Differential prognosis of single and multiple TP53 abnormalities in high-count MBL and untreated CLL

TP53 aberrations, including mutations and deletion of 17p13, are important adverse prognostic markers in chronic lymphocytic leukemia (CLL) but are less studied in high count monoclonal B-cell lymphocytosis (HCMBL), an asymptomatic pre-malignant stage of CLL. Here we estimated the prevalence and impact of TP53 aberrations in 1,230 newly diagnosed treatment-naïve individuals (849 CLL, 381 HCMBL). We defined TP53 state as: wild-type (no TP53 mutations and normal 17p), single-hit (del(17p) or one TP53 mutation), or multi-hit (TP53 mutation and del(17p), TP53 mutation and loss of heterozygosity, or multiple TP53 mutations). Cox regression was used to estimate hazard ratios (HR) and 95% confidence intervals (CI) for time to first treatment and overall survival by TP53 state. We found 64 (7.5%) CLL patients and 17 (4.5%) HCMBL individuals had TP53 mutations with variant allele fraction >10%. Del(17p) was present in 58 (6.8%) of CLL and 11 (2.9%) of HCMBL cases. Most individuals had wild-type (N=1,128, 91.7%) TP53 state, followed by multi-hit (N=55, 4.5%) and then single-hit (N=47, 3.8%) TP53 state. The risk of shorter time to therapy and death increased with the number of TP53 abnormalities. Compared to wild-type patients, multi-hit patients had 3-fold and single-hit patients had 1.5-fold increased risk of requiring therapy. Multi-hit patients also had 2.9-fold increased risk of death compared to wild-type. These results remained stable after accounting for other known poor prognostic factors. Both TP53 mutations and del(17p) may provide important prognostic information for HCMBL and CLL that would be missed if only one were measured.

Clinical outcomes in patients with chronic lymphocytic leukemia with disease progression on ibrutinib

Patients with chronic lymphocytic leukemia (CLL) with disease progression on ibrutinib have worse outcomes compared to patients stopping ibrutinib due to toxicity. A better understanding of expected outcomes in these patients is necessary to establish a benchmark for evaluating novel agents currently available and in development. We evaluated outcomes of 144 patients with CLL treated at Mayo Clinic with 2018 iwCLL disease progression on ibrutinib. The median overall survival (OS) for the entire cohort was 25.5 months; it was 29.8 months and 8.3 months among patients with CLL progression (n = 104) and Richter transformation (n = 38), respectively. Longer OS was observed among patients with CLL progression who had received ibrutinib in the frontline compared to relapsed/refractory setting (not reached versus 28.5 months; p = 0.04), but was similar amongst patients treated with 1, 2, or ≥3 prior lines (18.5, 30.9, and 26.0 months, respectively, p = 0.24). Among patients with CLL disease progression on ibrutinib, OS was significantly longer when next-line treatment was chimeric antigen receptor T-cell therapy (median not reached) or venetoclax-based treatment (median 29.8 months) compared to other approved treatments, such as chemoimmunotherapy, phosphoinositide 3'-kinase inhibitors, and anti-CD20 monoclonal antibodies (9.1 months; p = 0.03). These findings suggest an unmet need for this growing patient population.

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

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.

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

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.

MCIR1: A patient-derived mantle cell lymphoma line for discovering new treatments for ibrutinib resistance

BACKGROUND

Despite the unprecedented success of ibrutinib in lymphoma therapy, the development of ibrutinib resistance due to acquired BTK or PLCγ2 mutations has become a new clinical problem. However, not all resistance is mediated by these mutations and these mechanisms are poorly understood due to a lack of study tools that truly recapitulate this clinical scenario.

METHODS

We established a novel patient-derived ibrutinib-resistant mantle cell lymphoma (MCL) line named MCIR1. Using immunological, molecular, and cytogenetic approaches, we comprehensively characterized MCIR1 and further demonstrated its utility in the study of resistance mechanisms and treatments to overcome this resistance.

RESULTS

We show that MCIR1 is a bona fide ibrutinib-resistant MCL cell line with normal BTK-/PLCγ2 but ibrutinib-resistant ERK1/2 and AKT1 signaling. RNA-Seq analysis revealed a robust non-canonical NF-kB signaling that drives the ibrutinib resistance. We also demonstrate the potential utility of a MCIR1-based cell and mouse model for the discovery of new treatments to overcome BTK inhibitor resistance.

CONCLUSIONS

We have established the first patient-derived ibrutinib-resistant MCL cell line MCIR1 that lacks BTK or PLCγ2 mutations but exhibits a hyperactive non-canonical NF-kB pathway. We further demonstrate its utility in the discovery and validation of new drugs to overcome this resistance.

Conventional Cytogenetic Analysis of Hematologic Neoplasms: A 20-Year Review of Proficiency Test Results From the College of American Pathologists/American College of Medical Genetics and Genomics Cytogenetics Committee

CONTEXT.—

One goal of the joint College of American Pathologists/American College of Medical Genetics and Genomics Cytogenetics Committee is to ensure the accurate detection and description of chromosomal abnormalities in both constitutional and neoplastic specimens, including hematologic neoplasms.

OBJECTIVE.—

To report a 20-year performance summary (1999-2018) of conventional chromosome challenges focusing on hematologic neoplasms.

DESIGN.—

A retrospective review was performed from 1999 through 2018 to identify karyotype challenges specifically addressing hematologic neoplasms. The overall performance of participants was examined to identify potential recurring errors of clinical significance.

RESULTS.—

Of 288 total conventional chromosome challenges from 1999-2018, 87 (30.2%) were presented in the context of a hematologic neoplasm, based on the provided clinical history, specimen type, and/or chromosomal abnormalities. For these 87 hematologic neoplasm challenges, 91 individual cases were provided and graded on the basis of abnormality recognition and karyotype nomenclature (ISCN, International System for Human Cytogenomic [previously Cytogenetic] Nomenclature). Of the 91 cases, 89 (97.8%) and 87 (95.6%) exceeded the required 80% consensus for grading of abnormality recognition and correct karyotype nomenclature, respectively. The 2 cases (2 of 91; 2.2%) that failed to meet the 80% consensus for abnormality recognition had complex karyotypes. The 4 cases (4 of 91; 4.4%) that failed to meet the 80% consensus for correct karyotype nomenclature were the result of incorrect abnormality recognition (2 cases), missing brackets in the karyotype (1 case), and incorrect breakpoint designation (1 case).

