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Article ; Online: Novel identification of t(14;18)(q32;q21)/IGH::MALT1 in chronic lymphocytic leukaemia.

Kumar, Jyoti / Ewalt, Mark D / Zhang, Yanming / Yao, JinJuan / Thompson, Meghan C / Dogan, Ahmet

2023 Volume 204, Issue 2, Page(s) 561–565

Abstract: Chronic lymphocytic leukaemia (CLL) is a clonal B-cell malignancy and remains a chronic disease despite improvements in clinical outcomes since the use of targeted therapies. Both clinical and biological parameters are important for determining prognosis. ...

Abstract	Chronic lymphocytic leukaemia (CLL) is a clonal B-cell malignancy and remains a chronic disease despite improvements in clinical outcomes since the use of targeted therapies. Both clinical and biological parameters are important for determining prognosis. Unlike other mature B-cell lymphomas, translocations involving the immunoglobulin heavy chain (IGH) locus are uncommon in CLL. There have been few case reports of CLL harbouring t(14;18)/IGH::BCL2 and t(14;19)/IGH::BCL3. Here we describe the first two cases of patients with CLL with documented t(14;18)(q32;q21)/IGH::MALT1. Both cases in this report were associated with lower-risk biological parameters. Thus, FISH testing for MALT1 in cases with unknown IGH translocation partners in the setting of CLL should be implemented in clinical practice to better define such cases.
MeSH term(s)	Humans ; Leukemia, Lymphocytic, Chronic, B-Cell ; Caspases ; Lymphoma, B-Cell, Marginal Zone/pathology ; Translocation, Genetic ; Prognosis ; Chromosomes, Human, Pair 14 ; Mucosa-Associated Lymphoid Tissue Lymphoma Translocation 1 Protein
Chemical Substances	Caspases (EC 3.4.22.-) ; MALT1 protein, human (EC 3.4.22.-) ; Mucosa-Associated Lymphoid Tissue Lymphoma Translocation 1 Protein (EC 3.4.22.-)
Language	English
Publishing date	2023-11-29
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	80077-6
ISSN	1365-2141 ; 0007-1048
ISSN (online)	1365-2141
ISSN	0007-1048
DOI	10.1111/bjh.19235
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Article ; Online: Pan-Cancer Biomarkers: Changing the Landscape of Molecular Testing.

Yao, Jinjuan / Arcila, Maria E / Ladanyi, Marc / Hechtman, Jaclyn F

Archives of pathology & laboratory medicine

2020 Volume 145, Issue 6, Page(s) 692–698

Abstract: Context.—: The increasing use of large panel next-generation sequencing technologies in clinical settings has facilitated the identification of pan-cancer biomarkers, which can be diagnostic, prognostic, predictive, or most importantly, actionable.: ... ...

