID: PMC6372295 DOI: 10.3332/ecancer.2019.896] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 07/14/2018] [Indexed: 12/18/2022] Open
Abstract
Advances in high-throughput technologies and their involvement in the 'omics' of cancer have made possible the identification of hundreds of biomarkers and the development of predictive and prognostic platforms that model the management of cancer from evidence-based medicine to precision medicine. Latin America (LATAM) is a region characterised by fragmented healthcare, high rates of poverty and disparities to access to a basic standard of care not only for cancer but also for other complex diseases. Patients from the public setting cannot afford targeted therapy, the facilities offering genomic platforms are scarce and the use of high-precision radiotherapy is limited to few facilities. Despite the fact that LATAM oncologists are well-trained in the use of genomic platforms and constantly participate in genomic projects, a medical practice based in precision oncology is a great challenge and frequently limited to private practice. In breast cancer, we are waiting for the results of large basket trials to incorporate the detection of actionable mutations to select targeted treatments, in a similar way to the management of lung cancer. On the other hand and paradoxically, in the 'one fit is not for all' era, clinical and genomic studies continue grouping our patients under the single label 'Latin American' or 'Hispanic' despite the different ancestries and genomic backgrounds seen in the region. More regional cancer genomic initiatives and public availability of this data are needed in order to develop more precise oncology in locally advanced breast cancer.
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Affiliation(s)
- Joseph A Pinto
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Lima 15036, Perú
| | - César H Saravia
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Lima 15036, Perú
| | - Claudio Flores
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Lima 15036, Perú
| | - Jhajaira M Araujo
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Lima 15036, Perú
| | - David Martínez
- Departamento de Radioterapia, Oncosalud-AUNA, Lima 15036, Perú
| | - Luis J Schwarz
- Departamento de Medicina Oncológica, Oncosalud-AUNA, Lima 15036, Perú
| | - Alberto Casas
- Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima 15067, Perú
| | - Leny Bravo
- Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima 15067, Perú
| | - Jenny Zavaleta
- Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima 15067, Perú
| | | | - Hober Alvarado
- Facultad de Ciencias Biológicas, Universidad Nacional San Luis Gonzaga de Ica, Ica 11004, Perú
| | - Ricardo Fujita
- Centro de Genética y Biología Molecular, Universidad de San Martín de Porres, Lima 15024, Perú
| | - Henry L Gómez
- Departamento de Medicina Oncológica, Oncosalud-AUNA, Lima 15036, Perú.,Departamento de Medicina Oncológica, Instituto Nacional de Enfermedades Neoplásicas, 15038, Perú
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Schrauwen I, Kari E, Mattox J, Llaci L, Smeeton J, Naymik M, Raible DW, Knowles JA, Crump JG, Huentelman MJ, Friedman RA. De novo variants in GREB1L are associated with non-syndromic inner ear malformations and deafness. Hum Genet 2018; 137:459-470. [PMID: 29955957 PMCID: PMC6082420 DOI: 10.1007/s00439-018-1898-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 03/13/2018] [Accepted: 06/19/2018] [Indexed: 11/24/2022]
Abstract
Congenital inner ear malformations affecting both the osseous and membranous labyrinth can have a devastating impact on hearing and language development. With the exception of an enlarged vestibular aqueduct, non-syndromic inner ear malformations are rare, and their underlying molecular biology has thus far remained understudied. To identify molecular factors that might be important in the developing inner ear, we adopted a family-based trio exome sequencing approach in young unrelated subjects with severe inner ear malformations. We identified two previously unreported de novo loss-of-function variants in GREB1L [c.4368G>T;p.(Glu1410fs) and c.982C>T;p.(Arg328*)] in two affected subjects with absent cochleae and eighth cranial nerve malformations. The cochlear aplasia in these affected subjects suggests that a developmental arrest or problem at a very early stage of inner ear development exists, e.g., during the otic pit formation. Craniofacial Greb1l RNA expression peaks in mice during this time frame (E8.5). It also peaks in the developing inner ear during E13-E16, after which it decreases in adulthood. The crucial function of Greb1l in craniofacial development is also evidenced in knockout mice, which develop severe craniofacial abnormalities. In addition, we show that Greb1l-/- zebrafish exhibit a loss of abnormal sensory epithelia innervation. An important role for Greb1l in sensory epithelia innervation development is supported by the eighth cranial nerve deficiencies seen in both affected subjects. In conclusion, we demonstrate that GREB1L is a key player in early inner ear and eighth cranial nerve development. Abnormalities in cochleovestibular anatomy can provide challenges for cochlear implantation. Combining a molecular diagnosis with imaging techniques might aid the development of individually tailored therapeutic interventions in the future.