CONCLUSIONS.—

This 20-year review demonstrates clinical cytogenetics laboratories have been and continue to be highly proficient in the detection and description of chromosomal abnormalities associated with hematologic neoplasms.

Disease Flare During Temporary Interruption of Ibrutinib Therapy in Patients with Chronic Lymphocytic Leukemia

BACKGROUND

Approximately 25% of patients with chronic lymphocytic leukemia (CLL) experience a flare of disease following ibrutinib discontinuation. A critical question is whether this phenomenon may also occur when ibrutinib is temporarily held. This study aimed to determine the frequency and characteristics of disease flares in this setting and assess risk factors and clinical outcomes.

MATERIALS AND METHODS

We identified all patients with CLL seen at Mayo Clinic between October 2012 and March 2019 who received ibrutinib. Temporary interruptions in treatment and associated clinical findings were ascertained.

RESULTS

Among the 372 patients identified, 143 (38%) had at least one temporary interruption (median 1 hold, range 1-7 holds) in treatment. The median duration of interruption was 8 days (range 1-59 days) and the most common indication was periprocedural. Among the 143 patients with ≥1 hold, an associated disease flare was seen in 35 (25%) patients: mild (constitutional symptoms only) in 21 patients and severe (constitutional symptoms with exam/radiographic findings or laboratory changes) in 14 patients. Disease flare resolved with resuming ibrutinib in all patients. Predictive factors of disease flare included progressive disease at time of hold and ≥ 24 months of ibrutinib exposure. The occurrence of disease flare with an ibrutinib hold was associated with shorter event-free survival (hazard ratio 2.3; 95% confidence interval 1.3-4.1; p = .007) but not overall survival.

CONCLUSION

Temporary interruptions in ibrutinib treatment of patients with CLL are common, and one quarter of patients who held ibrutinib in this study experienced a disease flare. Resolution with resuming ibrutinib underscores the importance of awareness of this phenomenon for optimal management.

IMPLICATIONS FOR PRACTICE

Ibrutinib is a very effective treatment for chronic lymphocytic leukemia (CLL) but needs to be taken continuously. Side effects, such as increased bleeding risk with procedures, require temporary interruptions in this continuous treatment. Rapid CLL progression following ibrutinib discontinuation has been increasingly recognized. This study demonstrates that similar flares in disease signs or symptoms may occur during ibrutinib holds as well. Importantly, management with restarting ibrutinib led to quick clinical improvement. Awareness of this phenomenon among clinicians is critical to avoid associated patient morbidity and premature cessation of effective treatment with ibrutinib if the flare is misidentified as true progression of disease.

Abstract 650: MCIR1: A patient-derived ibrutinib-resistant mantle cell lymphoma line for the study of ibrutinib resistance and drug discovery

Constitutive activation of B-cell receptor (BCR) signaling is a major driving mechanism for the proliferation and survival of various B-cell lineage non-Hodgkin lymphomas (NHL). Blocking BCR signaling using the first-in-class Bruton's tyrosine kinase (BTK) inhibitor, ibrutinib, has proved effective and is currently FDA approved for the treatment of several B-cell lymphomas. Unfortunately, significant subsets of patients possess either primary or acquired resistance to ibrutinib, often resulting in worse prognosis and poorer responses to subsequent therapies. Therefore, overcoming ibrutinib resistance is an urgent clinical need requiring new tools to both delineate the molecular mechanisms of resistance and develop viable therapeutics.

To that end, we developed a mantle cell lymphoma (MCL) cell line, MCIR1, from a patient with clinically acquired ibrutinib resistance. MCIR1 is a bona fide MCL cell line featuring CD19+/CD5+/CD10-/CD23-/t(11;14)+/TP53+/-; and lacking the previously described mutations in BTK (C481S) and phospholipase C-gamma-2 (R665W, L845F). Importantly, MCIR1 cells possess hallmarks of ibrutinib resistance, including the insensitivity of ERK1/2 phosphorylation to ibrutinib in vitro, and the irresponsiveness of MCIR1 xenograft tumors to ibrutinib treatment in mice as compared with ibrutinib-sensitive Jeko-1 tumors. To delineate the molecular mechanism(s) of ibrutinib resistance, we identified by RNA-Seq analysis that MCIR1 cells possess robust activity of the non-canonical NFkB pathway and elevated expression of NFkB target genes, suggesting that this pathway likely drives their resistance to ibrutinib. Finally, we demonstrated the utility of MCIR1 as a tool for testing new drugs to combat ibrutinib resistance in vitro by showing its sensitivity to the anti-apoptotic B-cell lymphoma-2 (Bcl-2) protein inhibitor, venetoclax.

To our knowledge, MCIR1 is the first patient-derived ibrutinib-resistant cell line to be established. Hence, MCIR1 is especially useful because uniquely possesses the relevant clinical and biological features of patients with ibrutinib-resistant MCL. We propose MCIR1 as a tool to further the understanding of molecular mechanisms conferring ibrutinib resistance by providing a clinically relevant system with the capacity for molecular and genetic manipulations. Further, these features make MCIR1 an ideal model to screen drugs for combating ibrutinib resistance through both in vivo and in vitro approaches.

Citation Format: Kevin E. Nowakowski, Jithma P. Abeykoon, Mary J. Stenson, Michael M. Timm, Curtis A. Hanson, Daniel L. Van Dyke, Anne J. Novak, Xiaosheng Wu, Thomas E. Witzig. MCIR1: A patient-derived ibrutinib-resistant mantle cell lymphoma line for the study of ibrutinib resistance and drug discovery [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 650.

