1
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Gagnon MF, Midthun SM, Fangel JA, Schuh CM, Luoma IM, Pearce KE, Meyer RG, Ailawadhi S, Arribas MJ, Braggio E, Fonseca R, Rajkumar SV, Zepeda-Mendoza C, Xu X, Greipp PT, Timm MM, Otteson GE, Shi M, Jevremovic D, Olteanu H, Peterson JF, Ketterling RP, Kumar S, Baughn LB. Superior detection rate of plasma cell FISH using FACS-FISH. Am J Clin Pathol 2024; 161:60-70. [PMID: 37658775 DOI: 10.1093/ajcp/aqad108] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/26/2023] [Indexed: 09/05/2023] Open
Abstract
OBJECTIVES Fluorescence in situ hybridization (FISH) for plasma cell neoplasms (PCNs) requires plasma cell (PC) identification or purification strategies to optimize results. We compared the efficacy of cytoplasmic immunoglobulin FISH (cIg-FISH) and fluorescence-activated cell sorting FISH (FACS-FISH) in a clinical laboratory setting. METHODS The FISH analysis results of 14,855 samples from individuals with a suspected PCN subjected to cytogenetic evaluation between 2019 and 2022 with cIg-FISH (n = 6917) or FACS-FISH (n = 7938) testing were analyzed. RESULTS Fluorescence-activated cell sorting-FISH increased the detection rate of abnormalities in comparison with cIg-FISH, with abnormal results documented in 54% vs 50% of cases, respectively (P < .001). It improved the detection of IGH::CCND1 (P < .001), IGH::MAF (P < .001), IGH::MAFB (P < .001), other IGH rearrangements (P < .001), and gains/amplifications of 1q (P < .001), whereas the detection rates of IGH::FGFR3 fusions (P = .3), loss of 17p (P = .3), and other abnormalities, including hyperdiploidy (P = .5), were similar. Insufficient PC yield for FISH analysis was decreased between cIg-FISH and FACS-FISH (22% and 3% respectively, P < .001). Flow cytometry allowed establishment of ploidy status in 91% of cases. In addition, FACS-FISH decreased analysis times, workload efforts, and operating costs. CONCLUSIONS Fluorescence-activated cell sorting-FISH is an efficient PC purification strategy that affords significant improvement in diagnostic yield and decreases workflow requirements in comparison with cIg-FISH.
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Affiliation(s)
- Marie-France Gagnon
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, US
| | - Sally M Midthun
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, US
| | - James A Fangel
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, US
| | - Cynthia M Schuh
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, US
| | - Ivy M Luoma
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, US
| | - Kathryn E Pearce
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, US
| | - Reid G Meyer
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, US
| | - Sikander Ailawadhi
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Jacksonville, FL, US
| | - Mariano J Arribas
- Department of Internal Medicine, Division of Hematology, Mayo Clinic, Scottsdale, AZ, US
| | - Esteban Braggio
- Department of Internal Medicine, Division of Hematology, Mayo Clinic, Scottsdale, AZ, US
| | - Rafael Fonseca
- Department of Internal Medicine, Division of Hematology, Mayo Clinic, Scottsdale, AZ, US
| | - S Vincent Rajkumar
- Department of Internal Medicine, Division of Hematology, Mayo Clinic, Rochester, MN, US
| | - Cinthya Zepeda-Mendoza
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, US
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, US
| | - Xinjie Xu
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, US
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, US
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, US
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, US
| | - Michael M Timm
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, US
| | - Gregory E Otteson
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, US
| | - Min Shi
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, US
| | - Dragan Jevremovic
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, US
| | - Horatiu Olteanu
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, US
| | - Jess F Peterson
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, US
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, US
| | - Rhett P Ketterling
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, US
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, US
| | - Shaji Kumar
- Department of Internal Medicine, Division of Hematology, Mayo Clinic, Jacksonville, FL, US
| | - Linda B Baughn
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, US
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, US
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2
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Pitel BA, Zepeda-Mendoza C, Sachs Z, Tang H, Shivaram S, Sharma N, Smadbeck JB, Smoley SA, Pearce KE, Luoma IM, Cook J, Litzow MR, Hoppman NL, Viswanatha D, Xu X, Ketterling RP, Greipp PT, Peterson JF, Baughn LB. Prospective evaluation of genome sequencing to compare conventional cytogenetics in acute myeloid leukemia. Blood Cancer J 2023; 13:138. [PMID: 37673866 PMCID: PMC10482828 DOI: 10.1038/s41408-023-00908-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/07/2023] [Accepted: 08/24/2023] [Indexed: 09/08/2023] Open
Affiliation(s)
- Beth A Pitel
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Cinthya Zepeda-Mendoza
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Zohar Sachs
- Division of Hematology, Oncology, and Transplantation, Department of Medicine and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Hongwei Tang
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Suganti Shivaram
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Neeraj Sharma
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - Stephanie A Smoley
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Kathryn E Pearce
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Ivy M Luoma
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Joselle Cook
- Department of Medicine, Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Mark R Litzow
- Department of Medicine, Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - David Viswanatha
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Xinjie Xu
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Rhett P Ketterling
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Jess F Peterson
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, USA.
