1
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Farris J, Khanna C, Smadbeck JB, Johnson SH, Bothun E, Kaplan T, Hoffman F, Polonis K, Oliver G, Reis LM, Semina EV, Rust L, Hoppman NL, Vasmatzis G, Marcou CA, Schimmenti LA, Klee EW. Complex balanced intrachromosomal rearrangement involving PITX2 identified as a cause of Axenfeld-Rieger Syndrome. Am J Med Genet A 2024; 194:e63542. [PMID: 38234180 PMCID: PMC11003841 DOI: 10.1002/ajmg.a.63542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/15/2023] [Accepted: 01/07/2024] [Indexed: 01/19/2024]
Abstract
Axenfeld-Rieger Syndrome (ARS) type 1 is a rare autosomal dominant condition characterized by anterior chamber anomalies, umbilical defects, dental hypoplasia, and craniofacial anomalies, with Meckel's diverticulum in some individuals. Here, we describe a clinically ascertained female of childbearing age with ARS for whom clinical targeted sequencing and deletion/duplication analysis followed by clinical exome and genome sequencing resulted in no pathogenic variants or variants of unknown significance in PITX2 or FOXC1. Advanced bioinformatic analysis of the genome data identified a complex, balanced rearrangement disrupting PITX2. This case is the first reported intrachromosomal rearrangement leading to ARS, illustrating that for patients with compelling clinical phenotypes but negative genomic testing, additional bioinformatic analysis are essential to identify subtle genomic abnormalities in target genes.
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Affiliation(s)
- Joseph Farris
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Cheryl Khanna
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
| | - James B Smadbeck
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarah H Johnson
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Erick Bothun
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
| | - Tyler Kaplan
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
| | - Francis Hoffman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Katarzyna Polonis
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gavin Oliver
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Linda M Reis
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Wisconsin, Milwaukee, Wisconsin, USA
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Wisconsin, Milwaukee, Wisconsin, USA
- Department of Ophthalmology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Laura Rust
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - George Vasmatzis
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Cherisse A Marcou
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Lisa A Schimmenti
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
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2
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Points to consider in the detection of germline structural variants using next-generation sequencing: A statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100316. [PMID: 36507974 DOI: 10.1016/j.gim.2022.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022] Open
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3
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Venable ER, Gagnon MF, Pitel BA, Palmer JM, Peterson JF, Baughn LB, Hoppman NL, Greipp PT, Ketterling RP, Patnaik MS, Kelemen K, Xu X. A TRIP11:: FLT3 gene fusion in a patient with myeloid/lymphoid neoplasm with eosinophilia and tyrosine kinase gene fusions: a case report and review of the literature. Cold Spring Harb Mol Case Stud 2023; 9:mcs.a006243. [PMID: 36627146 PMCID: PMC10111796 DOI: 10.1101/mcs.a006243] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/13/2022] [Indexed: 01/12/2023] Open
Abstract
Myeloid/lymphoid neoplasms with FLT3 gene fusions have recently been included among myeloid/lymphoid neoplasms with eosinophilia and tyrosine kinase gene fusions (MLN-TK) in the World Health Organization classification and International Consensus Classification. As this entity remains remarkably rare, its scope and phenotypic features are evolving. In this report, we describe a 33-yr-old male with MLN-TK. Conventional chromosome analysis revealed a t(13;14)(q12;q32). Further analysis with mate-pair sequencing (MPseq) confirmed a TRIP11::FLT3 gene fusion. A diagnosis of MLN-TK was rendered. To the best of our knowledge, we report the third case of MLN-TK with a TRIP11::FLT3 gene fusion. In contrast to previously described cases, our case exhibited distinctly mild clinical features and disease behavior, emphasizing the diverse spectrum of MLN-TK at primary presentation and variability in disease course. MLN-TK with FLT3 gene fusions are a genetically defined entity which may be targetable with tyrosine kinase inhibitors with anti-FLT3 activity. Accordingly, from diagnostic and therapeutic viewpoints, genetic testing for FLT3 rearrangements using fluorescence in situ hybridization (FISH) or sequencing-based assays should be pursued for patients with chronic eosinophilia.
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Affiliation(s)
- Elise R Venable
- Division of Anatomic Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Marie-France Gagnon
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Beth A Pitel
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Jeanne M Palmer
- Division of Hematology and Oncology, Department of Medicine, Mayo Clinic, Phoenix, Arizona 85054, USA
| | - Jess F Peterson
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Rochester, Minnesota 55905, USA
| | - Linda B Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Rochester, Minnesota 55905, USA
| | - Nicole L Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Patricia T Greipp
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Rochester, Minnesota 55905, USA
| | - Rhett P Ketterling
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Rochester, Minnesota 55905, USA
| | - Mrinal S Patnaik
- Division of Hematology and Oncology, Department of Medicine Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Katalin Kelemen
- Division of Hematopathology, Department of Laboratory Medicine and Pathology; Mayo Clinic, Phoenix, Arizona 85054, USA
| | - Xinjie Xu
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Rochester, Minnesota 55905, USA;
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4
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Pitel BA, Zuckerman EZ, Baughn LB. Mate Pair Sequencing: Next-Generation Sequencing for Structural Variant Detection. Methods Mol Biol 2023; 2621:127-149. [PMID: 37041444 DOI: 10.1007/978-1-0716-2950-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Structural variant detection by next-generation sequencing (NGS) methods have a higher molecular resolution than conventional cytogenetic techniques (Aypar et al., Eur J Haematol 102(1):87-96, 2019; Smadbeck et al., Blood Cancer J 9(12):103, 2019) and are particularly helpful in characterizing genomic rearrangements. Mate pair sequencing (MPseq) leverages a unique library preparation chemistry involving circularization of long DNA fragments, allowing for a unique application of paired-end sequencing of reads that are expected to map 2-5 kb apart in the genome. The unique orientation of the reads allows the user to estimate the location of breakpoints involved in a structural variant either within the sequenced reads or between the two reads. The precision of structural variant and copy number detection by this method allows for characterization of cryptic and complex rearrangements that may be otherwise undetectable by conventional cytogenetic methods (Singh et al., Leuk Lymphoma 60(5):1304-1307, 2019; Peterson et al., Blood Adv 3(8):1298-1302, 2019; Schultz et al., Leuk Lymphoma 61(4):975-978, 2020; Peterson et al., Mol Case Studies 5(2), 2019; Peterson et al., Mol Case Studies 5(3), 2019).
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Affiliation(s)
- Beth A Pitel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| | | | - Linda B Baughn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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5
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Koleilat A, Smadbeck JB, Zepeda‐Mendoza CJ, Williamson CM, Pitel BA, Golden CL, Xu X, Greipp PT, Ketterling RP, Hoppman NL, Peterson JF, Harrison CJ, Akkari YMN, Tsuchiya KD, Shago M, Baughn LB. Characterization of unusual iAMP21 B-lymphoblastic leukemia (iAMP21-ALL) from the Mayo Clinic and Children's Oncology Group. Genes Chromosomes Cancer 2022; 61:710-719. [PMID: 35771717 PMCID: PMC9549522 DOI: 10.1002/gcc.23084] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/06/2022] [Accepted: 06/27/2022] [Indexed: 01/01/2023] Open
Abstract
Acute lymphoblastic leukemia (B-ALL) with intrachromosomal amplification of chromosome 21 (iAMP21-ALL) represents a recurrent high-risk cytogenetic abnormality and accurate identification is critical for appropriate clinical management. Identification of iAMP21-ALL has historically relied on fluorescence in situ hybridization (FISH) using a RUNX1 probe. Current classification requires ≥ five copies of RUNX1 per cell and ≥ three additional copies of RUNX1 on a single abnormal iAMP21-chromosome. We sought to evaluate the performance of the RUNX1 probe in the identification of iAMP21-ALL. This study was a retrospective evaluation of iAMP21-ALL in the Mayo Clinic and Children's Oncology Group cohorts. Of 207 cases of iAMP21-ALL, 188 (91%) were classified as "typical" iAMP21-ALL, while 19 (9%) cases were classified as "unusual" iAMP21-ALL. The "unusual" iAMP21 cases did not meet the current definition of iAMP21 by FISH but were confirmed to have iAMP21 by chromosomal microarray. Half of the "unusual" iAMP21-ALL cases had less than five RUNX1 signals, while the remainder had ≥ five RUNX1 signals with some located apart from the abnormal iAMP21-chromosome. Nine percent of iAMP21-ALL cases fail to meet the FISH definition of iAMP21-ALL demonstrating that laboratories are at risk of misidentification of iAMP21-ALL when relying only on the RUNX1 FISH probe. Incorporation of chromosomal microarray testing circumvents these risks.
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Affiliation(s)
- Alaa Koleilat
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - James B. Smadbeck
- Division of Computational Biology, Department of Quantitative Health SciencesMayo ClinicRochesterMinnesotaUSA
| | | | - Cynthia M. Williamson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Beth A. Pitel
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Crystal L. Golden
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Xinjie Xu
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Patricia T. Greipp
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Rhett P. Ketterling
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Nicole L. Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Jess F. Peterson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Christine J. Harrison
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research InstituteNewcastle University Centre for CancerNewcastle‐upon‐TyneUK
| | | | - Karen D. Tsuchiya
- Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWAUSA
| | - Mary Shago
- Department of Paediatric Laboratory Medicine, The Hospital for Sick ChildrenUniversity of TorontoTorontoOntarioCanada
| | - Linda B. Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
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6
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Identification of EWSR1 rearrangements in patients with immature hematopoietic neoplasms: A case series and review of literature. Ann Diagn Pathol 2022; 58:151942. [PMID: 35344861 DOI: 10.1016/j.anndiagpath.2022.151942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 11/20/2022]
Abstract
Rearrangement of the EWSR1 gene (22q12.2) is a well-recognized genetic lesion in bone and soft tissue tumors. However, few reports have suggested that EWSR1 rearrangements may also occur in the setting of hematopoietic tumors. We herein describe two cases of immature hematopoietic neoplasms presenting with EWSR1 rearrangements. The first occurred in a 41-year-old female diagnosed with mixed-phenotype acute leukemia, B/T/myeloid, in which conventional chromosome analysis revealed a t(2;22)(q35;q12). Further analysis with whole genome sequencing revealed that this rearrangement led to an EWSR1::FEV gene fusion. The second case was identified in an 18-year-old male with a high-grade B-cell lineage malignant neoplasm with immature features in which conventional chromosome analysis revealed a t(17;22)(q25;q12). Mate-pair sequencing, a next generation sequencing-based assay, was performed and revealed three in-frame chimeric gene fusions involving the EWSR1, TEF and STRADA gene regions. This report further expands the repertoire of hematopoietic neoplasms with EWSR1 fusions and partner genes involved in these rearrangements.
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7
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Kosari F, Disselhorst M, Yin J, Peikert T, Udell J, Johnson S, Smadbeck J, Murphy S, McCune A, Karagouga G, Desai A, Schaefer-Klein J, Borad MJ, Cheville J, Vasmatzis G, Baas P, Mansfield AS. Tumor Junction Burden and Antigen Presentation as Predictors of Survival in Mesothelioma Treated With Immune Checkpoint Inhibitors. J Thorac Oncol 2022; 17:446-454. [PMID: 34800701 PMCID: PMC8882146 DOI: 10.1016/j.jtho.2021.10.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/25/2021] [Accepted: 10/29/2021] [Indexed: 12/14/2022]
Abstract
INTRODUCTION The favorable outcomes with immunotherapy for mesothelioma were somewhat unexpected because this tumor has a low tumor mutation burden which has been associated with benefit in other cancers. Because chromosomal rearrangements are common in mesothelioma and have neoantigenic potential, we sought to determine whether they are associated with survival in patients treated with immunotherapy. METHODS Pleural biopsies of mesothelioma after at least one line of therapy were obtained from patients (n = 44) before treatment with nivolumab alone (NCT29908324) or in combination with ipilimumab (NCT30660511). RNA and whole-genome sequencing were performed to identify the junctions resulting from chromosomal rearrangements and antigen processing and presentation gene set expression. Associations with overall survival (OS) were estimated using Cox models. An OS cutoff of 1.5 years was used to distinguish patients with and without durable benefit for use in receiving operating characteristic curves. RESULTS Although tumor junction burdens were not predictive of OS, we identified significant interactions between the junction burdens and multiple antigen processing and presentation gene sets. The "regulation of antigen processing and presentation of peptide antigen" gene set revealed an interaction with tumor junction burden and was predictive of OS. This interaction also predicted 1.5-year or greater survival with an area under the receiving operating characteristic curve of 0.83. This interaction was not predictive of survival in a separate cohort of patients with mesothelioma who did not receive immune checkpoint inhibitors. CONCLUSIONS Analysis of structural variants and antigen presentation gene set expression may facilitate patient selection for immune checkpoint inhibitors.
