Detection of clonal IGH gene rearrangements: summary of molecular oncology surveys of the College of American Pathologists

Molecular Pathology of Mature Lymphoid Malignancies

Lymphoid malignancies are a broad and heterogeneous group of neoplasms. In the past decade, the genetic landscape of these tumors has been explored and cataloged in fine detail offering a glimpse into the mechanisms of lymphomagenesis and new opportunities to translate these findings into patient management. A myriad of studies have demonstrated both distinctive and overlapping molecular and chromosomal abnormalities that have influenced the diagnosis and classification of lymphoma, disease prognosis, and treatment selection.

A comparison of capillary electrophoresis and next-generation sequencing in the detection of immunoglobulin heavy chain H and light chain κ gene rearrangements in the diagnosis of classic hodgkin’s lymphoma

This study aimed to compare the application value of capillary electrophoresis and next-generation sequencing for immunoglobulin (IG) gene rearrangement in the diagnosis of classic Hodgkin’s lymphoma. Twenty paraffin-embedded specimens from patients with classic Hodgkin’s lymphoma were screened. For gene rearrangement detection, the ABI 3500 Genetic Analyzer and ABI Ion GeneStudio S5 Plus sequencing system were used, respectively, and the results were compared. Five cases with monoclonal rearrangements (25%, 5/20) were detected by Capillary Electrophoresis, and positivity for the FR1, FR2, FR3, and IGк loci was 5%, 10%, 10%, and 15%, respectively; 12 cases with monoclonal rearrangements (60%, 12/20) were detected by Next-generation Sequencing where the positivity of the above corresponding loci were 35%, 45%, 50%, and 30%, respectively. Among the 20 samples, 6 IGк clonal rearrangements were detected, and the usage frequency (66.7%) of IGкJ4 was the highest in the IGкJ subgroup. The usage frequency of IGкV1 and IGкV3 in the GкV sub-group was 33.3% and 33.3%, respectively. Twelve immunoglobulin heavy chain (IGH) clonal rearrangements were detected among the 20 samples, and the order of usage frequency in the IGH joining region J (IGHJ) subgroup was IGHJ4 > IGHJ5 > IGHJ6 > IGHJ3. The gene with the highest usage frequency in the IGH variable (IGHV) subgroup was IGHV3 (50%) and the percentage of IGHV mutations ranged from 0% ± 11.45% with an average frequency of 3.34%. Compared with Capillary Electrophoresis, Next-generation Sequencing showed a higher positivity in the detection of gene clonal rearrangements, was more accurate in the interpretation of results.

CloneRetriever: An Automated Algorithm to Identify Clonal B and T Cell Gene Rearrangements by Next-Generation Sequencing for the Diagnosis of Lymphoid Malignancies

BACKGROUND

Clonal immunoglobulin and T-cell receptor rearrangements serve as tumor-specific markers that have become mainstays of the diagnosis and monitoring of lymphoid malignancy. Next-generation sequencing (NGS) techniques targeting these loci have been successfully applied to lymphoblastic leukemia and multiple myeloma for minimal residual disease detection. However, adoption of NGS for primary diagnosis remains limited.

METHODS

We addressed the bioinformatics challenges associated with immune cell sequencing and clone detection by designing a novel web tool, CloneRetriever (CR), which uses machine-learning principles to generate clone classification schemes that are customizable, and can be applied to large datasets. CR has 2 applications-a "validation" mode to derive a clonality classifier, and a "live" mode to screen for clones by applying a validated and/or customized classifier. In this study, CR-generated multiple classifiers using 2 datasets comprising 106 annotated patient samples. A custom classifier was then applied to 36 unannotated samples.

RESULTS

The optimal classifier for clonality required clonal dominance ≥4.5× above background, read representation ≥8% of all reads, and technical replicate agreement. Depending on the dataset and analysis step, the optimal algorithm yielded sensitivities of 81%-90%, specificities of 97%-100%, areas under the curve of 91%-94%, positive predictive values of 92-100%, and negative predictive values of 88%-98%. Customization of the algorithms yielded 95%-100% concordance with gold-standard clonality determination, including rescue of indeterminate samples. Application to a set of unknowns showed concordance rates of 83%-96%.

