Whole-genome informed circulating tumor DNA analysis by multiplex digital PCR for disease monitoring in B-cell lymphomas: a proof-of-concept study

Introduction

Analyzing liquid biopsies for tumor-specific aberrations can facilitate detection of measurable residual disease (MRD) during treatment and at follow-up. In this study, we assessed the clinical potential of using whole-genome sequencing (WGS) of lymphomas at diagnosis to identify patient-specific structural (SVs) and single nucleotide variants (SNVs) to enable longitudinal, multi-targeted droplet digital PCR analysis (ddPCR) of cell-free DNA (cfDNA).

Methods

In 9 patients with B-cell lymphoma (diffuse large B-cell lymphoma and follicular lymphoma), comprehensive genomic profiling at diagnosis was performed by 30X WGS of paired tumor and normal specimens. Patient-specific multiplex ddPCR (m-ddPCR) assays were designed for simultaneous detection of multiple SNVs, indels and/or SVs, with a detection sensitivity of 0.0025% for SV assays and 0.02% for SNVs/indel assays. M-ddPCR was applied to analyze cfDNA isolated from serially collected plasma at clinically critical timepoints during primary and/or relapse treatment and at follow-up.

Results

A total of 164 SNVs/indels were identified by WGS including 30 variants known to be functionally relevant in lymphoma pathogenesis. The most frequently mutated genes included KMT2D, PIM1, SOCS1 and BCL2. WGS analysis further identified recurrent SVs including t(14;18)(q32;q21) (IGH::BCL2), and t(6;14)(p25;q32) (IGH::IRF4). Plasma analysis at diagnosis showed positive circulating tumor DNA (ctDNA) levels in 88% of patients and the ctDNA burden correlated with baseline clinical parameters (LDH and sedimentation rate, p-value <0.01). While clearance of ctDNA levels after primary treatment cycle 1 was observed in 3/6 patients, all patients analyzed at final evaluation of primary treatment showed negative ctDNA, hence correlating with PET-CT imaging. One patient with positive ctDNA at interim also displayed detectable ctDNA (average variant allele frequency (VAF) 6.9%) in the follow-up plasma sample collected 2 years after final evaluation of primary treatment and 25 weeks before clinical manifestation of relapse.

Conclusion

In summary, we demonstrate that multi-targeted cfDNA analysis, using a combination of SNVs/indels and SVs candidates identified by WGS analysis, provides a sensitive tool for MRD monitoring and can detect lymphoma relapse earlier than clinical manifestation.

Different prognostic impact of recurrent gene mutations in chronic lymphocytic leukemia depending on IGHV gene somatic hypermutation status: a study by ERIC in HARMONY

Recent evidence suggests that the prognostic impact of gene mutations in patients with chronic lymphocytic leukemia (CLL) may differ depending on the immunoglobulin heavy variable (IGHV) gene somatic hypermutation (SHM) status. In this study, we assessed the impact of nine recurrently mutated genes (BIRC3, EGR2, MYD88, NFKBIE, NOTCH1, POT1, SF3B1, TP53, and XPO1) in pre-treatment samples from 4580 patients with CLL, using time-to-first-treatment (TTFT) as the primary end-point in relation to IGHV gene SHM status. Mutations were detected in 1588 (34.7%) patients at frequencies ranging from 2.3-9.8% with mutations in NOTCH1 being the most frequent. In both univariate and multivariate analyses, mutations in all genes except MYD88 were associated with a significantly shorter TTFT. In multivariate analysis of Binet stage A patients, performed separately for IGHV-mutated (M-CLL) and unmutated CLL (U-CLL), a different spectrum of gene alterations independently predicted short TTFT within the two subgroups. While SF3B1 and XPO1 mutations were independent prognostic variables in both U-CLL and M-CLL, TP53, BIRC3 and EGR2 aberrations were significant predictors only in U-CLL, and NOTCH1 and NFKBIE only in M-CLL. Our findings underscore the need for a compartmentalized approach to identify high-risk patients, particularly among M-CLL patients, with potential implications for stratified management.

Precision diagnostics in lymphomas - Recent developments and future directions

Genetics is an integral part of the clinical diagnostics of lymphomas that improves disease subclassification and patient risk-stratification. With the introduction of high-throughput sequencing technologies, a rapid, in-depth portrayal of the genomic landscape in major lymphoma entities was achieved. Whilst a few lymphoma entities were characterized by a predominant gene mutation (e.g. Waldenström's macroglobulinemia and hairy cell leukemia), the vast majority demonstrated a very diverse genetic landscape with a high number of recurrent gene mutations (e.g. chronic lymphocytic leukemia and diffuse large B cell lymphoma), indeed reflecting the great clinical heterogeneity among lymphomas. These studies have allowed better understanding of the ontogeny and evolution of different lymphomas, while also identifying new genetic markers that can complement lymphoma diagnostics and improve prognostication. However, despite these efforts, there is still a limited number of gene mutations with predictive impact that can guide treatment selection. In this review, we will highlight clinically relevant diagnostic, prognostic and predictive markers in lymphomas that are used today in routine diagnostics. We will also discuss how comprehensive genomic characterization using broad sequencing panels, allowing for the simultaneous detection of different types of genetic aberrations, may aid future development of precision diagnostics in lymphomas. This may in turn pave the way for the implementation of tailored precision therapy strategies at the individual patient level.

