Literature DB >> 33742076

Inflation of tumor mutation burden by tumor-only sequencing in under-represented groups.

Yan W Asmann1,2, Kaushal Parikh3, P Leif Bergsagel4, Haidong Dong5, Alex A Adjei6, Mitesh J Borad2,4, Aaron S Mansfield7,8.   

Abstract

With the recent FDA approval of tumor mutational burden-high (TMB-H) status as a biomarker for treatment with a PD-1 inhibitor regardless of tumor type, accurate assessment of patient-specific TMB is more critical now more than ever. Using paired tumor and germline exome sequencing data from 701 patients newly diagnosed with multiple myeloma, including 575 self-reported White patients and 126 self-reported Black patients, we observed that compared to the gold standard of filtering germline variants with patient-paired germline sequencing data, TMB estimates were significantly higher in both Black and White patients when using public databases for filtering non-somatic mutations; however, TMB was more significantly inflated in Black patients compared to White patients. TMB as a biomarker for patient selection to receive immune checkpoint inhibitors (ICIs) therapy without patient-paired germline sequencing may introduce racial bias due to the under-representation of minority groups in public databases.

Entities:  

Year:  2021        PMID: 33742076      PMCID: PMC7979755          DOI: 10.1038/s41698-021-00164-5

Source DB:  PubMed          Journal:  NPJ Precis Oncol        ISSN: 2397-768X


  14 in total

1.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

Authors:  Aaron McKenna; Matthew Hanna; Eric Banks; Andrey Sivachenko; Kristian Cibulskis; Andrew Kernytsky; Kiran Garimella; David Altshuler; Stacey Gabriel; Mark Daly; Mark A DePristo
Journal:  Genome Res       Date:  2010-07-19       Impact factor: 9.043

2.  Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis.

Authors:  Samra Turajlic; Kevin Litchfield; Hang Xu; Rachel Rosenthal; Nicholas McGranahan; James L Reading; Yien Ning S Wong; Andrew Rowan; Nnennaya Kanu; Maise Al Bakir; Tim Chambers; Roberto Salgado; Peter Savas; Sherene Loi; Nicolai J Birkbak; Laurent Sansregret; Martin Gore; James Larkin; Sergio A Quezada; Charles Swanton
Journal:  Lancet Oncol       Date:  2017-07-07       Impact factor: 41.316

3.  Tumor mutational load predicts survival after immunotherapy across multiple cancer types.

Authors:  Robert M Samstein; Chung-Han Lee; Alexander N Shoushtari; Matthew D Hellmann; Ronglai Shen; Yelena Y Janjigian; David A Barron; Ahmet Zehir; Emmet J Jordan; Antonio Omuro; Thomas J Kaley; Sviatoslav M Kendall; Robert J Motzer; A Ari Hakimi; Martin H Voss; Paul Russo; Jonathan Rosenberg; Gopa Iyer; Bernard H Bochner; Dean F Bajorin; Hikmat A Al-Ahmadie; Jamie E Chaft; Charles M Rudin; Gregory J Riely; Shrujal Baxi; Alan L Ho; Richard J Wong; David G Pfister; Jedd D Wolchok; Christopher A Barker; Philip H Gutin; Cameron W Brennan; Viviane Tabar; Ingo K Mellinghoff; Lisa M DeAngelis; Charlotte E Ariyan; Nancy Lee; William D Tap; Mrinal M Gounder; Sandra P D'Angelo; Leonard Saltz; Zsofia K Stadler; Howard I Scher; Jose Baselga; Pedram Razavi; Christopher A Klebanoff; Rona Yaeger; Neil H Segal; Geoffrey Y Ku; Ronald P DeMatteo; Marc Ladanyi; Naiyer A Rizvi; Michael F Berger; Nadeem Riaz; David B Solit; Timothy A Chan; Luc G T Morris
Journal:  Nat Genet       Date:  2019-01-14       Impact factor: 38.330

4.  Association of tumour mutational burden with outcomes in patients with advanced solid tumours treated with pembrolizumab: prospective biomarker analysis of the multicohort, open-label, phase 2 KEYNOTE-158 study.

Authors:  Aurélien Marabelle; Marwan Fakih; Juanita Lopez; Manisha Shah; Ronnie Shapira-Frommer; Kazuhiko Nakagawa; Hyun Cheol Chung; Hedy L Kindler; Jose A Lopez-Martin; Wilson H Miller; Antoine Italiano; Steven Kao; Sarina A Piha-Paul; Jean-Pierre Delord; Robert R McWilliams; David A Fabrizio; Deepti Aurora-Garg; Lei Xu; Fan Jin; Kevin Norwood; Yung-Jue Bang
Journal:  Lancet Oncol       Date:  2020-09-10       Impact factor: 41.316

5.  Integrated genomic profiling expands clinical options for patients with cancer.

Authors:  Nike Beaubier; Martin Bontrager; Robert Huether; Catherine Igartua; Denise Lau; Robert Tell; Alexandria M Bobe; Stephen Bush; Alan L Chang; Derick C Hoskinson; Aly A Khan; Emily Kudalkar; Benjamin D Leibowitz; Ariane Lozachmeur; Jackson Michuda; Jerod Parsons; Jason F Perera; Ameen Salahudeen; Kaanan P Shah; Timothy Taxter; Wei Zhu; Kevin P White
Journal:  Nat Biotechnol       Date:  2019-09-30       Impact factor: 68.164