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3
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Horna P, Pearce KE, Ketterling RP, Shi M, Peterson JF. Recurrent Chromosomal Abnormalities in Tissues Involved by Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma. Am J Clin Pathol 2022; 157:286-292. [PMID: 34528680 DOI: 10.1093/ajcp/aqab128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/25/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Prognostically relevant chromosomal abnormalities in chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL) are routinely identified by fluorescence in situ hybridization (FISH) on peripheral blood or bone marrow specimens. We studied the prevalence of chromosomal abnormalities on extramedullary tissues involved by CLL/SLL and evaluated their association with prominent proliferation centers (PPCs). METHODS FISH for recurrent abnormalities in CLL/SLL was performed on formalin-fixed, paraffin-embedded biopsy sections. PPCs were identified on H&E-stained sections. Available FISH results on peripheral blood or bone marrow specimens were also reviewed. RESULTS Recurrent FISH abnormalities were detected in 69% of 320 CLL/SLL biopsy specimens studied, including +12 (35%), 13q- (24%), 11q- (15%), 17p- (6%), 6q- (2%), and IGH/BCL2 (0.9%). Forty-three patients had abnormal blood or bone marrow FISH analyses, of whom 7 (16%) had discordant +12 and/or 13q-, and 3 (7%) had discordant 17p- or 11q-. Morphology was positive (17%), negative (78%), or equivocal (6%) for PPCs on 247 evaluable biopsy specimens, a finding not significantly associated with FISH results (P = .7). CONCLUSIONS Trisomy 12 is overrepresented in tumoral CLL/SLL involvement, compared with the known predominance of 13q- in blood. Discrepancies between leukemic and tissue FISH findings are occasionally encountered. FISH results do not correlate with the presence of PPCs.
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Affiliation(s)
- Pedro Horna
- Division of Hematopathology, Rochester, MN, USA
| | - Kathryn E Pearce
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rhett P Ketterling
- Division of Hematopathology, Rochester, MN, USA
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Min Shi
- Division of Hematopathology, 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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4
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Gagnon MF, Pearce KE, Greipp PT, Xu X, Hoppman NL, Ketterling RP, McPhail ED, King RL, Baughn LB, Peterson JF. MYC break-apart FISH probe set reveals frequent unbalanced patterns of uncertain significance when evaluating aggressive B-cell lymphoma. Blood Cancer J 2021; 11:184. [PMID: 34819491 PMCID: PMC8613271 DOI: 10.1038/s41408-021-00578-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022] Open
Affiliation(s)
- Marie-France Gagnon
- grid.66875.3a0000 0004 0459 167XDivision of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Kathryn E. Pearce
- grid.66875.3a0000 0004 0459 167XDivision of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Patricia T. Greipp
- grid.66875.3a0000 0004 0459 167XDivision of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Xinjie Xu
- grid.66875.3a0000 0004 0459 167XDivision of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Nicole L. Hoppman
- grid.66875.3a0000 0004 0459 167XDivision of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Rhett P. Ketterling
- grid.66875.3a0000 0004 0459 167XDivision of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Ellen D. McPhail
- grid.66875.3a0000 0004 0459 167XDivision of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Rebecca L. King
- grid.66875.3a0000 0004 0459 167XDivision of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Linda B. Baughn
- grid.66875.3a0000 0004 0459 167XDivision of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Jess F. Peterson
- grid.66875.3a0000 0004 0459 167XDivision of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
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5
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Sharma N, Smadbeck JB, Abdallah N, Zepeda-Mendoza C, Binder M, Pearce KE, Asmann YW, Peterson JF, Ketterling RP, Greipp PT, Leif Bergsagel P, Vincent Rajkumar S, Kumar SK, Baughn LB. The Prognostic Role of MYC Structural Variants Identified by NGS and FISH in Multiple Myeloma. Clin Cancer Res 2021; 27:5430-5439. [PMID: 34233962 PMCID: PMC8738776 DOI: 10.1158/1078-0432.ccr-21-0005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 03/16/2021] [Accepted: 07/01/2021] [Indexed: 12/14/2022]
Abstract