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Affiliation(s)
- Farhad Kosari
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ
| | - Maria Disselhorst
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jun Yin
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Tobias Peikert
- Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - Julia Udell
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ
| | - Sarah Johnson
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ
| | - James Smadbeck
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ
| | - Stephen Murphy
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ
| | - Alexa McCune
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ
| | - Giannoula Karagouga
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ
| | - Aakash Desai
- Division of Medical Oncology, Mayo Clinic, Rochester, MN
| | - Janet Schaefer-Klein
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ
| | - Mitesh J. Borad
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ,Department of Medical Oncology, Mayo Clinic, Phoenix, Arizona
| | - John Cheville
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - George Vasmatzis
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ
| | - Paul Baas
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Aaron S. Mansfield
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic Rochester, MN and Phoenix, AZ,Division of Medical Oncology, Mayo Clinic, Rochester, MN
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8
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Koleilat A, McGarrah PW, Olteanu H, Van Dyke DL, Smadbeck JB, Johnson SH, Vasmatzis G, Hoppman NL, Xu X, Ketterling RP, Greipp PT, Baughn LB, Patnaik MS, Peterson JF. Utilizing next-generation sequencing to characterize a case of acute myeloid leukemia with t(4;12)(q12;p13) in the absence of ETV6/CHIC2 and ETV6/PDGFRA gene fusions. Cancer Genet 2022; 260-261:1-5. [PMID: 34781094 DOI: 10.1016/j.cancergen.2021.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/26/2021] [Accepted: 11/03/2021] [Indexed: 11/02/2022]
Abstract
The t(4;12)(q12;p13) has been rarely reported in both myeloid/lymphoid neoplasms with eosinophilia (ETV6/PDGFRA gene fusion) and acute myeloid leukemia (AML) (ETV6/CHIC2 gene fusion). The ability to accurately characterize t(4;12) is critical as myeloid neoplasms with PDGFRA rearrangements may be amenable to tyrosine kinase inhibitor (TKI) therapy. Herein, we describe a 60-year-old male with newly diagnosed AML and t(4;12)(q12;p13) by conventional chromosome studies. While the ETV6 break-apart fluorescence in situ hybridization (FISH) probe set demonstrated a balanced ETV6 gene rearrangement, the FIP1L1/CHIC2/PDGFRA tri-color and PDGFRA break-apart FISH probe sets could not resolve the ETV6 gene fusion partner. Mate-pair sequencing (MPseq), a next-generation sequencing assay, was subsequently performed and identified an ETV6 gene rearrangement (at 12p13) that involved an intergenic chromosomal region at 4q12, located between the CHIC2 and PDGFRA gene regions. Having excluded involvement by the PDGFRA gene region, the patient will not be considered for TKI therapy at any point during his medical management. The accurate characterization of structural rearrangements by NGS-based technologies, as demonstrated in this case, highlights the clinical relevance and potential impact on patient medical management of modern cytogenetic techniques.
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MESH Headings
- Chromosomes, Human, Pair 12/genetics
- Chromosomes, Human, Pair 4/genetics
- DNA-Binding Proteins/genetics
- High-Throughput Nucleotide Sequencing
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia, Myeloid, Acute/genetics
- Male
- Middle Aged
- Oncogene Proteins, Fusion/genetics
- Proto-Oncogene Proteins c-ets/genetics
- Receptor, Platelet-Derived Growth Factor alpha/genetics
- Repressor Proteins/genetics
- Sequence Analysis, DNA/methods
- Transcription Factors/genetics
- Translocation, Genetic
- ETS Translocation Variant 6 Protein
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Affiliation(s)
- Alaa Koleilat
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Patrick W McGarrah
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Horatiu Olteanu
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Daniel L Van Dyke
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - Sarah H Johnson
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Xinjie Xu
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rhett P Ketterling
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Patricia T Greipp
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Mrinal S Patnaik
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Jess F Peterson
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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9
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OUP accepted manuscript. Lab Med 2022; 53:e134-e138. [DOI: 10.1093/labmed/lmac010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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10
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Dalland JC, Smadbeck JB, Sharma N, Meyer RG, Pearce KE, Greipp PT, Peterson JF, Kumar S, Ketterling RP, King RL, Baughn LB. Increased complexity of t(11;14) rearrangements in plasma cell neoplasms compared with mantle cell lymphoma. Genes Chromosomes Cancer 2021; 60:678-686. [PMID: 34124820 PMCID: PMC8453742 DOI: 10.1002/gcc.22977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/14/2022] Open
Abstract
Plasma cell neoplasms (PCN) and mantle cell lymphoma (MCL) can both harbor t(11;14)(q13;q32) (CCND1/IGH), usually resulting in cyclin D1 overexpression. In some cases, particularly at low levels of disease, it can be morphologically challenging to distinguish between these entities in the bone marrow (BM) since PCN with t(11;14) are often CD20-positive with lymphoplasmacytic cytology, while MCL can rarely have plasmacytic differentiation. We compared the difference in CCND1/IGH by fluorescence in situ hybridization (FISH) in PCN and MCL to evaluate for possible differentiating characteristics. We identified 326 cases of MCL with t(11;14) and 279 cases of PCN with t(11;14) from either formalin-fixed, paraffin-embedded tissue or fresh BM specimens. The "typical," balanced CCND1/IGH FISH signal pattern was defined as three total CCND1 signals, three total IGH signals, and two total fusion signals. Any deviation from the "typical" pattern was defined as an "atypical" pattern, which was further stratified into "gain of fusion" vs "complex" patterns. There was a significantly higher proportion of cases that showed an atypical FISH pattern in PCN compared with MCL (53% vs 27%, P < .0001). There was also a significantly higher proportion of cases that showed a complex FISH pattern in PCN compared with MCL (47% vs 17%, P < .0001). We confirmed these findings using mate-pair sequencing of 25 PCN and MCL samples. PCN more often have a complex CCND1/IGH FISH pattern compared with MCL, suggesting possible differences in the genomic mechanisms underlying these rearrangements in plasma cells compared with B cells.
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Affiliation(s)
- Joanna C. Dalland
- Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - James B. Smadbeck
- Division of Computational Biology, Department of Quantitative Health SciencesMayo ClinicRochesterMinnesotaUSA
| | - Neeraj Sharma
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Reid G. Meyer
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Kathryn E. Pearce
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Patricia T. Greipp
- Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Jess F. Peterson
- Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Shaji Kumar
- Division of Hematology, Department of Internal MedicineMayo ClinicRochesterMinnesotaUSA
| | - Rhett P. Ketterling
- Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Rebecca L. King
- Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Linda B. Baughn
- Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
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11
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Cope H, Barseghyan H, Bhattacharya S, Fu Y, Hoppman N, Marcou C, Walley N, Rehder C, Deak K, Alkelai A, Vilain E, Shashi V. Detection of a mosaic CDKL5 deletion and inversion by optical genome mapping ends an exhaustive diagnostic odyssey. Mol Genet Genomic Med 2021; 9:e1665. [PMID: 33955715 PMCID: PMC8372083 DOI: 10.1002/mgg3.1665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Currently available structural variant (SV) detection methods do not span the complete spectrum of disease-causing SVs. Optical genome mapping (OGM), an emerging technology with the potential to resolve diagnostic dilemmas, was performed to investigate clinically-relevant SVs in a 4-year-old male with an epileptic encephalopathy of undiagnosed molecular origin. METHODS OGM was utilized to image long, megabase-size DNA molecules, fluorescently labeled at specific sequence motifs throughout the genome with high sensitivity for detection of SVs greater than 500 bp in size. OGM results were confirmed in a CLIA-certified laboratory via mate-pair sequencing. RESULTS OGM identified a mosaic, de novo 90 kb deletion and inversion on the X chromosome disrupting the CDKL5 gene. Detection of the mosaic deletion, which had been previously undetected by chromosomal microarray, an infantile epilepsy panel including exon-level microarray for CDKL5, exome sequencing as well as genome sequencing, resulted in a diagnosis of X-linked dominant early infantile epileptic encephalopathy-2. CONCLUSION OGM affords an effective technology for the detection of SVs, especially those that are mosaic, since these remain difficult to detect with current NGS technologies and with conventional chromosomal microarrays. Further research in undiagnosed populations with OGM is warranted.
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Affiliation(s)
- Heidi Cope
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Hayk Barseghyan
- Center for Genetic Medicine ResearchChildren’s National HospitalWashingtonDCUSA
- Department of genomics and Precision MedicineSchool of Medicine and Health SciencesGeorge Washington UniversityWashingtonDCUSA
- Bionano Genomics IncSan DiegoCAUSA
| | | | - Yulong Fu
- Center for Genetic Medicine ResearchChildren’s National HospitalWashingtonDCUSA
| | - Nicole Hoppman
- Division of Laboratory Genetics and GenomicsDepartment of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Cherisse Marcou
- Division of Laboratory Genetics and GenomicsDepartment of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Nicole Walley
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Catherine Rehder
- Department of PathologyDuke University Medical CenterDurhamNCUSA
| | - Kristen Deak
- Department of PathologyDuke University Medical CenterDurhamNCUSA
| | - Anna Alkelai
- Institute for Genomic MedicineColumbia University Medical CenterNew YorkNYUSA
| | - Eric Vilain
- Center for Genetic Medicine ResearchChildren’s National HospitalWashingtonDCUSA
- Department of genomics and Precision MedicineSchool of Medicine and Health SciencesGeorge Washington UniversityWashingtonDCUSA
| | - Vandana Shashi
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
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12
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Grassi T, Harris FR, Smadbeck JB, Murphy SJ, Block MS, Multinu F, Schaefer Klein JL, Zhang P, Karagouga G, Liu MC, Larish A, Lemens MA, Sommerfield MKS, Cappuccio S, Cheville JC, Vasmatzis G, Mariani A. Personalized tumor-specific DNA junctions to detect circulating tumor in patients with endometrial cancer. PLoS One 2021; 16:e0252390. [PMID: 34111149 PMCID: PMC8192008 DOI: 10.1371/journal.pone.0252390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 05/17/2021] [Indexed: 01/08/2023] Open
Abstract
INTRODUCTION There are no reliable blood biomarkers for monitoring endometrial cancer patients in the current clinical practice. Circulating tumor DNA (ctDNA) is emerging as a promising non-invasive method to measure tumor burden, define prognosis and monitor disease status in many solid cancers. In this pilot study, we investigated if unique tumor-specific DNA junctions can be used to detect ctDNA levels in patients with endometrial cancer. METHODS Chromosomal rearrangements in primary tumors of eleven patients with high-grade or advanced stage endometrial cancer were determined by whole-genome Mate-Pair sequencing. Identified unique tumor-specific junctions were evaluated in pre- and six-week post-surgery patient plasma using individualized quantitative polymerase chain reaction (qPCR) assays. The relationship between clinicopathological features and detection of ctDNA was investigated. RESULTS CtDNA was detected in 60% (6/10) of cases pre-surgery and in 27% (3/11) post-surgery. The detection of ctDNA pre-surgery was consistent with clinical indicators of aggressive disease such as advanced stage (80% - 4/5), lymphatic spread of disease (100% - 3/3), serous histology (80% - 4/5), deep myometrial invasion (100% - 3/3), lympho-vascular space invasion (75% - 3/4). All patients in which ctDNA was detected post-surgically had type II endometrial cancer. DISCUSSION This pilot study demonstrates the feasibility of using personalized tumor-specific junction panels for detecting ctDNA in the plasma of endometrial cancer patients. Larger studies and longer follow-up are needed to validate the potential association between pre-surgical ctDNA detection and the presence of cancers with aggressive pathologic tumor characteristics or advanced stage observed in this study.
