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Gagnon MF, Bruehl FK, Sill DR, Meyer RG, Greipp PT, Hoppman NL, Xu X, Baughn LB, Peterson JF, McPhail ED, Ketterling RP, King RL. Cytogenetic and pathologic characterization of MYC-rearranged B-cell lymphomas in pediatric and young adult patients. J Hematop 2024:10.1007/s12308-024-00579-6. [PMID: 38561469 DOI: 10.1007/s12308-024-00579-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
MYC-rearranged B-cell lymphoma (BCL) in the pediatric/young adult (YA) age group differs substantially in disease composition from adult cohorts. However, data regarding the partner genes, concurrent rearrangements, and ultimate diagnoses in these patients is scarce compared to that in adult cohorts. We aimed to characterize the spectrum of MYC-rearranged (MYC-R) mature, aggressive BCL in the pediatric/YA population. A retrospective study of morphologic, immunophenotypic, and fluorescence in situ hybridization (FISH) results of patients age ≤ 30 years with suspected Burkitt lymphoma (BL), diffuse large B-cell lymphoma (DLBCL) or high-grade B-cell lymphoma (HGBCL), and a MYC-R by FISH between 2013-2022 was performed. Two-hundred fifty-eight cases (129 (50%) pediatric (< 18 years) and 129 (50%) YA (18-30 years)) were included. Most MYC-R BCL in pediatric (89%) and YA (66%) cases were BL. While double-hit (DH) cytogenetics (MYC with BCL2 and/or BCL6-R, HGBCL-DH) was rare in the pediatric population (2/129, 2%), HGBCL-DH increased with age and was identified in 17/129 (13%) of YA cases. Most HGBCL-DH had MYC and BCL6-R, while BCL2-R were rare in both groups (3/258, 1%). MYC-R without an IG partner was more common in the YA group (14/116 (12%) vs 2/128 (2%), p = 0.001). The pediatric to YA transition is characterized by decreasing frequency in BL and increasing genetic heterogeneity of MYC-R BCL, with emergence of DH-BCL with MYC and BCL6-R. FISH to evaluate for BCL2 and BCL6 rearrangements is likely not warranted in the pediatric population but should continue to be applied in YA BCL.
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Affiliation(s)
- Marie-France Gagnon
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Frido K Bruehl
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Daniel R Sill
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Reid G Meyer
- Division of Laboratory Genetics and Genomics, 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
| | - 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
| | - Linda B Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jess F Peterson
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ellen D McPhail
- 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
| | - Rebecca L King
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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Akkari Y, Baughn LB, Kim A, Karaca E, Raca G, Shao L, Mikhail FM. Section E6.1-6.6 of the American College of Medical Genetics and Genomics (ACMG) Technical Laboratory Standards: Cytogenomic studies of acquired chromosomal abnormalities in neoplastic blood, bone marrow, and lymph nodes. Genet Med 2024; 26:101054. [PMID: 38349293 DOI: 10.1016/j.gim.2023.101054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 04/09/2024] Open
Abstract
Cytogenomic analyses of acquired clonal chromosomal abnormalities in neoplastic blood, bone marrow, and/or lymph nodes are instrumental in the clinical management of patients with hematologic neoplasms. Cytogenetic analyses assist in the diagnosis of such disorders and can provide important prognostic information. Furthermore, cytogenetic studies can provide crucial information regarding specific genetically defined subtypes of these neoplasms that may have targeted therapies. At time of relapse, cytogenetic analysis can confirm recurrence of the original neoplasm, detect clonal disease evolution, or uncover a new unrelated neoplastic process. This section deals specifically with the technical standards applicable to cytogenomic studies of acquired clonal chromosomal abnormalities in neoplastic blood, bone marrow, and/or lymph nodes. This updated Section E6.1-6.6 supersedes the previous Section E6 in Section E: Clinical Cytogenetics of the American College of Medical Genetics and Genomics Technical Standards for Clinical Genetics Laboratories.
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Affiliation(s)
- Yassmine Akkari
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Linda B Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Annette Kim
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Ender Karaca
- Department of Pathology, Baylor University Medical Center, Dallas, TX; Texas A&M School of Medicine, Texas A&M University, Dallas, TX
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA; Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Lina Shao
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
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Gagnon MF, Meyer RG, Weaver EJ, Wood AJ, Dupuy DA, Menachery SJ, Shi M, Baughn LB, Ketterling RP, Peterson JF. High-grade B-cell lymphoma with a quadruple-hit genetic profile including concurrent MYC, BCL2, BCL6, and CCND1 gene rearrangements. Lab Med 2024:lmae017. [PMID: 38522075 DOI: 10.1093/labmed/lmae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Abstract
Several reports of concurrent MYC, BCL2, BCL6, and CCND1 rearrangements in high-grade B-cell lymphoma (HGBL) have been recently described. Herein, we aimed to delineate the scope of this entity through a review of HGBL with a "quadruple-hit" genetic profile identified at our institution. We performed a retrospective review (2015-2023) at our institution of B-cell lymphoma (BCL) cases that were evaluated with concurrent MYC, BCL2, and BCL6 break-apart and IGH::MYC and IGH::CCND1 dual-color dual-fusion fluorescence in situ hybridization studies. Of 203 cases meeting inclusion criteria, 2 (1%) with a quadruple-hit genetic profile were identified. Case 1 represented a 59-year-old female with widespread lymphadenopathy and a diagnosis of HGBL who exhibited primary refractoriness to dose-adjusted etoposide, prednisone, vincristine, cyclophosphamide, doxorubicin, and rituximab (DA-EPOCH-R) chemotherapy. Case 2 represented a 58-year-old male with mediastinal and abdominal lymphadenopathy and a diagnosis of large BCL who died from disease after 1 cycle of DA-EPOCH-R chemotherapy. Similarly, a literature review of 7 previously reported cases of HGBL with a quadruple-hit profile also demonstrated aggressive disease behavior. Our study adds 2 new cases to the rarely encountered quadruple-hit HGBL, and a brief meta-analysis of the 9 available cases indicates aggressive disease behavior conferred by this constellation of genetic events.
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Affiliation(s)
- Marie-France Gagnon
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, US
| | - Reid G Meyer
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, US
| | - Eric J Weaver
- TidalHealth Outpatient Lab Services, Salisbury, MD, US
| | - Adam J Wood
- 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
| | - Linda B Baughn
- 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 Hematopathology, Mayo Clinic, Rochester, MN, US
| | - Jess F Peterson
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, US
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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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Gagnon MF, Penheiter AR, Harris F, Sadeghian D, Johnson SH, Karagouga G, McCune A, Zepeda-Mendoza C, Greipp PT, Xu X, Ketterling RP, McPhail ED, King RL, Peterson JF, Vasmatzis G, Baughn LB. Unraveling the genomic underpinnings of unbalanced MYC break-apart FISH results using whole genome sequencing analysis. Blood Cancer J 2023; 13:190. [PMID: 38114462 PMCID: PMC10730864 DOI: 10.1038/s41408-023-00967-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023] Open
Affiliation(s)
- Marie-France Gagnon
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Alan R Penheiter
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Faye Harris
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Dorsay Sadeghian
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sarah H Johnson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Alexa McCune
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Cinthya Zepeda-Mendoza
- 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
| | - 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
| | - Ellen D McPhail
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rebecca L King
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jess F Peterson
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - George Vasmatzis
- Center for Individualized Medicine, 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.
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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Yadav U, Kumar SK, Baughn LB, Dispenzieri A, Greipp P, Ketterling R, Jevremovic D, Buadi FK, Dingli D, Lacy MQ, Fonseca R, Bergsagel PL, Ailawadhi S, Roy V, Parrondo R, Sher T, Hayman SR, Kapoor P, Leung N, Cook J, Binder M, Muchtar E, Warsame R, Kourelis TV, Go RS, Lin Y, Seth A, Lester SC, Breen WG, Kyle RA, Gertz MA, Rajkumar SV, Gonsalves WI. Impact of cytogenetic abnormalities on the risk of disease progression in solitary bone plasmacytomas. Blood 2023; 142:1871-1878. [PMID: 37494698 PMCID: PMC10731916 DOI: 10.1182/blood.2023021187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/07/2023] [Accepted: 07/26/2023] [Indexed: 07/28/2023] Open
Abstract
Most patients with solitary bone plasmacytomas (SBP) progress to multiple myeloma (MM) after definitive radiation therapy as their primary treatment. Whether the presence of high-risk (HR) cytogenetic abnormalities by fluorescence in situ hybridization (FISH) in the clonal plasma cells, obtained either directly from the diagnostic SBP tissue or the corresponding bone marrow examination at the time of diagnosis, is associated with a shorter time to progression (TTP) to MM is unknown. This study evaluated all patients diagnosed with SBP at the Mayo Clinic from January 2012 to July 2022. The presence of del(17p), t(14;16), t(4;14), or +1q (gain or amplification) by FISH in clonal plasma cells was defined as HR. A total of 114 patients were included in this cohort, and baseline FISH was available for 55 patients (48%), of which 22 were classified as HR (40%). The median TTP to MM for patients with SBP and HR FISH was 8 months (95% confidence interval [CI], 6.3-26) compared with 42 months (95% CI, 25-not reached [NR]) in patients with SBP without HR FISH (P < .001). In a multivariate analysis, only HR FISH was a significant predictor for shorter TTP to MM, independent of minimal marrow involvement and an abnormal serum free light chain ratio at diagnosis. Deletion (17p) and gain 1q abnormalities were the most common FISH abnormalities responsible for the short TTP to MM. Thus, assessing for HR FISH abnormalities in clonal plasma cells derived from either the diagnostic SBP tissue or the staging bone marrow examination of patients with newly diagnosed SBP is feasible and prognostic for a shorter TTP to MM.
