Next-generation sequencing (NGS) of cell-free circulating tumor DNA and tumor tissue in patients with advanced urothelial cancer: a pilot assessment of concordance

Background

Advances in cancer genome sequencing have led to the development of various next-generation sequencing (NGS) platforms. There is paucity of data regarding concordance of different NGS tests carried out in the same patient.

Methods

Here, we report a pilot analysis of 22 patients with metastatic urinary tract cancer and available NGS data from paired tumor tissue [FoundationOne (F1)] and cell-free circulating tumor DNA (ctDNA) [Guardant360 (G360)].

Results

The median time between the diagnosis of stage IV disease and the first genomic test was 23.5 days (0-767), after a median number of 0 (0-3) prior systemic lines of treatment of advanced disease. Most frequent genomic alterations (GA) were found in the genes TP53 (50.0%), TERT promoter (36.3%); ARID1 (29.5%); FGFR2/3 (20.5%), PIK3CA (20.5%) and ERBB2 (18.2%). While we identified GA in both tests, the overall concordance between the two platforms was only 16.4% (0%-50%), and 17.1% (0%-50%) for those patients (n = 6) with both tests conducted around the same time (median difference = 36 days). On the contrary, in the subgroup of patients (n = 5) with repeated NGS in ctDNA after a median of 1 systemic therapy between the two tests, average concordance was 55.5% (12.1%-100.0%). Tumor tissue mutational burden was significantly associated with number of GA in G360 report (P < 0.001), number of known GA (P = 0.009) and number of variants of unknown significance (VUS) in F1 report (P < 0.001), and with total number of GA (non-VUS and VUS) in F1 report (P < 0.001).

Conclusions

This study suggests a significant discordance between clinically available NGS panels in advanced urothelial cancer, even when collected around the same time. There is a need for better understanding of these two possibly complementary NGS platforms for better integration into clinical practice.

An update on the management of sporadic desmoid-type fibromatosis: a European Consensus Initiative between Sarcoma PAtients EuroNet (SPAEN) and European Organization for Research and Treatment of Cancer (EORTC)/Soft Tissue and Bone Sarcoma Group (STBSG)

Desmoid-type fibromatosis is a rare and locally aggressive monoclonal, fibroblastic proliferation characterized by a variable and often unpredictable clinical course. Currently, there is no established or evidence-based treatment approach available for this disease. Therefore, in 2015 the European Desmoid Working Group published a position paper giving recommendations on the treatment of this intriguing disease. Here, we present an update of this consensus approach based on professionals' AND patients' expertise following a round table meeting bringing together sarcoma experts from the European Organization for Research and Treatment of Cancer/Soft Tissue and Bone Sarcoma Group with patients and patient advocates from Sarcoma PAtients EuroNet. In this paper, we focus on new findings regarding the prognostic value of mutational analysis in desmoid-type fibromatosis patients and new systemic treatment options.

Sinonasal Undifferentiated Carcinoma Invading the Orbit

Sinonasal undifferentiated carcinoma (SNUC) is an infrequent tumor described by Frierson et al. in 1986. Since its initial description, fewer than 100 patients have been reported. We present a case of a SNUC invading the orbit in a 57-year-old woman, for which the findings are documented by CT scan, light and electron microscopy.

Swift and NuSTAR observations of GW170817: Detection of a blue kilonova

With the first direct detection of merging black holes in 2015, the era of gravitational wave (GW) astrophysics began. A complete picture of compact object mergers, however, requires the detection of an electromagnetic (EM) counterpart. We report ultraviolet (UV) and x-ray observations by Swift and the Nuclear Spectroscopic Telescope Array of the EM counterpart of the binary neutron star merger GW170817. The bright, rapidly fading UV emission indicates a high mass (≈0.03 solar masses) wind-driven outflow with moderate electron fraction (Y_e ≈ 0.27). Combined with the x-ray limits, we favor an observer viewing angle of ≈30° away from the orbital rotation axis, which avoids both obscuration from the heaviest elements in the orbital plane and a direct view of any ultrarelativistic, highly collimated ejecta (a γ-ray burst afterglow).

Validity of code based algorithms to identify primary open angle glaucoma (POAG) in Veterans Affairs (VA) administrative databases

PURPOSE

The validity of the International Classification of Diseases, 9th revision, Clinical Modification (ICD-9) code for primary open angle glaucoma (POAG) in the Department of Veterans Affairs (VA) electronic medical record has not been examined. We determined the accuracy of the ICD-9 code for POAG and developed diagnostic algorithms for the detection of POAG.

METHODS

We conducted a retrospective study of abstracted data from the Michael E. DeBakey VA Medical Center's medical records of 334 unique patients with at least one visit to the Eye Clinic between 1999 and 2013. Algorithms were developed to validly identify POAG using ICD-9 codes and pharmacy data. The positive predictive value (PPV), negative predictive value (NPV), sensitivity, specificity and percent agreement of the various algorithms were calculated.

RESULTS

For the ICD-9 code 365.1x, the PPV was 65.9%, NPV was 95.2%, sensitivity was 100%, specificity was 82.6%, and percent agreement was 87.8%. The algorithm with the highest PPV was 76.3%, using pharmacy data in conjunction with two or more ICD-9 codes for POAG, but this algorithm also had the lowest NPV at 88.2%.

CONCLUSIONS

Various algorithms for identifying POAG in the VA administrative databases have variable validity. Depending on the type of research being done, the ICD-9 code 365.1x can be used for epidemiologic or health services database research.