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Affiliation(s)
- Tommaso Grassi
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
- Clinic of Obstetrics and Gynecology, University of Milan-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Faye R. Harris
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States of America
| | - James B. Smadbeck
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States of America
| | - Stephen J. Murphy
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States of America
| | - Matthew S. Block
- Department of Oncology, Mayo Clinic, Rochester, MN, United States of America
| | - Francesco Multinu
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
- Department of Gynecology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | | | - Piyan Zhang
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States of America
| | - Giannoula Karagouga
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States of America
| | - Minetta C. Liu
- Department of Oncology, Mayo Clinic, Rochester, MN, United States of America
| | - Alyssa Larish
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Maureen A. Lemens
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | | | - Serena Cappuccio
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
- Department of Women and Child Health, Catholic University of the Sacred Heart, Rome, Italy
| | - John C. Cheville
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - George Vasmatzis
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States of America
- * E-mail:
| | - Andrea Mariani
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
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13
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Freitag CE, Sukov WR, Bryce AH, Berg JV, Vanderbilt CM, Shen W, Smadbeck JB, Greipp PT, Ketterling RP, Jenkins RB, Herrera-Hernandez L, Costello BA, Thompson RH, Boorjian SA, Leibovich BC, Jimenez RE, Murphy SJ, Vasmatzis G, Cheville JC, Gupta S. Assessment of isochromosome 12p and 12p abnormalities in germ cell tumors using fluorescence in situ hybridization, single-nucleotide polymorphism arrays, and next-generation sequencing/mate-pair sequencing. Hum Pathol 2021; 112:20-34. [PMID: 33798590 DOI: 10.1016/j.humpath.2021.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 03/24/2021] [Indexed: 02/08/2023]
Abstract
The identification of isochromosome 12p [i(12p)] and 12p gains have significant clinical utility in the diagnosis of germ cell tumors (GCTs). We have summarized the results of fluorescence in situ hybridization (FISH) assays to identify i(12p), performed in a Clinical Laboratory Improvement Amendments (CLIA)-validated setting for 536 specimens. In addition, the American Association for Cancer Research (AACR) Project GENIE registry and The Cancer Genome Atlas (TCGA) data sets were evaluated for chromosome 12p gains, and a limited number of cases were concurrently evaluated using FISH, single-nucleotide polymorphism (SNP) arrays and next-generation sequencing (NGS; including mate-pair sequencing). Specimens submitted for FISH testing were frequently from potential sites of metastases (male: 70.9% and female: 69.3%), and polysomy of chromosome 12 with or without concurrent i(12p) was a frequent finding, seen in 3% (16/536) and 35% (186/536) of cases, respectively. Our analysis suggests that 12p gains are likely to be present in approximately 73% of male GCT and in 32% of female GCT (AACR GENIE, n = 555). When comparing TCGA cases of testicular GCT (n = 149) to combined cases of sarcoma, colorectal, prostate, and urothelial carcinoma (n = 1754), 12p gains had a sensitivity of 77.2% and specificity of 97.3% for GCT. Some advantages of FISH over SNP arrays/NGS include relatively lower cost, rapid turnaround time, the ability to analyze biopsy material with a limited number of tumor cells (50 cells), and the ability to distinguish i(12p) from polysomy. The ability to spatially restrict the analysis to cells of interest is critical, as specimens submitted for testing often have low tumor purity. Disadvantages include false negative results due to an inability to detect segmental gains due to FISH probe design. With the availability of numerous testing modalities, including FISH, SNP arrays, and NGS-based assays, a nuanced understanding of the advantages and disadvantages of each methodology, as has been presented in this study, may inform appropriate testing strategies.
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Affiliation(s)
- C Eric Freitag
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905 USA
| | - William R Sukov
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905 USA
| | - Alan H Bryce
- Division of Hematology and Medical Oncology, Mayo Clinic, Phoenix, AZ, 85054 USA
| | - Jamie V Berg
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905 USA
| | - Chad M Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065 USA
| | - Wei Shen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905 USA
| | - James B Smadbeck
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, 55905 USA
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905 USA
| | - Rhett P Ketterling
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905 USA
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905 USA
| | | | - Brian A Costello
- Division of Medical Oncology, Mayo Clinic, Rochester, MN, 55905 USA
| | | | | | | | - Rafael E Jimenez
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905 USA
| | - Stephen J Murphy
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, 55905 USA
| | - George Vasmatzis
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, 55905 USA
| | - John C Cheville
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905 USA
| | - Sounak Gupta
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905 USA.
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14
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Murphy SJ, Levy MJ, Smadbeck JB, Karagouga G, McCune AF, Harris FR, Udell JB, Johnson SH, Kerr SE, Cheville JC, Kipp BR, Vasmatzis G, Gleeson FC. Theragnostic chromosomal rearrangements in treatment-naive pancreatic ductal adenocarcinomas obtained via endoscopic ultrasound. J Cell Mol Med 2021; 25:4110-4123. [PMID: 33704908 PMCID: PMC8051743 DOI: 10.1111/jcmm.16381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 01/29/2021] [Accepted: 02/03/2021] [Indexed: 12/15/2022] Open
Abstract
A crucial mutational mechanism in malignancy is structural variation, in which chromosomal rearrangements alter gene functions that drive cancer progression. Herein, the presence and pattern of structural variations were investigated in twelve prospectively acquired treatment‐naïve pancreatic cancers specimens obtained via endoscopic ultrasound (EUS). In many patients, this diagnostic biopsy procedure and specimen is the only opportunity to identify somatic clinically relevant actionable alterations that may impact their care and outcome. Specialized mate pair sequencing (MPseq) provided genome‐wide structural variance analysis (SVA) with a view to identifying prognostic markers and possible therapeutic targets. MPseq was successfully performed on all specimens, identifying highly rearranged genomes with complete SVA on all specimens with > 20% tumour content. SVA identified chimeric fusion proteins and potentially immunogenic readthrough transcripts, change of function truncations, gains and losses of key genes linked to tumour progression. Complex localized rearrangements, termed chromoanagenesis, with broad pattern heterogeneity were observed in 10 (83%) specimens, impacting multiple genes with diverse cellular functions that could influence theragnostic evaluation and responsiveness to immunotherapy regimens. This study indicates that genome‐wide MPseq can be successfully performed on very limited clinically EUS obtained specimens for chromosomal rearrangement detection and potential theragnostic targets.
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Affiliation(s)
- Stephen J Murphy
- Biomarker Discovery Laboratory, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Michael J Levy
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN, USA
| | - James B Smadbeck
- Biomarker Discovery Laboratory, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Giannoula Karagouga
- Biomarker Discovery Laboratory, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Alexa F McCune
- Biomarker Discovery Laboratory, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Faye R Harris
- Biomarker Discovery Laboratory, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Julia B Udell
- Biomarker Discovery Laboratory, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sarah H Johnson
- Biomarker Discovery Laboratory, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sarah E Kerr
- Department of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - John C Cheville
- Biomarker Discovery Laboratory, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Benjamin R Kipp
- Department of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - George Vasmatzis
- Biomarker Discovery Laboratory, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ferga C Gleeson
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN, USA
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15
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Zepeda‐Mendoza CJ, Essendrup A, Smoley SA, Johnson SH, Hoppman NL, Vasmatzis G, Jackson DL, Kearney HM, Baughn LB. Prenatal characterization of a novel inverted SMAD2 duplication by mate pair sequencing in a fetus with dextrocardia. Clin Case Rep 2021; 9:769-774. [PMID: 33598243 PMCID: PMC7869371 DOI: 10.1002/ccr3.3608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/01/2020] [Indexed: 11/06/2022] Open
Abstract
This case report underlines the importance of molecular characterization of genomic duplications and other structural variants in the prenatal setting to guide clinical interpretation, genetic counseling, and perinatal medical care.
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Affiliation(s)
| | - Anna Essendrup
- Division of Laboratory GeneticsDepartment of Laboratory Medicine and Pathology, Mayo ClinicRochesterMNUSA
| | - Stephanie A. Smoley
- Division of Laboratory GeneticsDepartment of Laboratory Medicine and Pathology, Mayo ClinicRochesterMNUSA
| | - Sarah H. Johnson
- Center for Individualized Medicine‐Biomarker Discovery, Mayo ClinicRochesterMNUSA
| | - Nicole L Hoppman
- Division of Laboratory GeneticsDepartment of Laboratory Medicine and Pathology, Mayo ClinicRochesterMNUSA
| | - George Vasmatzis
- Center for Individualized Medicine‐Biomarker Discovery, Mayo ClinicRochesterMNUSA
- Department of Molecular MedicineMayo ClinicRochesterMNUSA
| | - Daniel L. Jackson
- Department of Obstetrics, Gynecology and Women's HealthUniversity of Missouri HealthColumbiaMOUSA
| | - Hutton M. Kearney
- Division of Laboratory GeneticsDepartment of Laboratory Medicine and Pathology, Mayo ClinicRochesterMNUSA
| | - Linda B. Baughn
- Division of Laboratory GeneticsDepartment of Laboratory Medicine and Pathology, Mayo ClinicRochesterMNUSA
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16
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Chromosomal Junction Detection from Whole-Genome Sequencing on Formalin-Fixed, Paraffin-Embedded Tumors. J Mol Diagn 2020; 23:375-388. [PMID: 33387698 DOI: 10.1016/j.jmoldx.2020.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 11/20/2020] [Accepted: 12/14/2020] [Indexed: 11/22/2022] Open
Abstract
DNA junctions (DNAJs) frequently impact clinically relevant genes in tumors and are important for diagnostic and therapeutic purposes. Although routinely screened through fluorescence in situ hybridization assays, such testing only allows the interrogation of single-gene regions or known fusion partners. Comprehensive assessment of DNAJs present across the entire genome can only be determined from whole-genome sequencing. Structural variance analysis from whole-genome paired-end sequencing data is, however, frequently restricted to copy number changes without DNAJ detection. Through optimized whole-genome sequencing and specialized bioinformatics algorithms, complete structural variance analysis is reported, including DNAJs, from formalin-fixed DNA. Selective library assembly from larger fragments (>500 bp) and economical sequencing depths (300 to 400 million reads) provide representative genomic coverage profiles and increased allelic coverage to levels compatible with DNAJ calling (40× to 60×). Although consistently fragmented, more recently formalin-fixed, specimens (<2 years' storage) revealed consistent populations of larger DNA fragments. Optimized bioinformatics efficiently detected >90% of DNAJs in two prostate tumors (approximately 60% tumor) previously analyzed by mate-pair sequencing on fresh frozen tissue, with evidence of at least one spanning-read in 99% of DNAJs. Rigorous masking with data from unrelated formalin-fixed tissue progressively eliminated many false-positive DNAJs, without loss of true positives, resulting in low numbers of false-positive passing current filters. This methodology enables more comprehensive clinical genomics testing on formalin-fixed clinical specimens.
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17
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Marla SS, Mishra P, Maurya R, Singh M, Wankhede DP, Kumar A, Yadav MC, Subbarao N, Singh SK, Kumar R. Refinement of Draft Genome Assemblies of Pigeonpea ( Cajanus cajan). Front Genet 2020; 11:607432. [PMID: 33384719 PMCID: PMC7770131 DOI: 10.3389/fgene.2020.607432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/23/2020] [Indexed: 11/13/2022] Open
Abstract
Genome assembly of short reads from large plant genomes remains a challenge in computational biology despite major developments in next generation sequencing. Of late several draft assemblies have been reported in sequenced plant genomes. The reported draft genome assemblies of Cajanus cajan have different levels of genome completeness, a large number of repeats, gaps, and segmental duplications. Draft assemblies with portions of genome missing are shorter than the referenced original genome. These assemblies come with low map accuracy affecting further functional annotation and the prediction of gene components as desired by crop researchers. Genome coverage, i.e., the number of sequenced raw reads mapped onto a certain location of the genome is an important quality indicator of completeness and assembly quality in draft assemblies. The present work aimed to improve the coverage in reported de novo sequenced draft genomes (GCA_000340665.1 and GCA_000230855.2) of pigeonpea, a legume widely cultivated in India. The two recently sequenced assemblies, A1 and A2 comprised 72% and 75% of the estimated coverage of the genome, respectively. We employed an assembly reconciliation approach to compare the draft assemblies and merge them, filling the gaps by employing an algorithm size sorting mate-pair library to generate a high quality and near complete assembly with enhanced contiguity. The majority of gaps present within scaffolds were filled with right-sized mate-pair reads. The improved assembly reduced the number of gaps than those reported in draft assemblies resulting in an improved genome coverage of 82.4%. Map accuracy of the improved assembly was evaluated using various quality metrics and for the presence of specific trait-related functional genes. Employed pair-end and mate-pair local libraries helped us to reduce gaps, repeats, and other sequence errors resulting in lengthier scaffolds compared to the two draft assemblies. We reported the prediction of putative host resistance genes against Fusarium wilt disease by their performance and evaluated them both in wet laboratory and field phenotypic conditions.
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Affiliation(s)
- Soma S. Marla
- Indian Council for Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Pallavi Mishra
- Indian Council for Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ranjeet Maurya
- Indian Council for Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Mohar Singh
- Indian Council for Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Anil Kumar
- Directorate of Education, Rani Lakshmi Bai Central Agricultural University, Jhansi, India
| | - Mahesh C. Yadav
- Indian Council for Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - N. Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sanjeev K. Singh
- Indian Council for Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rajesh Kumar
- Indian Council for Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
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18
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Berg HE, Blackburn PR, Smadbeck JB, Swanson KE, Rice CS, Webley MR, Johnson SH, Vasmatzis G, Xu X, Greipp PT, Hoppman NL, Ketterling RP, Baughn LB, Boston CH, Sutton LM, Peterson JF. Detection of a Cryptic EP300/ZNF384 Gene Fusion by Chromosomal Microarray and Next-Generation Sequencing Studies in a Pediatric Patient with B-Lymphoblastic Leukemia. Lab Med 2020; 52:297-302. [PMID: 33145596 DOI: 10.1093/labmed/lmaa085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Zinc-finger protein 384 (ZNF384) gene fusions with EP300 have recently been described as a recurrent fusion in B-cell acute lymphoblastic leukemia (B-ALL) with a good response to conventional chemotherapy, suggesting a favorable prognosis. Herein, we report on a female patient aged 12 years with uninformative conventional chromosome and B-ALL panel fluorescence in situ hybridization studies with chromosomal microarray showing multiple copy number gains, including relative gains in the ZNF384 (12p13.31) and EP300 (22q13.2) gene regions, suggesting a cryptic EP300/ZNF384 fusion. Ultimately, a next-generation sequencing assay, mate pair sequencing, was utilized to confirm EP300/ZNF384 fusion in this B-ALL clone, which may confer a favorable overall prognosis and potential targeted therapy.