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Affiliation(s)
- Udit Yadav
- Division of Hematology, Mayo Clinic, Rochester, MN
| | | | - Linda B. Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Patricia Greipp
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Rhett Ketterling
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Dragan Jevremovic
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - David Dingli
- Division of Hematology, Mayo Clinic, Rochester, MN
| | | | - Rafael Fonseca
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, AZ
| | | | | | - Vivek Roy
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL
| | - Ricardo Parrondo
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL
| | - Taimur Sher
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL
| | | | | | - Nelson Leung
- Division of Hematology, Mayo Clinic, Rochester, MN
- Division of Nephrology, Mayo Clinic, Rochester, MN
| | - Joselle Cook
- Division of Hematology, Mayo Clinic, Rochester, MN
| | | | - Eli Muchtar
- Division of Hematology, Mayo Clinic, Rochester, MN
| | | | | | - Ronald S. Go
- Division of Hematology, Mayo Clinic, Rochester, MN
| | - Yi Lin
- Division of Hematology, Mayo Clinic, Rochester, MN
| | | | - Scott C. Lester
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
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7
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Gao RW, Fleuranvil R, Harmsen WS, Greipp PT, Baughn LB, Jevremovic D, Gonsalves WI, Kourelis T, Stish BJ, Peterson JL, Rule WG, Hoppe BS, Breen W, Lester SC. Predictors of Local Control with Palliative Radiotherapy for Multiple Myeloma. Int J Radiat Oncol Biol Phys 2023; 117:S108. [PMID: 37784284 DOI: 10.1016/j.ijrobp.2023.06.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Palliative radiotherapy (RT) is employed for patients with multiple myeloma to improve or prevent symptoms. However, the optimal dose fractionation is not well defined. The role of cytogenetics in informing RT warrants further study. We performed an institutional analysis of patients with multiple myeloma receiving palliative RT and assessed factors associated with local progression, with a focus on dose fractionation and cytogenetic abnormalities. MATERIALS/METHODS We queried a prospectively maintained, departmental database for consecutive patients who received palliative RT for multiple myeloma at our institution from 2015 to 2020. Double- and triple-hit were defined as the presence of two and three high-risk cytogenetic abnormalities. RT dose fractionation data were extracted from the database. Follow-up imaging was used to evaluate for progression. RESULTS A total of 239 patients with 362 treated lesions were included. Twenty-five patients (10.4%) with 39 lesions had double-hit cytogenetics, and 4 patients (1.7%) with 7 lesions were triple-hit. Patients had the following number of lesions treated with RT: 1 (156, 65.3%), 2 (53, 22.2%), 3 (17, 7.1%), or >3 (13, 5.4%). The most commonly targeted sites were spine (125, 34.5%), abdomen/pelvis (67, 18.5%), and lower extremity (53, 14.6%). Most lesions received doses of 20 Gy/5 fx (132, 36.5%), 8 Gy/1 fx (93, 25.7%), or 30 Gy/10 fx (48, 13.3%). RT equivalent dose in 2 Gray fractions (EQD2) was <2000 cGy for 126 lesions (34.8%) and ≥2000 cGy for 236 lesions (65.2%). At a median follow-up of 4.3 years, the risk of local progression on a per lesion basis at 1 and 4 years was 7.8% (95% CI: 5.5-11.1) and 13.4% (10.3-17.5), respectively. No cytogenetic abnormalities were correlated with local progression. Factors significant on univariate analysis included female sex [hazard ratio (HR): 1.94 (1.02-3.71), p = .045], LDH at diagnosis [HR per 10 units/liter: 1.04 (1.09-1.08), p = .016], and number of treated lesions [HR per lesion: 1.38 (1.02-1.89), p = .039]. These three covariates were included on multivariable analysis, and the only covariate to approach significance was number of treated lesions [HR for >3 versus 1: 2.43 (0.88-6.74), p = .059]. In the overall cohort, EQD2 did not impact risk of progression. Among those with >3 treated lesions, EQD2 ≥2000 cGy was associated with a significantly lower risk of progression [HR: 0.05 (0.01-0.23), p<.001]. Double- and triple-hit status were not correlated with progression. Median overall survival in all patients was 4.1 years versus 1.5 and 0.6 years in those with double- and triple-hit disease, respectively. CONCLUSION In this large, institutional study of patients with multiple myeloma, palliative RT achieves durable long-term local control. Patients with high disease burden may be at increased risk of progression at treated sites. This group may benefit from an EQD ≥2000 cGy. Cytogenetics, including double- and triple-hit status, do not appear to influence RT response.
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Affiliation(s)
- R W Gao
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
| | | | - W S Harmsen
- Department of Biostatistics and Health Sciences Research, Mayo Clinic, Rochester, MN
| | | | | | | | | | | | - B J Stish
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
| | - J L Peterson
- Department of Radiation Oncology, Mayo Clinic, Jacksonville, FL
| | - W G Rule
- Department of Radiation Oncology, Mayo Clinic, Phoenix, AZ
| | - B S Hoppe
- Department of Radiation Oncology, Mayo Clinic, Jacksonville, FL
| | - W Breen
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
| | - S C Lester
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
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8
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Zhao CY, Gao RW, Fleuranvil R, Harmsen WS, Greipp PT, Baughn LB, Jevremovic D, Gonsalves WI, Kourelis T, Villasboas Bisneto J, Amundson A, Peterson JL, Rule WG, Hoppe BS, Lester SC, Breen W. Change in Blood Counts after Palliative Radiotherapy for Multiple Myeloma. Int J Radiat Oncol Biol Phys 2023; 117:e498-e499. [PMID: 37785567 DOI: 10.1016/j.ijrobp.2023.06.1740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Radiation therapy (RT) can provide effective palliation and prevent symptomatic local progression of multiple myeloma (MM). However, RT is sometimes avoided due to concerns for secondary impact to bone marrow, potentially decreasing blood cell counts and precluding ability to receive future systemic therapies. We reviewed a series of MM patients who received palliative RT to assess changes in blood counts from pre-RT to post-RT, hypothesizing that blood counts would not significantly decline after treatment with modern RT volumes and techniques. MATERIALS/METHODS We utilized a prospectively maintained departmental database and included patients who received palliative RT for MM from 2015 to 2020. Lab values immediately pre-RT (within one month of RT start date) and post-RT (within three months of RT completion) including hemoglobin, lymphocytes, neutrophils, and platelets were collected. Statistical differences from pre-RT to post-RT were assessed using t-tests. ANOVA was used to compare change in blood counts between common dose fractionation regimens (30 Gy in 10 Fractions, 20 Gy in 5, and 8 Gy in 1). RESULTS A total of 334 MM patients receiving 424 courses of RT were included in this analysis. The median age at start of first treatment was 67 (IQR: 60-76) years. One-hundred ninety-five (58%) were male. Median RT dose was 20 (IQR: 8-24.5) Gy delivered over a median 5 (IQR: 1-5) fractions. Between pre-RT and post-RT, there was no significant change in hemoglobin (+0.1 g/dL (IQR: -0.8, +0.5), p = .076), lymphocyte counts (-0.3*10^9 cells/L (IQR: -0.6, 0), p = .435), or neutrophil counts (-0.1*10^9 cells/L (IQR: -1.1, +0.9), p = .310). In contrast, platelet counts significantly decreased from pre-RT (median 165*10^9 cells/L, IQR: 112-210) to post-RT (median 146, IQR: 93-194) by a median of 17.5 *10^9 cells/L (IQR: -52.5, +14.0, p<0.0001). There were no differences in changes in hemoglobin, neutrophils, or platelets between the common dose fractionations. However, there was a significantly greater drop in lymphocytes after 30 Gy in 10 fractions (p = .039, mean lymphocyte count change (in 10^9 cells/L) for 30 Gy in 10: -0.87, 20 Gy in 5: -0.47, and 8 Gy in 1: -0.27). CONCLUSION In this large dataset of patients receiving modern palliative RT for MM, hemoglobin, lymphocytes, and neutrophils did not significantly decline from pre-RT to post-RT. In contrast, there was a statistically significant drop in platelet count by a median 17.5*10^9 cells/L from pre-RT to post-RT, which may or may not be clinically significant depending on clinical context. Patients receiving 30 Gy in 10 fractions had greater drops in lymphocytes than those receiving lower doses. Further analyses will be performed to determine clinical, dosimetric, and volumetric predictors of decline in blood counts after radiation.
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Affiliation(s)
| | - R W Gao
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
| | | | - W S Harmsen
- Department of Biostatistics and Health Sciences Research, Mayo Clinic, Rochester, MN
| | | | | | | | | | | | | | - A Amundson
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
| | - J L Peterson
- Department of Radiation Oncology, Mayo Clinic, Jacksonville, FL
| | - W G Rule
- Department of Radiation Oncology, Mayo Clinic, Phoenix, AZ
| | - B S Hoppe
- Department of Radiation Oncology, Mayo Clinic, Jacksonville, FL
| | - S C Lester
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
| | - W Breen
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
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9
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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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10
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Choate LA, Jiang L, Stein MI, Shen W, Baughn LB, Peterson JF. Detection of an MN1::ETV6 Gene Fusion in a Case of Acute Myeloid Leukemia with Erythroid Differentiation: A Case Report and Review of the Literature. Case Rep Hematol 2023; 2023:9771388. [PMID: 37434656 PMCID: PMC10332927 DOI: 10.1155/2023/9771388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/17/2023] [Accepted: 06/27/2023] [Indexed: 07/13/2023] Open
Abstract
The MN1::ETV6 gene fusion resulting from t(12;22)(p13;q12) has been rarely reported in myeloid neoplasms. We describe a 69-year-old male with newly diagnosed acute myeloid leukemia (AML) with erythroid differentiation and t(12;22)(p13;q12) demonstrated by conventional chromosome studies. Subsequent fluorescence in situ hybridization studies demonstrated a balanced ETV6 gene rearrangement (at 12p13). To further characterize this translocation, whole-genome sequencing was performed which confirmed t(12;22) with breakpoints involving the MN1 and ETV6 genes. Herein, we describe our case and review the literature to summarize the clinical and laboratory findings in patients with this rare but recurrent MN1::ETV6 gene fusion observed in myeloid neoplasms. Importantly, this case expands the clinical spectrum associated with the MN1::ETV6 gene fusion to include AML with erythroid differentiation. Lastly, this case demonstrates the importance of moving toward more comprehensive molecular testing to fully characterize the driver events in neoplastic genomes.