Clinical characteristics and outcomes of Richter transformation: experience of 204 patients from a single center

The natural history, prognostication and optimal treatment of Richter transformation developed from chronic lymphocytic leukemia (CLL) are not well defined. We report the clinical characteristics and outcomes of a large series of biopsy-confirmed Richter transformation (diffuse large B-cell lymphoma or high grade B-cell lymphoma, n=204) cases diagnosed from 1993 to 2018. After a median follow up of 67.0 months, the median overall survival (OS) was 12.0 months. Patients who received no prior treatment for CLL had significantly better OS (median 46.3 vs. 7.8 months; P<0.001). Patients with elevated lactate dehydrogenase (median 6.2 vs. 39.9 months; P<0.0001) or TP53 disruption (median 8.3 vs. 12.8 months; P=0.046) had worse OS than those without. Immunoglobulin heavy chain variable region gene mutation, cell of origin, Myc/Bcl-2 double expression and MYC/BCL2/BCL6 double-/triple-hit status were not associated with OS. In multivariable Cox regression, elevated lactate dehydrogenase [Hazard ratio (HR) 2.3, 95% Confidence Interval (CI): 1.3-4.1; P=0.01], prior CLL treatment (HR 2.0, 95%CI: 1.2-3.5; P=0.01), and older age (HR 1.03, 95%CI: 1.01-1.05; P=0.01) were associated with worse OS. Twenty-four (12%) patients underwent stem cell transplant (20 autologous and 4 allogeneic), and had a median post-transplant survival of 55.4 months. In conclusion, the overall outcome of Richter transformation is poor. Richter transformation developed in patients with untreated CLL has significantly better survival. Stem cell transplant may benefit select patients.

IGH translocations in chronic lymphocytic leukemia: Clinicopathologic features and clinical outcomes

The prevalence, clinicopathologic correlates, and outcomes of previously untreated chronic lymphocytic leukemia (CLL) patients with IGH-BCL2 and IGH-BCL3 translocations are not well known. Using the Mayo Clinic CLL database, we identified patients seen between March 1, 2002 and September 30, 2016 who had FISH testing performed within 3 years of CLL diagnosis. The prognostic profile, time to first therapy (TTT), and overall survival (OS) of patients with IGH-BCL2 and IGH-BCL3 translocation were compared to patients without these abnormalities (non-IGH group). Of 1684 patients who met the inclusion criteria, 38 (2.2%) had IGH-BCL2, and 16 (0.9%) had IGH-BCL3 translocation at diagnosis. Patients with IGH-BCL3 translocation were more likely to have high and very-high CLL-International Prognostic Index, compared to patients with IGH-BCL2 translocation and the non-IGH group. The 5-year probability of requiring therapy was significantly higher for IGH-BCL3 compared to IGH-BCL2 and non-IGH groups (84% vs 33% vs 29%, respectively, P < 0.0001). The 5-year OS was significantly shorter for IGH-BCL3 compared to IGH-BCL2 and non-IGH groups (45% vs 89% vs 86%, respectively, P < 0.0001). On multivariable analyses, IGH-BCL3 translocation was associated with a shorter TTT (hazard ratio [HR] = 2.7; P = 0.005) and shorter OS (HR = 5.5; P < 0.0001); IGH-BCL2 translocation did not impact TTT and OS. In conclusion, approximately 3% of all newly diagnosed CLL patients have either an IGH-BCL2 or IGH-BCL3 translocation. Patients with IGH-BCL3 translocations have a distinct prognostic profile and outcome. These results support the inclusion of an IGH probe during the routine evaluation of FISH abnormalities in newly diagnosed CLL.

Mate pair sequencing improves detection of genomic abnormalities in acute myeloid leukemia

OBJECTIVE

Acute myeloid leukemia (AML) can be subtyped based on recurrent cytogenetic and molecular genetic abnormalities with diagnostic and prognostic significance. Although cytogenetic characterization classically involves conventional chromosome and/or fluorescence in situ hybridization (FISH) assays, limitations of these techniques include poor resolution and the inability to precisely identify breakpoints.

METHOD

We evaluated whether an NGS-based methodology that detects structural abnormalities and copy number changes using mate pair sequencing (MPseq) can enhance the diagnostic yield for patients with AML.

RESULTS

Using 68 known abnormal and 20 karyotypically normal AML samples, each recurrent primary AML-specific abnormality previously identified in the abnormal samples was confirmed using MPseq. Importantly, in eight cases with abnormalities that could not be resolved by conventional cytogenetic studies, MPseq was utilized to molecularly define eight recurrent AML-fusion events. In addition, MPseq uncovered two cryptic abnormalities that were missed by conventional cytogenetic studies. Thus, MPseq improved the diagnostic yield in the detection of AML-specific structural rearrangements in 10/88 (11%) of cases analyzed.

CONCLUSION

Utilization of MPseq represents a precise, molecular-based technique that can be used as an alternative to conventional cytogenetic studies for newly diagnosed AML patients with the potential to revolutionize the diagnosis of hematologic malignancies.

The Utilization of Chromosomal Microarray Technologies for Hematologic Neoplasms: An ACLPS Critical Review

OBJECTIVES

Chromosome (G-banding) and fluorescence in situ hybridization (FISH) serve as the primary methodologies utilized for detecting genetic aberrations in hematologic neoplasms. Chromosomal microarray can detect copy number aberrations (CNAs) with greater resolution when compared to G-banding and FISH, and can also identify copy-neutral loss of heterozygosity (CN-LOH). The purpose of our review is to highlight a preselected group of hematologic neoplasms for which chromosomal microarray has the greatest clinical utility.

METHODS

A case-based approach and review of the literature was performed to identify the advantages and disadvantages of utilizing chromosomal microarray for specific hematologic neoplasms.

RESULTS

Chromosomal microarray identified CNAs and CN-LOH of clinical significance, and could be performed on fresh or paraffin-embedded tissue and liquid neoplasms. Microarray studies could not detect balanced rearrangements, low-level clones, or distinguish independent clones.

CONCLUSIONS

When utilized appropriately, chromosomal microarray can provide clinically significant information that complements traditional cytogenetic testing methodologies.

A Test Utilization Approach to the Diagnostic Workup of Isolated Eosinophilia in Otherwise Morphologically Unremarkable Bone Marrow: A Single Institutional Experience

OBJECTIVES

Determine ancillary test utilization for the workup of isolated eosinophilia in otherwise morphologically unremarkable bone marrow (BM).

METHODS

We evaluated BM ancillary testing performed in cases with isolated eosinophilia and otherwise morphologically unremarkable BM. Cases with abnormal morphology (eg, dysplasia, basophilia) and/or findings suggestive of a disorder (eg, unexplained thromboses, lymphoma) are specifically excluded.