Abstract	Context.—: The increasing use of large panel next-generation sequencing technologies in clinical settings has facilitated the identification of pan-cancer biomarkers, which can be diagnostic, prognostic, predictive, or most importantly, actionable. Objective.—: To discuss recently approved and emerging pan-cancer and multihistology biomarkers as well as testing methodologies. Data sources.—: The US Food and Drug Administration approval documents, National Comprehensive Cancer Network guidelines, literature, and authors' own publications. Conclusions.—: Since 2017, the US Food and Drug Administration has approved genotype-directed therapies for pan-cancer biomarkers, including microsatellite instability, neurotrophic receptor kinases fusions, and high-tumor mutation burden. Both the importance and rarity of these biomarkers have increased the prevalence of genomic profiling across solid malignancies. As an integral part of the management team of patients with advanced cancer, pathologists need to be aware of these emerging biomarkers, the therapies for which they determine eligibility, and the strengths and pitfalls of the available clinical assays.
MeSH term(s)	B7-H1 Antigen/genetics ; B7-H1 Antigen/metabolism ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism ; Fibroblast Growth Factors/genetics ; Fibroblast Growth Factors/metabolism ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Immunohistochemistry/methods ; In Situ Hybridization, Fluorescence/methods ; Microsatellite Instability ; Molecular Diagnostic Techniques/methods ; Molecular Diagnostic Techniques/trends ; Mutation ; Neoplasms/diagnosis ; Neoplasms/genetics ; Neoplasms/metabolism ; Programmed Cell Death 1 Receptor/genetics ; Programmed Cell Death 1 Receptor/metabolism ; Receptors, Fibroblast Growth Factor/genetics ; Receptors, Fibroblast Growth Factor/metabolism ; Reverse Transcriptase Polymerase Chain Reaction/methods
Chemical Substances	B7-H1 Antigen ; Biomarkers, Tumor ; CD274 protein, human ; PDCD1 protein, human ; Programmed Cell Death 1 Receptor ; Receptors, Fibroblast Growth Factor ; Fibroblast Growth Factors (62031-54-3)
Language	English
Publishing date	2020-12-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	194119-7
ISSN	1543-2165 ; 0363-0153 ; 0096-8528 ; 0003-9985
ISSN (online)	1543-2165
ISSN	0363-0153 ; 0096-8528 ; 0003-9985
DOI	10.5858/arpa.2020-0513-RA
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Article ; Online: A Brief Overview and Update on Major Molecular Genomic Alterations in Solid, Bone and Soft Tissue Tumors, and Hematopoietic As Well As Lymphoid Malignancies.

Zhang, Wei / Yao, Jinjuan / Zhong, Minghao / Zhang, Yaxia / Guo, Xiaoling / Wang, Huan-You

Archives of pathology & laboratory medicine

2021 Volume 145, Issue 11, Page(s) 1358–1366

Abstract: Context.—: Recent advances in comprehensive genomic profiling by next-generation sequencing have uncovered the genomic alterations at the molecular level for many types of tumors; as such, numerous small specific molecules that target these alterations ... ...

Abstract	Context.—: Recent advances in comprehensive genomic profiling by next-generation sequencing have uncovered the genomic alterations at the molecular level for many types of tumors; as such, numerous small specific molecules that target these alterations have been developed and widely used in the management of these cancers. Objective.—: To provide a concise molecular genomic update in solid, bone and soft tissue tumors, hematopoietic as well as lymphoid malignancies; discuss its clinical applications; and familiarize practicing pathologists with the emerging cancer biomarkers and their diagnostic utilities. Data sources.—: This review is based on the National Comprehensive Cancer Network guidelines and peer-reviewed English literature. Conclusions.—: Tumor-specific biomarkers and molecular/genomic alterations, including pan-cancer markers, have been significantly expanded in the past decade thanks to large-scale high-throughput technologies and will continue to emerge in the future. These biomarkers can be of great value in diagnosis, prognosis, and/or targeted therapy/treatment. Familiarization with these emerging and ever-changing tumor biomarkers will undoubtedly aid pathologists in making accurate and state-of-the-art diagnoses and enable them to be more actively involved in the care of cancer patients.
MeSH term(s)	Biomarkers, Tumor/genetics ; Bone Neoplasms/genetics ; Bone Neoplasms/pathology ; Gene Expression Profiling ; Genomics ; Hematologic Neoplasms/genetics ; Hematologic Neoplasms/pathology ; High-Throughput Nucleotide Sequencing ; Humans ; Lymphoproliferative Disorders/genetics ; Lymphoproliferative Disorders/pathology ; Molecular Diagnostic Techniques ; Predictive Value of Tests ; Soft Tissue Neoplasms/genetics ; Soft Tissue Neoplasms/pathology ; Transcriptome
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2021-07-16
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	194119-7
ISSN	1543-2165 ; 0363-0153 ; 0096-8528 ; 0003-9985
ISSN (online)	1543-2165
ISSN	0363-0153 ; 0096-8528 ; 0003-9985
DOI	10.5858/arpa.2021-0077-RA
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Article ; Online: YAP1-MAML2 fusion in a pediatric NF2-wildtype intraparenchymal brainstem schwannoma.

