Next Generation Sequencing Assay for Blood Cancers

Researchers Develop Targeted Next Generation Sequencing Assay for Myeloid Neoplasms

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Researchers from South Korea said they have developed a next-generation sequencing (NGS) assay to detect somatic mutations, translocations, and germline mutations in a single assay for the purpose of supplementing or replacing conventional tests in patients with myeloid neoplasms.

Writing in a recent issue of PLoS One, the researchers said were able to discover a high frequency of germline mutations in cancer predisposition genes. Patients with these mutations exhibited different clinical characteristics, suggesting that germline predisposition has significant clinical implications.

Deep sequencing of Adult Gliomas has promising results

Prospective Clinical Sequencing of Adult Glioma

Siyuan Zheng, Kristin Alfaro-Munoz, Wei Wei, Xiaojing Wang, Fang Wang, Agda Karina Eterovic, Kenna R Mills Shaw, Funda Meric-Bernstam, Gregory N Fuller, Ken Chen, Roel G. Verhaak, Gordon B. Mills, W.K. Alfred Yung, Shiao-Pei Weathers and John F. de Groot

Molecular Cancer Therapeutics (Research Article)

Abstract—Malignant gliomas are a group of intracranial cancers associated with disproportionately high mortality and morbidity. Here we report ultradeep targeted sequencing of a prospective cohort of 237 tumors from 234 patients consisting of both glioblastoma (GBM) and lower-grade glioma (LGG) using our customized gene panels. We identified 2485 somatic mutations including single nucleotide substitutions and small indels using a validated in-house protocol. Sixty one percent of the mutations were contributed by 12 hypermutators. The hypermutators were enriched for recurrent tumors, had comparable outcome, and most were associated with temozolomide exposure. TP53 was the most frequently mutated gene in our cohort, followed by IDH1 and EGFR. We detected at least one EGFR mutation in 23% of LGGs, which was significantly higher than 6% seen in TCGA, a pattern that can be partially explained by the different patient composition and sequencing depth. IDH hotspot mutations were found with higher frequencies in LGG (83%) and secondary GBM (77%) than primary GBM (9%). Multivariate analyses controlling for age, histology, and tumor grade confirm the prognostic value of IDH mutation. We predicted 1p/19q status using the panel sequencing data, and received only modest performance by benchmarking the prediction to Fluorescent In Situ Hybridization (FISH) results of 50 tumors. Targeted therapy based on the sequencing data resulted in three responders out of 14 participants. In conclusion, our study suggests ultradeep targeted sequencing can recapitulate previous findings and can be a useful approach in the clinical setting.

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Targeting Brain Tumors with Single-Cell RNA-seq

Brain Tumors Through the Single-Cell RNA Sequencing Lens: Researcher Interview with Mario Suvà

Read Peggy Wang’s interview with Mario Suvà for the National Cancer Institute. Dr. Suvà is an assistant professor of pathology at Massachusetts General Hospital and Harvard Medical School, an Institute Member at the Broad Institute, and uses single-cell RNA sequencing as a discovery tool for understanding brain cancer. Lean more about his work and this powerful new approach to understanding this important disease…

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Strata Oncology using NGS for advanced cancer

Strata Oncology Launches Expanded StrataNGS for Patients with Advanced Cancer

ANN ARBOR, Mich., March 19, 2019 /PRNewswire/ -- Strata OncologyTM, a leading precision oncology company, today announced the launch of version 3.0 of StrataNGSTM, its pan-cancer assay for solid tumors. The updated 500-gene assay utilizes DNA and RNA from tumor samples to detect all clinically actionable biomarkers — including microsatellite instability (MSI), tumor mutational burden (TMB), and PD-L1 — recommended by leading guidelines, in a single test. Test results are provided in a streamlined report that facilitates rapid, confident interpretation and identification of potential treatment options and clinical trials.

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Centers for Medicare & Medicaid Services cancer sequencing dust-up

CMS Acknowledges Stakeholder Concerns Over Decision Not to Cover Germline NGS in Early Cancer Patients

NEW YORK (GenomeWeb) – The Centers for Medicare & Medicaid Services issued a notice this week acknowledging the confusion over its coverage policy for germline next-generation sequencing for cancer patients.

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