PURPOSE Structural variants (SV) of the MYC gene region are common in multiple myeloma and influence disease progression. However, the prognostic significance of different MYC SVs in multiple myeloma has not been clearly established. EXPERIMENTAL DESIGN We conducted a retrospective study of multiple myeloma comparing MYC SV subtypes identified by next-generation sequencing (NGS) and FISH to MYC expression and disease survival using 140 cases from Mayo Clinic and 658 cases from the MMRF CoMMpass study. RESULTS MYC SVs were found in 41% of cases and were classified into nine subtypes. A correlation between the presence of a MYC SV and increased MYC expression was identified. Among the nine MYC subtypes, the non-immunoglobulin (non-Ig) insertion subtype was independently associated with improved outcomes, while the Ig insertion subtype, specifically involving the IgL gene partner, was independently associated with poorer outcomes compared with other MYC SV subtypes. Although the FISH methodology failed to detect approximately 70% of all MYC SVs, those detected by FISH were associated with elevated MYC gene expression and poor outcomes suggesting a different pathogenic role for FISH-detected MYC subtypes compared with other MYC subtypes. CONCLUSIONS Understanding the impact of different MYC SVs on disease outcome is necessary for the reliable interpretation of MYC SVs in multiple myeloma. NGS approaches should be considered as a replacement technique for a more comprehensive evaluation of the multiple myeloma clone.
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Affiliation(s)
- Neeraj Sharma
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - James B. Smadbeck
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Nadine Abdallah
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | | | - Moritz Binder
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Kathryn E. Pearce
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Yan W. Asmann
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL
| | - Jess F. Peterson
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN,Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Rhett P. Ketterling
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN,Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Patricia T. Greipp
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN,Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - P. Leif Bergsagel
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Scottsdale, AZ
| | - S. Vincent Rajkumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Shaji K. Kumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Linda B. Baughn
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN,Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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7
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Guenzel AJ, Smadbeck JB, Golden CL, Williamson CM, Benevides Demasi JC, Vasmatzis G, Pearce KE, Olteanu H, Xu X, Hoppman NL, Greipp PT, Baughn LB, Ketterling RP, Peterson JF. Clinical utility of next generation sequencing to detect IGH/IL3 rearrangements [t(5;14)(q31.1;q32.1)] in B-lymphoblastic leukemia/lymphoma. Ann Diagn Pathol 2021; 53:151761. [PMID: 33991782 DOI: 10.1016/j.anndiagpath.2021.151761] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 05/06/2021] [Indexed: 11/18/2022]
Abstract
The t(5;14)(q31.1;q32.1) associated with B-lymphoblastic leukemia/lymphoma (B-ALL/LBL) is a rare, recurrent genetic abnormality recognized as a distinct entity by the 2017 World Health Organization (WHO) classification. In these cases, the IGH enhancer region (14q32.1) is juxtaposed to the vicinity of the IL3 gene (5q31.1), resulting in increased production of interleukin-3 (IL3) and subsequently a characteristic reactive eosinophilia. B-ALL with t(5;14)(q31.1;q32.1) may have a low lymphoblast count that can complicate detection of t(5;14)(q31.1;q32.1) by conventional chromosome studies. We have identified four patients with IGH/IL3 rearrangements despite normal conventional chromosome studies in each case [one patient had a non-clonal t(5;14)(q31;q32) finding]. Fluorescence in situ hybridization utilizing a laboratory-developed IGH break-apart probe set identified IGH rearrangements in three of four cases, and a next generation sequencing (NGS) based assay, mate-pair sequencing (MPseq), was required to characterize the IGH/IL3 rearrangements in each case. Three patients demonstrated a balanced t(5;14)(q31.1;q32.1) while one patient had a cryptic insertion of the IL3 gene into the IGH region. These results demonstrate that NGS-based assays, such as MPseq, confer an advantage in the detection of IGH/IL3 rearrangements that are otherwise challenging to characterize by traditional cytogenetic methodologies.
