1
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Sheridan MB, Aksit MA, Pagel K, Hetrick K, Shultz-Lutwyche H, Myers B, Buckingham KJ, Pace RG, Ling H, Pugh E, O'Neal WK, Bamshad MJ, Gibson RL, Knowles MR, Blackman SM, Cutting GR, Raraigh KS. The clinical utility of sequencing the entirety of CFTR. J Cyst Fibros 2024:S1569-1993(24)00062-6. [PMID: 38734509 DOI: 10.1016/j.jcf.2024.04.018] [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: 12/12/2023] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND Cystic fibrosis (CF) is caused by deleterious variants in each CFTR gene. We investigated the utility of whole-gene CFTR sequencing when fewer than two pathogenic or likely pathogenic (P/LP) variants were detected by conventional testing (sequencing of exons and flanking introns) of CFTR. METHODS Individuals with features of CF and a CF-diagnostic sweat chloride concentration with zero or one P/LP variants identified by conventional testing enrolled in the CF Mutation Analysis Program (MAP) underwent whole-gene CFTR sequencing. Replication was performed on individuals enrolled in the CF Genome Project (CFGP), followed by phenotype review and interrogation of other genes. RESULTS Whole-gene sequencing identified a second P/LP variant in 20/43 MAP enrollees (47 %) and 10/22 CFGP enrollees (45 %) who had one P/LP variant after conventional testing. No P/LP variants were detected when conventional testing was negative (MAP: n = 43; CFGP: n = 13). Genome-wide analysis was unable to find an alternative etiology in CFGP participants with fewer than two P/LP CFTR variants and CF could not be confirmed in 91 % following phenotype re-review. CONCLUSIONS Whole-gene CFTR analysis is beneficial in individuals with one previously-identified P/LP variant and a CF-diagnostic sweat chloride. Negative conventional CFTR testing indicates that the phenotype should be re-evaluated.
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Affiliation(s)
- Molly B Sheridan
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Melis A Aksit
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Kymberleigh Pagel
- The Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kurt Hetrick
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Hannah Shultz-Lutwyche
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ben Myers
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Kati J Buckingham
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Rhonda G Pace
- Department of Medicine, Marsico Lung Institute/UNC CF Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hua Ling
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Elizabeth Pugh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Wanda K O'Neal
- Department of Medicine, Marsico Lung Institute/UNC CF Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Brotman-Baty Institute, Seattle, WA 98195, USA
| | - Ronald L Gibson
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Michael R Knowles
- Department of Medicine, Marsico Lung Institute/UNC CF Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Scott M Blackman
- Division of Pediatric Endocrinology and Diabetes, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Garry R Cutting
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Karen S Raraigh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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2
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Zhou YH, Gallins PJ, Pace RG, Dang H, Aksit MA, Blue EE, Buckingham KJ, Collaco JM, Faino AV, Gordon WW, Hetrick KN, Ling H, Liu W, Onchiri FM, Pagel K, Pugh EW, Raraigh KS, Rosenfeld M, Sun Q, Wen J, Li Y, Corvol H, Strug LJ, Bamshad MJ, Blackman SM, Cutting GR, Gibson RL, O’Neal WK, Wright FA, Knowles MR. Genetic Modifiers of Cystic Fibrosis Lung Disease Severity: Whole-Genome Analysis of 7,840 Patients. Am J Respir Crit Care Med 2023; 207:1324-1333. [PMID: 36921087 PMCID: PMC10595435 DOI: 10.1164/rccm.202209-1653oc] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 02/27/2023] [Indexed: 03/17/2023] Open
Abstract
Rationale: Lung disease is the major cause of morbidity and mortality in persons with cystic fibrosis (pwCF). Variability in CF lung disease has substantial non-CFTR (CF transmembrane conductance regulator) genetic influence. Identification of genetic modifiers has prognostic and therapeutic importance. Objectives: Identify genetic modifier loci and genes/pathways associated with pulmonary disease severity. Methods: Whole-genome sequencing data on 4,248 unique pwCF with pancreatic insufficiency and lung function measures were combined with imputed genotypes from an additional 3,592 patients with pancreatic insufficiency from the United States, Canada, and France. This report describes association of approximately 15.9 million SNPs using the quantitative Kulich normal residual mortality-adjusted (KNoRMA) lung disease phenotype in 7,840 pwCF using premodulator lung function data. Measurements and Main Results: Testing included common and rare SNPs, transcriptome-wide association, gene-level, and pathway analyses. Pathway analyses identified novel associations with genes that have key roles in organ development, and we hypothesize that these genes may relate to dysanapsis and/or variability in lung repair. Results confirmed and extended previous genome-wide association study findings. These whole-genome sequencing data provide finely mapped genetic information to support mechanistic studies. No novel primary associations with common single variants or rare variants were found. Multilocus effects at chr5p13 (SLC9A3/CEP72) and chr11p13 (EHF/APIP) were identified. Variant effect size estimates at associated loci were consistently ordered across the cohorts, indicating possible age or birth cohort effects. Conclusions: This premodulator genomic, transcriptomic, and pathway association study of 7,840 pwCF will facilitate mechanistic and postmodulator genetic studies and the development of novel therapeutics for CF lung disease.
