Description of the genetic variants identified in a cohort of patients diagnosed with localized anal squamous cell carcinoma and treated with panitumumab

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Abstract

Squamous cell carcinoma is the most frequent histologic type of anal carcinoma. The standard of care since the 1970s has been a combination of 5-fluorouracil, mitomycin C, and radiotherapy. This treatment is very effective in T1/T2 tumors (achieving complete regression in 80–90% of tumors). However, in T3/T4 tumors, the 3-year relapse free survival rate is only 50%. The VITAL trial aimed to assess the efficacy and safety of panitumumab in combination with this standard treatment. In this study, 27 paraffin-embedded samples from the VITAL trial and 18 samples from patients from daily clinical practice were analyzed by whole-exome sequencing and the influence of the presence of genetic variants in the response to panitumumab was studied. Having a moderate- or high-impact genetic variant in PIK3CA seemed to be related to the response to panitumumab. Furthermore, copy number variants in FGFR3, GRB2 and JAK1 were also related to the response to panitumumab. These genetic alterations have also been studied in the cohort of patients from daily clinical practice (not treated with panitumumab) and they did not have a predictive value. Therefore, in this study, a collection of genetic alterations related to the response with panitumumab was described. These results could be useful for patient stratification in new anti-EGFR clinical trials.

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The Sequence Alignment/Map format and SAMtools

Heng Li, Bob Handsaker, Alec Wysoker … (2009)

Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk

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Cutadapt removes adapter sequences from high-throughput sequencing reads

Marcel Martin (2011)

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Cancer statistics, 2019

Rebecca Siegel, Kimberly D Miller, Ahmedin Jemal (2019)

Each year, the American Cancer Society estimates the numbers of new cancer cases and deaths that will occur in the United States and compiles the most recent data on cancer incidence, mortality, and survival. Incidence data, available through 2015, were collected by the Surveillance, Epidemiology, and End Results Program; the National Program of Cancer Registries; and the North American Association of Central Cancer Registries. Mortality data, available through 2016, were collected by the National Center for Health Statistics. In 2019, 1,762,450 new cancer cases and 606,880 cancer deaths are projected to occur in the United States. Over the past decade of data, the cancer incidence rate (2006-2015) was stable in women and declined by approximately 2% per year in men, whereas the cancer death rate (2007-2016) declined annually by 1.4% and 1.8%, respectively. The overall cancer death rate dropped continuously from 1991 to 2016 by a total of 27%, translating into approximately 2,629,200 fewer cancer deaths than would have been expected if death rates had remained at their peak. Although the racial gap in cancer mortality is slowly narrowing, socioeconomic inequalities are widening, with the most notable gaps for the most preventable cancers. For example, compared with the most affluent counties, mortality rates in the poorest counties were 2-fold higher for cervical cancer and 40% higher for male lung and liver cancers during 2012-2016. Some states are home to both the wealthiest and the poorest counties, suggesting the opportunity for more equitable dissemination of effective cancer prevention, early detection, and treatment strategies. A broader application of existing cancer control knowledge with an emphasis on disadvantaged groups would undoubtedly accelerate progress against cancer.

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Author and article information

Contributors

Jaime Feliu: jaimefeliu@hotmail.com

Journal

Journal ID (nlm-ta): Sci Rep

Journal ID (iso-abbrev): Sci Rep

Title: Scientific Reports

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2045-2322

Publication date (Electronic): 1 April 2021

Publication date PMC-release: 1 April 2021

Publication date Collection: 2021

Volume: 11

Electronic Location Identifier: 7402

Affiliations

[1 ]Biomedica Molecular Medicine SL, Madrid, Spain

[2 ]GRID grid.81821.32, ISNI 0000 0000 8970 9163, Molecular Oncology and Pathology Lab, , Hospital Universitario La Paz-IdiPAZ, ; Madrid, Spain

