Literature DB >> 33317961

Next-Generation Liquid Biopsies: Embracing Data Science in Oncology.

Y R Im1, D W Y Tsui2, L A Diaz2, J C M Wan3.   

Abstract

Deeper and broader sequencing of circulating tumor DNA (ctDNA) has identified a wealth of cancer markers in the circulation, resulting in a paradigm shift towards data science-driven liquid biopsies in oncology. Although panel sequencing for actionable mutations in plasma is moving towards the clinic, the next generation of liquid biopsies is increasingly shifting from analyzing digital mutation signals towards analog signals, requiring a greater role for machine learning. Concomitantly, there is an increasing acceptance that these cancer signals do not have to arise from the tumor itself. In this Opinion, we discuss the opportunities and challenges arising from increasingly complex cancer liquid biopsy data.
Copyright © 2020 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  cancer; cell-free DNA; circulating tumor DNA; liquid biopsy; oncology

Mesh:

Year:  2020        PMID: 33317961      PMCID: PMC8408348          DOI: 10.1016/j.trecan.2020.11.001

Source DB:  PubMed          Journal:  Trends Cancer        ISSN: 2405-8025


  59 in total

1.  ctDNA monitoring using patient-specific sequencing and integration of variant reads.

Authors:  Jonathan C M Wan; Katrin Heider; Davina Gale; Suzanne Murphy; Eyal Fisher; Florent Mouliere; Andrea Ruiz-Valdepenas; Angela Santonja; James Morris; Dineika Chandrananda; Andrea Marshall; Andrew B Gill; Pui Ying Chan; Emily Barker; Gemma Young; Wendy N Cooper; Irena Hudecova; Francesco Marass; Richard Mair; Kevin M Brindle; Grant D Stewart; Jean E Abraham; Carlos Caldas; Doris M Rassl; Robert C Rintoul; Constantine Alifrangis; Mark R Middleton; Ferdia A Gallagher; Christine Parkinson; Amer Durrani; Ultan McDermott; Christopher G Smith; Charles Massie; Pippa G Corrie; Nitzan Rosenfeld
Journal:  Sci Transl Med       Date:  2020-06-17       Impact factor: 17.956

2.  Mutation tracking in circulating tumor DNA predicts relapse in early breast cancer.

Authors:  Isaac Garcia-Murillas; Gaia Schiavon; Britta Weigelt; Charlotte Ng; Sarah Hrebien; Rosalind J Cutts; Maggie Cheang; Peter Osin; Ashutosh Nerurkar; Iwanka Kozarewa; Javier Armisen Garrido; Mitch Dowsett; Jorge S Reis-Filho; Ian E Smith; Nicholas C Turner
Journal:  Sci Transl Med       Date:  2015-08-26       Impact factor: 17.956

3.  Enhanced detection of circulating tumor DNA by fragment size analysis.

Authors:  Florent Mouliere; Dineika Chandrananda; Anna M Piskorz; Elizabeth K Moore; James Morris; Lise Barlebo Ahlborn; Richard Mair; Teodora Goranova; Francesco Marass; Katrin Heider; Jonathan C M Wan; Anna Supernat; Irena Hudecova; Ioannis Gounaris; Susana Ros; Mercedes Jimenez-Linan; Javier Garcia-Corbacho; Keval Patel; Olga Østrup; Suzanne Murphy; Matthew D Eldridge; Davina Gale; Grant D Stewart; Johanna Burge; Wendy N Cooper; Michiel S van der Heijden; Charles E Massie; Colin Watts; Pippa Corrie; Simon Pacey; Kevin M Brindle; Richard D Baird; Morten Mau-Sørensen; Christine A Parkinson; Christopher G Smith; James D Brenton; Nitzan Rosenfeld
Journal:  Sci Transl Med       Date:  2018-11-07       Impact factor: 17.956

4.  Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli.

Authors:  Cayetano Pleguezuelos-Manzano; Jens Puschhof; Axel Rosendahl Huber; Arne van Hoeck; Henry M Wood; Jason Nomburg; Carino Gurjao; Freek Manders; Guillaume Dalmasso; Paul B Stege; Fernanda L Paganelli; Maarten H Geurts; Joep Beumer; Tomohiro Mizutani; Yi Miao; Reinier van der Linden; Stefan van der Elst; K Christopher Garcia; Janetta Top; Rob J L Willems; Marios Giannakis; Richard Bonnet; Phil Quirke; Matthew Meyerson; Edwin Cuppen; Ruben van Boxtel; Hans Clevers
Journal:  Nature       Date:  2020-02-27       Impact factor: 49.962