6.  The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation.

Authors:  Jean-Pierre A Kocher; Daniel J Quest; Patrick Duffy; Michael A Meiners; Raymond M Moore; David Rider; Asif Hossain; Steven N Hart; Valentin Dinu
Journal:  Bioinformatics       Date:  2014-03-10       Impact factor: 6.937

7.  Tumor Mutational Burden From Tumor-Only Sequencing Compared With Germline Subtraction From Paired Tumor and Normal Specimens.

Authors:  Kaushal Parikh; Robert Huether; Kevin White; Derick Hoskinson; Nike Beaubier; Haidong Dong; Alex A Adjei; Aaron S Mansfield
Journal:  JAMA Netw Open       Date:  2020-02-05

8.  Fast and accurate short read alignment with Burrows-Wheeler transform.

Authors:  Heng Li; Richard Durbin
Journal:  Bioinformatics       Date:  2009-05-18       Impact factor: 6.937

9.  CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting.

Authors:  Márton Münz; Elise Ruark; Anthony Renwick; Emma Ramsay; Matthew Clarke; Shazia Mahamdallie; Victoria Cloke; Sheila Seal; Ann Strydom; Gerton Lunter; Nazneen Rahman
Journal:  Genome Med       Date:  2015-07-28       Impact factor: 11.117

Review 10.  Evaluating the promise of inclusion of African ancestry populations in genomics.

Authors:  Amy R Bentley; Shawneequa L Callier; Charles N Rotimi
Journal:  NPJ Genom Med       Date:  2020-02-25       Impact factor: 8.617

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  6 in total

1.  Tumor Junction Burden and Antigen Presentation as Predictors of Survival in Mesothelioma Treated With Immune Checkpoint Inhibitors.

Authors:  Farhad Kosari; Maria Disselhorst; Jun Yin; Tobias Peikert; Julia Udell; Sarah Johnson; James Smadbeck; Stephen Murphy; Alexa McCune; Giannoula Karagouga; Aakash Desai; Janet Schaefer-Klein; Mitesh J Borad; John Cheville; George Vasmatzis; Paul Baas; Aaron S Mansfield
Journal:  J Thorac Oncol       Date:  2021-11-17       Impact factor: 15.609

2.  Ancestry-driven recalibration of tumor mutational burden and disparate clinical outcomes in response to immune checkpoint inhibitors.

Authors:  Amin H Nassar; Elio Adib; Sarah Abou Alaiwi; Talal El Zarif; Stefan Groha; Elie W Akl; Pier Vitale Nuzzo; Tarek H Mouhieddine; Tomin Perea-Chamblee; Kodi Taraszka; Habib El-Khoury; Muhieddine Labban; Christopher Fong; Kanika S Arora; Chris Labaki; Wenxin Xu; Guru Sonpavde; Robert I Haddad; Kent W Mouw; Marios Giannakis; F Stephen Hodi; Noah Zaitlen; Adam J Schoenfeld; Nikolaus Schultz; Michael F Berger; Laura E MacConaill; Guruprasad Ananda; David J Kwiatkowski; Toni K Choueiri; Deborah Schrag; Jian Carrot-Zhang; Alexander Gusev
Journal:  Cancer Cell       Date:  2022-09-29       Impact factor: 38.585

3.  Mutation burden-orthogonal tumor genomic subtypes delineate responses to immune checkpoint therapy.

Authors:  Shiro Takamatsu; Junzo Hamanishi; J B Brown; Ken Yamaguchi; Koji Yamanoi; Kosuke Murakami; Osamu Gotoh; Seiichi Mori; Masaki Mandai; Noriomi Matsumura
Journal:  J Immunother Cancer       Date:  2022-07       Impact factor: 12.469

4.  Lower Exome Sequencing Coverage of Ancestrally African Patients in The Cancer Genome Atlas.

Authors:  Daniel P Wickland; Mark E Sherman; Derek C Radisky; Aaron S Mansfield; Yan W Asmann
Journal:  J Natl Cancer Inst       Date:  2022-08-08       Impact factor: 11.816

5.  Visualization of the Effect of Assay Size on the Error Profile of Tumor Mutational Burden Measurement.

Authors:  Nathanael G Bailey
Journal:  Genes (Basel)       Date:  2022-02-26       Impact factor: 4.096

6.  RBM10 Deficiency Is Associated With Increased Immune Activity in Lung Adenocarcinoma.

Authors:  Bing Liu; Yaqi Wang; Han Wang; Zhongwu Li; Lujing Yang; Shi Yan; Xin Yang; Yuanyuan Ma; Xuan Gao; Yanfang Guan; Xin Yi; Xuefeng Xia; Jingjing Li; Nan Wu
Journal:  Front Oncol       Date:  2021-07-21       Impact factor: 6.244

  6 in total

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