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Affiliation(s)
- Yi-Hui Zhou
- Bioinformatics Research Center
- Department of Biological Sciences, and
| | | | - Rhonda G. Pace
- Marsico Lung Institute/UNC CF Research Center, School of Medicine
| | - Hong Dang
- Marsico Lung Institute/UNC CF Research Center, School of Medicine
| | | | - Elizabeth E. Blue
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Division of Medical Genetics, Department of Medicine
| | | | | | - Anna V. Faino
- Children’s Core for Biostatistics, Epidemiology and Analytics in Research and
| | | | - Kurt N. Hetrick
- Department of Genetic Medicine, Center for Inherited Disease Research, and
| | - Hua Ling
- Department of Genetic Medicine, Center for Inherited Disease Research, and
| | | | | | - Kymberleigh Pagel
- The Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland
| | - Elizabeth W. Pugh
- Department of Genetic Medicine, Center for Inherited Disease Research, and
| | | | - Margaret Rosenfeld
- Department of Pediatrics, and
- Center for Clinical and Translational Research, Seattle Children’s Research Institute, Seattle, Washington
| | | | | | - Yun Li
- Department of Biostatistics
- Department of Genetics, and
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Harriet Corvol
- Pediatric Pulmonary Department, Assistance Publique-Hôpitaux de Paris, Hôpital Trousseau, Paris, France
- Centre de Recherche Saint Antoine, Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Paris, France
| | - Lisa J. Strug
- Division of Biostatistics, Dalla Lana School of Public Health
- Department of Statistical Sciences, and
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada; and
- Program in Genetics and Genome Biology and
- The Center for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael J. Bamshad
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Division of Genetic Medicine, Department of Pediatrics
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Scott M. Blackman
- McKusick-Nathans Department of Genetic Medicine
- Division of Pediatric Endocrinology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Ronald L. Gibson
- Department of Pediatrics, and
- Center for Clinical and Translational Research, Seattle Children’s Research Institute, Seattle, Washington
| | - Wanda K. O’Neal
- Marsico Lung Institute/UNC CF Research Center, School of Medicine
| | - Fred A. Wright
- Bioinformatics Research Center
- Department of Biological Sciences, and
- Department of Statistics, North Carolina State University, Raleigh, North Carolina
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3
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Aksit MA, Ling H, Pace RG, Raraigh KS, Onchiri F, Faino AV, Pagel K, Pugh E, Stilp AM, Sun Q, Blue EE, Wright FA, Zhou YH, Bamshad MJ, Gibson RL, Knowles MR, Cutting GR, Blackman SM. Pleiotropic modifiers of age-related diabetes and neonatal intestinal obstruction in cystic fibrosis. Am J Hum Genet 2022; 109:1894-1908. [PMID: 36206743 PMCID: PMC9606479 DOI: 10.1016/j.ajhg.2022.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Received: 01/21/2022] [Accepted: 09/12/2022] [Indexed: 01/25/2023] Open
Abstract
Individuals with cystic fibrosis (CF) develop complications of the gastrointestinal tract influenced by genetic variants outside of CFTR. Cystic fibrosis-related diabetes (CFRD) is a distinct form of diabetes with a variable age of onset that occurs frequently in individuals with CF, while meconium ileus (MI) is a severe neonatal intestinal obstruction affecting ∼20% of newborns with CF. CFRD and MI are slightly correlated traits with previous evidence of overlap in their genetic architectures. To better understand the genetic commonality between CFRD and MI, we used whole-genome-sequencing data from the CF Genome Project to perform genome-wide association. These analyses revealed variants at 11 loci (6 not previously identified) that associated with MI and at 12 loci (5 not previously identified) that associated with CFRD. Of these, variants at SLC26A9, CEBPB, and PRSS1 associated with both traits; variants at SLC26A9 and CEBPB increased risk for both traits, while variants at PRSS1, the higher-risk alleles for CFRD, conferred lower risk for MI. Furthermore, common and rare variants within the SLC26A9 locus associated with MI only or CFRD only. As expected, different loci modify risk of CFRD and MI; however, a subset exhibit pleiotropic effects indicating etiologic and mechanistic overlap between these two otherwise distinct complications of CF.