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Affiliation(s)
- Isabelle Schrauwen
- Molecular and Human Genetics Department, Center for Statistical Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th str, Phoenix, AZ, 85004, USA.
| | - Elina Kari
- Division of Otolaryngology, Head and Neck Surgery, Department of Surgery, University of California, San Diego, ECOB-East Campus Office Building Room 3-013, 9444 Medical Center Drive, Mail Code 7220, La Jolla, CA, 92037, USA
| | - Jacob Mattox
- Tina and Rick Caruso Department of Otolaryngology-Head and Neck Surgery, Keck University of Southern California School of Medicine, 1975 Zonal Ave., Los Angeles, CA, 90033, USA
| | - Lorida Llaci
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th str, Phoenix, AZ, 85004, USA
| | - Joanna Smeeton
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, 1975 Zonal Ave., Los Angeles, CA, 90033, USA
| | - Marcus Naymik
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th str, Phoenix, AZ, 85004, USA
| | - David W Raible
- Department of Biological Structure, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
| | - James A Knowles
- Department of Cell Biology-MSC 5, SUNY Downstate Medical Center, 450 Clarkson Avenue, BSB 2-5, Brooklyn, NY, 11203, USA
| | - J Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, 1975 Zonal Ave., Los Angeles, CA, 90033, USA
| | - Matthew J Huentelman
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th str, Phoenix, AZ, 85004, USA
| | - Rick A Friedman
- Division of Otolaryngology, Head and Neck Surgery, Department of Surgery, University of California, San Diego, ECOB-East Campus Office Building Room 3-013, 9444 Medical Center Drive, Mail Code 7220, La Jolla, CA, 92037, USA
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Rabizadeh S, Garner C, Sanborn JZ, Benz SC, Reddy S, Soon-Shiong P. Comprehensive genomic transcriptomic tumor-normal gene panel analysis for enhanced precision in patients with lung cancer. Oncotarget 2018; 9:19223-19232. [PMID: 29721196 PMCID: PMC5922390 DOI: 10.18632/oncotarget.24973] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 11/30/2017] [Accepted: 03/15/2018] [Indexed: 02/06/2023] Open
Abstract
A CMS approved test for lung cancer is based on tumor-only analysis of a targeted 35 gene panel, specifically excluding the use of the patient's normal germline tissue. However, this tumor-only approach increases the risk of mistakenly identifying germline single nucleotide polymorphisms (SNPs) as somatically-derived cancer driver mutations (false positives). 621 patients with 30 different cancer types, including lung cancer, were studied to compare the precision of tumor somatic variant calling in 35 genes using tumor-only DNA sequencing versus tumor-normal DNA plus RNA sequencing. When sequencing of lung cancer was performed using tumor genomes alone without normal germline controls, 94% of variants identified were SNPs and thus false positives. Filtering for common SNPs still resulted in as high as 48% false positive variant calling. With tumor-only sequencing, 29% of lung cancer patients had a false positive variant call in at least one of twelve genes with directly targetable drugs. RNA analysis showed 18% of true somatic variants were not expressed. Thus, sequencing and analysis of both normal germline and tumor genomes is necessary for accurate identification of molecular targets. Treatment decisions based on tumor-only analysis may result in the administration of ineffective therapies while also increasing the risk of negative drug-related side effects.
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Affiliation(s)
| | | | | | | | | | - Patrick Soon-Shiong
- NantOmics, LLC, Culver City, CA, USA.,NantHealth, Inc., Culver City, CA, USA
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Yamato G, Shiba N, Yoshida K, Hara Y, Shiraishi Y, Ohki K, Okubo J, Park MJ, Sotomatsu M, Arakawa H, Kiyokawa N, Tomizawa D, Adachi S, Taga T, Horibe K, Miyano S, Ogawa S, Hayashi Y. RUNX1 mutations in pediatric acute myeloid leukemia are associated with distinct genetic features and an inferior prognosis. Blood 2018; 131:2266-70. [PMID: 29540347 DOI: 10.1182/blood-2017-11-814442] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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