RESULTS

A total of 132 cases met inclusion criteria. Ten cases had an ancillary testing abnormality that warranted a more specific hematologic diagnosis: four cases of lymphocytic variant of hypereosinophilic syndrome, three cases of myeloid neoplasm with PDGFRA rearrangement, and one case each of myeloid neoplasm with PDGFRB rearrangement, chronic eosinophilic leukemia, and morphologically occult systemic mastocytosis. No cases revealed a cryptic PDGFRB or BCR/ABL1 rearrangement or JAK2 V617F mutation.

CONCLUSIONS

Findings from our institutional experience support initial testing in isolated eosinophilia with otherwise unremarkable BM to include PDGFRA rearrangement, tryptase/CD25 immunohistochemistry, cytogenetics, and T-cell flow cytometry/receptor gene rearrangement. This approach achieves diagnostic quality and test utilization efficiency in our clinical practice.

A rapid and reliable chromosome analysis method for products of conception using interphase nuclei

BACKGROUND

Karyotype determination has a central role in the genetic workup of pregnancy loss, as aneuploidy (trisomy and monosomy) and polyploidy (triploidy and tetraploidy) are the cause in at least 50% of first trimester, 25% of second trimester, and 11% of third trimester miscarriages. There are several limitations with the current approaches of obtaining a karyotype using traditional cytogenetics, fluorescence in situ hybridization with a limited number of probes, and chromosomal microarray. These include culture failure, incomplete results, lower sensitivity, and longer reporting time.

METHODS

To overcome current limitations, a novel molecular assay is developed with a Standard Resolution Interphase Chromosome Profiling probe set which is a variation of the recently developed High Resolution probe set. It generates a molecular karyotype that can detect all major changes commonly associated with pregnancy loss. Initial familiarization of signal patterns from the probe set was used, followed by validation of the method using 83 samples from miscarriages in a blind study from three different laboratories. Finally, the clinical utility of the method was tested on 291 clinical samples in two commercial reference laboratory settings on two different continents.

RESULTS

The new molecular approach not only identified all the chromosome changes observed by current methods, but also significantly improved abnormality detection by characterizing derivative chromosomes and finding subtle subtelomeric rearrangements, balanced and unbalanced. All Robertsonian translocations were also detected. The abnormality rate was 54% on clinical samples from commercial laboratory 1 and 63% from laboratory 2.

CONCLUSION

The attributes of this method make it an ideal choice for the genetic workup of miscarriages, namely (1) near 100% successful results, (2) greater sensitivity than conventional chromosome analysis or FISH panels, (3) rapid reporting time, and (4) favorable comparisons with chromosomal microarray.

Low-grade fibromyxoid sarcoma arising within the median nerve

We report a case of low-grade fibromyxoid sarcoma arising within the median nerve. A 31-year-old woman presented with symptoms of carpal tunnel syndrome and an enlarging mass in her right palm over 1 year. MRI demonstrated a mass associated with the right median nerve with solid and cystic components. At surgery, the mass was located within the epineurium, could be bluntly dissected from the nerve fascicles, and was suspected to be a schwannoma. A 3.4 cm, tan-pink, glistening, smooth, homogenous mass was submitted to pathology. Microscopically, the tumor was a solid and cystic circumscribed nodule with a dense fibrous pseudocapsule. The tumor cells were uniformly bland and spindle-shaped, with small, hyperchromatic oval nuclei and were embedded in an alternating fibrous and myxoid stroma with a prominent curvilinear vasculature and perivascular sclerosis. The differential diagnosis for this lesion included myxoid neurofibroma, schwannoma, soft tissue perineurioma, low-grade malignant peripheral nerve sheath tumor and low-grade fibromyxoid sarcoma. The tumor cells expressed MUC4, GLUT-1, and vimentin and were negative for S-100 protein, epithelial membrane antigen, smooth muscle actin, desmin, claudin-1, neurofilament and SOX10. Fluorescence in situ hybridization, with a break-apart probe strategy, demonstrated FUS rearrangement, consistent in this morphological context with the low-grade fibromyxoid sarcoma-associated FUS-CREB3L2 or FUS-CREB3L1 fusions. Low-grade fibromyxoid sarcoma is exceptionally rare in the peripheral nerve, with only a single previously reported case. Nonetheless, as our case illustrates, this entity must be included in the differential diagnosis of unusual intraneural mesenchymal tumors. As in all other locations, intraneural low-grade fibromyxoid sarcomas should be excised with negative margins. Patients with this disease require long-term clinical follow-up, given this tumor's propensity for very late distant metastases to the lungs and other sites.

Interphase Chromosome Profiling: A Method for Conventional Banded Chromosome Analysis Using Interphase Nuclei

CONTEXT

- Chromosome analysis on bone marrow or peripheral blood samples fails in a small proportion of attempts. A method that is more reliable, with similar or better resolution, would be a welcome addition to the armamentarium of the cytogenetics laboratory.

OBJECTIVE

- To develop a method similar to banded metaphase chromosome analysis that relies only on interphase nuclei.

DESIGN

- To label multiple targets in an equidistant fashion along the entire length of each chromosome, including landmark subtelomere and centromere regions. Each label so generated by using cloned bacterial artificial chromosome probes is molecularly distinct with unique spectral characteristics, so the number and position of the labels can be tracked to identify chromosome abnormalities.

RESULTS

- Interphase chromosome profiling (ICP) demonstrated results similar to conventional chromosome analysis and fluorescence in situ hybridization in 55 previously studied cases and obtained useful ICP chromosome analysis results on another 29 cases in which conventional methods failed.

CONCLUSIONS

- ICP is a new and powerful method to karyotype peripheral blood and bone marrow aspirate preparations without reliance on metaphase chromosome preparations. It will be of particular value for cases with a failed conventional analysis or when a fast turnaround time is required.