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Affiliation(s)
- Holly E Berg
- Department of Laboratory Medicine and Pathology, Rochester, Minnesota
| | - Patrick R Blackburn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, Minnesota
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota
| | - Kirsten E Swanson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, Minnesota
| | - Christopher S Rice
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, Minnesota
| | - Matthew R Webley
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, Minnesota
| | - Sarah H Johnson
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota
| | - Xinjie Xu
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, Minnesota
| | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, Minnesota
| | - Nicole L Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, Minnesota
| | - Rhett P Ketterling
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, Minnesota
| | - Linda B Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, Minnesota
| | | | - Lisa M Sutton
- Department of Pathology and Laboratory Medicine, Driscoll Children's Hospital, Corpus Christi, Texas
| | - Jess F Peterson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, Minnesota
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19
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Murphy SJ, Harris FR, Smadbeck JB, Serla V, Karagouga G, Johnson SH, Kosari F, Pierson KE, Bungum AO, Edell ES, Mansfield AS, Wigle DA, Kipp BR, Vasmatzis G, Aubry MC. Optimizing clinical cytology touch preparations for next generation sequencing. Genomics 2020; 112:5313-5323. [PMID: 33144219 DOI: 10.1016/j.ygeno.2020.10.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/14/2020] [Accepted: 10/28/2020] [Indexed: 12/26/2022]
Abstract
Intraoperative diagnosis is routinely performed on cytology touch preparations (TPs) from core needle biopsies (CNBs). Current interest promotes their utility as an important source of patient tissue for clinical genomic testing. Herein we present whole genome structural variant analysis (SVA) from mate-pair sequencing (MPseq) and whole exome sequencing (WES) mutation calling in DNA directly whole genome amplified (WGA) from TPs. Chromosomal copy changes and somatic DNA junction detection from MPseq of TPs were highly consistent with associated CNBs and bulk resected tissues in all cases. While increased frequency coverage noise from limitations of amplification of limited sample input was significant, this was effectively compensated by natural tumor enrichment during the TP process, which also enhanced variant detection and loss of heterozygosity evaluations from WES. This novel TP methodology enables expanded utility of frequently limited CNB for both clinical and research genomic testing.
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Affiliation(s)
- Stephen J Murphy
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States.
| | - Faye R Harris
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - James B Smadbeck
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - Vishnu Serla
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States; Departments of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Giannoula Karagouga
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - Sarah H Johnson
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - Farhad Kosari
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - Karlyn E Pierson
- Departments of Thoracic Surgery, Mayo Clinic, Rochester, MN, United States
| | - Aaron O Bungum
- Departments of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, United States
| | - Eric S Edell
- Departments of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, United States
| | | | - Dennis A Wigle
- Departments of Thoracic Surgery, Mayo Clinic, Rochester, MN, United States
| | - Benjamin R Kipp
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - George Vasmatzis
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States.
| | - Marie Christine Aubry
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States.
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Berg HE, Blackburn PR, Baughn LB, Ketterling RP, Xu X, Greipp PT, Hoppman NL, Smadbeck JB, Vasmatzis G, Shi M, Reichard KK, Viswanatha DS, Jevremovic D, Maher GM, Peterson JF. Identification of a novel KMT2A/GIMAP8 gene fusion in a pediatric patient with acute undifferentiated leukemia. Genes Chromosomes Cancer 2020; 60:108-111. [PMID: 33078871 DOI: 10.1002/gcc.22902] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 01/05/2023] Open
Abstract
Acute undifferentiated leukemia (AUL) is a very rare hematologic neoplasm that expresses no markers specific for either myeloid or lymphoid lineages. While commonly observed in several acute leukemias, KMT2A rearrangements in AUL have been rarely reported in the literature. We report the third case to our knowledge of AUL harboring a KMT2A rearrangement. Furthermore, the KMT2A/GIMAP8 gene fusion identified in this case represents a novel KMT2A rearrangement.
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Affiliation(s)
- Holly E Berg
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Patrick R Blackburn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Linda B Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Rhett P Ketterling
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA.,Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Xinjie Xu
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Nicole L Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota, USA
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota, USA
| | - Min Shi
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Kaaren K Reichard
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - David S Viswanatha
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Dragan Jevremovic
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - George M Maher
- Divison of Pediatric Hematology/Oncology, Sanford Children's Hospital, Sioux Falls, South Dakota, USA
| | - Jess F Peterson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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21
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Parney IF, Gustafson MP, Solseth M, Bulur P, Peterson TE, Smadbeck JB, Johnson SH, Murphy SJ, Vasmatzis G, Dietz AB. Novel strategy for manufacturing autologous dendritic cell/allogeneic tumor lysate vaccines for glioblastoma. Neurooncol Adv 2020; 2:vdaa105. [PMID: 33134920 PMCID: PMC7592424 DOI: 10.1093/noajnl/vdaa105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Glioblastoma, the most common primary malignant brain tumor, is nearly universally fatal by 5 years. Dendritic cell vaccines are promising but often limited clinically by antigen choice, dendritic cell potency, and/or manufacturing yield. We optimized vaccine manufacture, generating potent mature autologous dendritic cells pulsed with allogeneic glioblastoma lysates. Methods Platelet lysate-based supplement was used to establish human glioblastoma cell lines. Phenotype and genotype were assessed. An improved culture technique to generate mature dendritic cells from glioblastoma patients’ monocytes was developed. The ability of T cells stimulated with autologous dendritic cells pulsed with allogeneic glioblastoma cell lysate to kill HLA-A2-matched glioblastoma cells was assessed. Results Glioblastoma cell lines established with platelet lysate supplement grew faster and expressed more stem-like markers than lines grown in neural stem cell media or in the presence of serum. They expressed a variety of glioma-associated antigens and had genomic abnormalities characteristic of glioblastoma stable up to 15 doublings. Unlike standard culture techniques, our optimized technique produced high levels of mature dendritic cells from glioblastoma patients’ monocytes. Autologous T cells stimulated with mature dendritic cells pulsed with allogeneic glioblastoma cell line lysate briskly killed HLA-A2-matched glioblastoma cells. Conclusions Our glioblastoma culture method provides a renewable source for a broad spectrum glioblastoma neoantigens while our dendritic cell culture technique results in more mature dendritic cells in glioblastoma patients than standard techniques. This broadly applicable strategy could be easily integrated into patient care.
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Affiliation(s)
- Ian F Parney
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
- Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA
- Corresponding Author: Ian F. Parney, MD, PhD or Allan B. Dietz, PhD, Mayo Clinic, 200 First Street SW, Rochester, MN 55902, USA ( or )
| | | | - Mary Solseth
- Division of Transfusion Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Peggy Bulur
- Division of Transfusion Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Timothy E Peterson
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - James B Smadbeck
- Division of Genetics and Bioinformatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarah H Johnson
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Stephen J Murphy
- Division of Genetics and Bioinformatics, Mayo Clinic, Rochester, Minnesota, USA
| | - George Vasmatzis
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Allan B Dietz
- Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Transfusion Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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22
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Snider JS, Znoyko I, Lindsey KG, Morse J, Baughn LB, Hoppman NL, Pitel BA, Pearce KE, Schandl CA, Wolff DJ. Integrated genomic analysis using chromosomal microarray, fluorescence in situ hybridization and mate pair analyses: Characterization of a cryptic t(9;22)(p24.1;q11.2)/BCR-JAK2 in myeloid/lymphoid neoplasm with eosinophilia. Cancer Genet 2020; 246-247:44-47. [PMID: 32827877 DOI: 10.1016/j.cancergen.2020.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/10/2020] [Accepted: 08/03/2020] [Indexed: 12/17/2022]
Abstract
The 2016 World Health Organization entity 'Myeloid/lymphoid neoplasms with eosinophilia and rearrangement of PDGFRA, PDGFRB or FGFR1, or with PCM1-JAK2' encompasses a group of rare neoplasms that result from the formation of a fusion gene that leads to expression of an aberrant tyrosine kinase. This entity also contains variant JAK2 fusion partners, and detection of this defining event can be facilitated by various cytogenetic and molecular methods. Cryptic rearrangements of 9p24/JAK2 can be particularly challenging to identify. We describe the use of chromosomal microarray analysis (CMA), fluorescence in situ hybridization (FISH) with a probe for JAK2, and genomic mate pair analysis to describe a complex karyotype with a t(9;22) that produced a functional BCR-JAK2 fusion, leading to the appropriate diagnosis for the patient. This case highlights the importance of using an integrated genomic approach to fully define complex aberrations to assign proper diagnoses.
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Affiliation(s)
- Jessica S Snider
- Medical University of South Carolina, Department of Pathology and Laboratory Medicine, 165 Ashley Ave, MSC 908, Charleston, SC 29425, United States.
| | - Iya Znoyko
- Medical University of South Carolina, Department of Pathology and Laboratory Medicine, 165 Ashley Ave, MSC 908, Charleston, SC 29425, United States.
| | - Kathryn G Lindsey
- Medical University of South Carolina, Department of Pathology and Laboratory Medicine, 165 Ashley Ave, MSC 908, Charleston, SC 29425, United States.
| | - Jennifer Morse
- Medical University of South Carolina, Department of Pathology and Laboratory Medicine, 165 Ashley Ave, MSC 908, Charleston, SC 29425, United States.
| | - Linda B Baughn
- Mayo Clinic, Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, 200 1st St SW, Rochester, MN 55905, United States.
| | - Nicole L Hoppman
- Mayo Clinic, Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, 200 1st St SW, Rochester, MN 55905, United States.
| | - Beth A Pitel
- Mayo Clinic, Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, 200 1st St SW, Rochester, MN 55905, United States.
| | - Kathryn E Pearce
- Mayo Clinic, Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, 200 1st St SW, Rochester, MN 55905, United States.
| | - Cynthia A Schandl
- Medical University of South Carolina, Department of Pathology and Laboratory Medicine, 165 Ashley Ave, MSC 908, Charleston, SC 29425, United States.
| | - Daynna J Wolff
- Medical University of South Carolina, Department of Pathology and Laboratory Medicine, 165 Ashley Ave, MSC 908, Charleston, SC 29425, United States.
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23
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Vaubel R, Zschernack V, Tran QT, Jenkins S, Caron A, Milosevic D, Smadbeck J, Vasmatzis G, Kandels D, Gnekow A, Kramm C, Jenkins R, Kipp BR, Rodriguez FJ, Orr BA, Pietsch T, Giannini C. Biology and grading of pleomorphic xanthoastrocytoma-what have we learned about it? Brain Pathol 2020; 31:20-32. [PMID: 32619305 PMCID: PMC8018001 DOI: 10.1111/bpa.12874] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/09/2020] [Accepted: 06/16/2020] [Indexed: 02/06/2023] Open
Abstract
Pleomorphic xanthoastrocytoma (PXA) is a rare astrocytoma predominantly affecting children and young adults. We performed comprehensive genomic characterization on a cohort of 67 patients with histologically defined PXA (n = 53, 79%) or anaplastic PXA (A-PXA, n = 14, 21%), including copy number analysis (ThermoFisher Oncoscan, n = 67), methylation profiling (Illumina EPIC array, n = 43) and targeted next generation sequencing (n = 32). The most frequent alterations were CDKN2A/B deletion (n = 63; 94%) and BRAF p.V600E (n = 51, 76.1%). In 7 BRAF p.V600 wild-type cases, alternative driver alterations were identified involving BRAF, RAF1 and NF1. Downstream phosphorylation of ERK kinase was uniformly present. Additional pathogenic alterations were rare, with TERT, ATRX and TP53 mutations identified in a small number of tumors, predominantly A-PXA. Methylation-based classification of 46 cases utilizing a comprehensive reference tumor allowed assignment to the PXA methylation class in 40 cases. A minority grouped with the methylation classes of ganglioglioma or pilocytic astrocytoma (n = 2), anaplastic pilocytic astrocytoma (n = 2) or control tissues (n = 2). In 9 cases, tissue was available from matched primary and recurrent tumors, including 8 with anaplastic transformation. At recurrence, two tumors acquired TERT promoter mutations and the majority demonstrated additional non-recurrent copy number alterations. Methylation class was preserved at recurrence. For 62 patients (92.5%), clinical follow-up data were available (median follow-up, 5.4 years). Overall survival was significantly different between PXA and A-PXA (5-year OS 80.8% vs. 47.6%; P = 0.0009) but not progression-free survival (5-year PFS 59.9% vs. 39.8%; P = 0.05). WHO grade remained a strong predictor of overall survival when limited to 38 cases defined as PXA by methylation-based classification. Our data confirm the importance of WHO grading in histologically and epigenetically defined PXA. Methylation-based classification may be helpful in cases with ambiguous morphology, but is largely confirmatory in PXA with well-defined morphology.