Diagnostic imaging trends in the emergency department: an extensive single-center experience

Background

Emergency Department imaging volume has increased significantly in North America and Asia.

Purpose

To assess Emergency Department imaging trends in a European center.

Material and Methods

The institutional radiological information system was queried for all computed tomography (CT), ultrasound (US), and magnetic resonance (MR) studies performed for the Emergency Department during 2002–2017. Descriptive statistics and linear regression analyses were used to assess overall study rates and temporal trends in overall and after-hours imaging after adjusting for patient visitations.

Results

CT use increased significantly from 38/1000 visits to 108/1000 at the end of the observation by 5.5 new exams per 1000 visits/year (P < 0.0001). US use increased gradually at a rate of 1.2/1000 per year during 2002–2008 with an accelerated annual increase of 6.4/1000 in 2009–2011 (P < 0.0001) raising US rates from 7/1000 to 28/1000 visits per year with stable rates from 2012 onwards. After on-site MR became available in 2004, its use increased from 0.3/1000 to 7/1000 at a rate of 1.9/1000 visits per year in 2005–2009 (P < 0.0001) and remained stable from 2010. While there was a significant increase in after-hours imaging, growth remained proportional to the overall trend in the use of CT, MR, and night-time CT with the exception of a slight decrease in after-hour US in favor of standard working hours (P < 0.0001).

Conclusion

All modalities increased significantly in volume adjusted usage. US and MR rates have been stable since 2012 and 2010, respectively, after periods of increase while CT use continues to increase. Demand for after-hours imaging was mostly proportional to the overall trend.

Abstract 3371: Analysis of telomere length and dysfunction in normal breast tissue from BRCA2 mutation carriers

The tumor suppressor protein BRCA2 is important for maintaining genomic stability. BRCA2 is essential for homologous recombination repair of DNA double strand breaks and also has a role in protection of stalled replication forks as well as in telomere protection and maintenance. Disruptions in telomere homeostasis can result in excessive telomere shortening and drive chromosome instability, a hallmark of BRCA2-related cancers. Germline mutations in the BRCA2 gene are associated with highly increased risk of breast cancer. A single deleterious founder mutation, BRCA2999del5, has been detected in the gene in the Icelandic population, making it feasible to study the influence of a single mutation at a population level. The BRCA2999del5 mutation is found in 6-7% of female breast cancer patients in Iceland and is associated with complex chromosomal changes in tumor tissue. Furthermore, the BRCA2999del5 mutation is associated with poor prognosis, although mutation carriers seem to differ with respect to age of onset and severity of disease. It is therefore of great interest to identify factors that influence breast cancer risk within the mutation carrier group. The aim of the study was to measure telomere length (TL) and levels of telomere dysfunction in tumor-adjacent normal breast tissue from BRCA2 mutation carriers and non-carriers and investigate their potential relationship with breast cancer risk. The study group consisted of 186 Icelandic breast cancer patients; BRCA2999del5 mutation carriers and sporadic cases, matched with respect to age and year of diagnosis. For TL measurements, paraffin embedded normal breast tissue samples were analyzed by Quantitative Fluorescence in Situ Hybridization. Telomere dysfunction induced foci (TIFs) can be detected where co-localization of telomere and DNA-damage signals occur. For this purpose, the samples were also immunofluorocently stained for the DNA damage repair protein 53BP1. In concordance with previously reported data in the literature, luminal epithelial cells showed the shortest TL and highest number TIFs of the cell types in normal breast tissue. This observation is highly relevant as these are the cells from which most breast cancers originate. No difference was detected in age-adjusted TL between BRCA2 mutation carriers and non-carriers. However, consistent with our recently published data from TL measurements in blood from the same study group, shorter TL is correlated with younger age at breast cancer diagnosis in BRCA2 mutation carriers but not in non-carriers. In conclusion, these results indicate that in BRCA2 mutation carriers, shorter TL in normal breast tissue is associated with earlier breast cancer occurrence.

Citation Format: Birna Thorvaldsdottir, Beth A. Cimini, Morgan E. Diolaiti, Katrin Olafsdottir, Jon G. Jonasson, Jorunn E. Eyfjörd. Analysis of telomere length and dysfunction in normal breast tissue from BRCA2 mutation carriers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3371.