5.  Integrating genomic features for non-invasive early lung cancer detection.

Authors:  Jacob J Chabon; Emily G Hamilton; David M Kurtz; Mohammad S Esfahani; Everett J Moding; Henning Stehr; Joseph Schroers-Martin; Barzin Y Nabet; Binbin Chen; Aadel A Chaudhuri; Chih Long Liu; Angela B Hui; Michael C Jin; Tej D Azad; Diego Almanza; Young-Jun Jeon; Monica C Nesselbush; Lyron Co Ting Keh; Rene F Bonilla; Christopher H Yoo; Ryan B Ko; Emily L Chen; David J Merriott; Pierre P Massion; Aaron S Mansfield; Jin Jen; Hong Z Ren; Steven H Lin; Christina L Costantino; Risa Burr; Robert Tibshirani; Sanjiv S Gambhir; Gerald J Berry; Kristin C Jensen; Robert B West; Joel W Neal; Heather A Wakelee; Billy W Loo; Christian A Kunder; Ann N Leung; Natalie S Lui; Mark F Berry; Joseph B Shrager; Viswam S Nair; Daniel A Haber; Lecia V Sequist; Ash A Alizadeh; Maximilian Diehn
Journal:  Nature       Date:  2020-03-25       Impact factor: 49.962

6.  Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution.

Authors:  Christopher Abbosh; Nicolai J Birkbak; Gareth A Wilson; Mariam Jamal-Hanjani; Tudor Constantin; Raheleh Salari; John Le Quesne; David A Moore; Selvaraju Veeriah; Rachel Rosenthal; Teresa Marafioti; Eser Kirkizlar; Thomas B K Watkins; Nicholas McGranahan; Sophia Ward; Luke Martinson; Joan Riley; Francesco Fraioli; Maise Al Bakir; Eva Grönroos; Francisco Zambrana; Raymondo Endozo; Wenya Linda Bi; Fiona M Fennessy; Nicole Sponer; Diana Johnson; Joanne Laycock; Seema Shafi; Justyna Czyzewska-Khan; Andrew Rowan; Tim Chambers; Nik Matthews; Samra Turajlic; Crispin Hiley; Siow Ming Lee; Martin D Forster; Tanya Ahmad; Mary Falzon; Elaine Borg; David Lawrence; Martin Hayward; Shyam Kolvekar; Nikolaos Panagiotopoulos; Sam M Janes; Ricky Thakrar; Asia Ahmed; Fiona Blackhall; Yvonne Summers; Dina Hafez; Ashwini Naik; Apratim Ganguly; Stephanie Kareht; Rajesh Shah; Leena Joseph; Anne Marie Quinn; Phil A Crosbie; Babu Naidu; Gary Middleton; Gerald Langman; Simon Trotter; Marianne Nicolson; Hardy Remmen; Keith Kerr; Mahendran Chetty; Lesley Gomersall; Dean A Fennell; Apostolos Nakas; Sridhar Rathinam; Girija Anand; Sajid Khan; Peter Russell; Veni Ezhil; Babikir Ismail; Melanie Irvin-Sellers; Vineet Prakash; Jason F Lester; Malgorzata Kornaszewska; Richard Attanoos; Haydn Adams; Helen Davies; Dahmane Oukrif; Ayse U Akarca; John A Hartley; Helen L Lowe; Sara Lock; Natasha Iles; Harriet Bell; Yenting Ngai; Greg Elgar; Zoltan Szallasi; Roland F Schwarz; Javier Herrero; Aengus Stewart; Sergio A Quezada; Karl S Peggs; Peter Van Loo; Caroline Dive; C Jimmy Lin; Matthew Rabinowitz; Hugo J W L Aerts; Allan Hackshaw; Jacqui A Shaw; Bernhard G Zimmermann; Charles Swanton
Journal:  Nature       Date:  2017-04-26       Impact factor: 49.962

7.  Swarm Intelligence-Enhanced Detection of Non-Small-Cell Lung Cancer Using Tumor-Educated Platelets.

Authors:  Myron G Best; Nik Sol; Sjors G J G In 't Veld; Adrienne Vancura; Mirte Muller; Anna-Larissa N Niemeijer; Aniko V Fejes; Lee-Ann Tjon Kon Fat; Anna E Huis In 't Veld; Cyra Leurs; Tessa Y Le Large; Laura L Meijer; Irsan E Kooi; François Rustenburg; Pepijn Schellen; Heleen Verschueren; Edward Post; Laurine E Wedekind; Jillian Bracht; Michelle Esenkbrink; Leon Wils; Francesca Favaro; Jilian D Schoonhoven; Jihane Tannous; Hanne Meijers-Heijboer; Geert Kazemier; Elisa Giovannetti; Jaap C Reijneveld; Sander Idema; Joep Killestein; Michal Heger; Saskia C de Jager; Rolf T Urbanus; Imo E Hoefer; Gerard Pasterkamp; Christine Mannhalter; Jose Gomez-Arroyo; Harm-Jan Bogaard; David P Noske; W Peter Vandertop; Daan van den Broek; Bauke Ylstra; R Jonas A Nilsson; Pieter Wesseling; Niki Karachaliou; Rafael Rosell; Elizabeth Lee-Lewandrowski; Kent B Lewandrowski; Bakhos A Tannous; Adrianus J de Langen; Egbert F Smit; Michel M van den Heuvel; Thomas Wurdinger
Journal:  Cancer Cell       Date:  2017-08-14       Impact factor: 31.743