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Affiliation(s)
- Adam J Guenzel
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, 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
| | - Crystal L Golden
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Cynthia M Williamson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Jonna C Benevides Demasi
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, United States of America
| | - Kathryn E Pearce
- 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, Department of Laboratory Medicine and Pathology, 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
| | - Nicole L Hoppman
- 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
| | - Linda B Baughn
- 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, 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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8
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Pitel BA, Sharma N, Zepeda-Mendoza C, Smadbeck JB, Pearce KE, Cook JM, Vasmatzis G, Sachs Z, Kanagal-Shamanna R, Viswanatha D, Xiao S, Jenkins RB, Xu X, Hoppman NL, Ketterling RP, Peterson JF, Greipp PT, Baughn LB. Myeloid malignancies with 5q and 7q deletions are associated with extreme genomic complexity, biallelic TP53 variants, and very poor prognosis. Blood Cancer J 2021; 11:18. [PMID: 33563889 PMCID: PMC7873204 DOI: 10.1038/s41408-021-00416-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/30/2020] [Accepted: 01/19/2021] [Indexed: 11/09/2022] Open
Affiliation(s)
- Beth A Pitel
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Neeraj Sharma
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Cinthya Zepeda-Mendoza
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA.,Cytogenetics and Genomic Microarray Laboratory, ARUP Laboratories, Salt Lake City, UT, USA
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - Kathryn E Pearce
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Joselle M Cook
- Department of Medicine, Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - Zohar Sachs
- Division of Hematology, Oncology, and Transplantation, Department of Medicine and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David Viswanatha
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Sheng Xiao
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Xinjie Xu
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Rhett P Ketterling
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Jess F Peterson
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA.
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Lopes JL, Webley M, Pitel BA, Pearce KE, Smadbeck JB, Johnson SH, Vasmatzis G, Sukov WR, Greipp PT, Hoppman NL, Ketterling RP, Baughn LB, Finn L, Peterson JF. Characterizing false-positive fluorescence in situ hybridization results by mate-pair sequencing in a patient with chronic myeloid leukemia and progression to myeloid blast crisis. Cancer Genet 2020; 243:48-51. [PMID: 32272434 DOI: 10.1016/j.cancergen.2020.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/23/2020] [Accepted: 02/27/2020] [Indexed: 12/21/2022]
Abstract
Traditional cytogenetic testing methodologies, including conventional chromosome analysis and fluorescence in situ hybridization (FISH), are invaluable for the detection or recurrent genetic abnormalities in various hematologic malignancies. However, technological advances, including a novel next-generation sequencing technique termed mate-pair sequencing (MPseq), continue to revolutionize the field of cytogenetics by enabling the characterization of structural variants at a significantly higher resolution compared to traditional methodologies. To illustrate the power of MPseq, we present a 27-year-old male diagnosed with chronic myeloid leukemia in myeloid blast crisis with multiple chromosomal abnormalities observed in all 20 metaphases from a peripheral blood specimen, including t(9;22)(q34;q11.2) and t(4;11)(q12;p15). Suspicious of a novel NUP98/PDGFRA fusion [t(4;11)(q12;p15)], break-apart FISH probe sets for the PDGFRA (4q12) and NUP98 (11p15.4) gene regions were performed and were both positive in approximately 86% of 200 interphase nuclei. However, subsequent MPseq testing revealed breakpoints located within the NUP98 gene and within an intergenic region (4q12) located between the CHIC2 and PDGFRA genes, indicating this 4;11 translocation does not result in the predicted NUP98/PDGFRA gene fusion as inferred from FISH and conventional chromosome results. This case demonstrates the clinical utility of MPseq, particularly for characterizing novel gene fusion events which may ultimately identify a false-positive FISH result.