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Affiliation(s)
- Rachael Vaubel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Valentina Zschernack
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
| | - Quynh T Tran
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sarah Jenkins
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Alissa Caron
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Dragana Milosevic
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - James Smadbeck
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - George Vasmatzis
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Daniela Kandels
- Swabian Children's Cancer Center, University Hospital Augsburg, Augsburg, Germany
| | - Astrid Gnekow
- Swabian Children's Cancer Center, University Hospital Augsburg, Augsburg, Germany
| | - Christof Kramm
- Division of Pediatric Hematology and Oncology, University of Goettingen, Goettingen, Germany
| | - Robert Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Fausto J Rodriguez
- Division of Neuropathology, Department of Pathology, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Torsten Pietsch
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
| | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.,Anatomic Pathology, Dipartimento di Scienze Biomediche e NeuroMotorie - DIBINEM, Alma Mater Studiorum - Università di Bologna, Bologna, Italy
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24
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Characterization of a cryptic IGH/CCND1 rearrangement in a case of mantle cell lymphoma with negative CCND1 FISH studies. Blood Adv 2020; 3:1298-1302. [PMID: 31015206 DOI: 10.1182/bloodadvances.2019031450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/10/2019] [Indexed: 01/06/2023] Open
Abstract
Key Points
This article characterizes a cryptic IGH/CCND1 rearrangement in MCL by NGS. Mate-pair sequencing can help in accurately diagnosing MCL in cases of cyclin-D1–positive B-cell lymphoma with negative CCND1 FISH studies.
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25
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Polonis K, Schultz MJ, Olteanu H, Smadbeck JB, Johnson SH, Vasmatzis G, Xu X, Greipp PT, Ketterling RP, Hoppman NL, Baughn LB, Peterson JF. Detection of cryptic CCND1 rearrangements in mantle cell lymphoma by next generation sequencing. Ann Diagn Pathol 2020; 46:151533. [PMID: 32408254 DOI: 10.1016/j.anndiagpath.2020.151533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 12/17/2022]
Abstract
The accurate detection of recurrent genetic abnormalities for most hematologic neoplasms is critical for diagnosis, prognosis and/or treatment. Rearrangements involving CCND1 are observed in a subset of mature B-cell neoplasms and can be reliably detected by fluorescence in situ hybridization (FISH) in most cases. However, cryptic and complex chromosomal rearrangements may pose a technical challenge for accurate diagnosis. Herein, we describe two patients with suspected mantle cell lymphoma that lacked obvious CCND1 rearrangements by FISH studies. A next generation sequencing (NGS) based assay, mate-pair sequencing (MPseq), was utilized in each case to investigate potential cryptic CCND1 rearrangements and revealed cryptic insertional events resulting in CCND1/IGH and CCND1/IGK rearrangements. These cases demonstrate that NGS-based assays, including MPseq, are a powerful approach to identify cryptic rearrangements of clinical importance that are not detected by current clinical genomics evaluation.
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Affiliation(s)
- Katarzyna Polonis
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Matthew J Schultz
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Horatiu Olteanu
- Division of Hematopathology, Mayo Clinic, Rochester, MN, United States of America
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, United States of America
| | - Sarah H Johnson
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, United States of America
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, United States of America
| | - Xinjie Xu
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Rhett P Ketterling
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America; Division of Hematopathology, Mayo Clinic, Rochester, MN, United States of America
| | - Nicole L Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Linda B Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Jess F Peterson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America.
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26
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Biliary tract cancer patient-derived xenografts: Surgeon impact on individualized medicine. JHEP Rep 2020; 2:100068. [PMID: 32181445 PMCID: PMC7066236 DOI: 10.1016/j.jhepr.2020.100068] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 01/08/2020] [Accepted: 01/08/2020] [Indexed: 02/08/2023] Open
Abstract
Background & Aims Biliary tract tumors are uncommon but highly aggressive malignancies with poor survival outcomes. Due to their low incidence, research into effective therapeutics has been limited. Novel research platforms for pre-clinical studies are desperately needed. We sought to develop a patient-derived biliary tract cancer xenograft catalog. Methods With appropriate consent and approval, surplus malignant tissues were obtained from surgical resection or radiographic biopsy and implanted into immunocompromised mice. Mice were monitored for xenograft growth. Established xenografts were verified by a hepatobiliary pathologist. Xenograft characteristics were correlated with original patient/tumor characteristics and oncologic outcomes. A subset of xenografts were then genomically characterized using Mate Pair sequencing (MPseq). Results Between October 2013 and January 2018, 87 patients with histologically confirmed biliary tract carcinomas were enrolled. Of the 87 patients, 47 validated PDX models were successfully generated. The majority of the PDX models were created from surgical resection specimens (n = 44, 94%), which were more likely to successfully engraft when compared to radiologic biopsies (p = 0.03). Histologic recapitulation of original patient tumor morphology was observed in all xenografts. Successful engraftment was an independent predictor for worse recurrence-free survival. MPseq showed genetically diverse tumors with frequent alterations of CDKN2A, SMAD4, NRG1, TP53. Sequencing also identified worse survival in patients with tumors containing tetraploid genomes. Conclusions This is the largest series of biliary tract cancer xenografts reported to date. Histologic and genomic analysis of patient-derived xenografts demonstrates accurate recapitulation of original tumor morphology with direct correlations to patient outcomes. Successful development of biliary cancer tumografts is feasible and may be used to direct subsequent therapy in high recurrence risk patients. Lay summary Patient biliary tract tumors grown in immunocompromised mice are an invaluable resource in the treatment of biliary tract cancers. They can be used to guide individualized cancer treatment in high-risk patients. Biliary tract tumors are uncommon but highly aggressive malignancies with poor survival outcomes. Patient-derived xenografts preserve the unique histology and genetic characteristics of the original patient tumor. Successful engraftment is an independent predictor for worse recurrence-free patient survival. Patients with tumors containing tetraploid genomes had worse overall survival.
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Key Words
- CCA, cholangiocarcinoma
- ECM, extracellular matrix
- GBCA, gallbladder carcinoma
- HRs, hazard ratios
- LOH, loss of heterozygosity
- MatePair sequencing
- OPTR, overall patient take rate
- OS, overall survival
- PDX, patient-derived xenograft
- Patient-derived xenografts
- TTF, time to tumor formation
- TTH, time to tumor harvest
- biliary tract
- cholangiocarcinoma
- dCCA, distal cholangiocarcinoma
- gallbladder carcinoma
- iCCA, intrahepatic cholangiocarcinoma
- pCCA, perihilar cholangiocarcinoma
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27
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Marla SS, Mishra P, Maurya R, Singh M, Wankhede DP, Kumar A, Yadav MC, Subbarao N, Singh SK, Kumar R. Refinement of Draft Genome Assemblies of Pigeonpea ( Cajanus cajan). Front Genet 2020. [PMID: 33384719 DOI: 10.1101/2020.08.10.243949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
Genome assembly of short reads from large plant genomes remains a challenge in computational biology despite major developments in next generation sequencing. Of late several draft assemblies have been reported in sequenced plant genomes. The reported draft genome assemblies of Cajanus cajan have different levels of genome completeness, a large number of repeats, gaps, and segmental duplications. Draft assemblies with portions of genome missing are shorter than the referenced original genome. These assemblies come with low map accuracy affecting further functional annotation and the prediction of gene components as desired by crop researchers. Genome coverage, i.e., the number of sequenced raw reads mapped onto a certain location of the genome is an important quality indicator of completeness and assembly quality in draft assemblies. The present work aimed to improve the coverage in reported de novo sequenced draft genomes (GCA_000340665.1 and GCA_000230855.2) of pigeonpea, a legume widely cultivated in India. The two recently sequenced assemblies, A1 and A2 comprised 72% and 75% of the estimated coverage of the genome, respectively. We employed an assembly reconciliation approach to compare the draft assemblies and merge them, filling the gaps by employing an algorithm size sorting mate-pair library to generate a high quality and near complete assembly with enhanced contiguity. The majority of gaps present within scaffolds were filled with right-sized mate-pair reads. The improved assembly reduced the number of gaps than those reported in draft assemblies resulting in an improved genome coverage of 82.4%. Map accuracy of the improved assembly was evaluated using various quality metrics and for the presence of specific trait-related functional genes. Employed pair-end and mate-pair local libraries helped us to reduce gaps, repeats, and other sequence errors resulting in lengthier scaffolds compared to the two draft assemblies. We reported the prediction of putative host resistance genes against Fusarium wilt disease by their performance and evaluated them both in wet laboratory and field phenotypic conditions.
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Affiliation(s)
- Soma S Marla
- Indian Council for Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Pallavi Mishra
- Indian Council for Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ranjeet Maurya
- Indian Council for Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Mohar Singh
- Indian Council for Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Anil Kumar
- Directorate of Education, Rani Lakshmi Bai Central Agricultural University, Jhansi, India
| | - Mahesh C Yadav
- Indian Council for Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - N Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sanjeev K Singh
- Indian Council for Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rajesh Kumar
- Indian Council for Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
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28
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Blackburn PR, Huang L, Dalovisio A, Pitel BA, Chen D, Oliveira JL, Wood AJ, Smadbeck JB, Johnson SH, Vasmatzis G, Haferlach C, Greipp PT, Hoppman NL, Ketterling RP, Baughn LB, Peterson JF. Secondary acquisition of BCR-ABL1 fusion in de novo GATA2-MECOM positive acute myeloid leukemia with subsequent emergence of a rare KMT2A-ASXL2 fusion. Cancer Genet 2019; 241:67-71. [PMID: 31902694 DOI: 10.1016/j.cancergen.2019.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/20/2019] [Accepted: 12/23/2019] [Indexed: 12/21/2022]
Abstract
Secondary acquisition of t(9;22)(q34;q11.2)/BCR-ABL1 fusion in the context of de novo acute myeloid leukemia (AML) with inv(3)(q21q26)/GATA2-MECOM rearrangement has been rarely reported. Furthermore, t(2;11)(p23;q23)/KMT2A-ASXL2 fusion has been rarely described with only a single case reported to date. We report a 45-year-old male with a diagnosis of de novo AML harboring GATA2-MECOM rearrangement in conjunction with a related subclone with concomitant inv(3) and t(9;22). The patient was treated with a tyrosine kinase inhibitor (TKI) which lead to disappearance of the inv(3)/t(9;22) subclone and subsequent expansion of the inv(3) ancestral clone. The patient was started on a 7+3 induction regimen with TKI but had persistent disease. He was placed on several additional treatment protocols and only achieved morphologic remission with a combination of fludarabine, cytarabine and filgrastim with TKI. Approximately 11.5 months after diagnosis the patient relapsed with the inv(3) clone predominating initially, followed by return of the inv(3)/t(9;22) subclone and the emergence of a second subclone with concomitant inv(3) and t(2;11)(p23;q23). Mate-pair sequencing was performed and identified a KMT2A-ASXL2 in-frame fusion, which was only recently described in a single case of therapy-related AML. For BCR-ABL1 positive AML, which generally carries a poor prognosis, treatment with TKIs has been proposed in combination with standard chemotherapy. In our case, treatment with TKI alone led to initial response of the BCR-ABL1 positive clone, but the ancestral clone quickly expanded and subsequent standard AML therapy may have led to further clonal evolution and re-emergence of the BCR-ABL1 clone in the absence of therapeutic selection.
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Affiliation(s)
- Patrick R Blackburn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, USA
| | - Li Huang
- Pathology and Laboratory Medicine William G. Helis Memorial Laboratories, Ochsner Medical Center, New Orleans, LA, USA
| | - Andrew Dalovisio
- Division of Hematology and Bone Marrow Transplant, Department of Internal Medicine, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Beth A Pitel
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, USA
| | - Dong Chen
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jennifer L Oliveira
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Adam J Wood
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - Sarah H Johnson
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | | | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, USA
| | - Nicole L Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, USA
| | - Rhett P Ketterling
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, USA; Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, USA
| | - Jess F Peterson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, USA.