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Affiliation(s)
- Lauren A. Choate
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Liuyan Jiang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, Florida, USA
| | - Mariam I. Stein
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Wei Shen
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Linda B. Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jess F. Peterson
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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11
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Baughn LB, Jessen E, Sharma N, Tang H, Smadbeck JB, Long MD, Pearce K, Smith M, Dasari S, Sachs Z, Linden MA, Cook J, Keith Stewart A, Chesi M, Mitra A, Leif Bergsagel P, Van Ness B, Kumar SK. Mass Cytometry reveals unique phenotypic patterns associated with subclonal diversity and outcomes in multiple myeloma. Blood Cancer J 2023; 13:84. [PMID: 37217482 PMCID: PMC10203138 DOI: 10.1038/s41408-023-00851-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 04/26/2023] [Accepted: 05/02/2023] [Indexed: 05/24/2023] Open
Abstract
Multiple myeloma (MM) remains an incurable plasma cell (PC) malignancy. Although it is known that MM tumor cells display extensive intratumoral genetic heterogeneity, an integrated map of the tumor proteomic landscape has not been comprehensively evaluated. We evaluated 49 primary tumor samples from newly diagnosed or relapsed/refractory MM patients by mass cytometry (CyTOF) using 34 antibody targets to characterize the integrated landscape of single-cell cell surface and intracellular signaling proteins. We identified 13 phenotypic meta-clusters across all samples. The abundance of each phenotypic meta-cluster was compared to patient age, sex, treatment response, tumor genetic abnormalities and overall survival. Relative abundance of several of these phenotypic meta-clusters were associated with disease subtypes and clinical behavior. Increased abundance of phenotypic meta-cluster 1, characterized by elevated CD45 and reduced BCL-2 expression, was significantly associated with a favorable treatment response and improved overall survival independent of tumor genetic abnormalities or patient demographic variables. We validated this association using an unrelated gene expression dataset. This study represents the first, large-scale, single-cell protein atlas of primary MM tumors and demonstrates that subclonal protein profiling may be an important determinant of clinical behavior and outcome.
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Affiliation(s)
- Linda B Baughn
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| | - Erik Jessen
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Neeraj Sharma
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Hongwei Tang
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - James B Smadbeck
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Mark D Long
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Kathryn Pearce
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Matthew Smith
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Surendra Dasari
- Division of Computational Biology, Department of Quantitative Health Sciences, 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
| | - Michael A Linden
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Joselle Cook
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Marta Chesi
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Amit Mitra
- Department of Drug Discovery and Development, Auburn University, Auburn, AL, USA
| | - P Leif Bergsagel
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Brian Van Ness
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Shaji K Kumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
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12
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Abdallah NH, Smith AN, Geyer S, Binder M, Greipp PT, Kapoor P, Dispenzieri A, Gertz MA, Baughn LB, Lacy MQ, Hayman SR, Buadi FK, Dingli D, Hwa YL, Lin Y, Kourelis T, Warsame R, Kyle RA, Rajkumar SV, Kumar SK. Conditional survival in multiple myeloma and impact of prognostic factors over time. Blood Cancer J 2023; 13:78. [PMID: 37188699 DOI: 10.1038/s41408-023-00852-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/22/2023] [Accepted: 05/03/2023] [Indexed: 05/17/2023] Open
Abstract
Overall survival estimates from diagnosis are valuable for guiding treatment, but do not consider the years already survived. Conditional survival (CS) provides dynamic survival predictions over time. This study was conducted to estimate CS at 1-8 years from diagnosis and the impact of baseline prognostic factors on CS in multiple myeloma (MM) patients. This is a retrospective study including 2556 MM patients diagnosed between 2004 and 2019. CS (t | s) was defined as the probability of surviving t years given survival of s years. Median age was 64 years. Median follow-up was 6.2 years and median overall survival from diagnosis was 7.5 years. The 5-year CS estimates at s = 0, 1, 2, 3, and 5 years were 0.64, 0.61, 0.61, 0.61, and 0.58, respectively. On multivariate analysis, age ≥ 65 and proteasome inhibitor+immunomodulatory-based induction were associated with decreased survival and increased survival, respectively, retained at 5 years. The adverse impact of 1q gain/amplification, high-risk IgH translocation, and ISS-3 was significant at 1 and 3 years but not 5 years. Chromosome 17 abnormality was associated with decreased survival only at 1 year. Among MM patients, 5-year CS was stable at 1-5 years from diagnosis. The prognostic impact of high-risk cytogenetic factors decreased with additional years survived.
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Affiliation(s)
| | | | - Susan Geyer
- Department of biostatistics, Mayo Clinic, Rochester, MN, USA
| | - Moritz Binder
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Morie A Gertz
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Martha Q Lacy
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | | | - David Dingli
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Yi L Hwa
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Yi Lin
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | - Rahma Warsame
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Robert A Kyle
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | - Shaji K Kumar
- Division of Hematology, Mayo Clinic, Rochester, MN, USA.
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13
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Panakkal V, Lakshman A, Shi M, Olteanu H, Horna P, Timm MM, Otteson GE, Baughn LB, Greipp PT, Gonsalves WI, Kapoor P, Gertz MA, Binder M, Buadi FK, Dispenzieri A, Rajkumar SV, Kumar SK, Jevremovic D. Utility of flow cytometry screening before MRD testing in multiple myeloma. Blood Cancer J 2023; 13:55. [PMID: 37080968 PMCID: PMC10119092 DOI: 10.1038/s41408-023-00832-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/22/2023] Open
Affiliation(s)
- Vandana Panakkal
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Arjun Lakshman
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Min Shi
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Horatiu Olteanu
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Pedro Horna
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Michael M Timm
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | | | - Linda B Baughn
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Patricia T Greipp
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Wilson I Gonsalves
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Prashant Kapoor
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Morie A Gertz
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Moritz Binder
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Francis K Buadi
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Angela Dispenzieri
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - S Vincent Rajkumar
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Shaji K Kumar
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
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14
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Levy B, Baughn LB, Akkari Y, Chartrand S, LaBarge B, Claxton D, Lennon PA, Cujar C, Kolhe R, Kroeger K, Pitel B, Sahajpal N, Sathanoori M, Vlad G, Zhang L, Fang M, Kanagal-Shamanna R, Broach JR. Optical genome mapping in acute myeloid leukemia: a multicenter evaluation. Blood Adv 2023; 7:1297-1307. [PMID: 36417763 PMCID: PMC10119592 DOI: 10.1182/bloodadvances.2022007583] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/25/2022] Open
Abstract
Detection of hallmark genomic aberrations in acute myeloid leukemia (AML) is essential for diagnostic subtyping, prognosis, and patient management. However, cytogenetic/cytogenomic techniques used to identify those aberrations, such as karyotyping, fluorescence in situ hybridization (FISH), or chromosomal microarray analysis (CMA), are limited by the need for skilled personnel as well as significant time, cost, and labor. Optical genome mapping (OGM) provides a single, cost-effective assay with a significantly higher resolution than karyotyping and with a comprehensive genome-wide analysis comparable with CMA and the added unique ability to detect balanced structural variants (SVs). Here, we report in a real-world setting the performance of OGM in a cohort of 100 AML cases that were previously characterized by karyotype alone or karyotype and FISH or CMA. OGM identified all clinically relevant SVs and copy number variants (CNVs) reported by these standard cytogenetic methods when representative clones were present in >5% allelic fraction. Importantly, OGM identified clinically relevant information in 13% of cases that had been missed by the routine methods. Three cases reported with normal karyotypes were shown to have cryptic translocations involving gene fusions. In 4% of cases, OGM findings would have altered recommended clinical management, and in an additional 8% of cases, OGM would have rendered the cases potentially eligible for clinical trials. The results from this multi-institutional study indicate that OGM effectively recovers clinically relevant SVs and CNVs found by standard-of-care methods and reveals additional SVs that are not reported. Furthermore, OGM minimizes the need for labor-intensive multiple cytogenetic tests while concomitantly maximizing diagnostic detection through a standardized workflow.
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Affiliation(s)
- Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Linda B. Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Yassmine Akkari
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH
| | - Scott Chartrand
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA
| | - Brandon LaBarge
- Department of Otolaryngology, Penn State College of Medicine, Hershey, PA
| | - David Claxton
- Department of Hematology and Oncology, Department of Medicine, Penn State College of Medicine, Hershey, PA
| | | | - Claudia Cujar
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA
| | - Kate Kroeger
- Cytogenetics Laboratory, Seattle Cancer Care Alliance, Seattle, WA
| | - Beth Pitel
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Nikhil Sahajpal
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA
| | | | - George Vlad
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Lijun Zhang
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA
| | - Min Fang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - James R. Broach
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA
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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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Gagnon MF, Tian S, Geyer S, Sharma N, Vachon CM, Kusne Y, Bergsagel PL, Stewart AK, Rajkumar SV, Kumar S, Ailawadhi S, Baughn LB. Distribution of clonal hematopoiesis of indeterminate potential (CHIP) is not associated with race in patients with plasma cell neoplasms. Blood Cancer J 2022; 12:112. [PMID: 35882836 PMCID: PMC9325693 DOI: 10.1038/s41408-022-00706-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/04/2022] [Accepted: 07/08/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Marie-France Gagnon
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Shulan Tian
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Susan Geyer
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Neeraj Sharma
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Celine M Vachon
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Yael Kusne
- 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
| | | | - S Vincent Rajkumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Shaji Kumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sikander Ailawadhi
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Linda B Baughn
- 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 Pathology, Mayo Clinic, Rochester, MN, USA.
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19
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Gagnon MF, Berg HE, Meyer RG, Sukov WR, Van Dyke DL, Jenkins RB, Greipp PT, Thorland EC, Hoppman NL, Xu X, Baughn LB, Reichard KK, Ketterling RP, Peterson JF. Typical, atypical and cryptic t(15;17)(q24;q21) (PML::RARA) observed in acute promyelocytic leukemia: a retrospective review of 831 patients with concurrent chromosome and PML::RARA dual-color dual-fusion FISH studies. Genes Chromosomes Cancer 2022; 61:629-634. [PMID: 35639830 DOI: 10.1002/gcc.23070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/07/2022] Open
Abstract
The diagnosis of acute promyelocytic leukemia (APL) relies on the identification of PML::RARA fusion. While the majority of APL cases harbor a typical t(15;17)(q24;q21), atypical genetic mechanisms leading to the oncogenic PML::RARA fusion have been reported yet their frequency and scope remain poorly characterized. We assessed the genetic findings of 831 cases with APL investigated with concurrent chromosome banding analysis and dual-color dual-fusion fluorescence in situ hybridization (D-FISH) analysis at our institution over an 18.5-year timeframe. Seven-hundred twenty-three (87%) cases had a typical balanced t(15;17) with both testing modalities. Atypical karyotypic results including complex translocations, unbalanced rearrangements and insertional events occurred in 50 (6%) cases, while 6 (0.7%) cases were cryptic by conventional chromosome studies despite PML::RARA fusion by D-FISH evaluation. Atypical FISH patterns were observed in 48 (6%) cases despite apparently balanced t(15;17) on chromosome banding analysis. Two-hundred fifty (30%) cases displayed additional chromosome abnormalities of which trisomy/tetrasomy 8 (37%), del(7q)/add(7q) (12%) and del(9q) (7%) were most frequent. Complex and very complex karyotypes were observed in 81 (10%) and 34 (4%) cases, respectively. In addition, 4 (0.5%) cases presented as an apparently doubled, near-tetraploid stemline clone. This report provides the largest appraisal of cytogenetic findings in APL with conventional chromosome and PML::RARA D-FISH analysis. By characterizing the frequency and breadth of typical and atypical results through the lens of these cytogenetic testing modalities, this study serves as a pragmatic source of information for those involved in the investigation of APL in both the clinical and research laboratory settings.