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Affiliation(s)
- Jaime L Lopes
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - Matthew Webley
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - Beth A Pitel
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - Kathryn E Pearce
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - James B Smadbeck
- Mayo Clinic, Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, United States
| | - Sarah H Johnson
- Mayo Clinic, Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, United States
| | - George Vasmatzis
- Mayo Clinic, Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, United States
| | - William R Sukov
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - Patricia T Greipp
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - Nicole L Hoppman
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - Rhett P Ketterling
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - Linda B Baughn
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - Laura Finn
- Division of Hematology and Bone Marrow Transplant, Department of Internal Medicine, Ochsner Medical Center, New Orleans, LA, United States
| | - Jess F Peterson
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States.
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11
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Affiliation(s)
- Amy W Xiao
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Yuyan Jia
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Linda B Baughn
- 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
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Sheng Xiao
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
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12
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Anagnostou T, Knudson RA, Pearce KE, Meyer RG, Pitel BA, Peterson JF, Baughn LB, Reichard KK, Ketterling RP, Kloft‐Nelson SM, Knutson DL, Khan SP, Gangat N, Litzow MR, Hogan WJ, Wolanskyj A, Al‐Kali A, Begna KH, Elliott M, Pardanani A, Foran J, Shah M, Tefferi A, Alkhateeb H, Halling K, Rodriguez V, Greipp PT, Patnaik MM. Clinical utility of fluorescence in situ hybridization-based diagnosis of BCR-ABL1 like (Philadelphia chromosome like) B-acute lymphoblastic leukemia. Am J Hematol 2020; 95:E68-E72. [PMID: 31919873 DOI: 10.1002/ajh.25729] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/03/2019] [Accepted: 12/05/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Theodora Anagnostou
- Bone Marrow Transplantation Service, Department of MedicineMemorial Sloan Kettering Cancer Center Mayo Clinic Rochester Minnesota
| | - Ryan A. Knudson
- Cytogenetics Core Laboratory, Medical Genome FacilityMayo Clinic Rochester Minnesota
| | - Kathryn E. Pearce
- Department of Laboratory Medicine and Pathology, Genomics LaboratoryMayo Clinic Rochester Minnesota
| | - Reid G. Meyer
- Department of Laboratory Medicine and Pathology, Genomics LaboratoryMayo Clinic Rochester Minnesota
| | - Beth A. Pitel
- Department of Laboratory Medicine and Pathology, Genomics LaboratoryMayo Clinic Rochester Minnesota
| | - Jess F. Peterson
- Department of Laboratory Medicine and Pathology, Genomics LaboratoryMayo Clinic Rochester Minnesota
| | - Linda B. Baughn
- Department of Laboratory Medicine and Pathology, Genomics LaboratoryMayo Clinic Rochester Minnesota
| | - Kaaren K. Reichard
- Department of Laboratory Medicine and Pathology, Genomics LaboratoryMayo Clinic Rochester Minnesota
| | - Rhett P. Ketterling
- Department of Laboratory Medicine and Pathology, Genomics LaboratoryMayo Clinic Rochester Minnesota
| | - Sara M. Kloft‐Nelson
- Cytogenetics Core Laboratory, Medical Genome FacilityMayo Clinic Rochester Minnesota
| | - Darlene L. Knutson
- Cytogenetics Core Laboratory, Medical Genome FacilityMayo Clinic Rochester Minnesota
| | - Shakila P. Khan
- Division of Pediatric Hematology/OncologyMayo Clinic Rochester Minnesota
| | | | | | | | | | - Aref Al‐Kali
- Division of HematologyMayo Clinic Rochester Minnesota
| | | | | | | | - James Foran
- Division of HematologyMayo Clinic Jacksonville Florida
| | - Mithun Shah
- Division of HematologyMayo Clinic Rochester Minnesota
| | | | | | - Kevin Halling
- Department of Laboratory Medicine and Pathology, Genomics LaboratoryMayo Clinic Rochester Minnesota
| | - Vilmarie Rodriguez
- Division of Pediatric Hematology/OncologyMayo Clinic Rochester Minnesota
| | - Patricia T. Greipp
- Department of Laboratory Medicine and Pathology, Genomics LaboratoryMayo Clinic Rochester Minnesota
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13
