Literature DB >> 34663944

Harnessing multimodal data integration to advance precision oncology.

Kevin M Boehm1, Pegah Khosravi1, Rami Vanguri1, Jianjiong Gao1, Sohrab P Shah2.   

Abstract

Advances in quantitative biomarker development have accelerated new forms of data-driven insights for patients with cancer. However, most approaches are limited to a single mode of data, leaving integrated approaches across modalities relatively underdeveloped. Multimodal integration of advanced molecular diagnostics, radiological and histological imaging, and codified clinical data presents opportunities to advance precision oncology beyond genomics and standard molecular techniques. However, most medical datasets are still too sparse to be useful for the training of modern machine learning techniques, and significant challenges remain before this is remedied. Combined efforts of data engineering, computational methods for analysis of heterogeneous data and instantiation of synergistic data models in biomedical research are required for success. In this Perspective, we offer our opinions on synthesizing complementary modalities of data with emerging multimodal artificial intelligence methods. Advancing along this direction will result in a reimagined class of multimodal biomarkers to propel the field of precision oncology in the coming decade.
© 2021. Springer Nature Limited.

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Year:  2021        PMID: 34663944      PMCID: PMC8810682          DOI: 10.1038/s41568-021-00408-3

Source DB:  PubMed          Journal:  Nat Rev Cancer        ISSN: 1474-175X            Impact factor:   69.800


  121 in total

1.  Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors.

Authors:  Pedram Razavi; Jared L Johnson; Hong Shao; Neil Vasan; Hardik Shah; Alesia Antoine; Erik Ladewig; Alexander Gorelick; Ting-Yu Lin; Eneda Toska; Guotai Xu; Abiha Kazmi; Matthew T Chang; Barry S Taylor; Maura N Dickler; Komal Jhaveri; Sarat Chandarlapaty; Raul Rabadan; Ed Reznik; Melissa L Smith; Robert Sebra; Frauke Schimmoller; Timothy R Wilson; Lori S Friedman; Lewis C Cantley; Maurizio Scaltriti; José Baselga
Journal:  Science       Date:  2019-11-08       Impact factor: 47.728

2.  High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.

Authors:  Yang Liu; Mingyu Yang; Yanxiang Deng; Graham Su; Archibald Enninful; Cindy C Guo; Toma Tebaldi; Di Zhang; Dongjoo Kim; Zhiliang Bai; Eileen Norris; Alisia Pan; Jiatong Li; Yang Xiao; Stephanie Halene; Rong Fan
Journal:  Cell       Date:  2020-11-13       Impact factor: 41.582

3.  Sensitive tumour detection and classification using plasma cell-free DNA methylomes.

Authors:  Shu Yi Shen; Rajat Singhania; Gordon Fehringer; Ankur Chakravarthy; Michael H A Roehrl; Dianne Chadwick; Philip C Zuzarte; Ayelet Borgida; Ting Ting Wang; Tiantian Li; Olena Kis; Zhen Zhao; Anna Spreafico; Tiago da Silva Medina; Yadon Wang; David Roulois; Ilias Ettayebi; Zhuo Chen; Signy Chow; Tracy Murphy; Andrea Arruda; Grainne M O'Kane; Jessica Liu; Mark Mansour; John D McPherson; Catherine O'Brien; Natasha Leighl; Philippe L Bedard; Neil Fleshner; Geoffrey Liu; Mark D Minden; Steven Gallinger; Anna Goldenberg; Trevor J Pugh; Michael M Hoffman; Scott V Bratman; Rayjean J Hung; Daniel D De Carvalho
Journal:  Nature       Date:  2018-11-14       Impact factor: 49.962

4.  Deep learning-based classification of mesothelioma improves prediction of patient outcome.

Authors:  Pierre Courtiol; Charles Maussion; Françoise Galateau-Sallé; Gilles Wainrib; Thomas Clozel; Matahi Moarii; Elodie Pronier; Samuel Pilcer; Meriem Sefta; Pierre Manceron; Sylvain Toldo; Mikhail Zaslavskiy; Nolwenn Le Stang; Nicolas Girard; Olivier Elemento; Andrew G Nicholson; Jean-Yves Blay
Journal:  Nat Med       Date:  2019-10-07       Impact factor: 53.440

5.  Multimodality computer-aided breast cancer diagnosis with FFDM and DCE-MRI.

Authors:  Yading Yuan; Maryellen L Giger; Hui Li; Neha Bhooshan; Charlene A Sennett
Journal:  Acad Radiol       Date:  2010-09       Impact factor: 3.173

6.  Assessment of Deep Natural Language Processing in Ascertaining Oncologic Outcomes From Radiology Reports.

Authors:  Kenneth L Kehl; Haitham Elmarakeby; Mizuki Nishino; Eliezer M Van Allen; Eva M Lepisto; Michael J Hassett; Bruce E Johnson; Deborah Schrag
Journal:  JAMA Oncol       Date:  2019-10-01       Impact factor: 31.777

7.  Multi-attention Recurrent Network for Human Communication Comprehension.

Authors:  Amir Zadeh; Paul Pu Liang; Soujanya Poria; Prateek Vij; Erik Cambria; Louis-Philippe Morency
Journal:  Proc Conf AAAI Artif Intell       Date:  2018-02

Review 8.  Multi-omics approaches to disease.

Authors:  Yehudit Hasin; Marcus Seldin; Aldons Lusis
Journal:  Genome Biol       Date:  2017-05-05       Impact factor: 13.583

9.  Classification and mutation prediction from non-small cell lung cancer histopathology images using deep learning.

Authors:  Nicolas Coudray; Paolo Santiago Ocampo; Theodore Sakellaropoulos; Navneet Narula; Matija Snuderl; David Fenyö; Andre L Moreira; Narges Razavian; Aristotelis Tsirigos
Journal:  Nat Med       Date:  2018-09-17       Impact factor: 53.440

10.  Correction for Magnetic Field Inhomogeneities and Normalization of Voxel Values Are Needed to Better Reveal the Potential of MR Radiomic Features in Lung Cancer.