Bone Marrow Conventional Karyotyping and Fluorescence In Situ Hybridization: Defining an Effective Utilization Strategy for Evaluation of Myelodysplastic Syndromes

OBJECTIVES

The current standard of practice for evaluation of myelodysplastic syndromes (MDS) includes peripheral blood and bone marrow morphology review and conventional karyotyping. Karyotype provides a global view of the chromosome complement while fluorescence in situ hybridization (FISH) targets specific abnormalities. The aim of this study was to determine if an MDS-FISH panel would add value beyond karyotype in MDS workup.

METHODS

We studied 505 patients who were evaluated for a possible MDS and had concurrent bone marrow examination, karyotyping, and MDS-FISH performed.

RESULTS

In total, 462 cases had adequate karyotyping (≥20 metaphases) and showed excellent concordance (96%, 445/462) between karyotyping and MDS-FISH. Additional FISH abnormalities had no impact on diagnosis and minimal impact on the cytogenetic prognostic scoring in the myeloid neoplasm cases (2%, 4/206). The concordance rate dropped to 82% (32/39) in the group with insufficient karyotyping (<20 metaphases), and additional FISH findings in this subgroup had no impact on the diagnosis but altered the cytogenetic prognostic scoring in 10% (2/20) of myeloid neoplasm cases.

CONCLUSIONS

In the evaluation of a possible MDS, FISH rarely provides additional value when karyotype is adequate. We propose a value-based, cost-effective algorithmic approach for conventional karyotyping and FISH testing in routine MDS workup.

The Dohner fluorescence in situ hybridization prognostic classification of chronic lymphocytic leukaemia (CLL): the CLL Research Consortium experience

This study revisited the Dohner prognostic hierarchy in a cohort of 1585 well-documented patients with chronic lymphocytic leukaemia. The duration of both time to first treatment (TTFT) and overall survival (OS) were significantly longer than observed previously, and this is at least partly due to improved therapeutic options. Deletion 13q remains the most favourable prognostic group with median TTFT and OS from fluorescence in situ hybridization (FISH) testing of 72 months and >12 years, respectively. Deletion 11q had the poorest median TTFT (22 months) and 17p deletion the poorest median OS (5 years). The percentages of abnormal nuclei were significantly associated with differential TTFT for the trisomy 12, 13q and 17p deletion cohorts but not for the 11q deletion cohort. From the date of the first FISH study, patients with >85% 13q deletion nuclei had a notably shorter TTFT (24 months). Patients with ≤20% 17p deletion nuclei had longer median TTFT and OS from the date of the first FISH study (44 months and 11 years), and were more likely to be IGHV mutated.

Hypogammaglobulinemia in newly diagnosed chronic lymphocytic leukemia: Natural history, clinical correlates, and outcomes

BACKGROUND

Although hypogammaglobulinemia is a well recognized complication in patients with chronic lymphocytic leukemia (CLL), its prevalence at the time of CLL diagnosis, and association with novel prognostic markers and clinical outcome is not well understood.

METHODS

All patients at the Mayo Clinic between January 1999 and July 2013 who had newly diagnosed CLL and had a baseline assessment of serum immunoglobulin G (IgG) were included. The relation between hypogammaglobulinemia at diagnosis and the novel prognostic parameters time to first treatment (TFT) and overall survival (OS) were evaluated.

RESULTS

Of 1485 patients who met the eligibility criteria, 382 (26%) had hypogammaglobulinemia (median IgG, 624 mg/dL), whereas the remaining 1103 patients (74%) had normal serum IgG levels (median IgG, 1040 mg/dL). Patients who had hypogammaglobulinemia at diagnosis were more likely to have advanced Rai stage (III-IV; P = .001) and higher expression of CD49d (P < .001) compared with patients who had normal IgG levels. Although the median TFT for patients who had hypogammaglobulinemia was shorter compared with that for patients who had normal IgG levels (3.8 years vs 7.4 years; P < .001), on multivariable analysis, there was no difference in OS between these 2 groups (12.8 years vs 11.3 years, respectively; P = .73). Of 1103 patients who had CLL with normal IgG levels at diagnosis and who did not receive CLL therapy, the risk of acquired hypogammaglobulinemia was 11% at 5 years and 23% at 10 years.

CONCLUSIONS

Hypogammaglobulinemia is present in 25% of patients with newly diagnosed CLL. Approximately 25% of patients who have CLL with normal IgG levels at diagnosis will subsequently develop hypogammaglobulinemia on long-term follow-up. The presence of hypogammaglobulinemia does not appear to impact overall survival.

Conventional karyotyping and fluorescence in situ hybridization: an effective utilization strategy in diagnostic adult acute myeloid leukemia

OBJECTIVES

Cytogenetics defines disease entities and predicts prognosis in acute myeloid leukemia (AML). Conventional karyotyping provides a comprehensive view of the genome, while fluorescence in situ hybridization (FISH) detects targeted abnormalities. The aim of this study was to compare the utility of karyotyping and FISH in adult AML.

METHODS

We studied 250 adult AML cases with concurrent karyotyping and FISH testing. Karyotyping was considered adequate when 20 or more metaphases were analyzed.

RESULTS

In total, 220 cases had adequate karyotyping and were classified as normal karyotype/normal FISH (n = 92), normal karyotype/abnormal FISH (n = 4), abnormal karyotype/normal FISH (n = 8), and abnormal karyotype/abnormal FISH (n = 116). The overall karyotype/FISH concordance rate was 97.7% with five discordant cases identified, four from the normal karyotype/abnormal FISH group and one from the abnormal karyotype/abnormal FISH group. No karyotype/FISH discordance was seen in the abnormal karyotype/normal FISH group for the FISH probes evaluated. FISH lent prognostic information in one (0.5%) of 220 cases with normal karyotype/abnormal FISH: CBFB-MYH11 fusion, indicating favorable prognosis.

CONCLUSIONS

In adult AML, FISH rarely provides additional information when karyotyping is adequate. We therefore propose an evidence-based, cost-effective algorithmic approach for routine conventional karyotype and FISH testing in adult AML workup.