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Peterson JF, Pearce KE, Meyer RG, Greipp PT, Knudson RA, Baughn LB, Ketterling RP, Feldman AL. Fluorescence in-situ hybridisation for TP63 rearrangements in T cell lymphomas: single-site experience of 470 patients and implications for clinical testing. Histopathology 2020; 76:481-485. [PMID: 31557339 DOI: 10.1111/his.14005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/15/2019] [Accepted: 09/26/2019] [Indexed: 12/28/2022]
Abstract
AIMS The aims of this study were to review our 5-year experience with clinical FISH testing for TP63 rearrangements using both TP63 break-apart (BAP) and TBL1XR1/TP63 dual-fusion (D-FISH) probes to evaluate the frequency of TP63 rearrangements and the distribution of TBL1XR1 vs. alternate partner loci, and to assess whether both probe sets are necessary in all cases undergoing FISH testing. METHODS AND RESULTS A retrospective review of the Mayo Clinic cytogenetic database identified 470 patients evaluated by FISH testing for TP63 rearrangements in formalin-fixed paraffin-embedded (FFPE) tissue using both BAP and D-FISH probes. Of these, 25 (5.3%) had TP63 rearrangements. All samples were being investigated for anaplastic large-cell lymphoma or other T cell lymphoma subtypes. A TBL1XR1 partner was identified by D-FISH in 12 (48%) of 25 cases. All cases positive by TBL1XR1/TP63 D-FISH were also positive by TP63 BAP FISH. CONCLUSION This is the largest series of TP63 rearrangements to date. The frequency of positive results among cases referred to a large reference laboratory for TP63 FISH testing was 5.3%. Approximately half of TP63 rearrangements have a TBL1XR1 partner. TP63 BAP FISH testing is sufficient for up-front testing of FFPE tissue samples. However, because of the genomic proximity of the TP63 and TBL1XR1 loci, we recommend reflex TBL1XR1/TP63 D-FISH testing in positive and equivocal cases.
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Affiliation(s)
- Jess F Peterson
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Kathryn E Pearce
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Reid G Meyer
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Ryan A Knudson
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Rhett P Ketterling
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Andrew L Feldman
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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Peterson JF, Blackburn PR, Webley MR, Pearce KE, Williamson CM, Vasmatzis G, Smadbeck JB, Bieliauskas SL, Reichard KK, Ketterling RP, Baughn LB, Greipp PT. Identification of a Novel ZBTB20-JAK2 Fusion by Mate-Pair Sequencing in a Young Adult With B-Lymphoblastic Leukemia/Lymphoma. Mayo Clin Proc 2019; 94:1381-1384. [PMID: 31272582 DOI: 10.1016/j.mayocp.2019.04.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 12/26/2022]
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16
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Xing D, Zheng G, Pallavajjala A, Schoolmeester JK, Liu Y, Haley L, Hu Y, Liu L, Logan L, Lin Y, Pearce KE, Sattler CA, Tsai YC, Vang R, Hung CF, Wu TC, Ronnett BM. Lineage-Specific Alterations in Gynecologic Neoplasms with Choriocarcinomatous Differentiation: Implications for Origin and Therapeutics. Clin Cancer Res 2019; 25:4516-4529. [DOI: 10.1158/1078-0432.ccr-18-4278] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/25/2019] [Accepted: 04/12/2019] [Indexed: 11/16/2022]
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17
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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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] [What about the content of this article? (0)] [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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19
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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: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [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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Peterson JF, Baughn LB, Pearce KE, Williamson CM, Benevides Demasi JC, Olson RM, Goble TA, Meyer RG, Greipp PT, Ketterling RP. KMT2A (MLL) rearrangements observed in pediatric/young adult T-lymphoblastic leukemia/lymphoma: A 10-year review from a single cytogenetic laboratory. Genes Chromosomes Cancer 2018; 57:541-546. [PMID: 30203571 DOI: 10.1002/gcc.22666] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/09/2018] [Accepted: 07/09/2018] [Indexed: 02/03/2023] Open
Abstract
