Aggressive Lymphoplasmacytic Neoplasm With an Unusual In-frame Deletion of MYD88 Associated With TRAF3 and TP53 Mutations and Complex Karyotype

Lymphoplasmacytic lymphoma often needs to be differentiated from other B-cell lymphomas with plasmacytic differentiation, especially marginal zone cell lymphoma. Molecular detection of MYD88 p.L265P hotspot mutation supports the diagnosis of lymphoplasmacytic lymphoma since it is seen in about 90% of such lymphoma, which is much higher than other B-cell lymphomas. MYD88 p.L265P is a gain-of-function mutation that enhances the activity of the NF-κB signaling pathway and therefore drives lymphomagenesis. Other mutations in MYD88 are rarely reported. This study aims to report an unusual MYD88 in-frame deletion in an aggressive lymphoplasmacytic neoplasm. This is an IgM-positive, CD5- and CD10-negative mature B-cell lymphoma with prominent plasmacytic differentiation and aggressive features. The clinical and pathologic findings were most consistent with lymphoplasmacytic lymphoma. Next-generation sequencing identified an unusual MYD88 in-frame deletion in the absence of the hotpot p.L265P mutation. Other concurrent pathogenic mutations also include truncating mutations of TRAF3, which is a negative regulator of the NF-κB signaling pathway, and a missense mutation of TP53. Karyotype analysis showed complex karyotypes, including chromosome 6q deletion. By searching literature and online cancer databases, we identified only 8 other mature B-cell lymphomas with MYD88 in-frame deletions, but none of them was diagnosed with lymphoplasmacytic lymphoma. Recognizing such in-frame deletions is necessary to help understand the mutational spectrum of MYD88 in B-cell lymphomas. It remains to be further investigated whether such MYD88 in-frame deletions are also overrepresented in lymphoplasmacytic lymphoma among other B-cell lymphomas.

Implementation of a precision medicine thoracic (PREDICT) service using reflex testing in a large academic-community practice network

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Background: Broad genomic testing is necessary for treatment of patients with stage IV non-small cell lung cancer (NSCLC). This quality improvement initiative aims to implement a precision medicine service for NSCLC patients at a hybrid academic-community practice oncology network. Methods: Following IRB approval, network tumor registries were queried for retrospective newly diagnosed stage IV NSCLC from 01/2016 through 12/2018. PREDICT was implemented in 08/2021. It consists of: 1) system-wide reflex testing of newly diagnosed stage IV NSCLC patients by an in-house solid tumor focused assay (hybrid DNA/RNA next-generation sequencing (NGS) panel previously reported) and PD-L1 testing, 2) PREDICT navigator, 3) molecular tumor board (MTB), 4) integrated information portal for real-time updates on samples processing, results and treatment recommendations by the MTB. We compared prospective data (08/2021 through 01/2022) after PREDICT with retrospective practice assessment. Comparisons between the groups were conducted using independent samples t-test / Wilcoxon rank sum test for continuous variables and Chi-square test/Fisher’s exact test for categorical variables. Results: Of 861 retrospective patients identified in the compiled registry of stage IV NSCLC, 626 were eligible. Since PREDICT launch in 08/2021, 103 eligible prospective patients have been identified. Prospective patients are slightly older (mean age 70.9 vs 68 years old; p = 0.013), with no other significant demographic or clinical differences identified. Rates of NGS testing obtained within 90 days of biopsy date (BxD) increased significantly (94.1% vs 60.8%; p < 0.0001) after PREDICT. Turnaround times (TAT) from BxD to test results were significantly shorter for both NGS (12 vs 18 days; p < 0.0001) and PD-L1 (7 vs 10 days; p = 0.007) after PREDICT. A trend towards higher rates of actionable alterations (EGFR, ALK, ROS1, RET, BRAF, MET14 skipping, NTRK1/2/3) was noted: 19.6% vs 13% (p = 0.071). Targeted therapy use increased from 6.8% to 15.6% (p = 0.002) in the overall cohort. No differences in time to treatment initiation (TTI) after PREDICT have been identified to this point, with a median of 34 and 35 days for the prospective and retrospective groups, respectively. Conclusions: Implementing a precision medicine service for thoracic oncology patients has led to significantly higher rates of NGS testing for patients with stage IV NSCLC in a large hybrid academic-community practice network. Launching of this initiative resulted in significantly shorter TAT for both NGS and PD-L1 test results. A trend towards higher rates of actionable alterations has been identified. Targeted therapy use has increased significantly overtime, potentially due to higher availability of precision medicine drugs in the current era.