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Affiliation(s)
- Melis A Aksit
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Hua Ling
- Department of Genetic Medicine, Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rhonda G Pace
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karen S Raraigh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Frankline Onchiri
- Children's Core for Biostatistics, Epidemiology and Analytics in Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Anna V Faino
- Children's Core for Biostatistics, Epidemiology and Analytics in Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Kymberleigh Pagel
- The Institute for Computational Medicine, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Elizabeth Pugh
- Department of Genetic Medicine, Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Elizabeth E Blue
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Fred A Wright
- Department of Statistics, North Carolina State University, Raleigh, NC 27797, USA; Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27797, USA; Department of Biological Sciences, North Carolina State University, Raleigh, NC 27797, USA
| | - Yi-Hui Zhou
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27797, USA
| | - Michael J Bamshad
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Center for Clinical and Translational Research, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Ronald L Gibson
- Center for Clinical and Translational Research, Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Pediatrics, Division of Pulmonary & Sleep Medicine, University of Washington School of Medicine/Seattle Children's Hospital, Seattle, WA, USA
| | - Michael R Knowles
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Garry R Cutting
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Scott M Blackman
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Division of Pediatric Endocrinology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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4
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Raraigh K, Sheridan M, Aksit M, Pagel K, Hetrick K, Shultz-Lutwyche H, Myers B, Buckingham K, Pace R, Ling H, Pugh E, Knowles M, Bamshad M, Blackman S, Cutting G. 152 My patient has an unresolved CFTR genotype … what next? J Cyst Fibros 2022. [DOI: 10.1016/s1569-1993(22)00843-8] [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: 11/05/2022]
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5
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Aksit M, Ling H, Pace R, Raraigh K, Onchiri F, Pagel K, Pugh E, Faino A, Stilp A, Blue E, Wright F, Bamshad M, Zhou Y, Gibson R, Knowles M, Cutting G, Blackman S. 654: Missense variant within SLC26A9 increases risk of meconium ileus but not age at onset of cystic fibrosis–related diabetes. J Cyst Fibros 2021. [DOI: 10.1016/s1569-1993(21)02077-4] [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: 10/20/2022]
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6
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Marrone K, Tao J, Canzoniero JV, Ghanem P, Nizialek E, Pagel K, Karchin R, Donehower RC, Anagnostou V. The Johns Hopkins Molecular Tumor Board Precision Oncology elective for Medical Oncology fellows. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.11035] [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
11035 Background: The accelerated impact of next generation sequencing (NGS) in clinical decision making requires the integration of cancer genomics and precision oncology focused training into medical oncology education. The Johns Hopkins Molecular Tumor Board (JH MTB) is a multi-disciplinary effort focused on integration of NGS findings with critical evidence interpretation to generate personalized recommendations tailored to the genetic footprint of individual patients. Methods: The JH MTB and the Medical Oncology Fellowship Program have developed a 3-month precision oncology elective for fellows in their research years. Commencing fall of 2020, the goals of this elective are to enhance the understanding of NGS platforms and findings, advance the interpretation and characterization of molecular assay outputs by use of mutation annotators and knowledgebases and ultimately master the art of matching NGS findings with available therapies. Fellow integration into the MTB focuses on mentored case-based learning in mutation characterization and ranking by levels of evidence for actionability, with culmination in form of verbal presentations and written summary reports of final MTB recommendations. A mixed methods questionnaire was administered to evaluate progress since elective initiation. Results: Three learners who have participated as of February 2021 were included. Of the two who had completed the MTB elective, each have presented at least 10 cases, with at least 1 scholarly publication planned. All indicated strong agreement that MTB elective had increased their comfort with interpreting clinical NGS reports as well as the use of knowledgebases and variant annotators. Exposure to experts in the field of molecular precision oncology, identification of resources necessary to interpret clinical NGS reports, development of ability to critically assess various NGS platforms, and gained familiarity with computational analyses relevant to clinical decision making were noted as strengths of the MTB elective. Areas of improvement included ongoing initiatives that involve streamlining variant annotation and transcription of information for written reports. Conclusions: A longitudinal elective in the JHU MTB has been found to be preliminarily effective in promoting knowledge mastery and creating academic opportunities related to the clinical application of precision medicine. Future directions will include leveraging of the MTB infrastructure for research projects, learner integration into computational laboratory meetings, and expansion of the MTB curriculum to include different levels of learners from multiple medical education programs. Continued elective participation will be key to understanding how best to facilitate adaptive expertise in assigning clinical relevance to genomic findings, ultimately improving precision medicine delivery in patient care and trial development.
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Affiliation(s)
- Kristen Marrone
- Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD
| | - Jessica Tao
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Emily Nizialek
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD
| | | | | | - Ross C. Donehower
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD
| | - Valsamo Anagnostou
- Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD
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7
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Pagel K, Kim R, Moad K, Busby B, Zheng L, Tolkheim C, Ryan M, Karchin R. 39. Integrated informatics analysis of cancer-related variants with OpenCRAVAT. Cancer Genet 2020. [DOI: 10.1016/j.cancergen.2020.04.043] [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: 11/24/2022]
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8
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Shao XM, Bhattacharya R, Huang J, Sivakumar A, Tokheim C, Zheng L, Hirsch D, Kaminow B, Omdahl A, Bonsack M, Riemer AB, Velculescu VE, Anagnostou V, Pagel K, Karchin R. Abstract A33: High-throughput prediction of MHC Class I and Class II neoantigens with MHCnuggets. Cancer Immunol Res 2020. [DOI: 10.1158/2326-6074.tumimm19-a33] [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
Computational prediction of binding between neoantigen peptides and major histocompatibility complex (MHC) proteins is an emerging biomarker for predicting patient response to cancer immunotherapy. Current neoantigen predictors focus on in silico estimation of MHC binding affinity and are limited by low positive predictive value for actual peptide presentation, inadequate support for rare MHC alleles, and poor scalability to high-throughput data sets. To address these limitations, we developed MHCnuggets, a deep neural network method to predict peptide-MHC binding. MHCnuggets is the only method to handle binding prediction for common or rare alleles of MHC Class I or II, with a single neural network architecture. Using a long short-term memory network (LSTM), MHCnuggets accepts peptides of variable length and is capable of faster performance than other methods. When compared to methods that integrate binding affinity and HLAp data from mass spectrometry, MHCnuggets yields a fourfold increase in positive predictive value on independent MHC-bound peptide (HLAp) data. We applied MHCnuggets to 26 cancer types in TCGA, processing 52.6 million allele-peptide comparisons in under 2.3 hours, yielding 103,587 candidate immunogenic missense mutations (IMMs). IMM hotspots occurred in 36 genes, including 22 driver genes. Predicted IMM load was significantly associated with increased immune cell infiltration (p<2e-16), including CD8+ T cells. Notably, only 0.15% of predicted immunogenic missense mutations were observed in >2 patients, with 65% of these derived from driver mutations. Our results provide a new method for neoantigen prediction with high performance characteristics and demonstrate its utility in large data sets across human cancers.