T-lymphoblastic leukemia/lymphoma (T-ALL/LBL) accounts for approximately 15% of pediatric and 25% of adult ALL. While the underlying frequency of KMT2A (MLL) gene rearrangements has been identified in approximately 4-8% of T-ALL/LBL cases, a paucity of literature is available to characterize further the KMT2A rearrangements in pediatric/young adult T-ALL/LBL. A 10-year retrospective review was performed to identify KMT2A rearrangements in specimens sent for T-ALL/LBL fluorescence in situ hybridization studies in patients under the age of 30 years. Of 806 T-ALL/LBL FISH studies performed on unique individuals, 27 (3.3%) harbored KMT2A rearrangements. Nineteen patients were male and eight were female (M:F ratio, 2.4:1) with ages ranging from 1 to 20 years (mean 12, median 12). Of the 27 cases, nine (33%) had KMT2A/MLLT1 fusions, eight (30%) had KMT2A/AFDN fusions, two (7%) had KMT2A/ELL fusions, and one (4%) had a KMT2A/MLLT10 fusion. In addition, five (19%) had KMT2A rearrangements with unidentified gene fusion partners and two (7%) had 3'KMT2A deletions. Our results indicate that MLLT1 and AFDN account for the majority (63%) of KMT2A gene partners in pediatric/young adult T-ALL/LBL, while no KMT2A/AFF1 or KMT2A/MLLT3 fusions were observed despite their common identification in B-ALL and acute myeloid leukemia, respectively. In addition to diagnostic and prognostic value, detecting specific KMT2A fusions may also be of clinical importance in the era of targeted therapies.
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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
| | - Linda B Baughn
- 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
| | - Cynthia M Williamson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jonna C Benevides Demasi
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Renee M Olson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Tony A Goble
- 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
| | - Patricia T Greipp
- 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
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González-Calle V, Slack A, Keane N, Luft S, Pearce KE, Ketterling RP, Jain T, Chirackal S, Reeder C, Mikhael J, Noel P, Mayo A, Adams RH, Ahmann G, Braggio E, Stewart AK, Bergsagel PL, Van Wier SA, Fonseca R. Evaluation of Revised International Staging System (R-ISS) for transplant-eligible multiple myeloma patients. Ann Hematol 2018; 97:1453-1462. [DOI: 10.1007/s00277-018-3316-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 03/22/2018] [Indexed: 10/17/2022]
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Cao Y, Pitel BA, Gliem TJ, Hughes EG, Pearce KE, Ketterling RP, Greipp PT, Kearney HM, Baughn LB. Development of a Clinical Grade Interpretive Tool for Neoplastic Genomic Microarray Testing. Cancer Genet 2016. [DOI: 10.1016/j.cancergen.2016.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Hodge JC, Bedroske PP, Pearce KE, Sukov WR. Molecular Cytogenetic Analysis of JAZF1, PHF1, and YWHAE in Endometrial Stromal Tumors: Discovery of Genetic Complexity by Fluorescence in Situ Hybridization. J Mol Diagn 2016; 18:516-26. [PMID: 27154512 DOI: 10.1016/j.jmoldx.2016.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 11/28/2015] [Accepted: 02/03/2016] [Indexed: 12/22/2022] Open
Abstract
Diagnosis of endometrial stromal tumors (ESTs) can be challenging, particularly endometrial stromal sarcomas (ESSs) because of variable histologic appearance, long latency to recurrence, frequent metastases with unknown primary, and overlap with endometrial stromal nodules and undifferentiated uterine sarcomas. To enhance EST diagnosis, a break-apart strategy fluorescence in situ hybridization panel to detect JAZF1, PHF1, and YWHAE rearrangements was applied to a cohort of primary or metastatic endometrial stromal nodules, ESSs, or undifferentiated uterine sarcomas (36 cases for JAZF1, 24 of which were also assessed for PHF1 and YWHAE), 24 myometrium/endometrium controls, and 37 non-ESTs in the differential diagnosis. JAZF1 was the most frequently altered gene and occurred in all EST types, JAZF1 and/or PHF1 were mutually exclusive from YWHAE involvement, and uterine and extrauterine ESTs have a shared pathogenesis. We further defined frequency of these rearrangements and provided a resource demonstrating the signal complexity that can manifest when evaluating JAZF1. Rearrangement of JAZF1 occurred in 47% of ESTs, most (70%) of which had atypical patterns representing multiple structural alterations and/or more than one clone. YWHAE and PHF1 rearrangements each occurred in 8% of ESTs. An exceptional case was an ESS without JAZF1 or MEAF6 disruption that further disputes correlation of PHF1 involvement with the sex cord-like variant. These results expand our understanding of the genetic heterogeneity that defines ESTs.