Telomere Length Is Predictive of Breast Cancer Risk in BRCA2 Mutation Carriers

Background: Germline BRCA2 mutations increase risk of breast cancer and other malignancies. BRCA2 has been shown to play a role in telomere protection and maintenance. Telomere length (TL) has been studied as a modifying factor for various diseases, including breast cancer. Previous research on TL in BRCA mutation carriers has produced contradicting results.Methods: We measured blood TL, using a high-throughput monochrome multiplex qPCR method, in a well-defined Icelandic cohort of female BRCA2 mutation carriers (n = 169), sporadic breast cancer patients (n = 561), and healthy controls (n = 537).Results: Breast cancer cases had significantly shorter TL than unaffected women (P < 0.0001), both BRCA2 mutation carriers (P = 0.0097) and noncarriers (P = 0.00006). Using exclusively samples acquired before breast cancer diagnosis, we found that shorter telomeres were significantly associated with increased breast cancer risk in BRCA2 mutation carriers [HR, 3.60; 95% confidence interval (CI), 1.17-11.28; P, 0.025] but not in non-carriers (HR,1.40; 95% CI, 0.89-2.22; P, 0.15). We found no association between TL and breast cancer-specific survival.Conclusions: Blood TL is predictive of breast cancer risk in BRCA2 mutation carriers. Breast cancer cases have significantly shorter TL than unaffected women, regardless of BRCA2 status, indicating that samples taken after breast cancer diagnosis should not be included in evaluations of TL and breast cancer risk.Impact: Our study is built on a well-defined cohort, highly accurate methods, and long follow-up and can therefore help to clarify some previously published, contradictory results. Our findings also suggest that BRCA2 has an important role in telomere maintenance, even in normal blood cells. Cancer Epidemiol Biomarkers Prev; 26(8); 1248-54. ©2017 AACR.

Abstract A26: Telomere length in normal and tumor breast tissue from BRCA2 mutation carriers and sporadic breast cancer cases

Germline mutations in the BRCA genes are associated with highly increased risk of breast and ovarian cancers and to a lesser extent to prostate and pancreatic cancers. Great number of mutations with variable impact on cancer risk and progression are known in these genes worldwide. A single founder mutation has been detected in each of the BRCA genes in the Icelandic population, making it feasible to study the influence of a single mutation at a population level. The BRCA2999del5 mutation is more frequent and can be found in approximately 6-7% of female breast cancer patients and 40% of male breast cancer patients in Iceland. The mutation leads to a non-functional protein product and is associated with complex chromosomal changes in tumor tissue. Furthermore, the BRCA2999del5 mutation has been associated with poor prognosis, both in breast and prostate cancers, although mutation carriers seem to differ with respect to age of onset and severity of disease.

Dysfunctional telomere maintenance can lead to excessive telomere shortening which causes chromosome instability. It is therefore a driving force behind cancer progression and is considered a hallmark of many human cancers. Telomere shortening has been shown to be an early and a common molecular alteration in epithelial cancers, including breast cancers. Previous results from our laboratory, amongst others, have shown that BRCA2 is associated with telomere protection and maintenance. Telomere dysfunction induced foci (TIFs) formation was detected in cell lines derived from heterozygous BRCA2999del5 mutation carriers1. Telomere length has been proposed as a possible predictive factor for cancer risk for various cancers. In the case of breast cancer and BRCA mutation carriers, the results have been conflicting.

The aim of the study was to investigate if telomere length in normal and tumor breast tissue is correlated with breast cancer progression and survival in a well-defined group of BRCA2 mutation carriers and sporadic breast cancer cases.

The study group consisted of breast cancer patients carrying the BRCA2999del5 Icelandic founder mutation and sporadic cases, matched with respect to age and year of diagnosis. Tumor and normal adjacent tissue samples from these patients were embedded in paraffin and Quantitative Fluorescence in Situ Hybridization method (Q-FISH) was used to carry out telomere length measurements. Telomeres were visualized using a telomeric sequence-specific fluorescence peptide nucleic acid (PNA) probe. A centromere-specific PNA probe was used as an inner control for hybridization efficiency.

The results show a clear difference in telomere length of different cell types in normal breast tissue with inner epithelial cells having shorter telomeres than both myoepithelial cells and fibroblasts. These findings support previously reported data in the literature2. The majority of examined tumors have very short telomeres. In mutation carriers, there are indications that less variable telomere length in normal adjacent tissue is associated with reduced breast cancer specific survival. This seems to be more pronounced in the mutation carrier group compared to the sporadic group. Telomere length in adjacent normal tissue appears to be shorter in cases with luminal type than with basal-like tumors.

References:

1. Bodvarsdottir, S. K., Steinarsdottir, M., Bjarnason, H. & Eyfjord, J. E. Dysfunctional telomeres in human BRCA2 mutated breast tumors and cell lines. Mutat. Res. Mol. Mech. Mutagen. 729, 90–99 (2012).

2. Kurabayashi, R. et al. Luminal and cancer cells in the breast show more rapid telomere shortening than myoepithelial cells and fibroblasts. Hum. Pathol. 39, 1647–1655 (2008).

Citation Format: Birna Thorvaldsdottir, Beth A. Cimini, Morgan E. Diolaiti, Margret Aradottir, Katrin Olafsdottir, Jon G. Jonasson, Elizabeth H. Blackburn, Jorunn E. Eyfjörd. Telomere length in normal and tumor breast tissue from BRCA2 mutation carriers and sporadic breast cancer cases. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr A26.