Clonal Characterization and Somatic Hypermutation (SHM) Assessment by Next Generation Sequencing in Chronic Lymphocytic Leukemia/ Small Lymphocytic Lymphoma (CLL/SLL): A Detailed Description of the Technical Performance, Clinical Utility, and Platform Comparison

Somatic hypermutation (SHM) status of the immunoglobulin heavy variable (IGHV) gene is essential for treating chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL) patients. Unlike the conventional low-throughput method, assessment of SHM by next generation sequencing (NGS) has potential for uniformity and scalability, however it lacks standardization or guidelines for routine clinical use. We critically assessed the performance of an amplicon-based NGS assay across 458 samples. Using a validation cohort (35 samples), the comparison of two platforms (Ion Torrent vs Illumina) and two primer sets (Leader vs FR1) in their ability to identify clonotypic IGHV rearrangement(s) revealed 97% concordance. The mutation rates were identical by both platforms when using the same primer set (FR1), while a slight overestimation bias (+0.326%) was found when comparing FR1 to Leader primers. However, for nearly all patients this did not affect the stratification into mutated or unmutated categories suggesting that use of FR1 may provide comparable results if Leader sequencing is not available, while also allowing for a simpler NGS laboratory workflow. In routine clinical practice (423 samples), the productive rearrangement was successfully detected by either primer set (Leader 97.7%, FR1 94.7%) and a combination of both in problematic cases reduced the failure rate to 1.2%. Higher sensitivity of the NGS-based analysis also detected a higher frequency of double IGHV rearrangements (19.1%) compared to traditional approaches.

Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell-free DNA via paired normal sequencing using MSK-ACCESS

Circulating cell-free DNA from blood plasma of cancer patients can be used to non-invasively interrogate somatic tumor alterations. Here we develop MSK-ACCESS (Memorial Sloan Kettering - Analysis of Circulating cfDNA to Examine Somatic Status), an NGS assay for detection of very low frequency somatic alterations in 129 genes. Analytical validation demonstrated 92% sensitivity in de-novo mutation calling down to 0.5% allele frequency and 99% for a priori mutation profiling. To evaluate the performance of MSK-ACCESS, we report results from 681 prospective blood samples that underwent clinical analysis to guide patient management. Somatic alterations are detected in 73% of the samples, 56% of which have clinically actionable alterations. The utilization of matched normal sequencing allows retention of somatic alterations while removing over 10,000 germline and clonal hematopoiesis variants. Our experience illustrates the importance of analyzing matched normal samples when interpreting cfDNA results and highlights the importance of cfDNA as a genomic profiling source for cancer patients.

Liquid biopsies allow the non-invasive detection of somatic mutations from tumours. Here, the authors develop and test MSK-ACCESS, an NGS-based clinical assay for identifying low frequency mutations in 129 genes and describe how it benefits patients in the clinic.

Establishment of Immunoglobulin Heavy (IGH) Chain Clonality Testing by Next-Generation Sequencing for Routine Characterization of B-Cell and Plasma Cell Neoplasms

Immunoglobulin heavy chain (IGH) clonality testing by next-generation sequencing (NGS) offers unique advantages over current low-throughput methods in the assessment of B-cell lineage neoplasms. Clinical use remains limited because assays are not standardized and validation/implementation guidelines are not yet developed. Herein, we describe our clinical validation and implementation of NGS IGH clonality testing and summarize our experience based on extensive routine use. NGS-based clonality testing targeting IGH FR1, FR2, FR3, and the conserved leader sequence upstream of FR1 was validated using commercially available kits. Data were analyzed by commercial and in-house-developed bioinformatics pipelines. Performance characteristics were evaluated directly comparing with capillary electrophoresis (CE) assays (BIOMED-2 primers). Assays were monitored after implementation (>1.5 years), concurrently testing by CE methods. A total of 1189 clinical samples were studied (94 validation, 1095 postimplementation). NGS showed superior performance compared with CE assays. For initial assessment, clonality detection rate was >97% for all malignancy types. Concordance with CE was 96%; discordances were related to higher sensitivity/resolution of NGS and improved detection in cases with high somatic hypermutation. Routine NGS clonality assessment is feasible and superior to existing assays, enabling accurate and specific index clone assessment and future tracking of all rearrangements in a patient sample. Successful implementation requires new standardization, validation, and implementation processes, which should be performed as a multicenter and multidisciplinary collaboration.

Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients

Tumor molecular profiling is a fundamental component of precision oncology, enabling the identification of genomic alterations in genes and pathways that can be targeted therapeutically. The existence of recurrent targetable alterations across distinct histologically defined tumor types, coupled with an expanding portfolio of molecularly targeted therapies, demands flexible and comprehensive approaches to profile clinically relevant genes across the full spectrum of cancers. We established a large-scale, prospective clinical sequencing initiative using a comprehensive assay, MSK-IMPACT, through which we have compiled tumor and matched normal sequence data from a unique cohort of more than 10,000 patients with advanced cancer and available pathological and clinical annotations. Using these data, we identified clinically relevant somatic mutations, novel noncoding alterations, and mutational signatures that were shared by common and rare tumor types. Patients were enrolled on genomically matched clinical trials at a rate of 11%. To enable discovery of novel biomarkers and deeper investigation into rare alterations and tumor types, all results are publicly accessible.

The ultrasound compression sign to diagnose temporal giant cell arteritis shows an excellent interobserver agreement

OBJECTIVES

To compare the diagnostic performance between a vascular specialist and a rheumatologist not familiar with vascular ultrasound when applying the compression sign for the diagnosis of temporal arteritis.

METHODS

Sixty consecutive patients with suspicion of giant cell arteritis were examined by both examiners. Compression of the temporal artery on both sides (stem and both branches) was performed to define whether signs of vasculitis, no vasculitis or an indefinite result were present. Each examiner was blinded to the result of the other.

RESULTS

In 59/60 patients, the examiners found an identical result. The interobserver agreement (Krippendorf alpha) was 0.92.

CONCLUSIONS

The new compression sign for the diagnosis of temporal arteritis is a simple and robust sonographic marker with an excellent interobserver agreement.

Temporal artery compression sign--a novel ultrasound finding for the diagnosis of giant cell arteritis

PURPOSE

In patients with suspected giant cell arteritis (GCA), a search for the perivascular halo sign, a sophisticated color duplex ultrasound (CDU) finding, at experienced centers reliably identifies inflamed temporal arteries (TA). We tested whether TA compression in patients with GCA, a simple, largely operator-independent maneuver, elicits contrasting echogenicity between the diseased artery wall and the surrounding tissue (compression sign).

MATERIALS AND METHODS

80 individuals with suspected GCA were prospectively enrolled in this single-center study. In all study participants, bilateral ultrasound examination of the TA established the presence/absence of the halo and compression sign. A positive compression sign was defined as visibility of the TA upon transducer-imposed compression of the artery. Based on ACR criteria, a team of specialized physicians independently grouped patients as GCA versus non-GCA.

RESULTS

43/80 study participants were grouped as GCA. Both the halo sign and the compression sign were positive in 34/43 patients in the GCA group, and negative in all 37/37 of the non-GCA group, resulting in a sensitivity of 79 % and a specificity of 100 % for both the halo and the compression sign.

CONCLUSION

In this cohort of individuals with suspected GCA, the halo sign and the compression sign were equal in their diagnostic performance. The simplicity of the compression sign suggests a level of reliability warranting further evaluation.

Use of biomarkers or echocardiography in pulmonary embolism: the Swiss Venous Thromboembolism Registry

BACKGROUND

Cardiac biomarkers and echocardiography for assessing right ventricular function are recommended to risk stratify patients with acute non-massive pulmonary embolism (PE), but it remains unclear if these tests are performed systematically in daily practice.

DESIGN AND METHODS

Overall, 587 patients with acute non-massive PE from 18 hospitals were enrolled in the Swiss Venous Thromboembolism Registry (SWIVTER): 178 (30%) neither had a biomarker test nor an echocardiographic evaluation, 196 (34%) had a biomarker test only, 47 (8%) had an echocardiogram only and 166 (28%) had both tests.

