Literature DB >> 35230680

The Architecture of a Precision Oncology Platform.

Alessandro Laganà1.   

Abstract

Precision oncology is a novel research field and approach to cancer care which leverages high-throughput sequencing technologies and bioinformatics pipelines to determine diagnosis, prognosis, and treatment of patients in a personalized manner. This chapter provides an overview of a typical precision oncology software platform, from raw data to patient reports. Standard and advanced analytical components are described and discussed, along with their strengths and limitations, in general and in the context of a precision oncology application for advanced cancer patients.
© 2022. Springer Nature Switzerland AG.

Entities:  

Keywords:  Actionable alterations; Biomarkers; Drug recommendations; High-throughput next-generation sequencing; Mutations; Patient reports; Precision oncology; RNA sequencing; Whole-exome sequencing; Whole-genome sequencing

Mesh：

Year:  2022        PMID： 35230680     DOI： 10.1007/978-3-030-91836-1_1

Source DB:  PubMed          Journal:  Adv Exp Med Biol        ISSN： 0065-2598            Impact factor:   2.622


  133 in total

Review 1.  Copy number alterations and copy number variation in cancer: close encounters of the bad kind.

Authors:  F Speleman; C Kumps; K Buysse; B Poppe; B Menten; K De Preter
Journal:  Cytogenet Genome Res       Date:  2009-03-11       Impact factor: 1.636

Review 2.  A primer on precision medicine informatics.

Authors:  Andrea Sboner; Olivier Elemento
Journal:  Brief Bioinform       Date:  2015-06-05       Impact factor: 11.622

3.  Nextflow enables reproducible computational workflows.

Authors:  Paolo Di Tommaso; Maria Chatzou; Evan W Floden; Pablo Prieto Barja; Emilio Palumbo; Cedric Notredame
Journal:  Nat Biotechnol       Date:  2017-04-11       Impact factor: 54.908

4.  Copy number variations and cancer.

Authors:  Adam Shlien; David Malkin
Journal:  Genome Med       Date:  2009-06-16       Impact factor: 11.117

5.  Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing.

Authors:  Garrett M Frampton; Alex Fichtenholtz; Geoff A Otto; Kai Wang; Sean R Downing; Jie He; Michael Schnall-Levin; Jared White; Eric M Sanford; Peter An; James Sun; Frank Juhn; Kristina Brennan; Kiel Iwanik; Ashley Maillet; Jamie Buell; Emily White; Mandy Zhao; Sohail Balasubramanian; Selmira Terzic; Tina Richards; Vera Banning; Lazaro Garcia; Kristen Mahoney; Zac Zwirko; Amy Donahue; Himisha Beltran; Juan Miguel Mosquera; Mark A Rubin; Snjezana Dogan; Cyrus V Hedvat; Michael F Berger; Lajos Pusztai; Matthias Lechner; Chris Boshoff; Mirna Jarosz; Christine Vietz; Alex Parker; Vincent A Miller; Jeffrey S Ross; John Curran; Maureen T Cronin; Philip J Stephens; Doron Lipson; Roman Yelensky
Journal:  Nat Biotechnol       Date:  2013-10-20       Impact factor: 54.908

6.  Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome.

Authors:  Michael Rusch; Joy Nakitandwe; Sheila Shurtleff; Scott Newman; Zhaojie Zhang; Michael N Edmonson; Matthew Parker; Yuannian Jiao; Xiaotu Ma; Yanling Liu; Jiali Gu; Michael F Walsh; Jared Becksfort; Andrew Thrasher; Yongjin Li; James McMurry; Erin Hedlund; Aman Patel; John Easton; Donald Yergeau; Bhavin Vadodaria; Ruth G Tatevossian; Susana Raimondi; Dale Hedges; Xiang Chen; Kohei Hagiwara; Rose McGee; Giles W Robinson; Jeffery M Klco; Tanja A Gruber; David W Ellison; James R Downing; Jinghui Zhang
Journal:  Nat Commun       Date:  2018-09-27       Impact factor: 14.919

7.  Implementation and use of whole exome sequencing for metastatic solid cancer.

Authors:  Manon Réda; Corentin Richard; Aurelie Bertaut; Julie Niogret; Thomas Collot; Jean David Fumet; Julie Blanc; Caroline Truntzer; Isabelle Desmoulins; Sylvain Ladoire; Audrey Hennequin; Laure Favier; Leila Bengrine; Julie Vincent; Alice Hervieu; Jean-Florian Guion Dusserre; Come Lepage; Pascal Foucher; Christophe Borg; Juliette Albuisson; Laurent Arnould; Sophie Nambot; Laurence Faivre; Romain Boidot; Francois Ghiringhelli
Journal:  EBioMedicine       Date:  2020-01-07       Impact factor: 8.143

Review 8.  Molecular profiling for precision cancer therapies.

Authors:  Eoghan R Malone; Marc Oliva; Peter J B Sabatini; Tracy L Stockley; Lillian L Siu
Journal:  Genome Med       Date:  2020-01-14       Impact factor: 11.117

9.  Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions.

Authors:  A Rose Brannon; Efsevia Vakiani; Brooke E Sylvester; Sasinya N Scott; Gregory McDermott; Ronak H Shah; Krishan Kania; Agnes Viale; Dayna M Oschwald; Vladimir Vacic; Anne-Katrin Emde; Andrea Cercek; Rona Yaeger; Nancy E Kemeny; Leonard B Saltz; Jinru Shia; Michael I D'Angelica; Martin R Weiser; David B Solit; Michael F Berger
Journal:  Genome Biol       Date:  2014-08-28       Impact factor: 13.583

10.  Performance comparison of four exome capture systems for deep sequencing.

Authors:  Chandra Sekhar Reddy Chilamakuri; Susanne Lorenz; Mohammed-Amin Madoui; Daniel Vodák; Jinchang Sun; Eivind Hovig; Ola Myklebost; Leonardo A Meza-Zepeda
Journal:  BMC Genomics       Date:  2014-06-09       Impact factor: 3.969
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