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Perez-Rodriguez D, Kalyva M, Leija-Salazar M, Lashley T, Tarabichi M, Chelban V, Gentleman S, Schottlaender L, Franklin H, Vasmatzis G, Houlden H, Schapira AHV, Warner TT, Holton JL, Jaunmuktane Z, Proukakis C. Investigation of somatic CNVs in brains of synucleinopathy cases using targeted SNCA analysis and single cell sequencing. Acta Neuropathol Commun 2019; 7:219. [PMID: 31870437 PMCID: PMC6929293 DOI: 10.1186/s40478-019-0873-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 12/17/2019] [Indexed: 12/17/2022] Open
Abstract
Synucleinopathies are mostly sporadic neurodegenerative disorders of partly unexplained aetiology, and include Parkinson's disease (PD) and multiple system atrophy (MSA). We have further investigated our recent finding of somatic SNCA (α-synuclein) copy number variants (CNVs, specifically gains) in synucleinopathies, using Fluorescent in-situ Hybridisation for SNCA, and single-cell whole genome sequencing for the first time in a synucleinopathy. In the cingulate cortex, mosaicism levels for SNCA gains were higher in MSA and PD than controls in neurons (> 2% in both diseases), and for MSA also in non-neurons. In MSA substantia nigra (SN), we noted SNCA gains in > 3% of dopaminergic (DA) neurons (identified by neuromelanin) and neuromelanin-negative cells, including olig2-positive oligodendroglia. Cells with CNVs were more likely to have α-synuclein inclusions, in a pattern corresponding to cell categories mostly relevant to the disease: DA neurons in Lewy-body cases, and other cells in the striatonigral degeneration-dominant MSA variant (MSA-SND). Higher mosaicism levels in SN neuromelanin-negative cells may correlate with younger onset in typical MSA-SND, and in cingulate neurons with younger death in PD. Larger sample sizes will, however, be required to confirm these putative findings. We obtained genome-wide somatic CNV profiles from 169 cells from the substantia nigra of two MSA cases, and pons and putamen of one. These showed somatic CNVs in ~ 30% of cells, with clonality and origins in segmental duplications for some. CNVs had distinct profiles based on cell type, with neurons having a mix of gains and losses, and other cells having almost exclusively gains, although control data sets will be required to determine possible disease relevance. We propose that somatic SNCA CNVs may contribute to the aetiology and pathogenesis of synucleinopathies, and that genome-wide somatic CNVs in MSA brain merit further study.
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Affiliation(s)
- Diego Perez-Rodriguez
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Maria Kalyva
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Melissa Leija-Salazar
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological disorders, UCL Queen Square Institute of Neurology, 1 Wakefield street, London, WC1N 1PJ, UK
| | - Maxime Tarabichi
- The Francis Crick Institute, Midland Road 1, London, NW1 1AT, UK
| | - Viorica Chelban
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | | | - Lucia Schottlaender
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Hannah Franklin
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - George Vasmatzis
- Center for Individualized Medicine, Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Anthony H V Schapira
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Thomas T Warner
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Queen Square Brain Bank for Neurological disorders, UCL Queen Square Institute of Neurology, 1 Wakefield street, London, WC1N 1PJ, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Janice L Holton
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Queen Square Brain Bank for Neurological disorders, UCL Queen Square Institute of Neurology, 1 Wakefield street, London, WC1N 1PJ, UK
| | - Zane Jaunmuktane
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Queen Square Brain Bank for Neurological disorders, UCL Queen Square Institute of Neurology, 1 Wakefield street, London, WC1N 1PJ, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Christos Proukakis
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.
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Smadbeck J, Peterson JF, Pearce KE, Pitel BA, Figueroa AL, Timm M, Jevremovic D, Shi M, Stewart AK, Braggio E, Riggs DL, Bergsagel PL, Vasmatzis G, Kearney HM, Hoppman NL, Ketterling RP, Kumar S, Rajkumar SV, Greipp PT, Baughn LB. Mate pair sequencing outperforms fluorescence in situ hybridization in the genomic characterization of multiple myeloma. Blood Cancer J 2019; 9:103. [PMID: 31844041 PMCID: PMC6914798 DOI: 10.1038/s41408-019-0255-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/21/2019] [Accepted: 11/04/2019] [Indexed: 02/07/2023] Open
Abstract
Fluorescence in situ hybridization (FISH) is currently the gold-standard assay to detect recurrent genomic abnormalities of prognostic significance in multiple myeloma (MM). Since most translocations in MM involve a position effect with heterogeneous breakpoints, we hypothesize that FISH has the potential to miss translocations involving these regions. We evaluated 70 bone marrow samples from patients with plasma cell dyscrasia by FISH and whole-genome mate-pair sequencing (MPseq). Thirty cases (42.9%) displayed at least one instance of discordance between FISH and MPseq for each primary and secondary abnormality evaluated. Nine cases had abnormalities detected by FISH that went undetected by MPseq including 6 tetraploid clones and three cases with missed copy number abnormalities. In contrast, 19 cases had abnormalities detected by MPseq that went undetected by FISH. Seventeen were MYC rearrangements and two were 17p deletions. MPseq identified 36 MYC abnormalities and 17 (50.0% of MYC abnormal group with FISH results) displayed a false negative FISH result. MPseq identified 10 cases (14.3%) with IgL rearrangements, a recent marker of poor outcome, and 10% with abnormalities in genes associated with lenalidomide response or resistance. In summary, MPseq was superior in the characterization of rearrangement complexity and identification of secondary abnormalities demonstrating increased clinical value compared to FISH.
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Affiliation(s)
- James Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - Jess F Peterson
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kathryn E Pearce
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Beth A Pitel
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Andrea Lebron Figueroa
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Michael Timm
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Dragan Jevremovic
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Min Shi
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - A Keith Stewart
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Esteban Braggio
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Daniel L Riggs
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - P Leif Bergsagel
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - Hutton M Kearney
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Hoppman
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rhett P Ketterling
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Shaji Kumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - S Vincent Rajkumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Patricia T Greipp
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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31
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Zepeda-Mendoza CJ, Cousin MA, Basu S, Jenkinson G, Oliver G, Pittock ST, Baughn LB, Klee EW, Babovic-Vuksanovic D. An intragenic duplication of TRPS1 leading to abnormal transcripts and causing trichorhinophalangeal syndrome type I. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004655. [PMID: 31662300 PMCID: PMC6913153 DOI: 10.1101/mcs.a004655] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/01/2019] [Indexed: 11/24/2022] Open
Abstract
Trichorhinophalangeal syndrome type I (TRPSI) is a rare disorder that causes distinctive ectodermal, facial, and skeletal features affecting the hair (tricho-), nose (rhino-), and fingers and toes (phalangeal) and is inherited in an autosomal dominant pattern. TRPSI is caused by loss of function variants in TRPS1, involved in the regulation of chondrocyte and perichondrium development. Pathogenic variants in TRPS1 include missense mutations and deletions with variable breakpoints, with only a single instance of an intragenic duplication reported to date. Here we report an affected individual presenting with a classic TRPSI phenotype who is heterozygous for a de novo intragenic ∼36.3-kbp duplication affecting exons 2–4 of TRPS1. Molecular analysis revealed the duplication to be in direct tandem orientation affecting the splicing of TRPS1. The aberrant transcripts are predicted to produce a truncated TRPS1 missing the nuclear localization signal and the GATA and IKAROS-like zinc-finger domains resulting in functional TRPS1 haploinsufficiency. Our study identifies a novel intragenic tandem duplication of TRPS1 and highlights the importance of molecular characterization of intragenic duplications.
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Affiliation(s)
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Shubham Basu
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Garrett Jenkinson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Gavin Oliver
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Siobhan T Pittock
- Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Linda B Baughn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Eric W Klee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Dusica Babovic-Vuksanovic
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
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32
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Schultz MJ, Blackburn PR, Cogbill CH, Pitel BA, Smadbeck JB, Johnson SH, Vasmatzis G, Rech KL, Sukov WR, Greipp PT, Hoppman NL, Baughn LB, Ketterling RP, Peterson JF. Characterization of a cryptic PML-RARA fusion by mate-pair sequencing in a case of acute promyelocytic leukemia with a normal karyotype and negative RARA FISH studies. Leuk Lymphoma 2019; 61:975-978. [PMID: 31809670 DOI: 10.1080/10428194.2019.1699081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Matthew J Schultz
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Patrick R Blackburn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Beth A Pitel
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - Sarah H Johnson
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - Karen L Rech
- Division of Hematopathology, Department of Laboratory Medicine and Genomics, Mayo Clinic, Rochester, MN, USA
| | - William R Sukov
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rhett P Ketterling
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.,Division of Hematopathology, Department of Laboratory Medicine and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Jess F Peterson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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33
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Rowsey RA, Smoley SA, Williamson CM, Vasmatzis G, Smadbeck JB, Ning Y, Greipp PT, Hoppman NL, Baughn LB, Ketterling RP, Peterson JF. Characterization of TCF3 rearrangements in pediatric B-lymphoblastic leukemia/lymphoma by mate-pair sequencing (MPseq) identifies complex genomic rearrangements and a novel TCF3/TEF gene fusion. Blood Cancer J 2019; 9:81. [PMID: 31575852 PMCID: PMC6773761 DOI: 10.1038/s41408-019-0239-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/13/2019] [Accepted: 08/15/2019] [Indexed: 11/17/2022] Open
Abstract
The TCF3/PBX1 gene fusion is a recurrent genetic abnormality in pediatric B-lymphoblastic leukemia/lymphoma (B-ALL/LBL). While dual-color, dual-fusion fluorescence in situ hybridization (D-FISH) probes can detect TCF3/PBX1 fusions, further characterization of atypical TCF3 FISH patterns as indicated by additional or diminished TCF3 signals is currently limited. Herein we describe the use of a next-generation sequencing assay, mate-pair sequencing (MPseq), to characterize typical and cryptic TCF3/PBX1 fusions and to identify TCF3 translocation partners based on results obtained from our laboratory-developed TCF3/PBX1 D-FISH probe set. MPseq was performed on 21 cases of pediatric B-ALL/LBL with either TCF3/PBX1 fusion, or no TCF3/PBX1 fusion but with additional or diminished TCF3 signals obtained by our PBX1/TCF3 D-FISH probe set. In addition, MPseq was performed on one pediatric B-ALL/LBL case with an apparently normal karyotype and abnormal TCF3 break-apart probe results. Of 22 specimens successfully evaluated by MPseq, 13 cases (59%) demonstrated TCF3/PBX1 fusion, including three cases with previously undescribed insertional rearrangements. The remaining nine cases (41%) harbored various TCF3 partners, including six cases with TCF3/ZNF384, and one case each with TCF3/HLF, TCF3/FLI1 and TCF3/TEF. Our results illustrate the power of MPseq to characterize TCF3 rearrangements with increased precision and accuracy over traditional cytogenetic methodologies.
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Affiliation(s)
- Ross A Rowsey
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Stephanie A Smoley
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Cynthia M Williamson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Mayo Clinic, Rochester, MN, USA
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Mayo Clinic, Rochester, MN, USA
| | - Yi Ning
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rhett P Ketterling
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jess F Peterson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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Peterson JF, Meyer RG, Smoley SA, Webley M, Smadbeck JB, Vasmatzis G, Pearce K, Greipp PT, Ketterling RP, Craig FE, Stewart AK, Baughn LB. Whole Genome Mate-pair Sequencing of Plasma Cell Neoplasm as a Novel Diagnostic Strategy: A Case of Unrecognized t(2;11) Structural Variation. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2019; 19:598-602. [DOI: 10.1016/j.clml.2019.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/17/2019] [Accepted: 06/07/2019] [Indexed: 02/04/2023]
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35
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Peterson JF, Pitel BA, Smoley SA, Smadbeck JB, Johnson SH, Vasmatzis G, Kearney HM, Greipp PT, Hoppman NL, Baughn LB, Ketterling RP. Use of mate-pair sequencing to characterize a complex cryptic BCR/ABL1 rearrangement observed in a newly diagnosed case of chronic myeloid leukemia. Hum Pathol 2019; 89:109-114. [DOI: 10.1016/j.humpath.2018.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/04/2018] [Accepted: 09/10/2018] [Indexed: 11/13/2022]
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36
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Peterson JF, He RR, Nayer H, Cuevo RS, Smadbeck JB, Vasmatzis G, Greipp PT, Ketterling RP, Hoppman NL, Baughn LB. Characterization of a rarely reported STAT5B/RARA gene fusion in a young adult with newly diagnosed acute promyelocytic leukemia with resistance to ATRA therapy. Cancer Genet 2019; 237:51-54. [PMID: 31447065 DOI: 10.1016/j.cancergen.2019.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/08/2019] [Accepted: 06/11/2019] [Indexed: 01/17/2023]
Abstract
The detection of PML/RARA or variant RARA rearrangements is critical for the diagnosis and treatment of patients with newly diagnosed acute promyelocytic leukemia (APL). While most cases of APL harboring the PML/RARA fusion respond to all-trans retinoic acid (ATRA), some variant RARA rearrangements are ATRA insensitive. Herein, we report a 27-year-old male with newly diagnosed, rapidly progressive APL and a rarely described STAT5B/RARA fusion with known resistance to ATRA therapy. While the PML/RARA dual-color dual-fusion fluorescence in situ hybridization (FISH) probe study was negative, the RARA break-apart probe study revealed an atypical RARA rearrangement in 95% of nuclei. A next generation sequencing assay, mate-pair sequencing, was subsequently performed to further characterize the RARA rearrangement and identified the RARA gene fusion partner STAT5B.