Karajannis, Matthias A / Li, Bryan K / Souweidane, Mark M / Liechty, Benjamin / Yao, JinJuan / Benhamida, Jamal K / Bale, Tejus A / Rosenblum, Marc K

Acta neuropathologica communications

2022 Volume 10, Issue 1, Page(s) 117

Abstract: Biallelic inactivation of NF2 represents the primary or sole oncogenic driver event in the vast majority of schwannomas. We report on a four-year-old female who underwent subtotal resection of a right medullary intraparenchymal schwannoma. RNA sequencing ...

Abstract	Biallelic inactivation of NF2 represents the primary or sole oncogenic driver event in the vast majority of schwannomas. We report on a four-year-old female who underwent subtotal resection of a right medullary intraparenchymal schwannoma. RNA sequencing revealed an in-frame fusion between exon 5 of YAP1 and exon 2 of MAML2. YAP1-MAML2 fusions have previously been reported in a variety of tumor types, but not schwannomas. Our report expands the spectrum of oncogenic YAP1 gene fusions an alternative to NF2 inactivation to include sporadic schwannoma, analogous to what has recently been described in NF2-wildtype pediatric meningiomas. Appropriate somatic and germline molecular testing should be undertaken in all young patients with solitary schwannoma and meningioma given the high prevalence of an underlying tumor predisposition syndrome. In such patients, the identification of a somatic non-NF2 driver alteration such as this newly described YAP1 fusion, can help ascertain the diagnosis of a sporadic schwannoma.
MeSH term(s)	Brain Stem/pathology ; Child ; Child, Preschool ; Female ; Gene Fusion ; Humans ; Meningeal Neoplasms/genetics ; Meningioma/genetics ; Neurilemmoma/genetics ; Neurilemmoma/pathology ; Neurilemmoma/surgery ; Neurofibromatosis 2/genetics ; Trans-Activators/genetics ; Transcription Factors/genetics ; YAP-Signaling Proteins
Chemical Substances	MAML2 protein, human ; Trans-Activators ; Transcription Factors ; YAP-Signaling Proteins ; YAP1 protein, human
Language	English
Publishing date	2022-08-19
Publishing country	England
Document type	Case Reports ; Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2715589-4
ISSN	2051-5960 ; 2051-5960
ISSN (online)	2051-5960
ISSN	2051-5960
DOI	10.1186/s40478-022-01423-7
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Article ; Online: A Primer on Gene Editing: What Does It Mean for Pathologists?

Cushman-Vokoun, Allison / Schmidt, Ryan J / Hiemenz, Matthew Charles / Fung, Mark / Zhang, Bing Melody / Bradshaw, Georganne / Gandhi, Manish / Yao, JinJuan / Yohe, Sophia / Beckman, Amy / Grody, Wayne W / Giannikopoulos, Petros

Archives of pathology & laboratory medicine

2023

Abstract: Context.—: Gene editing-based therapies are currently in development in the areas of oncology, inherited disease, and infectious disease. These potentially life-altering therapies are derived from decades of research in both academic and industry ... ...

Abstract	Context.—: Gene editing-based therapies are currently in development in the areas of oncology, inherited disease, and infectious disease. These potentially life-altering therapies are derived from decades of research in both academic and industry settings that developed technologies rooted in principles and products of nature. However, with such technologic developments come many important considerations, including adverse risks, high cost, and ethical questions. Objective.—: To educate pathologists about gene editing technologies, inform them of potential indications and risks, outline regulatory and practical issues that could affect hospital-based practice and laboratory testing, and advocate that pathologists need to be present at discussions among industry and regulators pertaining to gene editing-based therapies. Design.—: A Gene Editing Workgroup, facilitated by the College of American Pathologists Personalized Health Care Committee and consisting of pathologists of various backgrounds, was convened to develop an educational paper to serve as a stimulus to increase pathologist involvement and inquiry in gene editing therapeutic and diagnostic implementation. Results.—: Through multiple discussions and literature review, the workgroup identified potential gaps in pathologists' knowledge of gene editing. Additional topics that could impact pathology and laboratory medicine were also identified and summarized in order to facilitate pathologists as stakeholders in gene editing therapy administration and monitoring and potential use in diagnostics. Conclusions.—: Gene editing therapy is a complex but potentially transformative area of medicine. This article serves as an introduction to pathologists to assist them in future discussions with colleagues and potentially identify and alter pathology practices that relate to gene editing.
Language	English
Publishing date	2023-08-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	194119-7
ISSN	1543-2165 ; 0363-0153 ; 0096-8528 ; 0003-9985
ISSN (online)	1543-2165
ISSN	0363-0153 ; 0096-8528 ; 0003-9985
DOI	10.5858/arpa.2022-0410-CP
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Article ; Online: A Primer on Gene Editing.