RESULTS

Among the 409 (70%) patients with biomarkers or echocardiography, 210 (51%) had at least one positive test and 67 (16%) had positive biomarkers and right ventricular dysfunction. The ICU admission rates were 5.1% without vs. 5.6% with testing (P = 0.78), and thrombolysis or embolectomy were performed in 2.8% vs. 4.9%, respectively (P = 0.25). In multivariate analysis, syncope [odds ratio (OR): 3.49, 95% confidence interval (CI): 1.20-10.15; P = 0.022], tachycardia (OR: 2.31, 95% CI: 1.37-3.91; P = 0.002) and increasing age (OR: 1.02; 95% CI: 1.01-1.04; P < 0.001) were associated with testing of cardiac risk; outpatient status at the time of PE diagnosis (OR: 2.24, 95% CI: 1.49-3.36; P < 0.001), cancer (OR: 1.81, 95% CI: 1.17-2.79; P = 0.008) and provoked PE (OR: 1.58, 95% CI: 1.05-2.40; P = 0.029) were associated with its absence.

CONCLUSION

Although elderly patients and those with clinically severe PE were more likely to receive a biomarker test or an echocardiogram, these tools were used in only two-thirds of the patients with acute non-massive PE and rarely in combination.

[Check-up, what else?]

Evidence-based check-up does not only include medical history and physical examination but consultation with regard to recommended vaccinations, screening for cancer and cardiovascular risk factors. Patients with PAD are at high risk for cardiovascular events but frequently claudication is not mentioned during anamnesis, thus specific attention to exercise-dependent leg discomfort is necessary. Recognition of PAD related symptoms is important because it may implicate secondary cardiovascular prevention and specific therapeutic options including walking exercise and endovascular revascularisation exist.

["Good Morning, Doctor, I'm Flying to Australia Next Week!"]

Travel-related venous thromboembolism (VTE) is probably less frequent than previously suspected and becomes relevant when a flight lasts eight hours or more. Usually, general measures such as avoiding constrictive clothing or dehydration and doing gymnastics and walking around in the cabin are sufficient for preventing VTE. Compression stockings can be recommended when risk factors for VTE are present. Low molecular weight heparins in prophylactic dosage should be considered after previous VTE.

["Arteriosclerotic" aneurysm of the abdominal aorta]

We present a patient with an aortic aneurysm and the epidemiology, etiology, screening, symptoms and therapeutic options of abdominal aortic aneurysms are discussed. A widening of the abdominal aorta >3 cm is termed aortic aneurysm. As patients with aortic aneurysm are mostly oligosymptomatic until rupture occurs and an estimated 30,000 patients annually die from ruptured aortic aneurysm in the US a screening of the population at greatest risk (smokers, familial predisposition) is recommended. Screening is best done by ultrasound. Noninvasive therapy is limited to antiplatelet therapy and optimal adjustment of risk factors. For definitive treatment endovascular aortic repair (EVAR) is considered an established alternative to open surgery with lower 30 days mortality but higher reintervention rate.

Giant arteriovenous fistula after implantation of a percutaneous left ventricular assist device

INTRODUCTION

Percutaneous left ventricular assist devices are an important tool in the management of patients with severe cardiogenic shock. Limited experiences concerning vascular complications after long term implantation of these devices exist. We report on a large arteriovenous fistula after placement of a left ventricular assist device, which has not been described in the literature. The arteriovenous fistula was of clinical relevance because it represented a supplementary cardiac burden in a patient with impaired left ventricular function after a severe myocardial infarction.

Selective loss of extracellular matrix proteins is linked to biophysical properties of varicose veins assessed by ultrasonography

BACKGROUND

Dilatation and enhanced distensibility are specific biophysical properties of varicose veins. Both can be assessed by ultrasonography. The aim of this study was to analyse correlations between the vein wall protein content and these two biophysical properties of varicose veins.

METHODS

Twenty-seven patients having surgery for varicose veins and six control patients with normal veins undergoing arterial bypass surgery were examined clinically and with ultrasonography the day before surgery. Fifty-two varicose and six control vein rings were harvested and analysed histopathologically and morphometrically; vascular tissue microarrays incorporated 116 vein wall sectors.

RESULTS

Elastin loss in the adventitia (P = 0.010) and reduction of type III collagen in the intima and media (P = 0.004) were observed in varicose veins. Elastin loss correlated negatively with vein diameter at rest (P = 0.005), whereas loss of type III collagen in the intima correlated negatively with the increase in vein diameter at the Valsalva manoeuvre (P < 0.001).

CONCLUSION

Loss of elastin and type III collagen occurs in varicose veins and can be assessed with ultrasonography in vivo by measuring vein diameter and distensibility.