Authors:  Maxime Lacroix; Frédérique Frouin; Anne-Sophie Dirand; Christophe Nioche; Fanny Orlhac; Jean-François Bernaudin; Pierre-Yves Brillet; Irène Buvat
Journal:  Front Oncol       Date:  2020-01-31       Impact factor: 6.244

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  17 in total

1.  Multimodal integration of radiology, pathology and genomics for prediction of response to PD-(L)1 blockade in patients with non-small cell lung cancer.

Authors:  Rami S Vanguri; Jia Luo; Andrew T Aukerman; Jacklynn V Egger; Christopher J Fong; Natally Horvat; Andrew Pagano; Jose de Arimateia Batista Araujo-Filho; Luke Geneslaw; Hira Rizvi; Ramon Sosa; Kevin M Boehm; Soo-Ryum Yang; Francis M Bodd; Katia Ventura; Travis J Hollmann; Michelle S Ginsberg; Jianjiong Gao; Matthew D Hellmann; Jennifer L Sauter; Sohrab P Shah
Journal:  Nat Cancer       Date:  2022-08-29

2.  Swarm learning for decentralized artificial intelligence in cancer histopathology.

Authors:  Oliver Lester Saldanha; Philip Quirke; Nicholas P West; Jacqueline A James; Maurice B Loughrey; Heike I Grabsch; Manuel Salto-Tellez; Elizabeth Alwers; Didem Cifci; Narmin Ghaffari Laleh; Tobias Seibel; Richard Gray; Gordon G A Hutchins; Hermann Brenner; Marko van Treeck; Tanwei Yuan; Titus J Brinker; Jenny Chang-Claude; Firas Khader; Andreas Schuppert; Tom Luedde; Christian Trautwein; Hannah Sophie Muti; Sebastian Foersch; Michael Hoffmeister; Daniel Truhn; Jakob Nikolas Kather
Journal:  Nat Med       Date:  2022-04-25       Impact factor: 87.241

Review 3.  Challenges and the Evolving Landscape of Assessing Blood-Based PD-L1 Expression as a Biomarker for Anti-PD-(L)1 Immunotherapy.

Authors:  Tao Wang; Desirée Denman; Silvia M Bacot; Gerald M Feldman
Journal:  Biomedicines       Date:  2022-05-20

4.  Weakly supervised end-to-end artificial intelligence in gastrointestinal endoscopy.

Authors:  Lukas Buendgens; Didem Cifci; Narmin Ghaffari Laleh; Marko van Treeck; Maria T Koenen; Henning W Zimmermann; Till Herbold; Thomas Joachim Lux; Alexander Hann; Christian Trautwein; Jakob Nikolas Kather
Journal:  Sci Rep       Date:  2022-03-22       Impact factor: 4.379

Review 5.  Navigate Towards the Immunotherapy Era: Value of Immune Checkpoint Inhibitors in Non-Small Cell Lung Cancer Patients With Brain Metastases.

Authors:  Guanqun Yang; Ligang Xing; Xiaorong Sun
Journal:  Front Immunol       Date:  2022-03-29       Impact factor: 7.561

6.  A benchmark study of deep learning-based multi-omics data fusion methods for cancer.

Authors:  Dongjin Leng; Linyi Zheng; Yuqi Wen; Yunhao Zhang; Lianlian Wu; Jing Wang; Meihong Wang; Zhongnan Zhang; Song He; Xiaochen Bo
Journal:  Genome Biol       Date:  2022-08-09       Impact factor: 17.906

7.  Multimodal data integration using machine learning improves risk stratification of high-grade serous ovarian cancer.

Authors:  Kevin M Boehm; Emily A Aherne; Lora Ellenson; Ines Nikolovski; Mohammed Alghamdi; Ignacio Vázquez-García; Dmitriy Zamarin; Kara Long Roche; Ying Liu; Druv Patel; Andrew Aukerman; Arfath Pasha; Doori Rose; Pier Selenica; Pamela I Causa Andrieu; Chris Fong; Marinela Capanu; Jorge S Reis-Filho; Rami Vanguri; Harini Veeraraghavan; Natalie Gangai; Ramon Sosa; Samantha Leung; Andrew McPherson; JianJiong Gao; Yulia Lakhman; Sohrab P Shah
Journal:  Nat Cancer       Date:  2022-06-28

Review 8.  Beyond the snapshot: optimizing prognostication and prediction by moving from fixed to functional multidimensional cancer pathology.

Authors:  Cjh Kramer; Mpg Vreeswijk; B Thijssen; T Bosse; J Wesseling
Journal:  J Pathol       Date:  2022-05-23       Impact factor: 9.883

9.  iCEMIGE: Integration of CEll-morphometrics, MIcrobiome, and GEne biomarker signatures for risk stratification in breast cancers.

Authors:  Xuan-Yu Mao; Jesus Perez-Losada; Mar Abad; Marta Rodríguez-González; Cesar A Rodríguez; Jian-Hua Mao; Hang Chang
Journal:  World J Clin Oncol       Date:  2022-07-24

10.  Noncoding RNAs and Deep Learning Neural Network Discriminate Multi-Cancer Types.

Authors:  Anyou Wang; Rong Hai; Paul J Rider; Qianchuan He
Journal:  Cancers (Basel)       Date:  2022-01-12       Impact factor: 6.575

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