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Affiliation(s)
- Marie-France Gagnon
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Holly E Berg
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Reid G Meyer
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, 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
| | - Daniel L Van Dyke
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Robert B Jenkins
- Division of Laboratory Genetics and Genomics, 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
| | - Erik C Thorland
- 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
| | - Xinjie Xu
- 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
| | - Kaaren K Reichard
- 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
| | - Jess F Peterson
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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20
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Kumar H, Mazumder S, Sharma N, Chakravarti S, Long MD, Meurice N, Petit J, Liu S, Chesi M, Sanyal S, Stewart AK, Kumar S, Bergsagel L, Rajkumar SV, Baughn LB, Van Ness BG, Mitra AK. Single-Cell Proteomics and Tumor RNAseq Identify Novel Pathways Associated With Clofazimine Sensitivity in PI- and IMiD- Resistant Myeloma, and Putative Stem-Like Cells. Front Oncol 2022; 12:842200. [PMID: 35646666 PMCID: PMC9130773 DOI: 10.3389/fonc.2022.842200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/28/2022] [Indexed: 12/14/2022] Open
Abstract
Multiple myeloma (MM) is an incurable plasma cell malignancy with dose-limiting toxicities and inter-individual variation in response/resistance to the standard-of-care/primary drugs, proteasome inhibitors (PIs), and immunomodulatory derivatives (IMiDs). Although newer therapeutic options are potentially highly efficacious, their costs outweigh the effectiveness. Previously, we have established that clofazimine (CLF) activates peroxisome proliferator-activated receptor-γ, synergizes with primary therapies, and targets cancer stem-like cells (CSCs) in drug-resistant chronic myeloid leukemia (CML) patients. In this study, we used a panel of human myeloma cell lines as in vitro model systems representing drug-sensitive, innate/refractory, and clonally-derived acquired/relapsed PI- and cereblon (CRBN)-negative IMiD-resistant myeloma and bone marrow-derived CD138+ primary myeloma cells obtained from patients as ex vivo models to demonstrate that CLF shows significant cytotoxicity against drug-resistant myeloma as single-agent and in combination with PIs and IMiDs. Next, using genome-wide transcriptome analysis (RNA-sequencing), single-cell proteomics (CyTOF; Cytometry by time-of-flight), and ingenuity pathway analysis (IPA), we identified novel pathways associated with CLF efficacy, including induction of ER stress, autophagy, mitochondrial dysfunction, oxidative phosphorylation, enhancement of downstream cascade of p65-NFkB-IRF4-Myc downregulation, and ROS-dependent apoptotic cell death in myeloma. Further, we also showed that CLF is effective in killing rare refractory subclones like side populations that have been referred to as myeloma stem-like cells. Since CLF is an FDA-approved drug and also on WHO's list of safe and effective essential medicines, it has strong potential to be rapidly re-purposed as a safe and cost-effective anti-myeloma drug.
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Affiliation(s)
- Harish Kumar
- Department of Drug Discovery and Development, Harrison College of Pharmacy, Auburn University, Auburn, AL, United States
| | - Suman Mazumder
- Department of Drug Discovery and Development, Harrison College of Pharmacy, Auburn University, Auburn, AL, United States
- Center for Pharmacogenomics and Single-Cell Omics (AUPharmGx), Harrison College of Pharmacy, Auburn University, Auburn, AL, United States
| | - Neeraj Sharma
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Sayak Chakravarti
- Department of Drug Discovery and Development, Harrison College of Pharmacy, Auburn University, Auburn, AL, United States
| | - Mark D. Long
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Nathalie Meurice
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ, United States
| | - Joachim Petit
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ, United States
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Marta Chesi
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ, United States
| | - Sabyasachi Sanyal
- Biochemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - A. Keith Stewart
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ, United States
| | - Shaji Kumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Leif Bergsagel
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, AZ, United States
| | - S. Vincent Rajkumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Linda B. Baughn
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Brian G. Van Ness
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, United States
| | - Amit Kumar Mitra
- Department of Drug Discovery and Development, Harrison College of Pharmacy, Auburn University, Auburn, AL, United States
- Center for Pharmacogenomics and Single-Cell Omics (AUPharmGx), Harrison College of Pharmacy, Auburn University, Auburn, AL, United States
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21
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Gagnon MF, Smadbeck JB, Sharma N, Blackburn PR, Demasi Benevides J, Akkari YMN, Jaroscak JJ, Znoyko I, Wolff DJ, Schandl CA, Meyer R, Greipp PT, Xu X, Hoppman NL, Ketterling RP, Peterson JF, Baughn LB. Apparent coexistence of ETV6::RUNX1 and KMT2A::MLLT3 fusions due to a nonproductive KMT2A rearrangement in B-ALL. Leuk Lymphoma 2022; 63:2243-2246. [DOI: 10.1080/10428194.2022.2064991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Marie-France Gagnon
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, USA
| | - James B. Smadbeck
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Neeraj Sharma
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, USA
| | | | - Jonna Demasi Benevides
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, USA
| | | | - Jennifer J. Jaroscak
- Division of Pediatric Hematology-Oncology, College of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Iya Znoyko
- Department of Pathology and Laboratory Medicine, Division of Cytogenetics and Genomics, Medical University of South Carolina, Charleston, SC, USA
| | - Daynna J. Wolff
- Department of Pathology and Laboratory Medicine, Division of Cytogenetics and Genomics, Medical University of South Carolina, Charleston, SC, USA
| | - Cynthia A. Schandl
- Department of Pathology and Laboratory Medicine, Division of Cytogenetics and Genomics, Medical University of South Carolina, Charleston, SC, USA
| | - Reid Meyer
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, USA
| | - Patricia T. Greipp
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, USA
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Xinjie Xu
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, USA
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole L. Hoppman
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, USA
| | - Rhett P. Ketterling
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, USA
- 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 Laboratory Genetics, Mayo Clinic, Rochester, MN, USA
- 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 Laboratory Genetics, Mayo Clinic, Rochester, MN, USA
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
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22
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Tyner JW, Haderk F, Kumaraswamy A, Baughn LB, Van Ness B, Liu S, Marathe H, Alumkal JJ, Bivona TG, Chan KS, Druker BJ, Hutson AD, Nelson PS, Sawyers CL, Willey CD. Understanding Drug Sensitivity and Tackling Resistance in Cancer. Cancer Res 2022; 82:1448-1460. [PMID: 35195258 PMCID: PMC9018544 DOI: 10.1158/0008-5472.can-21-3695] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/21/2022] [Accepted: 02/15/2022] [Indexed: 11/16/2022]
Abstract
Decades of research into the molecular mechanisms of cancer and the development of novel therapeutics have yielded a number of remarkable successes. However, our ability to broadly assign effective, rationally targeted therapies in a personalized manner remains elusive for many patients, and drug resistance persists as a major problem. This is in part due to the well-documented heterogeneity of cancer, including the diversity of tumor cell lineages and cell states, the spectrum of somatic mutations, the complexity of microenvironments, and immune-suppressive features and immune repertoires, which collectively require numerous different therapeutic approaches. Here, we describe a framework to understand the types and biological causes of resistance, providing translational opportunities to tackle drug resistance by rational therapeutic strategies.
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Affiliation(s)
- Jeffrey W. Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Franziska Haderk
- Department of Medicine, University of California, San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California
| | | | - Linda B. Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Brian Van Ness
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Himangi Marathe
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Joshi J. Alumkal
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Trever G. Bivona
- Department of Medicine, University of California, San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California
| | - Keith Syson Chan
- Cedars-Sinai Samuel Oschin Comprehensive Cancer Institute, Los Angeles, California
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Brian J. Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Alan D. Hutson
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Peter S. Nelson
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Charles L. Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York City, New York
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Christopher D. Willey
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, Alabama
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23
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Akkari YM, Baughn LB, Dubuc AM, Smith AC, Mallo M, Dal Cin P, Diez Campelo M, Gallego MS, Granada Font I, Haase DT, Schlegelberger B, Slavutsky I, Mecucci C, Levine RL, Hasserjian RP, Solé F, Levy B, Xu X. Guiding the global evolution of cytogenetic testing for hematologic malignancies. Blood 2022; 139:2273-2284. [PMID: 35167654 PMCID: PMC9710485 DOI: 10.1182/blood.2021014309] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 02/03/2022] [Indexed: 12/15/2022] Open
Abstract
Cytogenetics has long represented a critical component in the clinical evaluation of hematologic malignancies. Chromosome banding studies provide a simultaneous snapshot of genome-wide copy number and structural variation, which have been shown to drive tumorigenesis, define diseases, and guide treatment. Technological innovations in sequencing have ushered in our present-day clinical genomics era. With recent publications highlighting novel sequencing technologies as alternatives to conventional cytogenetic approaches, we, an international consortium of laboratory geneticists, pathologists, and oncologists, describe herein the advantages and limitations of both conventional chromosome banding and novel sequencing technologies and share our considerations on crucial next steps to implement these novel technologies in the global clinical setting for a more accurate cytogenetic evaluation, which may provide improved diagnosis and treatment management. Considering the clinical, logistic, technical, and financial implications, we provide points to consider for the global evolution of cytogenetic testing.
