Red Cell Transfusions in the Genomics Era.

Red cell genotyping has become widely available and now contributes to support transfusion of patients with hematologic diseases. This technology has facilitated the immunohematologic approach to antibody prevention, detection and identification. Donors, particularly rare donors, are most efficiently screened and identified by red cell genotyping. In transfused patients with challenging serologic reactivity, antibodies are more reliably identified when molecular typing information is available. Red cell genotyping of both donors and patients augments the selection of blood components. This technology, serving at the core of a real-time database inventory, is resulting in blood supply efficiencies. However, there is limited published evidence on the extent to which red cell genotyping has translated into improved clinical outcomes. Red cell alloimmunized patients may benefit the most in enhanced safety. For patients with antibodies to high-prevalence antigens, other than Rh, blood centers realized supply-chain efficiencies in the past decade. Prospective clinical trials and cost-effectiveness studies would contribute to further clarifying the optimal role of molecular testing in providing transfusion support for patients with hematologic diseases.

Beyond sequence variation: assessment of copy number variation in adult glioblastoma through targeted tumor somatic profiling.

Glioblastoma is the most common primary malignancy of the adult central nervous system. Gliomagenesis involves a complex range of alterations, including sequence changes, copy number variations (CNVs), and epigenetic modifications, that have clinical implications for disease classification and prognosis. Thus, multiple testing modalities are required to support a complete diagnostic workup. The goal of this study was to streamline the multipart workflow by predicting both sequence changes and CNVs (specifically EGFR amplifications) from a single next-generation sequencing (NGS) test. Eighty-six primary and secondary glioblastomas were submitted for clinical NGS to report sequence variants from a concise panel of cancer-relevant genes. Most specimens underwent concomitant testing by methylation-specific polymerase chain reaction, immunohistochemistry, and fluorescence in situ hybridization. Using data generated during the course of clinical testing, we found that NGS-based variant predictions were concordant with immunohistochemistry and fluorescence in situ hybridization for IDH mutation and EGFR amplification status, respectively. We also noted that EGFR amplifications correlated with polysomy of chromosome 7, 19, and 20, and loss of PTEN and CDKN2A. EGFR-unamplified cases had lower rates of chromosome 7 polysomy, and PTEN and CDKN2A loss, but more CNVs overall. TP53, NF1, ATRX, and PDGFRA mutations were nearly exclusive to specimens without EGFR amplification. EGFR amplification was not associated with longer progression-free survival in this cohort, but amplifications were enriched in a group with slightly longer overall survival despite radiographic evidence of disease progression. Further study is needed to explore the mechanisms responsible for noted patterns of co-occurring variants and to correlate them with specific clinical outcomes.

FGFR2 amplification in colorectal adenocarcinoma.

FGFR2 is recurrently amplified in 5% of gastric cancers and 1%-4% of breast cancers; however, this molecular alteration has never been reported in a primary colorectal cancer specimen. Preclinical studies indicate that several FGFR tyrosine-kinase inhibitors (TKIs), such as AZD4547, have in vitro activity against the FGFR2-amplified colorectal cell line, NCI-H716. The efficacy of these inhibitors is currently under investigation in clinical trials for breast and gastric cancer. Thus, better characterizing colorectal tumors for FGFR2 amplification could identify a subset of patients who may benefit from FGFR TKI therapies. Here, we describe a novel FGFR2 amplification identified by clinical next-generation sequencing in a primary colorectal cancer. Further characterization of the tumor by immunohistochemistry showed neuroendocrine differentiation, similar to the reported properties of the NCI-H716 cell line. These findings demonstrate that the spectrum of potentially clinically actionable mutations detected by targeted clinical sequencing panels is not limited to only single-nucleotide polymorphisms and insertions/deletions but also to copy-number alterations.

Targeted Next-Generation Sequencing in Molecular Subtyping of Lower-Grade Diffuse Gliomas: Application of the World Health Organization's 2016 Revised Criteria for Central Nervous System Tumors.

The 2007 World Health Organization Classification of Tumours of the Central Nervous System classifies lower-grade gliomas [LGGs (grades II to III diffuse gliomas)] morphologically as astrocytomas or oligodendrogliomas, and tumors with unclear ambiguous morphology as oligoastrocytomas. The World Health Organization's newly released (2016) classification incorporates molecular data. A single, targeted next-generation sequencing (NGS) panel was used for detecting single-nucleotide variation and copy number variation in 50 LGG cases originally classified using the 2007 criteria, including 36 oligoastrocytomas, 11 oligodendrogliomas, 2 astrocytomas, and 1 LGG not otherwise specified. NGS results were compared with those from IHC analysis and fluorescence in situ hybridization to assess concordance and to categorize the tumors according to the 2016 criteria. NGS results were concordant with those from IHC analysis in all cases. In 3 cases, NGS was superior to fluorescence in situ hybridization in distinguishing segmental chromosomal losses from whole-arm deletions. The NGS approach was effective in reclassifying 36 oligoastrocytomas as 30 astrocytomas (20 IDH1/2 mutant and 10 IDH1/2 wild type) and 6 oligodendrogliomas, and 1 oligodendroglioma as an astrocytoma (IDH1/2 mutant). Here we show that a single, targeted NGS assay can serve as the sole testing modality for categorizing LGG according to the World Health Organization's 2016 diagnostic scheme. This modality affords greater accuracy and efficiency while reducing specimen tissue requirements compared with multimodal approaches.

Radiographic response of brain metastasis after linear accelerator radiosurgery.

BACKGROUND: Radiographic response of brain metastasis to stereotactic radiosurgery (SRS) over time has not been well characterized. Being able to predict SRS-induced changes in tumor size over time may allow improved counseling of patients and potentially earlier recognition of poor response to SRS. OBJECTIVE: To quantify the rate of change in size of metastatic brain tumors after treatment with a linear accelerator (LINAC) SRS. METHODS: We performed a retrospective analysis of patients with single metastatic brain tumors treated with LINAC SRS at the University of Florida between 1992 and 2009 who had at least one MRI after treatment. A total of 218 patients with 406 follow-up MRI scans were included in the study. Tumor area was calculated by measuring the largest tumor area on axial imaging and using the equation for area of an ellipse. Primary outcome was percent change in tumor size. The contribution of several factors including gender, primary tumor histology, synchronous or asynchronous presentation, prior treatment, primary tumor control, and SRS dose were examined using multivariate analysis. RESULTS: Mean patient age was 58.3 years (range 4-86), and 48.6% of patients were female. Sixty-three percent of patients had primary tumor control and 70.6% had asynchronous presentation of their brain metastases. SRS peripheral dose range was 1,000-2,250 cGy with a median of 1,750 cGy. The mean percent size change was -22.6% with a mean rate of change of -7.0% per month. The median percent change was -49.7% with a median rate of change of -8.8% per month. The median follow-up was 4.8 months (range 0.3-52.5). Female gender and melanoma histology were found to be significant predictors of an increase in tumor size. Lack of previous surgical resection was a significant predictor of a decrease in tumor size after SRS. Other factors tested with multivariate analysis, including age, synchronicity of presentation, dose, dose volume, Karnofsky performance score, and primary tumor control, were not significant in predicting tumor size change after SRS. CONCLUSION: In this study, brain metastases decreased in size by a median of 50% for a median follow-up of 4.8 months after SRS. The overall rate of decrease was 9% per month after treatment with SRS. Melanoma histology was a predictor of poor tumor control.