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Geospatial immune variability illuminates differential evolution of lung adenocarcinoma.
(NATURE PORTFOLIO, 2020-07-01)
Remarkable progress in molecular analyses has improved our understanding of the evolution of cancer cells toward immune escape1-5. However, the spatial configurations of immune and stromal cells, which may shed light on ...
REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants.
(CELL PRESS, 2016-10-06)
The vast majority of coding variants are rare, and assessment of the contribution of rare variants to complex traits is hampered by low statistical power and limited functional data. Improved methods for predicting the ...
Genomic evolution and chemoresistance in germ-cell tumours.
(NATURE PUBLISHING GROUP, 2016-11-30)
Germ-cell tumours (GCTs) are derived from germ cells and occur most frequently in the testes. GCTs are histologically heterogeneous and distinctly curable with chemotherapy. Gains of chromosome arm 12p and aneuploidy are ...
FFPE breast tumour blocks provide reliable sources of both germline and malignant DNA for investigation of genetic determinants of individual tumour responses to treatment.
(SPRINGER, 2018-08-01)
BACKGROUND: Bio-banked formalin-fixed paraffin-embedded (FFPE) tissues provide an excellent opportunity for translational genomic research. Historically matched blood has not always been collected as a source of germline ...
Neutral tumor evolution in myeloma is associated with poor prognosis.
(AMER SOC HEMATOLOGY, 2017-10-05)
Recent studies suggest that the evolutionary history of a cancer is important in forecasting clinical outlook. To gain insight into the clonal dynamics of multiple myeloma (MM) and its possible influence on patient outcomes, ...
CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting.
(BMC, 2015-07-28)
BACKGROUND: Next-generation sequencing (NGS) offers unprecedented opportunities to expand clinical genomics. It also presents challenges with respect to integration with data from other sequencing methods and historical ...
Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma.
(CELL PRESS, 2017-10-09)
We collated data from 157 unpublished cases of pediatric high-grade glioma and diffuse intrinsic pontine glioma and 20 publicly available datasets in an integrated analysis of >1,000 cases. We identified co-segregating ...
Search for rare protein altering variants influencing susceptibility to multiple myeloma.
(IMPACT JOURNALS LLC, 2017-05-30)
The genetic basis underlying the inherited risk of developing multiple myeloma (MM) is largely unknown. To examine the impact of rare protein altering variants on the risk of developing MM we analyzed high-coverage exome ...
The Spectrum and Clinical Impact of Epigenetic Modifier Mutations in Myeloma.
(AMER ASSOC CANCER RESEARCH, 2016-12-01)
PURPOSE: Epigenetic dysregulation is known to be an important contributor to myeloma pathogenesis but, unlike other B-cell malignancies, the full spectrum of somatic mutations in epigenetic modifiers has not been reported ...
Between-region genetic divergence reflects the mode and tempo of tumor evolution.
(NATURE PUBLISHING GROUP, 2017-06-05)
Given the implications of tumor dynamics for precision medicine, there is a need to systematically characterize the mode of evolution across diverse solid tumor types. In particular, methods to infer the role of natural ...