CONCLUSIONS

CR is an out-of-the-box ready and user-friendly software designed to identify clonal rearrangements in large NGS datasets for the diagnosis of lymphoid malignancies.

Molecular Pathology of Mature Lymphoid Malignancies

Lymphoid malignancies are a broad and heterogeneous group of neoplasms. In the past decade, the genetic landscape of these tumors has been explored and cataloged in fine detail offering a glimpse into the mechanisms of lymphomagenesis and new opportunities to translate these findings into patient management. A myriad of studies have demonstrated both distinctive and overlapping molecular and chromosomal abnormalities that have influenced the diagnosis and classification of lymphoma, disease prognosis, and treatment selection.

Vitreoretinal Lymphoma: A Literature Review and Introduction of a New Diagnostic Method

PURPOSE

The aim of this study was to briefly review the clinical and diagnostic features of vitreoretinal lymphoma (VRL) and to introduce the recent introduction of metagenomic deep sequencing in this ocular lymphomatous disease.

DESIGN AND METHODS

Review and description of the process of using metagenomic deep sequencing for ocular specimens at the Proctor Foundation, University of California, San Francisco, CA.

RESULTS

VRL masquerades as a uveitis, but clinical signs of subretinal lesions, and vitritis should prompt the inclusion of VRL in a differential diagnosis. Imaging features such as hyporeflective infiltrative lesions between the retinal pigment epithelium and Bruch's membrane are compatible with VRL, but diagnosis requires satisfying specific cytopathological and immunohistochemical or molecular features. Diagnosis, then, is subject to the cellularity, viability, and volume of the specimen submitted for these tests. Metagenomic deep sequencing has the ability to detect numerous lymphoma-associated mutations and is able to utilize minute volume samples and cell-free nucleic acid, so is well-suited for ocular tissues.

CONCLUSIONS

Metagenomic deep sequencing may offer an additional tool in the future with which to diagnose VRL.

PCR Analysis of IgH and TCR-γ Gene Rearrangements as a Confirmatory Diagnostic Tool for Lymphoproliferative Disorders

This study investigates PCR analysis of immunoglobulin heavy chain (IgH) and T cell receptor (TCR) gene rearrangements on paraffin-embedded tissue sections and bone marrow aspirates of patients suspected to have lymphoproliferative disorders but with inconclusive diagnosis in histopathological examination. 130 samples of patients with inconclusive immunohistochemistry results were evaluated for clonal rearrangement of IgH and TCR genes. Based on histopathology examination, the patients were divided into three groups: the first group without any definite diagnosis of lymphoproliferative disorders (60 cases, 46.2 %), the second group suspected to have a lymphoproliferative disorder but in favor of benign disorders (19 cases, 14.6 %) and the third group suspect to lymphoproliferative disorders but relatively in favor of malignant disorders (51 cases, 39.2 %). After DNA extraction and quality control, semi-nested PCR was performed using consensus primers for amplification of TCR-γ and CDR-3 regions of IgH genes. PCR products were analyzed after heteroduplex analysis using polyacrylamide gel electrophoresis, and were subject to silver staining. Totally, in over half of the cases (55.4 %), a monoclonal pattern was found in IgH or TCR-γ genes rearrangements. Monoclonal IgH gene rearrangement was detected in 48.1 % of patients, whereas monoclonal TCR-γ gene rearrangement was found in 33.6 % of them, which was not statistically significant (P = 0.008). Only in 32 patients (24.6 %) were the results of TCR-γ and IgH gene rearrangements consistent with respect to the presence (2.3 %) or absence (22.3 %) of monoclonality. Finally, PCR analysis of TCR-γ and IgH gene rearrangements led to definite diagnosis in 105 patients (80.8 %), and only 25 cases (19.2 %) remained inconclusive. Our results emphasize the usefulness of gene rearrangement study in cases without a definite diagnosis in immunohistochemistry studies. Multiple PCR analysis results when combined with patient's clinical course and immunohistochemistry can lead to early diagnosis and subsequent therapy.