Citation Format: Xiaoshan M. Shao, Rohit Bhattacharya, Justin Huang, Ashok Sivakumar, Collin Tokheim, Lily Zheng, Dylan Hirsch, Ben Kaminow, Ashton Omdahl, Maria Bonsack, Angelika B. Riemer, Victor E. Velculescu, Valsamo Anagnostou, Kymberleigh Pagel, Rachel Karchin. High-throughput prediction of MHC Class I and Class II neoantigens with MHCnuggets [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr A33.
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Affiliation(s)
| | | | | | | | | | - Lily Zheng
- 1Johns Hopkins University, Baltimore, MD,
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9
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Carraro M, Monzon AM, Chiricosta L, Reggiani F, Aspromonte MC, Bellini M, Pagel K, Jiang Y, Radivojac P, Kundu K, Pal LR, Yin Y, Limongelli I, Andreoletti G, Moult J, Wilson SJ, Katsonis P, Lichtarge O, Chen J, Wang Y, Hu Z, Brenner SE, Ferrari C, Murgia A, Tosatto SC, Leonardi E. Assessment of patient clinical descriptions and pathogenic variants from gene panel sequences in the CAGI-5 intellectual disability challenge. Hum Mutat 2019; 40:1330-1345. [PMID: 31144778 PMCID: PMC7341177 DOI: 10.1002/humu.23823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 02/18/2019] [Revised: 05/07/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022]
Abstract
The Critical Assessment of Genome Interpretation-5 intellectual disability challenge asked to use computational methods to predict patient clinical phenotypes and the causal variant(s) based on an analysis of their gene panel sequence data. Sequence data for 74 genes associated with intellectual disability (ID) and/or autism spectrum disorders (ASD) from a cohort of 150 patients with a range of neurodevelopmental manifestations (i.e. ID, autism, epilepsy, microcephaly, macrocephaly, hypotonia, ataxia) have been made available for this challenge. For each patient, predictors had to report the causative variants and which of the seven phenotypes were present. Since neurodevelopmental disorders are characterized by strong comorbidity, tested individuals often present more than one pathological condition. Considering the overall clinical manifestation of each patient, the correct phenotype has been predicted by at least one group for 93 individuals (62%). ID and ASD were the best predicted among the seven phenotypic traits. Also, causative or potentially pathogenic variants were predicted correctly by at least one group. However, the prediction of the correct causative variant seems to be insufficient to predict the correct phenotype. In some cases, the correct prediction has been supported by rare or common variants in genes different from the causative one.
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Affiliation(s)
- Marco Carraro
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | | | - Luigi Chiricosta
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Francesco Reggiani
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- Department of Information Engineering, University of Padua, Padua, Italy
| | | | - Mariagrazia Bellini
- Department of Woman and Child Health, University of Padua, Padua, Italy
- Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
| | - Kymberleigh Pagel
- Khoury College of Computer and Information Sciences, Northeastern University, 440, Huntington Avenue, Boston, MA 02115, USA
| | - Yuxiang Jiang
- Khoury College of Computer and Information Sciences, Northeastern University, 440, Huntington Avenue, Boston, MA 02115, USA
| | - Predrag Radivojac
- Khoury College of Computer and Information Sciences, Northeastern University, 440, Huntington Avenue, Boston, MA 02115, USA
| | - Kunal Kundu
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Lipika R. Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Yizhou Yin
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
| | | | - Gaia Andreoletti
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - John Moult
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Stephen J. Wilson
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA
| | - Panagiotis Katsonis
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA
| | - Olivier Lichtarge
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA
| | - Jingqi Chen
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Yaqiong Wang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Zhiqiang Hu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Steven E. Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Carlo Ferrari
- Department of Information Engineering, University of Padua, Padua, Italy
| | - Alessandra Murgia
- Department of Woman and Child Health, University of Padua, Padua, Italy
- Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
| | - Silvio C.E. Tosatto
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- CNR Institute of Neuroscience, Padua, Italy
| | - Emanuela Leonardi
- Department of Woman and Child Health, University of Padua, Padua, Italy
- Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
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Struwe WB, Baldauf C, Hofmann J, Rudd PM, Pagel K. Ion mobility separation of deprotonated oligosaccharide isomers - evidence for gas-phase charge migration. Chem Commun (Camb) 2018; 52:12353-12356. [PMID: 27711324 DOI: 10.1039/c6cc06247d] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
There has been increasing evidence that certain isomeric glycans can be separated efficiently by ion mobility-mass spectrometry when deprotonated ions are analyzed. To better understand the fundamentals behind these separations, we here investigate the impact of ionisation mode and adduct formation using IM-MS, density-functional theory and ab initio molecular dynamics.