Patients with chronic lymphocytic leukaemia and clonal deletion of both 17p13.1 and 11q22.3 have a very poor prognosis

Detection of a 17p13.1 deletion (loss of TP53) or 11q22.3 deletion (loss of ATM), by fluorescence in situ hybridization (FISH), in chronic lymphocytic leukaemia (CLL) patients is associated with a poorer prognosis. Because TP53 and ATM are integral to the TP53 pathway, we hypothesized that 17p13.1- (17p-) and 11q22.3- (11q-) occurring in the same cell (clonal 17p-/11q-) would confer a worse prognosis than either 17p- or 11q-. We studied 2184 CLL patients with FISH (1995-2012) for the first occurrence of 17p-, 11q-, or clonal 17p-/11q-. Twenty (1%) patients had clonal 17p-/11q-, 158 (7%) had 17p- (including 4 with 17p- and 11q- in separate clones), 247 (11%) had 11q-, and 1759 (81%) had neither 17p- nor 11q-. Eleven of 15 (73%) tested patients with clonal 17p-/11q- had dysfunctional TP53 mutations. Overall survival for clonal 17p-/11q- was significantly shorter (1·9 years) than 17p- (3·1 years, P = 0·04), 11q- (4·8 years, P ≤ 0·0001), or neither 17p- nor 11q- (9·3 years, P ≤ 0·0001). Clonal 17p-/11q- thus conferred significantly worse prognosis, suggesting that loss of at least one copy of both TP53 and ATM causes more aggressive disease. Use of an ATM/TP53 combination FISH probe set could identify these very-high risk patients.

Long QT syndrome-associated mutations in intrauterine fetal death

IMPORTANCE

Intrauterine fetal death or stillbirth occurs in approximately 1 out of every 160 pregnancies and accounts for 50% of all perinatal deaths. Postmortem evaluation fails to elucidate an underlying cause in many cases. Long QT syndrome (LQTS) may contribute to this problem.

OBJECTIVE

To determine the spectrum and prevalence of mutations in the 3 most common LQTS susceptible genes (KCNQ1, KCNH2, and SCN5A) for a cohort of unexplained cases.

DESIGN, SETTING, AND PATIENTS

In this case series, retrospective postmortem genetic testing was conducted on a convenience sample of 91 unexplained intrauterine fetal deaths (mean [SD] estimated gestational age at fetal death, 26.3 [8.7] weeks) that were collected from 2006-2012 by the Mayo Clinic, Rochester, Minnesota, or the Fondazione IRCCS Policlinico San Matteo, Pavia, Italy. More than 1300 ostensibly healthy individuals served as controls. In addition, publicly available exome databases were assessed for the general population frequency of identified genetic variants.

MAIN OUTCOMES AND MEASURES

Comprehensive mutational analyses of KCNQ1 (KV7.1, LQTS type 1), KCNH2 (HERG/KV11.1, LQTS type 2), and SCN5A (NaV1.5, LQTS type 3) were performed using denaturing high-performance liquid chromatography and direct DNA sequencing on genomic DNA extracted from decedent tissue. Functional analyses of novel mutations were performed using heterologous expression and patch-clamp recording.

RESULTS

The 3 putative LQTS susceptibility missense mutations (KCNQ1, p.A283T; KCNQ1, p.R397W; and KCNH2 [1b], p.R25W), with a heterozygous frequency of less than 0.05% in more than 10 000 publicly available exomes and absent in more than 1000 ethnically similar control patients, were discovered in 3 intrauterine fetal deaths (3.3% [95% CI, 0.68%-9.3%]). Both KV7.1-A283T (16-week male) and KV7.1-R397W (16-week female) mutations were associated with marked KV7.1 loss-of-function consistent with in utero LQTS type 1, whereas the HERG1b-R25W mutation (33.2-week male) exhibited a loss of function consistent with in utero LQTS type 2. In addition, 5 intrauterine fetal deaths hosted SCN5A rare nonsynonymous genetic variants (p.T220I, p.R1193Q, involving 2 cases, and p.P2006A, involving 2 cases) that conferred in vitro electrophysiological characteristics consistent with potentially proarrhythmic phenotypes.

CONCLUSIONS AND RELEVANCE

In this molecular genetic evaluation of 91 cases of intrauterine fetal death, missense mutations associated with LQTS susceptibility were discovered in 3 cases (3.3%) and overall, genetic variants leading to dysfunctional LQTS-associated ion channels in vitro were discovered in 8 cases (8.8%). These preliminary findings may provide insights into mechanisms of some cases of stillbirth.

When are apparently non-clonal abnormalities in bone marrow chromosome studies actually clonal?

The observation of an apparently non-clonal abnormal cell in a cytogenetic study for a hematologic neoplasm opens the possibility of a small, or slowly proliferating, abnormal clone. Many laboratories analyze additional cells or reflex to fluorescence in situ hybridization (FISH) to evaluate this possibility further. In a retrospective study of 500 cases with a non-clonal abnormal cell identified in a 20-cell analysis, we found that the benefit of additional metaphase analysis was limited to specific categories of abnormal karyotypes, including those with a complex karyotype or a classic abnormality known to be a recurring finding in hematologic neoplasms, and excluding all other categories.

Clinical diagnostic testing for the cytogenetic and molecular causes of male infertility: the Mayo Clinic experience

PURPOSE

Approximately 8% of couples attempting to conceive are infertile and male infertility accounts for approximately 50% of infertility among couples. Up to 25% of males with non-obstructive infertility have chromosomal abnormalities and/or microdeletions of the long arm of the Y-chromosome. These are detected by conventional chromosome and Y-microdeletion analysis. In this study, we reviewed the results of testing performed in the Mayo Clinic Cytogenetics and Molecular Genetics Laboratories and compared our findings with previously published reports.

METHODS

This study includes 2,242 chromosome studies from males ≥18 years of age referred for infertility between 1989 and 2000 and 2,749 Y-deletion molecular studies performed between 2002 and 2009.

RESULTS

14.3% of infertile males tested by karyotyping had abnormalities identified. These include: (258) 47,XXY and variants consistent with Klinefelter syndrome, (3) combined 47,XXY and balanced autosomal rearrangements, (9) 47,XYY, (9) Y-deletions, (7) 46,XX males, (32) balanced rearrangements, and (1) unbalanced rearrangement. 3.6% of males tested for Y-microdeletion analysis had abnormalities identified, 90% of which included a deletion of the AZFc region.

CONCLUSIONS

This study highlights the need of males suffering from non-obstructive infertility to have laboratory genetic testing performed. An abnormal finding can have significant consequences to assisted reproductive techniques and fertility treatment, and provide a firm diagnosis to couples with longstanding infertility.