Archives of pathology & laboratory medicine

2023

Abstract: Context—: Gene editing-based therapies are currently in development in the areas of oncology, inherited disease, and infectious disease. These potentially life-altering therapies are derived from decades of research in both academic and industry ... ...

Abstract	Context—: Gene editing-based therapies are currently in development in the areas of oncology, inherited disease, and infectious disease. These potentially life-altering therapies are derived from decades of research in both academic and industry settings that developed technologies rooted in principles and products of nature. However, with such technologic developments come many important considerations, including adverse risks, high cost, and ethical questions. Objective—: To educate pathologists about gene editing technologies, inform them of potential indications and risks, outline regulatory and practical issues that could affect hospital-based practice and laboratory testing, and advocate that pathologists need to be present at discussions among industry and regulators pertaining to gene editing-based therapies. Design—: A Gene Editing Workgroup, facilitated by the College of American Pathologists Personalized Health Care Committee and consisting of pathologists of various backgrounds, was convened to develop an educational paper to serve as a stimulus to increase pathologist involvement and inquiry in gene editing therapeutic and diagnostic implementation. Results—: Through multiple discussions and literature review, the workgroup identified potential gaps in pathologists' knowledge of gene editing. Additional topics that could impact pathology and laboratory medicine were also identified and summarized in order to facilitate pathologists as stakeholders in gene editing therapy administration and monitoring and potential use in diagnostics. Conclusions—: Gene editing therapy is a complex but potentially transformative area of medicine. This article serves as an introduction to pathologists to assist them in future discussions with colleagues and potentially identify and alter pathology practices that relate to gene editing.
Language	English
Publishing date	2023-08-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	194119-7
ISSN	1543-2165 ; 0363-0153 ; 0096-8528 ; 0003-9985
ISSN (online)	1543-2165
ISSN	0363-0153 ; 0096-8528 ; 0003-9985
DOI	10.5858/arpa.2022-0410-CP
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Article ; Online: Getting Your Laboratory on Track With Neurotrophic Receptor Tyrosine Kinase.

Eyerer, Frederick Inglis Rudolf / Bradshaw, Georganne / Vasalos, Patricia / Laser, Jordan Seth / Chang, Chung-Che / Kim, Annette Sunhi / Olson, Damon R / Paler, Ronald Joseph / Rosenbaum, Jason N / Walk, Eric E / Willis, Joseph E / Yao, Jinjuan / Yohe, Sophia Louise

Archives of pathology & laboratory medicine

2022 Volume 147, Issue 8, Page(s) 872–884

Abstract: Context.—: Neurotrophic receptor tyrosine kinase (NTRK) fusion testing has both diagnostic and therapeutic implications for patient care. With 2 tumor-agnostic US Food and Drug Administration-approved tropomyosin receptor kinase (TRK) inhibitors, ... ...