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Affiliation(s)
- W B Struwe
- National Institute of Bioprocessing, Research and Training (NIBRT), Fosters Avenue, Dublin, Ireland.
| | - C Baldauf
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany.
| | - J Hofmann
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany.
| | - P M Rudd
- National Institute of Bioprocessing, Research and Training (NIBRT), Fosters Avenue, Dublin, Ireland.
| | - K Pagel
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany. and Institut für Chemie und Biochemie der Freien Universität Berlin, Takustr. 3, 14195 Berlin, Germany.
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11
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Hinneburg H, Hofmann J, Struwe WB, Thader A, Altmann F, Varón Silva D, Seeberger PH, Pagel K, Kolarich D. Distinguishing N-acetylneuraminic acid linkage isomers on glycopeptides by ion mobility-mass spectrometry. Chem Commun (Camb) 2016; 52:4381-4. [PMID: 26926577 DOI: 10.1039/c6cc01114d] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Differentiating the structure of isobaric glycopeptides represents a major challenge for mass spectrometry-based characterisation techniques. Here we show that the regiochemistry of the most common N-acetylneuraminic acid linkages of N-glycans can be identified in a site-specific manner from individual glycopeptides using ion mobility-mass spectrometry analysis of diagnostic fragment ions.
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Affiliation(s)
- H Hinneburg
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany. and Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany.
| | - J Hofmann
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany. and Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - W B Struwe
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, OX1 3QZ, Oxford, UK
| | - A Thader
- Department of Chemistry, University of Natural Resources and Applied Life Sciences, Vienna, Austria
| | - F Altmann
- Department of Chemistry, University of Natural Resources and Applied Life Sciences, Vienna, Austria
| | - D Varón Silva
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.
| | - P H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany. and Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany.
| | - K Pagel
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany. and Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - D Kolarich
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.
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12
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Struwe WB, Benesch JL, Harvey DJ, Pagel K. Collision cross sections of high-mannose N-glycans in commonly observed adduct states--identification of gas-phase conformers unique to [M-H](-) ions. Analyst 2016; 140:6799-803. [PMID: 26159123 DOI: 10.1039/c5an01092f] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We report collision cross sections (CCS) of high-mannose N-glycans as [M + Na](+), [M + K](+), [M + H](+), [M + Cl](-), [M + H2PO4](-) and [M - H](-) ions, measured by drift tube (DT) ion mobility-mass spectrometry (IM-MS) in helium and nitrogen gases. Further analysis using traveling wave (TW) IM-MS reveal the existence of distinct conformers exclusive to [M - H](-) ions.
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Affiliation(s)
- W B Struwe
- Department of Chemistry, University of Oxford, Oxford, UKOX1 3TA.
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14
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Slovak ML, Bedell V, Pagel K, Chang KL, Somlo G. Targeted plasma cell FISH analysis detects residual disease in multiple myeloma missed by standard FISH. J Clin Oncol 2004. [DOI: 10.1200/jco.2004.22.90140.6553] [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
Affiliation(s)
- M. L. Slovak
- City of Hope National Medical Center, Duarte, CA
| | - V. Bedell
- City of Hope National Medical Center, Duarte, CA
| | - K. Pagel
- City of Hope National Medical Center, Duarte, CA
| | - K. L. Chang
- City of Hope National Medical Center, Duarte, CA
| | - G. Somlo
- City of Hope National Medical Center, Duarte, CA
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