Next-Generation Pathology.

@article{Caie2016NextGenerationP,
  title={Next-Generation Pathology.},
  author={Peter David Caie and David J. Harrison},
  journal={Methods in molecular biology},
  year={2016},
  volume={1386},
  pages={
          61-72
        }
}
The field of pathology is rapidly transforming from a semiquantitative and empirical science toward a big data discipline. Large data sets from across multiple omics fields may now be extracted from a patient's tissue sample. Tissue is, however, complex, heterogeneous, and prone to artifact. A reductionist view of tissue and disease progression, which does not take this complexity into account, may lead to single biomarkers failing in clinical trials. The integration of standardized multi-omics… 

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References

SHOWING 1-10 OF 21 REFERENCES

High-Content Phenotypic Profiling of Drug Response Signatures across Distinct Cancer Cells

TLDR
The utility of a cell-based assay and custom designed image analysis algorithms designed to monitor morphologic phenotypic response in detail across distinct cancer cell types are shown and have the potential to drive the development of a new generation of novel therapeutic classes encompassing pharmacologic compositions or polypharmacology in appropriate disease context.

Predictive, personalized, preventive, participatory (P4) cancer medicine

TLDR
One powerful approach to this challenge is the crowd-sourced recruitment of patients by bringing large clinical centers together with patient-advocate groups.

Modelling the spatial heterogeneity and molecular correlates of lymphocytic infiltration in triple-negative breast cancer

  • Yinyin Yuan
  • Biology, Medicine
    Journal of The Royal Society Interface
  • 2015
TLDR
A quantitative measure of intratumour lymphocyte ratio is developed and found to be significantly associated with disease-specific survival in both TNBC cohorts independent to standard clinical parameters, and support the fusion of high-throughput image analysis and statistical modelling to offer reproducible and robust biomarkers for the objective identification of patients with poor prognosis and treatment options.

A Big Bang model of human colorectal tumor growth

TLDR
A 'Big Bang' model is presented, whereby tumors grow predominantly as a single expansion producing numerous intermixed subclones that are not subject to stringent selection and where both public and most detectable private alterations arise early during growth.

Genetic and phenotypic diversity in breast tumor metastases.

TLDR
The integrative method that couples ecologic models with experimental data in human tissue samples could be used for the improved prognostication of patients with cancer and for the design of more effective therapies for progressive disease.

Systems biology reveals new strategies for personalizing cancer medicine and confirms the role of PTEN in resistance to trastuzumab.

TLDR
Quantitative PTEN protein expression was found to be the key determinant of resistance to anti-HER2 therapy in silico, which was predictive of unseen experiments in vitro using the PTEN inhibitor bp(V), further compelling evidence that PTEN, appropriately measured in the clinical setting, refines clinical decision making in patients treated with anti- HER2 therapies.

Stromal gene expression defines poor-prognosis subtypes in colorectal cancer

TLDR
It is shown that the use of TGF-β signaling inhibitors to block the cross-talk between cancer cells and the microenvironment halts disease progression, and all poor-prognosis CRC subtypes share a gene program induced by T GF-β in tumor stromal cells.

Triple negative breast cancer: a multi-omics network discovery strategy for candidate targets and driving pathways.

TLDR
The multi-omics molecular target and biomarker discovery approach presented here can offer ways forward on novel diagnostics and potentially help to design personalized therapeutics for TNBC in the future.

Towards the introduction of the ‘Immunoscore’ in the classification of malignant tumours

TLDR
In colorectal cancer, the Immunoscore may add to the significance of the current AJCC/UICC TNM classification, since it has been demonstrated to be a prognostic factor superior to the AJCC or UICCTNM classification.

Genomic classifier ColoPrint predicts recurrence in stage II colorectal cancer patients more accurately than clinical factors.

BACKGROUND Approximately 20% of patients with stage II colorectal cancer will experience a relapse. Current clinical-pathologic stratification factors do not allow clear identification of these