Abstract	Context.—: Neurotrophic receptor tyrosine kinase (NTRK) fusion testing has both diagnostic and therapeutic implications for patient care. With 2 tumor-agnostic US Food and Drug Administration-approved tropomyosin receptor kinase (TRK) inhibitors, testing is increasingly used for therapeutic decision making. However, the testing landscape for NTRK fusions is complex, and optimal testing depends on the clinicopathologic scenario. Objective.—: To compare different NTRK testing methods to help pathologists understand test features and performance characteristics and make appropriate selections for NTRK fusion detection for their laboratory and individual patient specimens. Data sources.—: A literature search for NTRK gene fusions and TRK protein was performed, including papers that discussed treatment, testing methodology, and detection or prevalence of fusion-positive cases. Conclusions.—: As standard of care in some tumor types, next-generation sequencing (NGS) panel testing is a cost effective and reliable way to detect a broad range of NTRK fusions. The design of the panel and use of DNA or RNA will affect performance characteristics. Pan-TRK immunohistochemistry may be used as a rapid, less expensive screen in cases that will not undergo routine NGS testing, or on specimens unsuitable for NGS testing. Fluorescence in situ hybridization may be appropriate for low-tumor-content specimens that are unsuitable for NGS testing. Quantitative reverse transcription polymerase chain reaction is best suited for monitoring low-level disease of a specific, previously identified target. This information should help laboratories develop a laboratory-specific NTRK testing algorithm that best suits their practice setting and patients' needs.
MeSH term(s)	Humans ; Receptor, trkA/genetics ; Receptor, trkC/genetics ; In Situ Hybridization, Fluorescence ; Laboratories ; Neoplasms/diagnosis ; Neoplasms/genetics ; Neoplasms/drug therapy ; Oncogene Proteins, Fusion/genetics
Chemical Substances	Receptor, trkA (EC 2.7.10.1) ; Receptor, trkC (EC 2.7.10.1) ; Oncogene Proteins, Fusion
Language	English
Publishing date	2022-12-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	194119-7
ISSN	1543-2165 ; 0363-0153 ; 0096-8528 ; 0003-9985
ISSN (online)	1543-2165
ISSN	0363-0153 ; 0096-8528 ; 0003-9985
DOI	10.5858/arpa.2022-0042-CP
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Article ; Online: Rare and novel RUNX1 fusions in myeloid neoplasms: A single-institute experience.

Aypar, Umut / Yao, Jinjuan / Londono, Dory M / Khoobyar, Rose / Scalise, Angela / Arcila, Maria E / Roshal, Mikhail / Xiao, Wenbin / Zhang, Yanming

Genes, chromosomes & cancer

2020 Volume 60, Issue 2, Page(s) 100–107

Abstract: Chromosome translocations involving the RUNX1 gene at 21q22 are recurring abnormalities in acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS), that is, t(8;21) and t(3;21) and in B-cell acute lymphoblastic leukemia with t(12;21). These ... ...

Abstract	Chromosome translocations involving the RUNX1 gene at 21q22 are recurring abnormalities in acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS), that is, t(8;21) and t(3;21) and in B-cell acute lymphoblastic leukemia with t(12;21). These translocations result in the fusion of RUNX1 with RUNX1T1, MECOM, and ETV6, respectively, and are implicated in leukemogenesis. Here we describe 10 rare RUNX1 fusion gene partners, including six novel fusions, in myeloid neoplasia. Comprehensive molecular testing revealed the partner genes and features of these fusions in all the tested patients, and detected various recurring myeloid related gene mutations in eight patients. In two patients, RUNX1 mutations were identified. Most of these fusions were detected in patients with high-grade MDS and AML with a relatively short survival. Integration of conventional chromosome analysis, FISH testing and molecular genetic studies allow a comprehensive characterization of these rare RUNX1 fusions. Our study may help define myeloid neoplasms with rare and novel RUNX1 translocations and support appropriate patient management.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Core Binding Factor Alpha 2 Subunit/genetics ; Female ; Humans ; Male ; Middle Aged ; Mutation ; Myelodysplastic Syndromes/genetics ; Myelodysplastic Syndromes/pathology ; Neoplasm Grading ; Oncogene Proteins, Fusion/genetics ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/pathology
Chemical Substances	Core Binding Factor Alpha 2 Subunit ; Oncogene Proteins, Fusion ; RUNX1 protein, human
Language	English
Publishing date	2020-10-21
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1018988-9
ISSN	1098-2264 ; 1045-2257
ISSN (online)	1098-2264
ISSN	1045-2257
DOI	10.1002/gcc.22901
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Article: A case of acute myeloid leukemia with e6a2 BCR-ABL fusion transcript acquired after progressing from chronic myelomonocytic leukemia.