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Affiliation(s)
- Yassmine M.N. Akkari
- Departments of Cytogenetics and Molecular Pathology, Legacy Health, Portland, OR
| | - Linda B. Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Adrian M. Dubuc
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Adam C. Smith
- Laboratory Medicine Program, University Health Network and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Mar Mallo
- MDS Group, Microarrays Unit, Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Maria Diez Campelo
- Hematology Department University Hospital of Salamanca, IBSAL, Salamanca, Spain
| | - Marta S. Gallego
- Laboratory of Cytogenetics and Molecular Cytogenetics, Department of Clinical Pathology, Italian Hospital, Buenos Aires, Argentina
| | - Isabel Granada Font
- Hematology Laboratory, Germans Trias i Pujol University Hospital–Catalan Institute of Oncology, Josep Carreras Leukemia Research Institute, Barcelona, Spain
| | - Detlef T. Haase
- Clinics of Hematology and Medical Oncology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Irma Slavutsky
- Laboratory Genetics of Lymphoid Malignancies, Institute of Experimental Medicine, Buenos Aires, Argentina
| | - Cristina Mecucci
- Laboratory of Cytogenetics and Molecular Medicine, Hematology University of Perugia, Perugia, Italy
| | - Ross L. Levine
- Department of Medicine, Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Francesc Solé
- MDS Group, Microarrays Unit, Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Brynn Levy
- College of Physicians and Surgeons, Columbia University Medical Center and the New York Presbyterian Hospital, New York, NY
| | - Xinjie Xu
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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24
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Abdallah NH, Binder M, Rajkumar SV, Greipp PT, Kapoor P, Dispenzieri A, Gertz MA, Baughn LB, Lacy MQ, Hayman SR, Buadi FK, Dingli D, Go RS, Hwa YL, Fonder AL, Hobbs MA, Lin Y, Leung N, Kourelis T, Warsame R, Siddiqui MA, Kyle RA, Bergsagel PL, Fonseca R, Ketterling RP, Kumar SK. A simple additive staging system for newly diagnosed multiple myeloma. Blood Cancer J 2022; 12:21. [PMID: 35102148 PMCID: PMC8803917 DOI: 10.1038/s41408-022-00611-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/07/2021] [Accepted: 01/12/2022] [Indexed: 11/21/2022] Open
Abstract
Risk stratification in multiple myeloma is important for prognostication, patient selection for clinical trials, and comparison of treatment approaches. We developed and validated a staging system that incorporates additional FISH abnormalities not included in the R-ISS and reflects the additive effects of co-occurring high-risk disease features. We first evaluated the prognostic value of predefined cytogenetic and laboratory abnormalities in 2556 Mayo Clinic patients diagnosed between February 2004 and June 2019. We then used data from 1327 patients to develop a risk stratification model and validated this in 502 patients enrolled in the MMRF CoMMpass study. On multivariate analysis, high-risk IgH translocations [risk ratio (RR): 1.7], 1q gain/amplification (RR: 1.4), chromosome17 abnormalities (RR: 1.6), ISS III (RR: 1.7), and elevated LDH (RR: 1.3) were independently associated with decreased overall survival (OS). Among 1327 evaluable patients, OS was 11.0 (95% CI: 9.2–12.6), 7.0 (95% CI: 6.3–9.2), and 4.5 (95% CI: 3.7–5.2) years in patients with 0 (stage I), 1 (stage II), and ≥2 (stage III) high-risk factors, respectively. In the MMRF cohort, median OS was 7.8 (95% CI: NR-NR), 6.0 (95% CI: 5.7-NR), and 4.3 (95% CI: 2.7-NR) years in the 3 groups, respectively (P < 0.001). This 5-factor, 3-tier system is easy to implement in practice and improves upon the current R-ISS.
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Affiliation(s)
| | - Moritz Binder
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | - Morie A Gertz
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Department of Laboratory Medicine and Pathology, Rochester, MN, USA
| | - Martha Q Lacy
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | | | - David Dingli
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Ronald S Go
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Yi L Hwa
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Amie L Fonder
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | - Yi Lin
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Nelson Leung
- Division of Hematology, Mayo Clinic, Rochester, MN, USA.,Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | | | - Rahma Warsame
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | - Robert A Kyle
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Shaji K Kumar
- Division of Hematology, Mayo Clinic, Rochester, MN, USA.
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25
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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26
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Audil HY, Cook JM, Greipp PT, Kapoor P, Baughn LB, Dispenzieri A, Gertz MA, Buadi FK, Lacy MQ, Dingli D, Fonder AL, Hayman SR, Hobbs MA, Muchtar E, Siddiqui M, Gonsalves WI, Hwa YL, Leung N, Lin Y, Kourelis TV, Warsame R, Kyle RA, Ketterling RP, Rajkumar SV, Kumar SK. Prognostic significance of acquired 1q22 gain in multiple myeloma. Am J Hematol 2022; 97:52-59. [PMID: 34710241 DOI: 10.1002/ajh.26391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/22/2021] [Accepted: 10/24/2021] [Indexed: 11/08/2022]
Abstract
Gain of 1q22 at diagnosis portends poorer outcomes in multiple myeloma (MM), but the prognostic significance of acquired 1q22 gain is unknown. We identified 63 MM patients seen at Mayo Clinic from 1/2004 to 12/2019 without 1q22 gain at diagnosis who acquired it during follow up and compared them to 63 control patients who did not acquire 1q22 gain with similar follow up. We also compared outcomes in the acquired 1q22 gain group with outcomes in 126 patients with 1q22 gain present at diagnosis. The incidence of acquired 1q22 gain was 6.1% (median follow-up 6.8 years); median time to acquisition was 5.0 years (range: 0.7-11.5 years). Abnormalities on baseline fluorescence in situ hybridization (FISH) included trisomies (54%) and monosomy 13 (39%); 16 (25%) had high-risk (HR) translocations or del(17p). Median progression-free survival with front line therapy was 29.5 months in patients with acquired 1q22 gain, versus 31.4 months in control patients (p = .34) and 31.2 months in patients with de novo 1q22 gain (p = .04). Median overall survival (OS) from diagnosis was 10.9 years in patients with acquired 1q22 gain, versus 13.0 years in control patients (p = .03) and 6.3 years in patients with de novo 1q22 gain (p = .01). Presence of HR FISH at baseline increased risk of 1q22 gain acquisition. We demonstrate that acquisition of 1q22 gain is a significant molecular event in MM, associated with reduced OS. Among HR patients for whom this clonal evolution is determined, a risk-adapted approach and/or clinical trial should be considered.
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Affiliation(s)
- Hadiyah Y. Audil
- Department of Internal Medicine Mayo Clinic Rochester Minnesota USA
| | - Joselle M. Cook
- Department of Hematology Mayo Clinic Rochester Minnesota USA
| | - Patricia T. Greipp
- Department of Laboratory Medicine and Pathology Mayo Clinic Rochester Minnesota USA
| | - Prashant Kapoor
- Department of Hematology Mayo Clinic Rochester Minnesota USA
| | - Linda B. Baughn
- Department of Laboratory Medicine and Pathology Mayo Clinic Rochester Minnesota USA
| | | | - Morie A. Gertz
- Department of Hematology Mayo Clinic Rochester Minnesota USA
| | | | - Martha Q. Lacy
- Department of Hematology Mayo Clinic Rochester Minnesota USA
| | - David Dingli
- Department of Hematology Mayo Clinic Rochester Minnesota USA
| | - Amie L. Fonder
- Department of Hematology Mayo Clinic Rochester Minnesota USA
| | | | - Miriam A. Hobbs
- Department of Hematology Mayo Clinic Rochester Minnesota USA
| | - Eli Muchtar
- Department of Hematology Mayo Clinic Rochester Minnesota USA
| | | | | | - Yi Lisa Hwa
- Department of Hematology Mayo Clinic Rochester Minnesota USA
| | - Nelson Leung
- Department of Hematology Mayo Clinic Rochester Minnesota USA
| | - Yi Lin
- Department of Hematology Mayo Clinic Rochester Minnesota USA
| | | | - Rahma Warsame
- Department of Hematology Mayo Clinic Rochester Minnesota USA
| | - Robert A. Kyle
- Department of Hematology Mayo Clinic Rochester Minnesota USA
| | - Rhett P. Ketterling
- Department of Laboratory Medicine and Pathology Mayo Clinic Rochester Minnesota USA
| | | | - Shaji K. Kumar
- Department of Hematology Mayo Clinic Rochester Minnesota USA
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27
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Berg HE, Greipp PT, Baughn LB, Falcon CP, Jackson CC, Peterson JF. Detection of a Cryptic KMT2A/AFDN Gene Fusion [ins(6;11)(q27;q23q23)] in a Pediatric Patient with Newly Diagnosed Acute Myeloid Leukemia. Lab Med 2021; 53:e95-e99. [PMID: 34894139 DOI: 10.1093/labmed/lmab109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
KMT2A gene rearrangements are a major oncogenic driver in multiple hematologic neoplasms. Apart from t(9;11)(p21;q23) (KMT2A/MLLT3) in acute myeloid leukemia (AML), KMT2A gene rearrangements are considered to convey high risk and poor overall survival. Herein, we report a case of a 7 year old boy with newly diagnosed AML and a cryptic KMT2A/AFDN gene fusion resulting from a 5'KMT2A insertional event. The results of conventional chromosome studies revealed trisomy 8 in all 20 metaphases, with normal-appearing chromosomes 6 and 11. A KMT2A break-apart FISH probe identified 2 intact copies of the KMT2A gene region and an extra 5'KMT2A signal in 85% of interphase nuclei. Subsequent FISH studies using a KMT2A/AFDN dual-color dual-fusion FISH probe revealed positive results for a single fusion in 82% of interphase nuclei, indicating a KMT2A/AFDN gene fusion. Subsequently, metaphase FISH confirmed the location of the KMT2A/AFDN fusion at 6q27. To our knowledge, this represents only the second time in the literature that a cryptic KMT2A/AFDN gene fusion resulting from a 5'KMT2A insertional event was reported.