8.  Noninvasive blood tests for fetal development predict gestational age and preterm delivery.

Authors:  Thuy T M Ngo; Mira N Moufarrej; Marie-Louise H Rasmussen; Joan Camunas-Soler; Wenying Pan; Jennifer Okamoto; Norma F Neff; Keli Liu; Ronald J Wong; Katheryne Downes; Robert Tibshirani; Gary M Shaw; Line Skotte; David K Stevenson; Joseph R Biggio; Michal A Elovitz; Mads Melbye; Stephen R Quake
Journal:  Science       Date:  2018-06-08       Impact factor: 47.728

9.  Microbiome analyses of blood and tissues suggest cancer diagnostic approach.

Authors:  Gregory D Poore; Evguenia Kopylova; Qiyun Zhu; Carolina Carpenter; Serena Fraraccio; Stephen Wandro; Tomasz Kosciolek; Stefan Janssen; Jessica Metcalf; Se Jin Song; Jad Kanbar; Sandrine Miller-Montgomery; Robert Heaton; Rana Mckay; Sandip Pravin Patel; Austin D Swafford; Rob Knight
Journal:  Nature       Date:  2020-03-11       Impact factor: 49.962

10.  Size-tagged preferred ends in maternal plasma DNA shed light on the production mechanism and show utility in noninvasive prenatal testing.

Authors:  Kun Sun; Peiyong Jiang; Ada I C Wong; Yvonne K Y Cheng; Suk Hang Cheng; Haiqiang Zhang; K C Allen Chan; Tak Y Leung; Rossa W K Chiu; Y M Dennis Lo
Journal:  Proc Natl Acad Sci U S A       Date:  2018-05-14       Impact factor: 11.205

View more
  9 in total

Review 1.  Detection of Cell Types Contributing to Cancer From Circulating, Cell-Free Methylated DNA.

Authors:  Megan E Barefoot; Netanel Loyfer; Amber J Kiliti; A Patrick McDeed; Tommy Kaplan; Anton Wellstein
Journal:  Front Genet       Date:  2021-07-27       Impact factor: 4.772

Review 2.  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

3.  Circulating Plasma Tumor DNA Is Superior to Plasma Tumor RNA Detection in Ewing Sarcoma Patients: ptDNA and ptRNA in Ewing Sarcoma.

Authors:  Avery Bodlak; Kyle Chang; Jessica Channel; Amy L Treece; Nathan Donaldson; Carrye R Cost; Timothy P Garrington; Brian Greffe; Sandra Luna-Fineman; Jenna Sopfe; David M Loeb; Masanori Hayashi
Journal:  J Mol Diagn       Date:  2021-04-20       Impact factor: 5.341

Review 4.  Prognostic Biomarkers in Uveal Melanoma: The Status Quo, Recent Advances and Future Directions.

Authors:  Nuno Jorge Lamas; Arnaud Martel; Sacha Nahon-Estève; Samantha Goffinet; Adam Macocco; Corine Bertolotto; Sandra Lassalle; Paul Hofman
Journal:  Cancers (Basel)       Date:  2021-12-25       Impact factor: 6.639

Review 5.  Tracing the Origin of Cell-Free DNA Molecules through Tissue-Specific Epigenetic Signatures.

Authors:  Angela Oberhofer; Abel J Bronkhorst; Carsten Uhlig; Vida Ungerer; Stefan Holdenrieder
Journal:  Diagnostics (Basel)       Date:  2022-07-29

Review 6.  Liquid biopsies to predict CDK4/6 inhibitor efficacy and resistance in breast cancer.

Authors:  Sasha C Main; David W Cescon; Scott V Bratman
Journal:  Cancer Drug Resist       Date:  2022-06-22

7.  Liquid biopsy: from discovery to clinical implementation.

Authors:  Catherine Alix-Panabières; Klaus Pantel
Journal:  Mol Oncol       Date:  2021-06       Impact factor: 6.603

8.  NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA.

Authors:  Mariya Shtumpf; Kristan V Piroeva; Shivam P Agrawal; Divya R Jacob; Vladimir B Teif
Journal:  Chromosoma       Date:  2022-01-21       Impact factor: 2.919

9.  Liquid biopsy: Precise diagnosis and therapy for cholangiocarcinoma.

Authors:  Si-Qin Wang; Chu-Xing Chai; Bi-Rong Wang; Feng Zhu; Dan Shang; Min Li
Journal:  World J Gastrointest Oncol       Date:  2022-01-15
  9 in total

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