Standardization of fluorescence in situ hybridization studies on chronic lymphocytic leukemia (CLL) blood and marrow cells by the CLL Research Consortium

Five laboratories in the Chronic Lymphocytic Leukemia (CLL) Research Consortium (CRC) investigated standardizing and pooling of fluorescence in situ hybridization (FISH) results as a collaborative research project. This investigation used fixed bone marrow and blood cells available from previous conventional cytogenetic or FISH studies in two pilot studies, a one-day workshop, and proficiency test. Multiple FISH probe strategies were used to detect 6q-, 11q-, +12, 13q-, 17p-, and IGH rearrangements. Ten specimens were studied by participants who used their own probes (pilot study 1). Of 312 FISH interpretations, 224 (72%) were true-negative, 74 (24%) true-positive, 6 (2%) false-negative, and 8 (3%) false-positive. In pilot study no. 2, each participant studied two specimens using identical FISH probe sets to control for variation due to probe sets and probe strategies. Of 80 FISH interpretations, no false interpretations were identified. At a subsequent workshop, discussions produced agreement on scoring criteria. The proficiency test that followed produced no false-negative results and 4% (3/68) false-positive interpretations. Interpretation disagreements among laboratories were primarily attributable to inadequate normal cutoffs, inconsistent scoring criteria, and the use of different FISH probe strategies. Collaborative organizations that use pooled FISH results may wish to impose more conservative empiric normal cutoff values or use an equivocal range between the normal cutoff and the abnormal reference range to eliminate false-positive interpretations. False-negative results will still occur, and would be expected in low-percentage positive cases; these would likely have less clinical significance than false positive results. Individual laboratories can help by closely following rigorous quality assurance guidelines to ensure accurate and consistent FISH studies in their clinical practice and research.

Stimulation of chronic lymphocytic leukemia cells with CpG oligodeoxynucleotide gives consistent karyotypic results among laboratories: a CLL Research Consortium (CRC) Study

Cytogenetic abnormalities are important prognostic indicators in CLL. Historically, only interphase cytogenetics was clinically useful in CLL, because traditional mitogens are not effective mitotic stimulants. Recently, CpG-oligodeoxynucleotide (ODN) stimulation has shown effectiveness in CLL cells. The CLL Research Consortium tested the effectiveness and reproducibility of CpG-ODN stimulation for detecting chromosomally abnormal clones by five laboratories. More clonal abnormalities were observed after culture of CLL cells with CpG-ODN than with the traditional pokeweed mitogen plus 12-O-tetradecanoylphorbol-13-acetate (PWM+TPA). All clonal abnormalities in PWM+TPA cultures were observed in CpG-ODN cultures, whereas CpG-ODN identified some clones not found by PWM+TPA. CpG-ODN stimulation of one normal control sample and 12 CLL samples showed that, excepting clones of del(13q) in low frequencies and one translocation, results in all five laboratories were consistent, and all abnormalities were concordant with FISH. Abnormal clones in CLL were more readily detected with CpG-ODN stimulation than with traditional B-cell mitogens. With CpG-ODN stimulation, abnormalities were reproducible among cytogenetic laboratories. CpG-ODN did not appear to induce aberrations in cell culture, but did enhance detection of abnormalities and complexity in CLL. Because karyotypic complexity is prognostic and is not detectable by standard FISH analyses, stimulation with CpG-ODN is useful for identifying this additional prognostic factor in CLL.

Nearly identical near-haploid karyotype in a peritoneal mesothelioma and a retroperitoneal malignant peripheral nerve sheath tumor

The presence of a near-haploid karyotype is a rare finding in human malignancies, most frequently occurring in acute leukemia. In solid tumors, a near-haploid karyotype has been reported in fewer than 40 cases. We report two nearly identical near-haploid karyotypes from two distinctly different tumor types. The first case is a biphasic malignant mesothelioma from a 53-year-old white woman forming a large retroperitoneal mass. Cytogenetic evaluation revealed a primary hyperdiploid cell population as well as near-haploid and hypertetraploid populations with an overall karyotype of 27,XX,i(5)(p10),+7,add(15)(p11.2),+dic(1;20)(p13;p13)[2]/54,idemx2[90]/101-108,idemx4[19]. The second case is a large pelvic mass from a 48-year-old man. Histologic examination identified a malignant peripheral nerve sheath tumor displaying a karyotype of 26,X,+i(5)(p10),+7,der(15)t(1;15)(q12;p12),+20[5]/52,idemx2[20]. Herein we discuss the potential relationship between these two disparate neoplasms with nearly identical near-haploid karyotypes and present a literature review.

Dosage regulation of the active X chromosome in human triploid cells

In mammals, dosage compensation is achieved by doubling expression of X-linked genes in both sexes, together with X inactivation in females. Up-regulation of the active X chromosome may be controlled by DNA sequence–based and/or epigenetic mechanisms that double the X output potentially in response to autosomal factor(s). To determine whether X expression is adjusted depending on ploidy, we used expression arrays to compare X-linked and autosomal gene expression in human triploid cells. While the average X:autosome expression ratio was about 1 in normal diploid cells, this ratio was lower (0.81–0.84) in triploid cells with one active X and higher (1.32–1.4) in triploid cells with two active X's. Thus, overall X-linked gene expression in triploid cells does not strictly respond to an autosomal factor, nor is it adjusted to achieve a perfect balance. The unbalanced X:autosome expression ratios that we observed could contribute to the abnormal phenotypes associated with triploidy. Absolute autosomal expression levels per gene copy were similar in triploid versus diploid cells, indicating no apparent global effect on autosomal expression. In triploid cells with two active X's our data support a basic doubling of X-linked gene expression. However, in triploid cells with a single active X, X-linked gene expression is adjusted upward presumably by an epigenetic mechanism that senses the ratio between the number of active X chromosomes and autosomal sets. Such a mechanism may act on a subset of genes whose expression dosage in relation to autosomal expression may be critical. Indeed, we found that there was a range of individual X-linked gene expression in relation to ploidy and that a small subset (∼7%) of genes had expression levels apparently proportional to the number of autosomal sets.