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Affiliation(s)
- Holly E Berg
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Patricia T Greipp
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Linda B Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Corey P Falcon
- Department of Pediatric Hematology and Oncology, Ochsner Health Center for Children, New Orleans, Louisiana
| | - Courtney C Jackson
- Department of Laboratory Medicine and Pathology, Ochsner Medical Center, New Orleans, Louisiana
| | - Jess F Peterson
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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28
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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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29
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Macke EL, Meyer RG, Hoppman NL, Ketterling RP, Greipp PT, Xu X, Baughn LB, Shafer DA, He RR, Peterson JF. Identification of a Cryptic t(8;20;21)(q22;p13;q22) Resulting in RUNX1T1/RUNX1 Fusion in a Patient with Newly Diagnosed Acute Myeloid Leukemia. Lab Med 2021; 53:e87-e90. [PMID: 34791328 DOI: 10.1093/labmed/lmab105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The detection of recurrent genetic abnormalities in acute myeloid leukemia (AML), including RUNX1T1/RUNX1 gene fusion, is critical for optimal medical management. Herein, we report a 45 year old woman with newly diagnosed AML and conventional chromosome studies that revealed an apparently balanced t(8;20)(q22;p13) in all 20 metaphases analyzed. A RUNX1T1/RUNX1 dual-color dual-fusion fluorescence in situ hybridization (FISH) probe set was subsequently performed and revealed a RUNX1T1/RUNX1 gene fusion. Metaphase FISH studies performed on abnormal metaphases revealed a cryptic, complex translocation resulting in RUNX1T1/RUNX1 fusion, t(8;20;21)(q22;p13;q22). This case study shows the importance of performing FISH studies or other high-resolution genetic testing concurrently with conventional chromosome studies for the detection of cryptic recurrent gene fusions in AML, particularly a focused genetic evaluation such as RUNX1T1/RUNX1 gene fusion, when specific abnormalities involving 8q22 are identified.
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Affiliation(s)
- Erica L Macke
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, US
| | - Reid G Meyer
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, US
| | - Nicole L Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, US
| | - Rhett P Ketterling
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, US
| | - Patricia T Greipp
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, US
| | - Xinjie Xu
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, US
| | - Linda B Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, US
| | - Danielle A Shafer
- Inova Schar Cancer Institute, Inova Fairfax Hospital, Falls Church, Virginia, US
| | - Rui R He
- Department of Pathology, Inova Fairfax Hospital, Falls Church, Virginia, US
| | - Jess F Peterson
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, US
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30
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Visram A, Vachon C, Baughn LB, Larson D, Smadbeck J, Dispenzieri A, Kapoor P, Lacy MQ, Gertz MA, Buadi FK, Hayman SR, Dingli D, Kourelis T, Gonsalves W, Warsame R, Muchtar E, Leung N, Kyle RA, Rajkumar SV, Kumar S. Family history of plasma cell disorders is associated with improved survival in MGUS, multiple myeloma, and systemic AL amyloidosis. Leukemia 2021; 36:1058-1065. [PMID: 34764424 DOI: 10.1038/s41375-021-01454-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 10/11/2021] [Accepted: 10/15/2021] [Indexed: 12/19/2022]
Abstract
The association between familial plasma cell disorders (PCD) and prognosis in patients with MGUS, multiple myeloma (MM), and systemic light chain (AL) amyloidosis has not been well described. This study retrospectively reviewed outcomes of 25,423 patients (16,744 MGUS, 6194 MM, 2955 AL amyloidosis). Overall, 2.7% of patients reported having a family member with a PCD (defined as MGUS, MM, or AL amyloidosis). Family history was documented in 94% of MGUS, 92% of MM, and 88% of AL amyloidosis patients. The overall survival was consistently longer in patients with versus without familial PCD (crude hazard ratios: 0.52, 95% CI 0.40-0.67, p < 0.001 for MGUS patients; 0.68, 95% CI 0.57-0.79, p < 0.001 for MM patients; 0.60, 95% CI 0.43-0.84, p = 0.003 for AL patients). This association remained consistent when adjusting for baseline patient and disease characteristics. In MGUS patients, the risk of progression to MM, AL amyloidosis, or a lymphoproliferative disorder was higher in patients with familial PCD when accounting for death as a competing risk (cause-specific HR 1.9, 95% 1.3-2.7, p < 0.001). This is the first study to demonstrate that in a cohort of MGUS, MM, and systemic AL amyloidosis, patients with a PCD family history have an improved overall survival.
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Affiliation(s)
- Alissa Visram
- Division of Hematology, University of Ottawa, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Celine Vachon
- Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA.,Division of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Dirk Larson
- Division of Biostatistics, Mayo Clinic, Rochester, MN, USA
| | - James Smadbeck
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | | | | | - Martha Q Lacy
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Morie A Gertz
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | | | - David Dingli
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Rahma Warsame
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Eli Muchtar
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Nelson Leung
- Division of Nephrology, Mayo Clinic, Rochester, MN, USA
| | - Robert A Kyle
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | - Shaji Kumar
- Division of Hematology, Mayo Clinic, Rochester, MN, USA.
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31
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Abdel Rahman ZH, Parrondo RD, Heckman MG, Wieczorek M, Miller KC, Alkhateeb H, Sproat LZ, Murthy H, Hogan WJ, Kharfan-Dabaja MA, Peterson JF, Baughn LB, Hoppman N, Litzow MR, Ketterling RP, Greipp PT, Foran JM. Comparative study of therapy-related and de novo adult b-cell acute lymphoblastic leukaemia. Br J Haematol 2021; 196:963-968. [PMID: 34697797 PMCID: PMC9034764 DOI: 10.1111/bjh.17906] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 01/18/2023]
Abstract
We report a comparative analysis of patients with therapy‐related acute lymphoblastic leukaemia (tr‐ALL) vs de novo ALL. We identified 331 patients with B‐ALL; 69 (21%) were classified as tr‐ALL. The most common prior malignancies were breast (23·2%) and plasma cell disorders (20·3%). Patients with tr‐ALL were older (median 63·2 vs. 46·2 years, P < 0.001), more often female (66·7% vs. 43·5%, P < 0·001), and more likely to have hypodiploid cytogenetics (18·8% vs. 5·0%, P < 0·001). In multivariable analysis, patients with tr‐ALL were less likely to achieve complete remission [odds ratio (OR) = 0·16, P < 0·001] and more likely to be minimal residual disease‐positive (OR = 4·86, P = 0·01) but had similar OS after diagnosis and allo‐haematopoietic cell transplantation.
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Affiliation(s)
| | | | - Michael G Heckman
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, FL, USA
| | - Mikolaj Wieczorek
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, FL, USA
| | - Kevin C Miller
- Department of Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Lisa Z Sproat
- Division of Hematology and Medical Oncology, Mayo Clinic, Phoenix, AZ, USA
| | - Hemant Murthy
- Division of Hematology and Medical Oncology, Mayo Clinic, USA
| | | | | | - Jess F Peterson
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Nicole Hoppman
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Mark R Litzow
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | | | - James M Foran
- Division of Hematology and Medical Oncology, Mayo Clinic, USA
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32
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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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33
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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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34
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Abdel-Rahman ZH, Heckman MG, Anagnostou T, White LJ, Kloft-Nelson SM, Knudson RA, Alkhateeb HB, Sproat LZ, Khera N, Murthy HS, Ayala E, Hogan WJ, Roy V, Peterson JF, Kharfan-Dabaja MA, Ketterling RP, Litzow MR, Baughn LB, Patnaik M, Greipp PT, Foran JM. Identification of adult Philadelphia-like acute lymphoblastic leukemia using a FISH-based algorithm distinguishes prognostic groups and outcomes. Blood Cancer J 2021; 11:156. [PMID: 34548472 PMCID: PMC8455651 DOI: 10.1038/s41408-021-00538-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 06/10/2021] [Revised: 07/23/2021] [Accepted: 07/29/2021] [Indexed: 01/02/2023] Open
Affiliation(s)
- Zaid H Abdel-Rahman
- Division of Hematology and Medical Oncology, Mayo Clinic, Jacksonville, FL, USA
| | - Michael G Heckman
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, FL, USA
| | - Theodora Anagnostou
- Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Launia J White
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, FL, USA
| | - Sara M Kloft-Nelson
- Cytogenetics Core Laboratory, Medical Genome Facility, Mayo Clinic, Rochester, MN, USA
| | - Ryan A Knudson
- Cytogenetics Core Laboratory, Medical Genome Facility, Mayo Clinic, Rochester, MN, USA
| | | | - Lisa Z Sproat
- Division of Hematology and Medical Oncology, Mayo Clinic, Phoenix, AZ, USA
| | - Nandita Khera
- Division of Hematology and Medical Oncology, Mayo Clinic, Phoenix, AZ, USA
| | - Hemant S Murthy
- Division of Hematology and Medical Oncology, Mayo Clinic, Jacksonville, FL, USA
| | - Ernesto Ayala
- Division of Hematology and Medical Oncology, Mayo Clinic, Jacksonville, FL, USA
| | | | - Vivek Roy
- Division of Hematology and Medical Oncology, Mayo Clinic, Jacksonville, FL, USA
| | - Jess F Peterson
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Rhett P Ketterling
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Mark R Litzow
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - James M Foran
- Division of Hematology and Medical Oncology, Mayo Clinic, Jacksonville, FL, USA.
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35
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Wagner AH, Vlachos IS, Sonkin D, Terraf P, Kesserwan C, Sboner A, Coard T, Reich C, Ritter DI, Horak P, Zou YS, Tanska A, Berlin AM, Lu A, Cameron D, Williams HE, Lin WH, Toruner G, Danos A, Saliba J, Xu H, Xu X, Ryland G, Ceccarelli M, Zhang L, Rapisardo S, Rehder C, Liu X, Pallavajjala A, Park N, Satgunaseelan L, Lee K, Liu J, Griffith O, Freimuth RR, Stenzinger A, Baughn LB, Baudis M, Lee J, Li M, Roy A, Raca G. Abstract 449: A standard operating procedure for the curation of gene fusions. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Despite the well-established role of recurrent gene fusions as oncogenic drivers, current practices for characterizing and interpreting gene fusion events in clinical testing and in biomedical literature are inconsistent. From the conceptual definition of gene fusions to the salient elements that characterize these alterations, a lack of community-driven standards for the curation of gene fusions has resulted in a disparate landscape of fusion representations and supporting tools. Consequently, the evidence-based clinical evaluation of gene fusions requires extensive expert review for accurate interpretation of observed gene fusions with respect to putative evidence from biomedical literature. Furthermore, the lack of these standards inhibits the interoperability of tools, resources, and pipelines - impeding data sharing and downstream utility.To address these challenges, a cross-consortia initiative between the Variant Interpretation for Cancer Consortium and ClinGen was formed to develop a standard operating procedure (SOP) for the curation of gene fusions. The SOP is under development by an international and diverse set of experts in the representation, detection, and clinical interpretation of gene fusions. Participating stakeholders across academic, government, and industry sectors showcased challenges and solutions, and participated in community surveys and discussions to define and develop the SOP for this diverse class of alterations.An initial result of this effort was the precise molecular definition of genomic events and features constituting gene fusions. We distinguish these from similar but distinct classes of structural alterations through clinically-relevant examples. Next, we discuss our findings on community practices around the description and evaluation of gene fusions. We provide our recommendations for characterization and representation of gene fusions from these practices, and compare these recommendations to existing variant representation standards and formats (e.g. HGVS variant nomenclature). We also discuss the concurrent application of formats for standardized human- and machine-readable representations of gene fusion events.We conclude with discussion of the salient elements to enable rapid, scalable, and consistent evaluation of fusions curated from the biomedical literature. Recommendations are provided for the standardized capture of these elements to enable both intuitive and precise characterization of this diverse class of alterations in clinical reporting and literature. In summary, we provide a clinical-practice driven framework and nomenclature for gene fusions, including recommendations for human readability, computational precision, and data integrity within the SOP. This work is a substantial advancement towards standardized communication, investigation, and sharing of gene fusion data across clinical and research domains and specialties.