Flow Cytometric Findings in Clonal Cytopenia of Undetermined Significance

OBJECTIVES

To examine flow cytometric (FCM) findings in clonal cytopenia of undetermined significance (CCUS) in relation to variant allele fraction (VAF) and mutation risk.

METHODS

Nine FCM parameters, including 5 FCM metrics (Meyerson-Alayed scoring scheme [MASS] parameters) we previously used to identify myelodysplastic syndromes (MDS), were compared among 96 CCUS samples, 100 low-grade MDS samples and 100 samples from patients without somatic alterations (controls).

RESULTS

FCM findings did not differ between CCUS samples with less than 20% VAF and controls. CCUS samples with more than 20% VAF (CCUS >20% VAF) demonstrated more than 1 abnormal FCM parameter at a frequency between MDS and controls. Abnormalities in CCUS with high-risk alterations (CCUS(hi)) were similar to MDS, with no statistical difference in the percentage of cases with more than 1 FCM abnormality or a positive MASS score. The positive predictive value (PPV) for clinically significant myeloid processes; MDS, CCUS(hi), and CCUS >20% VAF compared with other CCUS samples and controls was 94.8%, with 96.5% specificity and 61% sensitivity using a modified MASS score. A subset of MDS (43%) was distinguished from CCUS(hi) and CCUS >20% VAF using 3 parameters, with a 93.5% PPV and 83.3% specificity.

CONCLUSIONS

FCM abnormalities can distinguish high-risk CCUS based on VAF or alteration type from low-risk CCUS and MDS in many cases. The findings are of potential utility in the evaluation of patients with cytopenias.

Tiny but mighty: use of next generation sequencing on discarded cytocentrifuged bile duct brushing specimens to increase sensitivity of cytological diagnosis

Bile duct brushing (BDB) is used to evaluate pancreatobiliary lesions as it widely samples lesions with a low complication rate. Cytological evaluation of BDB is a specific but insensitive test. There is limited literature on the use of post-cytocentrifuged (PCC) samples, which are usually discarded, for next-generation sequencing (NGS) as an adjunct to cytological diagnosis of BDB. In this study we investigate whether molecular analysis by NGS of PCC specimens improves the sensitivity of diagnosis. PCC samples from 100 consecutive BDB specimens spanning 93 unique patients were retained. DNA was extracted and mutational analysis was performed agnostic of morphologic or clinical findings. Each BDB specimen was characterized as negative, atypical or positive based on morphological analysis by trained cytopathologists. Performance characteristics for mutational profiling and morphological analysis were calculated on the basis of clinicopathologic follow-up. There was sufficient clinicopathologic follow-up to classify 94 of 100 cases as either malignant (n = 43) or benign (n = 51). Based on morphologic analysis of cytology, these 94 cases were classified as either benign (n = 55), atypical (n = 18), or as at least suspicious or positive for malignancy (n = 21). Morphologic analysis of cytology showed a sensitivity of 49% and a specificity of 100% if atypical cases were considered negative. NGS revealed oncogenic alterations in 40/43 (93%) of malignant cases based on clinicopathologic follow-up. The most common alterations were in KRAS and TP53, observed in 77% and 49% of malignant cases respectively. No alterations were observed in the 51 benign cases classified based on clinicopathologic follow-up. Supplementing cytomorphologic analysis with molecular profiling of PCC by targeted NGS analysis increased the sensitivity to 93% and maintained specificity at 100%. This study provides evidence for the utility of NGS molecular profiling of PCC specimens to increase the sensitivity of BDB cytology samples, although studies with larger cohorts are needed to verify these findings.