Many organisms have a single X chromosome in males and two in females, leading to a chromosome imbalance between autosomes and sex chromosomes and between the sexes. In mammals, this dosage imbalance is adjusted by doubling expression of X-linked genes in both sexes and by silencing one X chromosome in females. We used expression array analyses of human triploid cultures to test X chromosome expression in the presence of three sets of autosomes and address the question of an autosomal counting factor. We found that overall X-linked gene expression is not tripled in the presence of three sets of autosomes. However, in triploid cells with a single active X chromosome, its expression is adjusted upward presumably by an epigenetic mechanism that senses the active X/autosome ratio. Based on the range of individual gene expression we identified a subset of dosage-sensitive genes whose expression is apparently proportional to the ploidy. Our findings are important for understanding the regulation of the X chromosome and the role of ploidy in the balance of gene expression and associated phenotypes.

A comprehensive evaluation of the prognostic significance of 13q deletions in patients with B-chronic lymphocytic leukaemia

Deletion 13q14 on fluorescence in situ hybridization (FISH) analysis is the most common cytogenetic abnormality in chronic lymphocytic leukaemia (CLL), and is a favourable prognostic biomarker when detected as a sole abnormality. We intensively interrogated clinical outcome in 323 consecutive, untreated CLL patients with isolated 13q- identified within 2 years of diagnosis. We also analyzed outcome in 217 additional patients with deletion 11q22.3 or 17p13.1, or trisomy 12, based on whether these occurred in isolation or in conjunction with 13q-. Patients with a heterozygous 13q- and those with a homozygous deletion had similar time to first treatment (TFT) and overall survival (OS). In contrast, a higher percentage of 13q- nuclei was associated with significantly shorter TFT (P < 0.001). The 5-year untreated rate was 79% for patients with isolated 13q- in < or =65.5% of nuclei compared to 38% among those with 13q- in >65.5% of nuclei (P < 0.001). The percentage of nuclei exhibiting 13q- remained an independent predictor of TFT after controlling for ZAP-70, IGHV, or CD38 (all P < 0.001). Among patients with 13q- plus one other FISH abnormality, concomitant 13q- appeared to attenuate the shorter survival associated with 17p- (P = 0.019). The clinical implications of 13q- in CLL appear more complex than originally appreciated.

Fluorescence in situ hybridization to visualize genetic abnormalities in interphase cells of acinar cell carcinoma, ductal adenocarcinoma, and islet cell carcinoma of the pancreas

OBJECTIVE

To use fluorescence in situ hybridization (FISH) to visualize genetic abnormalities in interphase cell nuclei (interphase FISH) of acinar cell carcinoma, ductal adenocarcinoma, and islet cell carcinoma of the pancreas.

PATIENTS AND METHODS

Between April 4, 2007, and December 4, 2008, interphase FISH was used to study paraffin-embedded preparations of tissue obtained from 18 patients listed in the Mayo Clinic Biospecimen Resource for Pancreas Research with a confirmed diagnosis of acinar cell carcinoma, ductal adenocarcinoma, islet cell carcinoma, or pancreas without evidence of neoplasia. FISH probes were used for chromosome loci of APC (see glossary at end of article for expansion of all gene symbols), BRCA2, CTNNB1, EGFR, ERBB2, CDKN2A, TP53, TYMP, and TYMS. These FISH probes were used with control probes to distinguish among various kinds of chromosome abnormalities of number and structure.

RESULTS

FISH abnormalities were observed in 12 (80%) of 15 patients with pancreatic cancer: 5 of 5 patients with acinar cell carcinoma, 5 of 5 patients with ductal adenocarcinoma, and 2 (40%) of 5 patients with islet cell carcinoma. All 3 specimens of pancreatic tissue without neoplasia had normal FISH results. Gains of CTNNB1 due to trisomy 3 occurred in each tumor with acinar cell carcinoma but in none of the other tumors in this study. FISH abnormalities of all other cancer genes studied were observed in all forms of pancreatic tumors in this investigation.

CONCLUSION

FISH abnormalities of CTNNB1 due to trisomy 3 were observed only in acinar cell carcinoma. FISH abnormalities of genes implicated in familial cancer, tumor progression, and the 5-fluorouracil pathway were common but were not associated with specific types of pancreatic cancer.

Fluorescence in situ hybridization to visualize genetic abnormalities in interphase cells of acinar cell carcinoma, ductal adenocarcinoma, and islet cell carcinoma of the pancreas

OBJECTIVE

To use fluorescence in situ hybridization (FISH) to visualize genetic abnormalities in interphase cell nuclei (interphase FISH) of acinar cell carcinoma, ductal adenocarcinoma, and islet cell carcinoma of the pancreas.

PATIENTS AND METHODS

Between April 4, 2007, and December 4, 2008, interphase FISH was used to study paraffin-embedded preparations of tissue obtained from 18 patients listed in the Mayo Clinic Biospecimen Resource for Pancreas Research with a confirmed diagnosis of acinar cell carcinoma, ductal adenocarcinoma, islet cell carcinoma, or pancreas without evidence of neoplasia. FISH probes were used for chromosome loci of APC (see glossary at end of article for expansion of all gene symbols), BRCA2, CTNNB1, EGFR, ERBB2, CDKN2A, TP53, TYMP, and TYMS. These FISH probes were used with control probes to distinguish among various kinds of chromosome abnormalities of number and structure.

RESULTS

FISH abnormalities were observed in 12 (80%) of 15 patients with pancreatic cancer: 5 of 5 patients with acinar cell carcinoma, 5 of 5 patients with ductal adenocarcinoma, and 2 (40%) of 5 patients with islet cell carcinoma. All 3 specimens of pancreatic tissue without neoplasia had normal FISH results. Gains of CTNNB1 due to trisomy 3 occurred in each tumor with acinar cell carcinoma but in none of the other tumors in this study. FISH abnormalities of all other cancer genes studied were observed in all forms of pancreatic tumors in this investigation.

CONCLUSION

FISH abnormalities of CTNNB1 due to trisomy 3 were observed only in acinar cell carcinoma. FISH abnormalities of genes implicated in familial cancer, tumor progression, and the 5-fluorouracil pathway were common but were not associated with specific types of pancreatic cancer.