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Affiliation(s)
- Jess F Peterson
- Division of Laboratory Medicine and Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, United States.
| | - Rui R He
- Department of Pathology, Inova Fairfax Hospital, Falls Church, VA, United States
| | - Hassan Nayer
- Department of Pathology, Inova Fairfax Hospital, Falls Church, VA, United States
| | - Raymund S Cuevo
- Inova Schar Cancer Institute, Inova Fairfax Hospital, Falls Church, VA, United States
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, United States
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, United States
| | - Patricia T Greipp
- Division of Laboratory Medicine and Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, United States
| | - Rhett P Ketterling
- Division of Laboratory Medicine and Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, United States
| | - Nicole L Hoppman
- Division of Laboratory Medicine and Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, United States
| | - Linda B Baughn
- Division of Laboratory Medicine and Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, United States
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37
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Peterson JF, Pitel BA, Smoley SA, Vasmatzis G, Smadbeck JB, Greipp PT, Ketterling RP, Macon WR, Baughn LB. Elucidating a false-negative MYC break-apart fluorescence in situ hybridization probe study by next-generation sequencing in a patient with high-grade B-cell lymphoma with IGH/MYC and IGH/BCL2 rearrangements. Cold Spring Harb Mol Case Stud 2019; 5:a004077. [PMID: 31160360 PMCID: PMC6549546 DOI: 10.1101/mcs.a004077] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 03/27/2019] [Indexed: 12/15/2022] Open
Abstract
The identification of MYC rearrangements in several mature B-cell neoplasms is critical for diagnostic and prognostic purposes. Commercially available fluorescence in situ hybridization (FISH) probe sets, including IGH/MYC dual-color dual-fusion (D-FISH) and MYC break-apart probes (BAPs), serve as the primary methodology utilized to detect MYC rearrangements. However, performing either IGH/MYC D-FISH or MYC BAP FISH studies in isolation has been reported to result in false-negative results because of the complex nature of 8q24 rearrangements involving the MYC gene region. We report a 60-yr-old male with newly diagnosed high-grade B-cell lymphoma with a negative MYC BAP study, but with positive BCL2 and BCL6 BAP studies. Per our current laboratory algorithm to concurrently interrogate the MYC gene region with both MYC BAP and IGH/MYC D-FISH probe sets, we performed IGH/MYC D-FISH studies and detected an IGH/MYC fusion. To further characterize the discrepant MYC results obtained by FISH, a next-generation sequencing strategy, mate-pair sequencing (MPseq), was performed and revealed a small insertion (∼200 kb) of the IGH locus downstream from the MYC gene that was undetectable by MYC BAP studies. This case highlights the importance of utilizing both IGH/MYC D-FISH and MYC BAP sets to detect potential cryptic MYC rearrangements and also demonstrates the power of MPseq to characterize complex structural rearrangements and copy-number abnormalities unappreciable by FISH.
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Affiliation(s)
- Jess F Peterson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Beth A Pitel
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Stephanie A Smoley
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Rhett P Ketterling
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - William R Macon
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Linda B Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
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38
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Murphy SJ, Harris FR, Kosari F, Barreto Siqueira Parrilha Terra S, Nasir A, Johnson SH, Serla V, Smadbeck JB, Halling GC, Karagouga G, Sukov WR, Leventakos K, Yang P, Peikert T, Mansfield AS, Wigle DA, Yi ES, Kipp BR, Vasmatzis G, Aubry MC. Using Genomics to Differentiate Multiple Primaries From Metastatic Lung Cancer. J Thorac Oncol 2019; 14:1567-1582. [PMID: 31103780 DOI: 10.1016/j.jtho.2019.05.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 04/01/2019] [Accepted: 05/06/2019] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Genomic technologies present a promising mechanism of resolving the clinical dilemma of distinguishing independent primary tumors from intrapulmonary metastases in NSCLC. We evaluated the utility of discordant mapping somatic junctions from chromosomal rearrangements in diagnosing metastatic disease compared to the current standard histologic review. MATERIAL AND METHODS Mate-pair sequencing was performed on DNA extracted from 76 distinct tumors from 37 cases of multiple lung cancers. Discordant mapping junctions and chromosomal copy levels were assessed for each tumor. Blood-derived DNA was available on 22 of these cases for germline assessments. A lung cancer next-generation sequencing panel was additionally performed on tumor pairs from 17 patients. RESULTS Whereas mate-pair sequencing was able to classify lineage in all tumor pairs, histologic review appeared to misclassify lineage in 9 of 33 (27%) same-histology tumor pair comparisons. Based on disagreement between the reviewing pathologists, histopathologic lineage was classified as indeterminate in seven cases. In two cases where pathologists agreed on a metastatic call, no shared junctions were found suggesting independent primaries. Although germline junctions passing algorithmic filters were common, on average less than three were present and all had predictable structures of small focal rearrangements or transposons. Evaluation of shared chromosomal copy changes and driver mutations through a lung cancer next-generation sequencing panel, while informative, were nondefinitive in calling lineage in all cases. CONCLUSIONS The highly unique nature and prevalence of chromosomal rearrangement in lung cancers provide a useful and definitive technique for calling lineage in multifocal lung cancer.
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Affiliation(s)
- Stephen J Murphy
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota
| | - Faye R Harris
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Farhad Kosari
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota
| | - Simone Barreto Siqueira Parrilha Terra
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Aqsa Nasir
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota
| | - Sarah H Johnson
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota
| | - Vishnu Serla
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - James B Smadbeck
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota
| | - Geoffrey C Halling
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota
| | - Giannoula Karagouga
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota
| | - William R Sukov
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Ping Yang
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Tobias Peikert
- Department of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Dennis A Wigle
- Department of General Thoracic Surgery, Mayo Clinic, Rochester, Minnesota
| | - Eunhee S Yi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - George Vasmatzis
- Center for Individualized Medicine, Biomarker Discovery Program, Mayo Clinic, Rochester, Minnesota
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39
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Characterization of a cryptic KMT2A/AFF1 gene fusion by mate-pair sequencing (MPseq) in a young adult with newly diagnosed B-lymphoblastic leukemia. J Hematop 2019. [DOI: 10.1007/s12308-019-00355-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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40
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Peterson JF, Pitel BA, Smoley SA, Smadbeck JB, Johnson SH, Vasmatzis G, Koon SJ, Webley MR, McGrath M, Bayerl MG, Baughn LB, Rowsey RA, Ketterling RP, Greipp PT, Hoppman NL. Detection of a cryptic NUP214/ABL1 gene fusion by mate-pair sequencing (MPseq) in a newly diagnosed case of pediatric T-lymphoblastic leukemia. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a003533. [PMID: 30936193 PMCID: PMC6549564 DOI: 10.1101/mcs.a003533] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/05/2018] [Indexed: 02/06/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematopoietic neoplasm involving the bone marrow and blood that accounts for ∼15% of childhood and 25% of adult ALL. Whereas multiple, recurrent genetic abnormalities have been described in T-ALL, their clinical significance is unclear or controversial. Importantly, ABL1 rearrangements, most commonly described in BCR/ABL1-positive B-ALL and BCR-ABL1-like B-ALL, have been observed in T-ALL and may respond to tyrosine kinase inhibitor (TKI) therapy. We describe a newly diagnosed case of pediatric T-ALL with a fluorescence in situ hybridization abnormality suggesting a partial ABL1 deletion by a BCR/ABL1 dual-color dual-fusion probe but that demonstrated a normal result using an ABL1 break-apart probe. Mate-pair sequencing (MPseq), a next-generation sequencing (NGS)-based technology utilized to detect copy number and structural abnormalities with high resolution and precision throughout the genome, was performed and revealed a NUP214/ABL1 gene fusion that has been demonstrated to be sensitive to TKI therapy. This case demonstrates the power of MPseq to resolve chromosomal abnormalities unappreciable by traditional cytogenetic methodologies and highlights the clinical value of this novel NGS-based technology.
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Affiliation(s)
- Jess F Peterson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology
| | - Beth A Pitel
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology
| | - Stephanie A Smoley
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Sarah H Johnson
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Sarah J Koon
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology
| | - Matthew R Webley
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology
| | - Mary McGrath
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Penn State Children's Hospital, Hershey, Pennsylvania 17033, USA
| | - Michael G Bayerl
- Department of Pathology and Laboratory Medicine, Penn State Milton S. Hershey Medical Center, Hershey, Pennsylvania 17033, USA
| | - Linda B Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology
| | - Ross A Rowsey
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology
| | - Rhett P Ketterling
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology
| | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology
| | - Nicole L Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology
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41
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Peterson JF, Sukov WR, Pitel BA, Smoley SA, Pearce KE, Meyer RG, Williamson CM, Smadbeck JB, Vasmatzis G, Hoppman NL, Greipp PT, Baughn LB, Ketterling RP. Acute leukemias harboring KMT2A/MLLT10 fusion: a 10-year experience from a single genomics laboratory. Genes Chromosomes Cancer 2019; 58:567-577. [PMID: 30707474 DOI: 10.1002/gcc.22741] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/16/2019] [Accepted: 01/30/2019] [Indexed: 02/05/2023] Open
Abstract
The MLLT10 (formerly AF10) gene is the fourth most common KMT2A fusion partner across all acute leukemias and requires at least 3 breaks to form an in-frame KMT2A/MLLT10 fusion due to the opposite orientation of each gene. A 10-year retrospective review was performed to identify individuals from all age groups that harbor KMT2A/MLLT10 fusion obtained by our KMT2A/MLLT10 dual-color dual-fusion fluorescence in situ hybridization (D-FISH) assay. Of the 60 unique individuals identified, 31 were male and 29 were female (M:F ratio, 1.1:1) with ages ranging from 3 days to 86 years (mean 21.5 years, median 5.5 years). The diagnoses included acute myeloid leukemia (AML) (49 patients, 82%), B- or T-lymphoblastic leukemia/lymphoma (7 patients, 12%), myeloid sarcoma (3 patients, 5%), and a single case (2%) of undifferentiated leukemia. Twenty-seven of 49 patients (55%) with AML were in the infant or pediatric age group. Fifty-three of 60 patients (88%) had KMT2A/MLLT10 D-FISH signal patterns mostly consisting of single fusions. In addition, 10 (26%) of 38 patients with conventional chromosome studies had "normal" (5 patients) or abnormal (5 patients) chromosome studies that lacked structural or numeric abnormalities involving chromosomes 10 or 11, implying cryptic cytogenetic mechanisms for KMT2A/MLLT10 fusion. Lastly, mate-pair sequencing was performed on 4 AML cases, 2 of which had "normal" chromosome studies and cryptic KMT2A/MLLT10 fusion as detected by KMT2A/MLLT10 D-FISH studies, and verified the multiple breaks required to generate KMT2A/MLLT10 fusion.
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Affiliation(s)
- Jess F Peterson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - William R Sukov
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Beth A Pitel
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Stephanie A Smoley
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kathryn E Pearce
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Reid G Meyer
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Cynthia M Williamson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota
| | - Nicole L Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Linda B Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Rhett P Ketterling
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.,Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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42
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Blackburn PR, Davila JI, Jackson RA, Fadra N, Atiq MA, Pitel BA, Nair AA, VanDeWalker TJ, Hessler MG, Hovel SK, Wehrs RN, Fritchie KJ, Jenkins RB, Halling KC, Geiersbach KB. RNA sequencing identifies a novel
USP9X‐USP6
promoter swap gene fusion in a primary aneurysmal bone cyst. Genes Chromosomes Cancer 2019; 58:589-594. [DOI: 10.1002/gcc.22742] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 12/23/2022] Open
Affiliation(s)
| | - Jaime I. Davila
- Department of Health Science ResearchMayo Clinic Rochester Minnesota
| | - Rory A. Jackson
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
| | - Numrah Fadra
- Department of Health Science ResearchMayo Clinic Rochester Minnesota
| | - Mazen A. Atiq
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
| | - Beth A. Pitel
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
| | - Asha A. Nair
- Department of Health Science ResearchMayo Clinic Rochester Minnesota
| | - Todd J. VanDeWalker
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
| | - Mark G. Hessler
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
| | - Sara K. Hovel
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
| | - Rebecca N. Wehrs
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
| | - Karen J. Fritchie
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
| | - Robert B. Jenkins
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
| | - Kevin C. Halling
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
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43
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Shared and unique genomic structural variants of different histological components within testicular germ cell tumours identified with mate pair sequencing. Sci Rep 2019; 9:3586. [PMID: 30837548 PMCID: PMC6400951 DOI: 10.1038/s41598-019-39956-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 02/01/2019] [Indexed: 12/12/2022] Open
Abstract
Post-pubertal testicular germ-cell tumours (TGCTs) can present with a variety of distinct histologies which are nevertheless lineage related and often co-occurring. The exact lineage relationships and developmental pathways leading to the different histologies is debated. In order to investigate the relationship of histologic populations, mate-pair sequencing (MPseq) and exome sequencing (ExomeSeq) were conducted on different histological populations within the same tumour. Ten TGCTs with 1–3 histologic types/tumour were sequenced. Junctions of somatic chromosomal rearrangements were identified on a per genome basis, with germ cell neoplasia in situ possessing the least (median 1, range 0–4) and embryonal carcinoma the most (median 8.5, range 6–12). Copy number variation revealed gains and losses, including isoform 12p (i12p) (10/10 samples), and chromosomes 7, 8, and 21 gains (7/10 samples). Mapping of shared junctions within a tumour revealed lineage relationships, but only i12p was shared between patients. ExomeSeq from two cases demonstrated a high level of copy-neutral loss of heterozygosity. Parallel assessment of separate histologies within a single TGCT demonstrated cumulative and divergent changes, suggesting the importance of parallel sequencing for detection of relevant biomarkers.