Yao, Jinjuan / Douer, Dan / Wang, Lu / Arcila, Maria E / Nafa, Khedoudja / Chiu, April

Leukemia research reports

2017 Volume 7, Page(s) 17–19

Abstract: Philadelphia (Ph) chromosome is a cytogenetic hallmark of chronic myeloid leukemia (CML). Most patients with CML harbor either the e13a2 or e14a2 BCR-ABL fusion product, while a small subset of the cases expresses e1a2 or e19a2 transcripts. We report a ... ...

Abstract	Philadelphia (Ph) chromosome is a cytogenetic hallmark of chronic myeloid leukemia (CML). Most patients with CML harbor either the e13a2 or e14a2 BCR-ABL fusion product, while a small subset of the cases expresses e1a2 or e19a2 transcripts. We report a patient with chronic myelomonocytic leukemia (CMML), initially Ph chromosome negative at presentation, with rapid disease progression to acute myeloid leukemia (AML) and appearance of Ph chromosome and BCR-ABL e6a2, a very uncommon fusion transcript. The AML was refractory to treatment with subsequent emergence and dominance of a Ph negative leukemic clone. The patient expired shortly after disease progression.
Language	English
Publishing date	2017-01-31
Publishing country	Netherlands
Document type	Case Reports
ZDB-ID	2706248-X
ISSN	2213-0489
ISSN	2213-0489
DOI	10.1016/j.lrr.2017.01.003
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Article ; Online: Quantification of Measurable Residual Disease Detection by Next-Generation Sequencing-Based Clonality Testing in B-Cell and Plasma Cell Neoplasms.

The Journal of molecular diagnostics : JMD

2023 Volume 26, Issue 3, Page(s) 168–178

Abstract: Next-generation sequencing (NGS)-based measurable residual disease (MRD) monitoring in post-treatment settings can be crucial for relapse risk stratification in patients with B-cell and plasma cell neoplasms. Prior studies have focused on validation of ... ...

Abstract	Next-generation sequencing (NGS)-based measurable residual disease (MRD) monitoring in post-treatment settings can be crucial for relapse risk stratification in patients with B-cell and plasma cell neoplasms. Prior studies have focused on validation of various technical aspects of the MRD assays, but more studies are warranted to establish the performance characteristics and enable standardization and broad utilization in routine clinical practice. Here, the authors describe an NGS-based IGH MRD quantification assay, incorporating a spike-in calibrator for monitoring B-cell and plasma cell neoplasms based on their unique IGH rearrangement status. Comparison of MRD status (positive or undetectable) by NGS and flow cytometry (FC) assays showed high concordance (91%, 471/519 cases) and overall good linear correlation in MRD quantitation, particularly for chronic lymphocytic leukemia and B-lymphoblastic leukemia/lymphoma (R = 0.85). Quantitative correlation was lower for plasma cell neoplasms, where underestimation by FC is a known limitation. No significant effects on sequencing efficiency by the spike-in calibrator were observed, with excellent inter- and intra-assay reproducibility within the authors' laboratory, and in comparison to an external laboratory, using the same assay and protocols. Assays performed both at internal and external laboratories showed highly concordant MRD detection (100%) and quantitation (R = 0.97). Overall, this NGS-based MRD assay showed highly reproducible results with quantitation that correlated well with FC MRD assessment, particularly for B-cell neoplasms.
MeSH term(s)	Humans ; Reproducibility of Results ; Multiple Myeloma ; Leukemia, Lymphocytic, Chronic, B-Cell ; High-Throughput Nucleotide Sequencing/methods ; Neoplasm, Residual/diagnosis ; Neoplasm, Residual/genetics
Language	English
Publishing date	2023-12-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	2000060-1
ISSN	1943-7811 ; 1525-1578
ISSN (online)	1943-7811
ISSN	1525-1578
DOI	10.1016/j.jmoldx.2023.11.009
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