Primary diffuse large B-cell lymphoma developing within a rectal tubular adenoma with low-grade dysplasia: a case report

Introduction

Colorectal lymphomas represent only 5% to 10% of gastrointestinal lymphomas, after the stomach and small intestine. Primary lymphoma of the colon and rectum is an unusual observation, constituting only 0.2% to 0.5% of all malignant tumors arising from the colorectal region. Very little is known about the correlation between adenoma and lymphoma in the colorectal tract. We report here a rare case of diffuse large B-cell lymphoma developing within a solitary tubular adenoma with low-grade dysplasia of the rectum.

Case presentation

An 83-year-old Caucasian man was referred to our hospital intermittent anal bleeding and irregular bowel. Colonoscopy revealed a 1cm solitary rectal polyp, which was completely removed by endoscopic resection. Histologic studies revealed low-grade intraepithelial dysplasia; the stroma of adenoma showed focal localization by highly proliferative lymphoid cells. Immunohistochemical analyses demonstrated that lymphoid cells were positive for CD20 and bcl2, whereas they were negative for CD3, CD5, CD10, CD23, CD30, CD138 and cyclin D1. Approximately 90% of the neoplastic cells reacted positively when stained with an antibody to Ki-67. Molecular studies showed the presence of a monoclonal immunoglobulin heavy chain gene rearrangement.

To determine primary or secondary lymphoma localization, Dawson’s criteria were applied to the case. A diagnosis of primary diffuse large B- lymphoma Ann Arbor stage 1A was established. Subsequently, the patient was referred to oncology to establish the stage and to select appropriate treatment.

Conclusions

The case of diffuse large B-cell lymphoma developing within a tubular adenoma, as reported here, is considered a rare event. Little about the prognosis of primary colorectal lymphomas is available and therapeutic treatment protocol is unclear. This case report provides more information on the history and macroscopic appearance of lymphomas presenting in an unusual location. To report additional cases in the future would be helpful in redefining the diagnostic, prognostic and therapeutic approach.

Primary follicular lymphoma of the epididymis positive for t(14;18)(q32;q21)/IGH-BCL2 and negative for BCL2 protein expression: a case report

Introduction

Non-Hodgkin lymphoma (NHL) can involve the paratesticular organs as the primary disease, as primary testicular lymphoma that secondarily involves the paratesticular structures, as the initial site of presentation of occult nodal disease or as the result of disease dissemination. Primary follicular lymphoma of the epididymis in an adult is extremely rare. Little is known about primary adult paratesticular/epididimal lymphomas.

Case presentation

We report a rare case of primary follicular non-Hodgkin lymphoma of the epididymis in a 90-year-old Caucasian man who presented with a left scrotal mass. Bone marrow biopsy was negative and computed tomography of the total body revealed no evidence of extratesticular involvement. Macroscopically, the epididymis was replaced completely by a uniform mass. Histologic studies revealed a dense lymphoid infiltrate predominantly composed of centrocytes with admixed centroblasts. Immunohistochemical analyses demonstrated that neoplastic cells strongly expressed CD45RB, CD20, CD79a, bcl-6 and CD10; bcl-2 immunostaining was negative. Molecular studies showed the presence of the monoclonal IgH gene rearrangement and the IgH/BCL2 rearrangement. The lymphoma was classified as follicular lymphoma, low grade, grade 1-2. The patient subsequently underwent radical orchiectomy, did not receive chemotherapy and post-operative follow-up showed absence of disease recurrence.

Conclusions

The case of primary follicular lymphoma of epididymis, reported here, is considered a very rare event. It is characterized by clinically indolent localized disease, a good clinical outcome, lack of expression of BCL2 protein and the presence of the t(14;18)(q32;q21)/IGH-BCL2. Even if it is a single case, the primary follicular lymphoma epididymis with t(14;18) could represent either a variant of the previously reported t(14;18)-negative primary paratesticular follicular lymphoma or a distinct biological entity. To report additional cases in the future would be helpful in resolving this question.