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44
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Ren H, Hou X, Eiken PW, Zhang J, Pierson KE, Nair AA, Davila JI, Kovarikova H, Jang JS, Johnson SH, Molina JR, Marks RS, Yang P, Yi JE, Mansfield AS, Jen J. Identification and Development of a Lung Adenocarcinoma PDX Model With STRN-ALK Fusion. Clin Lung Cancer 2019; 20:e142-e147. [PMID: 30581091 DOI: 10.1016/j.cllc.2018.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/29/2018] [Accepted: 11/12/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Hongzheng Ren
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Biomarker Discovery Program, Mayo Clinic, Rochester, MN; Cancer Research Center, Shantou University Medical College, Shantou, China
| | - Xiaonan Hou
- Department of Medical Oncology, Mayo Clinic, Rochester, MN
| | | | - Jin Zhang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | | | - Asha A Nair
- Department of Health Science Research, Mayo Clinic, Rochester, MN
| | - Jaime I Davila
- Department of Health Science Research, Mayo Clinic, Rochester, MN
| | - Helena Kovarikova
- Institute of Clinical Biochemistry and Diagnostics, Charles University, Faculty of Medicine, Hradec Kralove, Czech Republic; Institute of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Jin Sung Jang
- The Genome Analysis Core, Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | | | | | | | - Ping Yang
- Department of Health Science Research, Mayo Clinic, Rochester, MN
| | - Joanne E Yi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Jin Jen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Biomarker Discovery Program, Mayo Clinic, Rochester, MN; The Genome Analysis Core, Center for Individualized Medicine, Mayo Clinic, Rochester, MN.
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45
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Characterization of a t(1;2)(p36;p21) involving the PRDM16 gene region by mate-pair sequencing (MPseq) in a patient with newly diagnosed acute myeloid leukemia with myelodysplasia-related changes. J Hematop 2019. [DOI: 10.1007/s12308-019-00348-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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46
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Peterson JF, Pitel BA, Smoley SA, Smadbeck JB, Johnson SH, Vasmatzis G, Pearce KE, He R, Kelemen K, Al-Mondhiry HA, Lamparella NE, Hoppman NL, Kearney HM, Baughn LB, Ketterling RP, Greipp PT. Constitutional chromosome rearrangements that mimic the 2017 world health organization “acute myeloid leukemia with recurrent genetic abnormalities”: A study of three cases and review of the literature. Cancer Genet 2019; 230:37-46. [DOI: 10.1016/j.cancergen.2018.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/16/2018] [Accepted: 11/14/2018] [Indexed: 01/28/2023]
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47
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King RL, McPhail ED, Meyer RG, Vasmatzis G, Pearce K, Smadbeck JB, Ketterling RP, Smoley SA, Greipp PT, Hoppman NL, Peterson JF, Baughn LB. False-negative rates for MYC fluorescence in situ hybridization probes in B-cell neoplasms. Haematologica 2018; 104:e248-e251. [PMID: 30523057 DOI: 10.3324/haematol.2018.207290] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Rebecca L King
- Division of Hematopathology, Department of Laboratory Medicine and Pathology
| | - Ellen D McPhail
- Division of Hematopathology, Department of Laboratory Medicine and Pathology
| | - Reid G Meyer
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - Kathryn Pearce
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - Rhett P Ketterling
- Division of Hematopathology, Department of Laboratory Medicine and Pathology.,Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology
| | - Stephanie A Smoley
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology
| | - Patricia T Greipp
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology
| | - Nicole L Hoppman
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology
| | - Jess F Peterson
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology
| | - Linda B Baughn
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology
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48
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Aypar U, Smoley SA, Pitel BA, Pearce KE, Zenka RM, Vasmatzis G, Johnson SH, Smadbeck JB, Peterson JF, Geiersbach KB, Van Dyke DL, Thorland EC, Jenkins RB, Ketterling RP, Greipp PT, Kearney HM, Hoppman NL, Baughn LB. Mate pair sequencing improves detection of genomic abnormalities in acute myeloid leukemia. Eur J Haematol 2018; 102:87-96. [PMID: 30270457 PMCID: PMC7379948 DOI: 10.1111/ejh.13179] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Acute myeloid leukemia (AML) can be subtyped based on recurrent cytogenetic and molecular genetic abnormalities with diagnostic and prognostic significance. Although cytogenetic characterization classically involves conventional chromosome and/or fluorescence in situ hybridization (FISH) assays, limitations of these techniques include poor resolution and the inability to precisely identify breakpoints. METHOD We evaluated whether an NGS-based methodology that detects structural abnormalities and copy number changes using mate pair sequencing (MPseq) can enhance the diagnostic yield for patients with AML. RESULTS Using 68 known abnormal and 20 karyotypically normal AML samples, each recurrent primary AML-specific abnormality previously identified in the abnormal samples was confirmed using MPseq. Importantly, in eight cases with abnormalities that could not be resolved by conventional cytogenetic studies, MPseq was utilized to molecularly define eight recurrent AML-fusion events. In addition, MPseq uncovered two cryptic abnormalities that were missed by conventional cytogenetic studies. Thus, MPseq improved the diagnostic yield in the detection of AML-specific structural rearrangements in 10/88 (11%) of cases analyzed. CONCLUSION Utilization of MPseq represents a precise, molecular-based technique that can be used as an alternative to conventional cytogenetic studies for newly diagnosed AML patients with the potential to revolutionize the diagnosis of hematologic malignancies.
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Affiliation(s)
- Umut Aypar
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Stephanie A Smoley
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Beth A Pitel
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Kathryn E Pearce
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Roman M Zenka
- Bioinformatics Systems, Mayo Clinic, Rochester, Minnesota
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota
| | - Sarah H Johnson
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota
| | - Jess F Peterson
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Katherine B Geiersbach
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Daniel L Van Dyke
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Erik C Thorland
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Rhett P Ketterling
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Hutton M Kearney
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
| | - Linda B Baughn
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota
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49
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Mansfield AS, Peikert T, Smadbeck JB, Udell JBM, Garcia-Rivera E, Elsbernd L, Erskine CL, Van Keulen VP, Kosari F, Murphy SJ, Ren H, Serla VV, Schaefer Klein JL, Karagouga G, Harris FR, Sosa C, Johnson SH, Nevala W, Markovic SN, Bungum AO, Edell ES, Dong H, Cheville JC, Aubry MC, Jen J, Vasmatzis G. Neoantigenic Potential of Complex Chromosomal Rearrangements in Mesothelioma. J Thorac Oncol 2018; 14:276-287. [PMID: 30316012 DOI: 10.1016/j.jtho.2018.10.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 09/19/2018] [Accepted: 10/02/2018] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Malignant pleural mesothelioma is a disease primarily associated with exposure to the carcinogen asbestos. Whereas other carcinogen-related tumors are associated with a high tumor mutation burden, mesothelioma is not. We sought to resolve this discrepancy. METHODS We used mate-pair (n = 22), RNA (n = 28), and T cell receptor sequencing along with in silico predictions and immunologic assays to understand how structural variants of chromosomes affect the transcriptome. RESULTS We observed that inter- or intrachromosomal rearrangements were present in every specimen and were frequently in a pattern of chromoanagenesis such as chromoplexy or chromothripsis. Transcription of rearrangement-related junctions was predicted to result in many potential neoantigens, some of which were proven to bind patient-specific major histocompatibility complex molecules and to expand intratumoral T cell clones. T cells responsive to these predicted neoantigens were also present in a patient's circulating T cell repertoire. Analysis of genomic array data from the mesothelioma cohort in The Cancer Genome Atlas suggested that multiple chromothriptic-like events negatively impact survival. CONCLUSIONS Our findings represent the discovery of potential neoantigen expression driven by structural chromosomal rearrangements. These results may have implications for the development of novel immunotherapeutic strategies and the selection of patients to receive immunotherapies.
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Affiliation(s)
| | - Tobias Peikert
- Division of Pulmonary Medicine and Critical Care, Mayo Clinic, Rochester, Minnesota
| | - James B Smadbeck
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota
| | - Julia B M Udell
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
| | | | - Laura Elsbernd
- Department of Immunology, Mayo Clinic, Rochester, Minnesota
| | | | | | - Farhad Kosari
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota
| | - Stephen J Murphy
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota
| | - Hongzheng Ren
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Vishnu V Serla
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota
| | - Janet L Schaefer Klein
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota
| | - Giannoula Karagouga
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota
| | - Faye R Harris
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota
| | - Carlos Sosa
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota
| | - Sarah H Johnson
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota
| | - Wendy Nevala
- Department of Immunology, Mayo Clinic, Rochester, Minnesota
| | | | - Aaron O Bungum
- Division of Pulmonary Medicine and Critical Care, Mayo Clinic, Rochester, Minnesota
| | - Eric S Edell
- Division of Pulmonary Medicine and Critical Care, Mayo Clinic, Rochester, Minnesota
| | - Haidong Dong
- Department of Immunology, Mayo Clinic, Rochester, Minnesota; Department of Urology, Mayo Clinic, Rochester, Minnesota
| | - John C Cheville
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Jin Jen
- Medical Genome Facility, Mayo Clinic, Rochester, Minnesota
| | - George Vasmatzis
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota.
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50
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Smadbeck JB, Johnson SH, Smoley SA, Gaitatzes A, Drucker TM, Zenka RM, Kosari F, Murphy SJ, Hoppman N, Aypar U, Sukov WR, Jenkins RB, Kearney HM, Feldman AL, Vasmatzis G. Copy number variant analysis using genome-wide mate-pair sequencing. Genes Chromosomes Cancer 2018; 57:459-470. [PMID: 29726617 DOI: 10.1002/gcc.5] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 04/23/2018] [Accepted: 04/29/2018] [Indexed: 02/06/2023] Open
Abstract
Copy number variation (CNV) is a common form of structural variation detected in human genomes, occurring as both constitutional and somatic events. Cytogenetic techniques like chromosomal microarray (CMA) are widely used in analyzing CNVs. However, CMA techniques cannot resolve the full nature of these structural variations (i.e. the orientation and location of associated breakpoint junctions) and must be combined with other cytogenetic techniques, such as karyotyping or FISH, to do so. This makes the development of a next-generation sequencing (NGS) approach capable of resolving both CNVs and breakpoint junctions desirable. Mate-pair sequencing (MPseq) is a NGS technology designed to find large structural rearrangements across the entire genome. Here we present an algorithm capable of performing copy number analysis from mate-pair sequencing data. The algorithm uses a step-wise procedure involving normalization, segmentation, and classification of the sequencing data. The segmentation technique combines both read depth and discordant mate-pair reads to increase the sensitivity and resolution of CNV calls. The method is particularly suited to MPseq, which is designed to detect breakpoint junctions at high resolution. This allows for the classification step to accurately calculate copy number levels at the relatively low read depth of MPseq. Here we compare results for a series of hematological cancer samples that were tested with CMA and MPseq. We demonstrate comparable sensitivity to the state-of-the-art CMA technology, with the benefit of improved breakpoint resolution. The algorithm provides a powerful analytical tool for the analysis of MPseq results in cancer.
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Affiliation(s)
- James B Smadbeck
- Center for Individualized Medicine - Biomarker Discovery, Mayo Clinic, Rochester, Minnesota
| | - Sarah H Johnson
- Center for Individualized Medicine - Biomarker Discovery, Mayo Clinic, Rochester, Minnesota
| | - Stephanie A Smoley
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | | | - Roman M Zenka
- Bioinformatics Systems, Mayo Clinic, Rochester, Minnesota
| | - Farhad Kosari
- Center for Individualized Medicine - Biomarker Discovery, Mayo Clinic, Rochester, Minnesota
| | - Stephen J Murphy
- Center for Individualized Medicine - Biomarker Discovery, Mayo Clinic, Rochester, Minnesota
| | - Nicole Hoppman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Umut Aypar
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - William R Sukov
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Hutton M Kearney
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Andrew L Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - George Vasmatzis
- Center for Individualized Medicine - Biomarker Discovery, Mayo Clinic, Rochester, Minnesota.,Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
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