Citation Format: Alex H. Wagner, Ioannis S. Vlachos, Dmitriy Sonkin, Panieh Terraf, Chimene Kesserwan, Andrea Sboner, Thomas Coard, Christian Reich, Deborah I. Ritter, Peter Horak, Ying S. Zou, Anna Tanska, Aaron M. Berlin, Anna Lu, Daniel Cameron, Heather E. Williams, Wan-Hsin Lin, Gokce Toruner, Arpad Danos, Jason Saliba, Huiling Xu, Xinjie Xu, Georgina Ryland, Michele Ceccarelli, Liying Zhang, Sarah Rapisardo, Catherine Rehder, Xuelu Liu, Aparna Pallavajjala, Nicole Park, Laveniya Satgunaseelan, Kristy Lee, Jie Liu, Obi Griffith, Robert R. Freimuth, Albrecht Stenzinger, Linda B. Baughn, Michael Baudis, Jennifer Lee, Marilyn Li, Angshumoy Roy, Gordana Raca. A standard operating procedure for the curation of gene fusions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 449.
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Affiliation(s)
| | | | | | - Panieh Terraf
- 4Memorial Sloan kettering Cancer Center, New York, NY
| | | | | | | | | | | | - Peter Horak
- 9NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Ying S. Zou
- 10The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Anna Tanska
- 11Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Anna Lu
- 13Frederick National Laboratory of Cancer Research, Frederick, MD
| | - Daniel Cameron
- 14Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | | | | | | | - Arpad Danos
- 18Washington University School of Medicine, St. Louis, MO
| | - Jason Saliba
- 18Washington University School of Medicine, St. Louis, MO
| | - Huiling Xu
- 11Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | | | | | - Liying Zhang
- 21UCLA David Geffen School of Medicine, Los Angeles, CA
| | | | | | - Xuelu Liu
- 23Dana-Farber Cancer Institute, Boston, MA
| | | | - Nicole Park
- 24University Health Network, Toronto, Ontario, Canada
| | | | - Kristy Lee
- 1Nationwide Children's Hospital, Columbus, OH
| | - Jie Liu
- 26Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Obi Griffith
- 18Washington University School of Medicine, St. Louis, MO
| | | | | | | | | | | | - Marilyn Li
- 29Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Gordana Raca
- 30Keck School of Medicine of USC, Los Angeles, CA
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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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37
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Ravindran A, Greipp PT, Wongchaowart N, Smadbeck JB, Peterson JF, Ketterling RP, Kumar SK, Baughn LB. Dual Primary IGH Translocations in Multiple Myeloma: A Novel Finding. Clin Lymphoma Myeloma Leuk 2021; 21:e710-e713. [PMID: 34172422 DOI: 10.1016/j.clml.2021.05.001] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/13/2021] [Accepted: 05/01/2021] [Indexed: 10/21/2022]
Affiliation(s)
- Aishwarya Ravindran
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, 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
| | - Jess F Peterson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Rhett P Ketterling
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Shaji K Kumar
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN
| | - Linda B Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN.
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38
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Koleilat A, Williamson CM, Demasi JCB, Xu X, Greipp PT, Ketterling RP, Hoppman NL, Peterson JF, Baughn LB. 30. Characterization of atypical iAMP21 observed in B-Lymphoblastic Leukemia (B-ALL): a 2.5-year retrospective study from the Mayo Clinic. Cancer Genet 2021. [DOI: 10.1016/j.cancergen.2021.01.041] [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: 11/26/2022]
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39
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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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40
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Johannsen EB, Baughn LB, Sharma N, Zjacic N, Pirooznia M, Elhaik E. The Genetics of Sudden Infant Death Syndrome-Towards a Gene Reference Resource. Genes (Basel) 2021; 12:216. [PMID: 33540853 PMCID: PMC7913088 DOI: 10.3390/genes12020216] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/21/2021] [Accepted: 01/29/2021] [Indexed: 12/16/2022] Open
Abstract
Sudden infant death syndrome (SIDS) is the unexpected death of an infant under one year of age that remains unexplained after a thorough investigation. Despite SIDS remaining a diagnosis of exclusion with an unexplained etiology, it is widely accepted that SIDS can be caused by environmental and/or biological factors, with multiple underlying candidate genes. However, the lack of biomarkers raises questions as to why genetic studies on SIDS to date are unable to provide a clearer understanding of the disease etiology. We sought to improve the identification of SIDS-associated genes by reviewing the SIDS genetic literature and objectively categorizing and scoring the reported genes based on the strength of evidence (from C1 (high) to C5 (low)). This was followed by analyses of function, associations between genes, the enrichment of gene ontology (GO) terms, and pathways and gender difference in tissue gene expression. We constructed a curated database for SIDS gene candidates consisting of 109 genes, 14 of which received a category 4 (C4) and 95 genes received the lowest category of C5. That none of the genes was classified into the higher categories indicates the low level of supporting evidence. We found that genes of both scoring categories show distinct networks and are highly diverse in function and involved in many GO terms and pathways, in agreement with the perception of SIDS as a heterogeneous syndrome. Genes of both scoring categories are part of the cardiac system, muscle, and ion channels, whereas immune-related functions showed enrichment for C4 genes. A limited association was found with neural development. Overall, inconsistent reports and missing metadata contribute to the ambiguity of genetic studies. Considering those parameters could help improve the identification of at-risk SIDS genes. However, the field is still far from offering a full-pledged genetic test to identify at-risk infants and is still hampered with methodological challenges and misunderstandings of the vulnerabilities of vital biological mechanisms.
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Affiliation(s)
| | - Linda B. Baughn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; (L.B.B.); (N.S.)
| | - Neeraj Sharma
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; (L.B.B.); (N.S.)
| | - Nicolina Zjacic
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK;
| | - Mehdi Pirooznia
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Eran Elhaik
- Department of Biology, Lund University, 22362 Lund, Sweden;
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41
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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] [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: 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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42
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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43
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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44
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Abdallah N, Baughn LB, Rajkumar SV, Kapoor P, Gertz MA, Dispenzieri A, Lacy MQ, Hayman SR, Buadi FK, Dingli D, Go RS, Hwa YL, Fonder A, Hobbs M, Lin Y, Leung N, Kourelis T, Warsame R, Siddiqui M, Lust J, Kyle RA, Ketterling R, Bergsagel L, Greipp P, Kumar SK. Implications of MYC Rearrangements in Newly Diagnosed Multiple Myeloma. Clin Cancer Res 2020; 26:6581-6588. [PMID: 33008815 DOI: 10.1158/1078-0432.ccr-20-2283] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/20/2020] [Accepted: 09/29/2020] [Indexed: 12/18/2022]
Abstract
PURPOSE Rearrangements involving the MYC protooncogene are common in newly diagnosed multiple myeloma, but their prognostic significance is still unclear. The purpose of this study was to assess the impact of MYC rearrangement on clinical characteristics, treatment response, and survival in patients with newly diagnosed multiple myeloma. EXPERIMENTAL DESIGN This is a retrospective study including 1,342 patients seen in Mayo Clinic in Rochester, MN, from January 2006 to January 2018, who had cytogenetic testing by FISH at diagnosis, including MYC testing using the break apart FISH probe (8q24.1). RESULTS A rearrangement involving MYC was found in 8% of patients and was associated with elevated β2-microglobulin, ≥50% bone marrow plasma cells, IgA multiple myeloma, and the cooccurrence of trisomies. There were no differences in overall response rates between patients with and without MYC rearrangement when induction chemotherapy was proteasome inhibitor (PI)-based, immunomodulatory drug (IMiD)-based or PI + IMiD-based. Overall survival was shorter in patients with MYC rearrangement compared with patients without MYC rearrangement (5.3 vs. 8.0 years, P < 0.001). MYC rearrangement was associated with increased risk of death on multivariate analysis when high-risk cytogenetic abnormalities, ISS stage III, and ≥70 years of age were included (risk ratio: 1.5; P = 0.007). CONCLUSIONS MYC rearrangement is associated with high disease burden and is an independent adverse prognostic factor in patients with newly diagnosed multiple myeloma.
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Affiliation(s)
| | - Linda B Baughn
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | | | - Morie A Gertz
- Division of Hematology, Mayo Clinic, Rochester, Minnesota
| | | | - Martha Q Lacy
- Division of Hematology, Mayo Clinic, Rochester, Minnesota
| | | | | | - David Dingli
- Division of Hematology, Mayo Clinic, Rochester, Minnesota
| | - Ronald S Go
- Division of Hematology, Mayo Clinic, Rochester, Minnesota
| | - Yi L Hwa
- Division of Hematology, Mayo Clinic, Rochester, Minnesota
| | - Amie Fonder
- Division of Hematology, Mayo Clinic, Rochester, Minnesota
| | - Miriam Hobbs
- Division of Hematology, Mayo Clinic, Rochester, Minnesota
| | - Yi Lin
- Division of Hematology, Mayo Clinic, Rochester, Minnesota
| | - Nelson Leung
- Division of Hematology, Mayo Clinic, Rochester, Minnesota.,Division of Nephrology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Rahma Warsame
- Division of Hematology, Mayo Clinic, Rochester, Minnesota
| | | | - John Lust
- Division of Hematology, Mayo Clinic, Rochester, Minnesota
| | - Robert A Kyle
- Division of Hematology, Mayo Clinic, Rochester, Minnesota
| | - Rhett Ketterling
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Leif Bergsagel
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Phoenix, Arizona
| | - Patricia Greipp
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Shaji K Kumar
- Division of Hematology, Mayo Clinic, Rochester, Minnesota.