Polymerase chain reaction-based clonality analysis of cutaneous B-cell lymphoproliferative processes

INTRODUCTION

The differential diagnosis of B-cell lymphoproliferative processes remains a challenge for pathologists, dermatologists and oncologists, despite advances in histology, immunohistochemistry and molecular biology.

OBJECTIVE

Evaluate aid and limitations of clonality analysis in the diagnosis of primary cutaneous B-cell lymphomas and B-cell pseudolymphomas.

METHODS

This study included 29 cases of B-cell lymphoproliferative processes classified as primary cutaneous B-cell lymphomas (13), B-cell pseudolymphomas (6) and inconclusive cases (10) using histology and immunohistochemistry. The clonality analysis was performed by polymerase chain reaction analysis of immunoglobulin light chain and heavy chain rearrangements.

RESULTS

DNA quality was shown to be generally poor; eight samples were inadequate for polymerase chain reaction analysis. The results showed monoclonality in eight of the primary cutaneous B-cell lymphomas and polyclonality in four of the B-cell pseudolymphomas. In addition, monoclonality was shown in two of the inconclusive cases by histology and immunohistochemistry, demonstrating the utility of polymerase chain reaction as an ancillary diagnostic tool for primary cutaneous B-cell lymphomas.

DISCUSSION

The low quality DNA extracted from these cases demanded the use of an IgH protocol that yielded small fragments and IgK. Both methods used together improved detection.

CONCLUSION

Use of the two protocols, immunoglobulin heavy chain FR3-trad and immunoglobulin light chain-Kappa Biomed protocols for clonality analysis improved diagnostic accuracy.

Primary T-cell lymphoma of the retina and cerebellum: immunophenotypic and gene rearrangement confirmation

PURPOSE

To document fully the first credible primary T-cell lymphoma of the retina and central nervous system in a 71-year-old man.

DESIGN

Interventional, retrospective report.

METHODS

Critical analysis of clinical history and findings, which included bilateral vitreitis with anterior chamber reaction, creamy intraretinal infiltrates, and retinal detachment; complete blood counts and other blood studies (anti-neutrophil cytoplasmic antibody [ANCA], angiotensin-converting enzyme levels, and Lyme and fluorescent treponemal antibody absorption titers); magnetic resonance imaging (MRI) scanning of the brain with total body computed tomographic and positron emission tomographic scanning; interleukin (IL) level determinations (IL-10 and IL-6); cytologic and electron microscopic evaluations; immunophenotyping of cells; and polymerase chain reaction studies for viral deoxyribonucleic acid and ribonucleic acid, and immunoglobulin heavy-chain, and T-cell receptor (TCR) gene rearrangements.

RESULTS

The first vitreous specimen was diagnosed mistakenly as cytologically reactive and contained elevated levels of IL-10 and IL-6 in a ratio of 7 to 1. T cells predominated on immunophenotypic analysis. Computed tomographic and positron emission tomographic whole body scanning showed negative results for lymphoma. An MRI scan of the brain eventually revealed a cerebellar lesion. A retinal biopsy harbored cytologically atypical pleomorphic cells that were almost all immunophenotypically T cells; polymerase chain reaction studies demonstrated a clonal TCR gene rearrangement. T-cell lymphocytes in the biopsy specimen of the cerebellum had an identical clonal TCR gene rearrangement.

CONCLUSIONS

This case unequivocally establishes that primary retinal T-cell lymphoma accompanied by central nervous system involvement can occur. Elevation in the IL-10 to IL-6 ratio in the face of inconclusive or confusing vitreous cytologic and immunophenotypic findings (a predominance of "reactive T cells with some atypicality") should lead to gene rearrangement studies on biopsies of involved tissues for the detection of T-cell clonality.