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Affiliation(s)
- Jennelle C Hodge
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota; Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California.
| | - Patrick P Bedroske
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kathryn E Pearce
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - William R Sukov
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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Aypar U, Knudson RA, Pearce KE, Wiktor AE, Ketterling RP. Development of an NPM1/MLF1 D-FISH Probe Set for the Detection of t(3;5)(q25;q35) Identified in Patients with Acute Myeloid Leukemia. J Mol Diagn 2014; 16:527-532. [DOI: 10.1016/j.jmoldx.2014.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 04/25/2014] [Accepted: 05/16/2014] [Indexed: 11/27/2022] Open
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Hodge JC, Pearce KE, Clayton AC, Taran FA, Stewart EA. Uterine cellular leiomyomata with chromosome 1p deletions represent a distinct entity. Am J Obstet Gynecol 2014; 210:572.e1-7. [PMID: 24412114 DOI: 10.1016/j.ajog.2014.01.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/15/2013] [Accepted: 01/07/2014] [Indexed: 11/29/2022]
Abstract
OBJECTIVE This study aimed to determine whether 1p deletion defines a subset of cellular leiomyomata (CL), which is a hypercellular variant of uterine leiomyomata that may have delayed malignant potential, and to correlate this genetic change with clinical and pathologic characteristics including those present in uterine sarcomas. STUDY DESIGN Available CL cases at the Mayo Clinic (n = 101) and variant cases reported in another article (n = 16) were identified. Each case with sufficient tissue that met histologic criteria for CL when reviewed by a single pathologist underwent interphase fluorescence in situ hybridization to determine the presence of 1p deletion. Clinical characteristics of women with confirmed CL were compared on the basis of 1p deletion status using univariate analysis. RESULTS Of the Mayo Clinic cohort of histologically confirmed CL, 23% had deletion of 1p. Women with this subset of CL, when compared to those without 1p deletion, were more likely to be postmenopausal (P = .049) and their uteri tended to be heavier (P = .039) with a larger dominant leiomyoma (P = .030). The pathologic features associated with 1p deletion were high cellularity (P = .036) and hyaline necrosis (P = .047), which remained significant after inclusion of the CL cases from a previously published series. CONCLUSION Deletion of 1p occurs in approximately one-quarter of CL cases. This genetic alteration is potentially associated with clinicopathologic features that are present in uterine sarcomas, which suggests a distinct clinical entity that may have malignant potential. Our findings are particularly pertinent considering the increased preference for uterine-sparing options in leiomyoma treatment, suggesting assessment of 1p deletion status in CL may influence clinical surveillance decisions.
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Affiliation(s)
- Jennelle C Hodge
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA.
| | - Kathryn E Pearce
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Amy C Clayton
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Florin A Taran
- Department of Obstetrics and Gynecology and Surgery, Mayo Clinic, Rochester, MN; Department of Obstetrics and Gynecology, University Women's Clinic, Tübingen, Germany
| | - Elizabeth A Stewart
- Department of Obstetrics and Gynecology and Surgery, Mayo Clinic, Rochester, MN
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Hodge JC, Pearce KE, Sukov WR. Distinct ALK-rearranged and VCL-negative papillary renal cell carcinoma variant in two adults without sickle cell trait. Mod Pathol 2013; 26:604-5. [PMID: 23542520 DOI: 10.1038/modpathol.2012.144] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Wynne-Jones M, Pearce KE, Bhalla AK. Bone-fracture risk in a wheelchair user. Practitioner 2001; 245:687, 690-2, 695-6. [PMID: 11584582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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Pearce KE. Osteoporosis is a risk factor, not a disease. BMJ 2001; 322:862. [PMID: 11290653 PMCID: PMC1120023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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Pearce KE, Charlton JS. Screening for hyperlipidaemia in childhood. J R Coll Physicians Lond 1996; 30:268-269. [PMID: 8811608 PMCID: PMC5401425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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