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45
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Martig DS, Williamson CM, Xu X, Sukov WR, Greipp PT, Hoppman NL, Baughn LB, Ketterling RP, Peterson JF. Siblings with ETV6/RUNX1-positive B-lymphoblastic leukemia: A single site experience and review of the literature. Ann Diagn Pathol 2020; 48:151588. [PMID: 32836179 DOI: 10.1016/j.anndiagpath.2020.151588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 11/19/2022]
Abstract
Siblings diagnosed with B-lymphoblastic leukemia (B-ALL) that share the same driver abnormality have been rarely described in the literature. Herein, we report three pairs of siblings (one non-identical pair, one maternal half-sibling pair, and one identical pair) all diagnosed with ETV6/RUNX1-positive B-ALL. Considering that ETV6/RUNX1 fusion is thought to represent a prenatal event and necessitates additional genomic alterations to result in leukemia, siblings of patient's with known ETV6/RUNX1-positive B-ALL may be at increased risk of ETV6/RUNX1-positive B-ALL due to common exposures (environmental or infectious) or shared germline polymorphisms.
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Affiliation(s)
- Daniel S Martig
- Division of Hematopathology, 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
| | - Xinjie Xu
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - William R Sukov
- 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
| | - 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
| | - Rhett P Ketterling
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America; 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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46
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Kaya EA, Baughn LB, Pham T, Ketterling RP, Kumar SK, Jevremovic D. Lymphoma-like double-hit genetic abnormalities ( MYC/IGH and IGH/BCL2) in a case of non-secretory multiple myeloma. Leuk Lymphoma 2020; 62:243-246. [PMID: 32955382 DOI: 10.1080/10428194.2020.1821012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Erin A Kaya
- Elson S Floyd College of Medicine (ESFCOM), Washington State University (WSU), Spokane, WA, USA
| | - Linda B Baughn
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Truc Pham
- Pathology, Incyte Diagnostics, Spokane Valley, WA, USA
| | - Rhett P Ketterling
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Shaji K Kumar
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Dragan Jevremovic
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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47
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Ustun C, Morgan EA, Ritz EM, Vestergaard H, Pullarkat S, Kluin PM, Ohgami R, Baughn LB, Kim Y, Ku NK, Czuchlewski D, Boe Møller M, Schiefer AI, Mrózek K, Horny HP, George TI, Kielsgaard Kristensen T, Beck T, Nathan S, Arana Yi C, Yeung C, Pullarkat V, Gotlib J, Akin C, Kohlschmidt J, Salhotra A, Soma L, Chen D, Han SY, Cho C, Sperr W, Broesby-Olsen S, Linden MA, Dolan M, Hoermann G, Hornick JL, Bloomfield C, Nakamura R, Joachim Deeg H, Litzow MR, Borthakur G, Weisdorf D, Huls G, Perales MA, Valent P, Marcucci G. Core-binding factor acute myeloid leukemia with inv(16): Older age and high white blood cell count are risk factors for treatment failure. Int J Lab Hematol 2020; 43:e19-e25. [PMID: 32926565 DOI: 10.1111/ijlh.13338] [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: 05/15/2020] [Revised: 08/11/2020] [Accepted: 08/18/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Celalettin Ustun
- Division of Hematology, Oncology and Cellular Therapy, Rush University, Chicago, IL, USA.,Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Elizabeth A Morgan
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ethan M Ritz
- Rush Bioinformatics and Biostatistics Core, Rush University, Chicago, IL, USA
| | - Hanne Vestergaard
- Department of Hematology, Odense University Hospital, Odense, Denmark
| | - Sheeja Pullarkat
- Department of Pathology, University of California, Los Angeles, CA, USA
| | - Philip M Kluin
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Robert Ohgami
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Linda B Baughn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Young Kim
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - Nam K Ku
- Department of Pathology, University of California, Los Angeles, CA, USA
| | - David Czuchlewski
- Department of Pathology, University of New Mexico, Albuquerque, NM, USA
| | - Michael Boe Møller
- Department of Hematology, Odense University Hospital, Odense, Denmark.,Department of Pathology, Odense University Hospital, Odense, Denmark.,Mastocytosis Center Odense University Hospital, Odense, Denmark
| | - Ana-Iris Schiefer
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Krzysztof Mrózek
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Hans-Peter Horny
- Institute of Pathology, Ludwig-Maximilians-University, Munich, Germany
| | - Tracy I George
- Department of Pathology, University of New Mexico, Albuquerque, NM, USA.,Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Thomas Kielsgaard Kristensen
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Mastocytosis Center, Odense University Hospital, Odense, Denmark
| | - Todd Beck
- Rush Bioinformatics and Biostatistics Core, Rush University, Chicago, IL, USA
| | - Sunita Nathan
- Division of Hematology, Oncology and Cellular Therapy, Rush University, Chicago, IL, USA
| | - Cecilia Arana Yi
- Department of Pathology, University of New Mexico, Albuquerque, NM, USA
| | - Cecilia Yeung
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,University of Washington School of Medicine, Seattle, WA, USA
| | - Vinod Pullarkat
- Division of Hematology and HCT, City of Hope, Duarte, CA, USA
| | - Jason Gotlib
- Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA, USA
| | - Cem Akin
- Division of Allergy and Clinical Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Jessica Kohlschmidt
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.,Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Amandeep Salhotra
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - Lori Soma
- University of Washington School of Medicine, Seattle, WA, USA
| | - Dong Chen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Se Y Han
- Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Christina Cho
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Wolfgang Sperr
- Department of Internal Medicine I, Division of Hematology & Hemostaseology and Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Sigurd Broesby-Olsen
- Mastocytosis Center Odense University Hospital, Odense, Denmark.,Department of Dermatology and Allergy Centre, Odense Research Center for Anaphylaxis, Odense, Denmark
| | - Michael A Linden
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Michelle Dolan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Gregor Hoermann
- Division of Medical and Chemical Laboratory Diagnostics - Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Clara Bloomfield
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Ryo Nakamura
- Division of Hematology and HCT, City of Hope, Duarte, CA, USA
| | - H Joachim Deeg
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,University of Washington School of Medicine, Seattle, WA, USA
| | - Mark R Litzow
- Department of Internal Medicine and Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Gautam Borthakur
- Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Daniel Weisdorf
- Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Gerwin Huls
- Department of Hematology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Peter Valent
- Department of Internal Medicine I, Division of Hematology & Hemostaseology and Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Guido Marcucci
- Division of Hematology and HCT, City of Hope, Duarte, CA, USA
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48
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Abstract
Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has rapidly caused a global pandemic associated with a novel respiratory infection: coronavirus disease-19 (COVID-19). Angiotensin-converting enzyme-2 (ACE2) is necessary to facilitate SARS-CoV-2 infection, but-owing to its essential metabolic roles-it may be difficult to target it in therapies. Transmembrane protease serine 2 (TMPRSS2), which interacts with ACE2, may be a better candidate for targeted therapies. Using publicly available expression data, we show that both ACE2 and TMPRSS2 are expressed in many host tissues, including lung. The highest expression of ACE2 is found in the testes, whereas the prostate displays the highest expression of TMPRSS2. Given the increased severity of disease among older men with SARS-CoV-2 infection, we address the potential roles of ACE2 and TMPRSS2 in their contribution to the sex differences in severity of disease. We show that expression levels of ACE2 and TMPRSS2 are overall comparable between men and women in multiple tissues, suggesting that differences in the expression levels of TMPRSS2 and ACE2 in the lung and other non-sex-specific tissues may not explain the gender disparities in severity of SARS CoV-2. However, given their instrumental roles for SARS-CoV-2 infection and their pleiotropic expression, targeting the activity and expression levels of TMPRSS2 is a rational approach to treat COVID-19.
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Affiliation(s)
- Linda B Baughn
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Neeraj Sharma
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Eran Elhaik
- Department of Biology, Lund University, Lund, Sweden
| | | | - Alan H Bryce
- Division of Hematology and Medical Oncology, Mayo Clinic, Phoenix, AZ
| | - Rafael Fonseca
- Division of Hematology and Medical Oncology, Mayo Clinic, Phoenix, AZ.
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49
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Marcou CA, Pitel B, Hagen CE, Boczek NJ, Rowsey RA, Baughn LB, Hoppman NL, Thorland EC, Kearney HM. Limited diagnostic impact of duplications <1 Mb of uncertain clinical significance: a 10-year retrospective analysis of reporting practices at the Mayo Clinic. Genet Med 2020; 22:2120-2124. [PMID: 32820244 DOI: 10.1038/s41436-020-0932-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/26/2020] [Accepted: 07/28/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Copy-number variants (CNVs) of uncertain clinical significance are routinely reported in a clinical setting only when exceeding predetermined reporting thresholds, typically based on CNV size. Given that very few genes are associated with triplosensitive phenotypes, it is not surprising that many interstitial duplications <1 Mb are found to be inherited and anticipated to be of limited or no clinical significance. METHODS In an effort to further refine our reporting criteria to maximize diagnostic yield while minimizing the return of uncertain variants, we performed a retrospective analysis of all clinical microarray cases reported in a 10-year window. A total of 1112 reported duplications had parental follow-up, and these were compared by size, RefSeq gene content, and inheritance pattern. De novo origin was used as a rough proxy for pathogenicity. RESULTS Approximately 6% of duplications 500 kb-1 Mb were de novo observations, compared with approximately 14% for 1-2 Mb duplications (p = 0.0005). On average, de novo duplications had higher gene counts than inherited duplications. CONCLUSION Our data reveal limited diagnostic utility for duplications of uncertain significance <1 Mb. Considerations for revised reporting criteria are discussed and are applicable to CNVs detected by any genome-wide exploratory methodology, including exome/genome sequencing.
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Affiliation(s)
- Cherisse A Marcou
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| | - Beth Pitel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Clinton E Hagen
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Nicole J Boczek
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ross A Rowsey
- 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
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Erik C Thorland
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Hutton M Kearney
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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50
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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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