Advanced search

Filter By:

Journal Check one or more journals to show results from those journals only.

Choose more journals

Article type Check one or more article types to show results from those article types only.
Subject Check one or more subjects to show results from those subjects only.
Date Choose a date option to show results from those dates only.

Custom date range

Clear all filters
Sort by:
Showing 1–19 of 19 results
Advanced filters: Author: Debyani Chakravarty Clear advanced filters

  • Precision oncology knowledge bases provide cancer clinicians with a point-of-care interpretation of the therapeutic actionability of clinical genomic sequencing results. These knowledge bases are now positioned to expand beyond the annotation of individual somatic molecular alterations, however, important gaps remain. Here, Suehnholz and Chakravarty discuss key deficiencies in current precision oncology knowledge bases that present opportunities for the next generation of data annotation.

    • Sarah Suehnholz
    • Debyani Chakravarty
    Comments & Opinion
    Nature Reviews Cancer
    Volume: 25, P: 651-652

  • It remains unclear whether machine learning methods can accurately identify cancer driver alterations. Here, the authors compare machine learning-based approaches to other computational methods to determine their utility for annotating variants of unknown significance and identifying driver alterations in real-world cancer patient data, demonstrating superior performance.

    • Thinh N. Tran
    • Chris Fong
    • Justin Jee
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-10

  • Targeted sequencing panels such as MSK-IMPACT have been successfully used to profile solid tumours in clinical settings. Here, the authors develop and implement the MSK-IMPACT Heme sequencing panel and platform to profile haematologic malignancies using paired tumor and normal tissues.

    • Ryan N. Ptashkin
    • Mark D. Ewalt
    • Maria E. Arcila
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-16

  • Analysis of exomes and transcriptomes from 100 African American patients with acute myeloid leukemia identifies ancestry-related variation in mutation profiles and survival. Refined risk classification suggests clinical relevance of these ancestry-associated differences.

    • Andrew Stiff
    • Maarten Fornerod
    • Ann-Kathrin Eisfeld
    ResearchOpen Access
    Nature Genetics
    Volume: 56, P: 2434-2446

  • A study generates a clinicogenomics dataset resource, MSK-CHORD, that combines natural language processing-derived clinical annotations with patient medical data from various sources to improve models of cancer outcome.

    • Justin Jee
    • Christopher Fong
    • Xinran Bi
    ResearchOpen Access
    Nature
    Volume: 636, P: 728-736

  • How different oncogenic Akt mutants can affect the response to Akt inhibitors is currently unclear. Here, the authors analyse somatic mutations of Akt1-3 isoforms in several human cancers, investigate their oncogenic effects and therapeutic relevance in vitro and confirm some of their data in a clinical trial testing the AKT inhibitor capivasertib in patients with solid tumors harboring AKT alterations.

    • Tripti Shrestha Bhattarai
    • Tambudzai Shamu
    • Barry S. Taylor
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-11

  • MSK-IMPACT is a clinical sequencing platform able to detect genomic mutations, copy number alterations and structural variants in a panel of cancer-related genes. This assay is implemented prospectively to inform patient enrollment in genomically matched clinical trials at Memorial Sloan Kettering Cancer Center (MSKCC). Sequencing results of tumor and matched normal tissue from a cohort of >10,000 patients with detailed clinical annotation provide an overview of the genomic landscape of advanced solid cancers and bring new insights into molecularly guided cancer therapy.

    • Ahmet Zehir
    • Ryma Benayed
    • Michael F Berger
    Research
    Nature Medicine
    Volume: 23, P: 703-713

  • This analysis presents a harmonized meta-knowledgebase to facilitate clinical interpretation of somatic genomic variants in cancer. This community-based project highlights the need for cooperative efforts to curate clinical interpretations of somatic variants for robust practice of precision oncology.

    • Alex H. Wagner
    • Brian Walsh
    • Adam A. Margolin
    ResearchOpen Access
    Nature Genetics
    Volume: 52, P: 448-457

  • Meta-analysis of exome sequencing data identifies new recurrently mutated driver genes for prostate cancer. Comparison of primary and metastatic tumors further identifies genomic markers for advanced prostate cancer that may inform risk stratification.

    • Joshua Armenia
    • Stephanie A. M. Wankowicz
    • Eliezer M. Van Allen
    Research
    Nature Genetics
    Volume: 50, P: 645-651

  • The Cancer Genome Atlas Research Network report integrated genomic and molecular analyses of 164 squamous cell carcinomas and adenocarcinomas of the oesophagus; they find genomic and molecular features that differentiate squamous and adenocarcinomas of the oesophagus, and strong similarities between oesophageal adenocarcinomas and the chromosomally unstable variant of gastric adenocarcinoma, suggesting that gastroesophageal adenocarcinoma is a single disease entity.

    • Jihun Kim
    • Reanne Bowlby
    • Jiashan Zhang
    ResearchOpen Access
    Nature
    Volume: 541, P: 169-175

  • Profiling tumours by next-generation sequencing can improve diagnostic accuracy, assess for heritable cancer risk and guide treatment selection. The authors review efforts to enhance the clinical utility of cancer genomic profiling through integrative analyses of tumour and germline variants, as well as by characterizing allelic context and mutational signatures that influence therapy response.

    • Debyani Chakravarty
    • David B. Solit
    Reviews
    Nature Reviews Genetics
    Volume: 22, P: 483-501