Literature DB >> 30364881

BREAST CANCER HISTOPATHOLOGY IMAGE ANALYSIS PIPELINE FOR TUMOR PURITY ESTIMATION.

Vahid Azimi1, Young Hwan Chang1, Guillaume Thibault1, Jaclyn Smith1, Takahiro Tsujikawa1, Benjamin Kukull1, Bradden Jensen1, Christopher Corless1, Adam Margolin1, Joe W Gray1.   

Abstract

The translation of genomic sequencing technology to the clinic has greatly advanced personalized medicine. However, the presence of normal cells in tumors is a confounding factor in genome sequence analysis. Tumor purity, or the percentage of cancerous cells in whole tissue section, is a correction factor that can be used to improve the clinical utility of genomic sequencing. Currently, tumor purity is estimated visually by expert pathologists; however, it has been shown that there exist vast inter-observer discrepancies in tumor purity scoring. In this paper, we propose a quantitative image analysis pipeline for tumor purity estimation and provide a systematic comparison between pathologists' scores and our image-based tumor purity estimation.

Entities:  

Keywords:  Histopathology; Quantitative Image Analysis

Year:  2017        PMID： 30364881      PMCID： PMC6198647          DOI： 10.1109/ISBI.2017.7950717

Source DB:  PubMed          Journal:  Proc IEEE Int Symp Biomed Imaging        ISSN： 1945-7928


  13 in total

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Journal:  Cancer Res       Date:  2004-05-01       Impact factor: 12.701

2.  The estimation of tumor cell percentage for molecular testing by pathologists is not accurate.

Authors:  Alexander J J Smits; J Alain Kummer; Peter C de Bruin; Mijke Bol; Jan G van den Tweel; Kees A Seldenrijk; Stefan M Willems; G Johan A Offerhaus; Roel A de Weger; Paul J van Diest; Aryan Vink
Journal:  Mod Pathol       Date:  2013-07-26       Impact factor: 7.842

3.  Impact of TP53 mutation variant allele frequency on phenotype and outcomes in myelodysplastic syndromes.

Authors:  D A Sallman; R Komrokji; C Vaupel; T Cluzeau; S M Geyer; K L McGraw; N H Al Ali; J Lancet; M J McGinniss; S Nahas; A E Smith; A Kulasekararaj; G Mufti; A List; J Hall; E Padron
Journal:  Leukemia       Date:  2015-10-30       Impact factor: 11.528

4.  Quantitative analysis of histological tissue image based on cytological profiles and spatial statistics.

Authors:  Guillaume Thibault; Vahid Azimi; Brett Johnson; Danielle Jorgens; Jason Link; Adam Margolin; Joe W Gray
Journal:  Conf Proc IEEE Eng Med Biol Soc       Date:  2016-08

5.  Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling.

Authors:  Yinyin Yuan; Henrik Failmezger; Oscar M Rueda; H Raza Ali; Stefan Gräf; Suet-Feung Chin; Roland F Schwarz; Christina Curtis; Mark J Dunning; Helen Bardwell; Nicola Johnson; Sarah Doyle; Gulisa Turashvili; Elena Provenzano; Sam Aparicio; Carlos Caldas; Florian Markowetz
Journal:  Sci Transl Med       Date:  2012-10-24       Impact factor: 17.956

6.  Pan-cancer patterns of somatic copy number alteration.

Authors:  Travis I Zack; Stephen E Schumacher; Scott L Carter; Andre D Cherniack; Gordon Saksena; Barbara Tabak; Michael S Lawrence; Cheng-Zhong Zhsng; Jeremiah Wala; Craig H Mermel; Carrie Sougnez; Stacey B Gabriel; Bryan Hernandez; Hui Shen; Peter W Laird; Gad Getz; Matthew Meyerson; Rameen Beroukhim
Journal:  Nat Genet       Date:  2013-10       Impact factor: 38.330

7.  Variant allele frequency enrichment analysis in vitro reveals sonic hedgehog pathway to impede sustained temozolomide response in GBM.

Authors:  Nidhan K Biswas; Vikas Chandra; Neeta Sarkar-Roy; Tapojyoti Das; Rabindra N Bhattacharya; Laxmi N Tripathy; Sunandan K Basu; Shantanu Kumar; Subrata Das; Ankita Chatterjee; Ankur Mukherjee; Pryiadarshi Basu; Arindam Maitra; Ansuman Chattopadhyay; Analabha Basu; Surajit Dhara
Journal:  Sci Rep       Date:  2015-01-21       Impact factor: 4.379

8.  Identification of rare germline copy number variations over-represented in five human cancer types.

Authors:  Richard W Park; Tae-Min Kim; Simon Kasif; Peter J Park
Journal:  Mol Cancer       Date:  2015-02-03       Impact factor: 27.401

9.  Collaborative analysis of multi-gigapixel imaging data using Cytomine.

Authors:  Raphaël Marée; Loïc Rollus; Benjamin Stévens; Renaud Hoyoux; Gilles Louppe; Rémy Vandaele; Jean-Michel Begon; Philipp Kainz; Pierre Geurts; Louis Wehenkel
Journal:  Bioinformatics       Date:  2016-01-10       Impact factor: 6.937

10.  Systematic pan-cancer analysis of tumour purity.

Authors:  Dvir Aran; Marina Sirota; Atul J Butte
Journal:  Nat Commun       Date:  2015-12-04       Impact factor: 14.919
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  4 in total

1.  Correlation analysis of tumor purity with clinicopathological, molecular, and imaging features in high-grade gliomas.

Authors:  Qing Zhou; Peng Zhang; Jiangwei Man; Bin Zhang; Caiqiang Xue; Xiaoai Ke; Junlin Zhou
Journal:  Neurosurg Rev       Date:  2022-09-26       Impact factor: 2.800

Review 2.  Digital pathology and artificial intelligence in translational medicine and clinical practice.

Authors:  Vipul Baxi; Robin Edwards; Michael Montalto; Saurabh Saha
Journal:  Mod Pathol       Date:  2021-10-05       Impact factor: 7.842

3.  Obtaining spatially resolved tumor purity maps using deep multiple instance learning in a pan-cancer study.

Authors:  Mustafa Umit Oner; Jianbin Chen; Egor Revkov; Anne James; Seow Ye Heng; Arife Neslihan Kaya; Jacob Josiah Santiago Alvarez; Angela Takano; Xin Min Cheng; Tony Kiat Hon Lim; Daniel Shao Weng Tan; Weiwei Zhai; Anders Jacobsen Skanderup; Wing-Kin Sung; Hwee Kuan Lee
Journal:  Patterns (N Y)       Date:  2021-12-09

4.  Artificial intelligence-augmented histopathologic review using image analysis to optimize DNA yield from formalin-fixed paraffin-embedded slides.

Authors:  Bolesław L Osinski; Aïcha BenTaieb; Irvin Ho; Ryan D Jones; Rohan P Joshi; Andrew Westley; Michael Carlson; Caleb Willis; Luke Schleicher; Brett M Mahon; Martin C Stumpe
Journal:  Mod Pathol       Date:  2022-10-05       Impact factor: 8.209
  4 in total

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