Integrated RNA and DNA sequencing improves mutation detection in low purity tumors

Identifying somatic mutations is critical for cancer genome characterization and for prioritizing patient treatment. DNA whole exome sequencing (DNA-WES) is currently the most popular technology; however, this yields low sensitivity in low purity tumors. RNA sequencing (RNA-seq) covers the expressed exome with depth proportional to expression. We hypothesized that integrating DNA-WES and RNA-seq would enable superior mutation detection versus DNA-WES alone. We developed a first-of-its-kind method, called UNCeqR, that detects somatic mutations by integrating patient-matched RNA-seq and DNA-WES. In simulation, the integrated DNA and RNA model outperformed the DNA-WES only model. Validation by patient-matched whole genome sequencing demonstrated superior performance of the integrated model over DNA-WES only models, including a published method and published mutation profiles. Genome-wide mutational analysis of breast and lung cancer cohorts (n = 871) revealed remarkable tumor genomics properties. Low purity tumors experienced the largest gains in mutation detection by integrating RNA-seq and DNA-WES. RNA provided greater mutation signal than DNA in expressed mutations. Compared to earlier studies on this cohort, UNCeqR increased mutation rates of driver and therapeutically targeted genes (e.g. PIK3CA, ERBB2 and FGFR2). In summary, integrating RNA-seq with DNA-WES increases mutation detection performance, especially for low purity tumors

Differential Pathogenesis of Lung Adenocarcinoma Subtypes Involving Sequence Mutations, Copy Number, Chromosomal Instability, and Methylation

Lung adenocarcinoma (LAD) has extreme genetic variation among patients, which is currently not well understood, limiting progress in therapy development and research. LAD intrinsic molecular subtypes are a validated stratification of naturally-occurring gene expression patterns and encompass different functional pathways and patient outcomes. Patients may have incurred different mutations and alterations that led to the different subtypes. We hypothesized that the LAD molecular subtypes co-occur with distinct mutations and alterations in patient tumors.The LAD molecular subtypes (Bronchioid, Magnoid, and Squamoid) were tested for association with gene mutations and DNA copy number alterations using statistical methods and published cohorts (n = 504). A novel validation (n = 116) cohort was assayed and interrogated to confirm subtype-alteration associations. Gene mutation rates (EGFR, KRAS, STK11, TP53), chromosomal instability, regional copy number, and genomewide DNA methylation were significantly different among tumors of the molecular subtypes. Secondary analyses compared subtypes by integrated alterations and patient outcomes. Tumors having integrated alterations in the same gene associated with the subtypes, e.g. mutation, deletion and underexpression of STK11 with Magnoid, and mutation, amplification, and overexpression of EGFR with Bronchioid. The subtypes also associated with tumors having concurrent mutant genes, such as KRAS-STK11 with Magnoid. Patient overall survival, cisplatin plus vinorelbine therapy response and predicted gefitinib sensitivity were significantly different among the subtypes.The lung adenocarcinoma intrinsic molecular subtypes co-occur with grossly distinct genomic alterations and with patient therapy response. These results advance the understanding of lung adenocarcinoma etiology and nominate patient subgroups for future evaluation of treatment response

The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer

Abstract: Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM−/− patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors

Central Nervous System Tumors

Introduction: Chemotherapy, immunotherapy, and biological response modifiers were tested in clinical trials for brain tumors. Results of these studies published in 2003 and 2004 are reviewed. Materials and methods: Major peer-reviewed journals in the disciplines of neurosurgery, neurology, medical oncology, and radiation oncology were surveyed. Results of phase II and phase III clinical trials testing chemotherapy, gene therapy, immunotherapy, and radiosensitizers for adults and children with malignant and low-grade glioma, primary central nervous system lymphoma (PCNSL), brain metastasis, medulloblastoma/primitive neuroectodermal tumor (PNET), and germ cell tumors were reviewed. Results: Nitrosourea and temozolomide were tested as monotherapy or in combination with other agents as neoadjuvant, concurrent, and adjuvant treatment with radiotherapy for newly diagnosed malignant glioma in adults, including high-risk treatment groups, such as the elderly. Trials for recurrent malignant glioma included novel therapies, dendritic vaccine therapy, gene therapy and immunotherapy. High-dose chemotherapy with bone marrow rescue was tested in anaplastic oligodendroglioma (AO). Seven additional studies were performed to treat recurrent oligodendroglioma (O). Nine clinical trials for PCNSL emphasized the use of high-dose systemic methotrexate, temozolomide, and rituxin. Chemotherapy and immunotherapy were used to treat low-grade glioma in 7 studies. Intra-arterial and (IT) chemotherapy were used for metastatic disease. Treatment protocols for children were compared using multi-agent chemotherapy for malignant glioma, brainstem glioma, medulloblastoma, and germ cell tumors. Conclusion: Multi-agent chemotherapy is successful for some pediatric brain tumors and PCNSL in adults. Vaccine, immunotherapy, and other gene therapies are still under investigation. Temozolomide and nitrosourea, specifically degradable polymer wafers, had the best results for malignant gliomas in adults. Treatment standards have been established for medulloblastoma/PNET. Treating malignant glioma in children remains problematic

Supporting American Academy of Neurology’s new clinical practice guideline on evaluation and management of insomnia in children with autism

Rosen CL, Aurora RN, Kapur VK, et al. Supporting American Academy of Neurology’s new clinical practice guideline on evaluation and management of insomnia in children with autism. J Clin Sleep Med . 2020;16(6):989–990