[3 ]GRID grid.5841.8, ISNI 0000 0004 1937 0247, Medical Oncology Department, Hospital Clinic of Barcelona, Translational Genomics and Targeted Therapeutics in Solid Tumors Group, IDIBAPS, , University of Barcelona, ; Barcelona, Spain

[4 ]GRID grid.144756.5, ISNI 0000 0001 1945 5329, Medical Oncology Department, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), UCM, CNIO, CIBERONC, , Hospital Universitario 12 de Octubre, ; Madrid, Spain

[5 ]GRID grid.411083.f, ISNI 0000 0001 0675 8654, Medical Oncology Service, Vall Hebron Institute of Oncology (VHIO), , Vall Hebron University Hospital, ; Barcelona, Spain

[6 ]GRID grid.81821.32, ISNI 0000 0000 8970 9163, Pathology Department, , Hospital Universitario La Paz, ; Madrid, Spain

[7 ]GRID grid.81821.32, ISNI 0000 0000 8970 9163, Molecular Pathology and Therapeutic Targets Group, , Hospital Universitario La Paz-IdiPAZ, ; Madrid, Spain

[8 ]GRID grid.413448.e, ISNI 0000 0000 9314 1427, Biomedical Research Networking Center On Oncology-CIBERONC, , ISCIII, ; Madrid, Spain

[9 ]GRID grid.410458.c, ISNI 0000 0000 9635 9413, Pathology Department, , Hospital Clínic Universitat de Barcelona, ; Villarroel 170, 08036 Barcelona, Spain

[10 ]GRID grid.410526.4, ISNI 0000 0001 0277 7938, Medical Oncology Department, , Hospital General Universitario Gregorio Marañón, ; Madrid, Spain

[11 ]Genomics Unit Cantoblanco, Parque Científico de Madrid, C/ Faraday 7, 28049 Madrid, Spain

[12 ]Biotechvana SL, Parque Científico de Madrid, C/ Faraday 7, 28049 Madrid, Spain

[13 ]GRID grid.81821.32, ISNI 0000 0000 8970 9163, Medical Oncology Department, , Hospital Universitario La Paz, ; Paseo de la Castellana 261, 28046 Madrid, Spain

[14 ]GRID grid.410458.c, ISNI 0000 0000 9635 9413, Radiotherapy Oncology Department, , Hospital Clinic of Barcelona, ; Carrer de Villarroel 170, 08036 Barcelona, Spain

[15 ]GRID grid.81821.32, ISNI 0000 0000 8970 9163, Translational Oncology Group, , Hospital Universitario La Paz-IdiPAZ, ; Madrid, Spain

[16 ]GRID grid.81821.32, ISNI 0000 0000 8970 9163, Institute of Medical and Molecular Genetics, IdiPAZ, Unit 753, ISCIII, , Hospital Universitario La Paz /& CIBERER, ; Paseo de la Castellana 261, 28046 Madrid, Spain

[17 ]GRID grid.5515.4, ISNI 0000000119578126, Cátedra UAM-Amgen, , Universidad Autónoma de Madrid, ; Madrid, Spain

Article

Publisher ID: 86966

DOI: 10.1038/s41598-021-86966-w

PMC ID: 8016846

SO-VID: 5b3d1e5d-5bdf-4232-b88a-2db7c10d1f30

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 6 May 2020

Date accepted : 11 March 2021

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100003329, Ministerio de Economía y Competitividad;

Award ID: DI-15-07614

Award Recipient : Lucía Trilla-Fuertes

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ScienceOpen disciplines: Uncategorized

Keywords: cancer,medical genetics,predictive markers

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ScienceOpen disciplines: Uncategorized

Keywords: cancer, medical genetics, predictive markers

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Description of the genetic variants identified in a cohort of patients diagnosed with localized anal squamous cell carcinoma and treated with panitumumab

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Most cited references 31

The Sequence Alignment/Map format and SAMtools

Cutadapt removes adapter sequences from high-throughput sequencing reads

Cancer statistics, 2019

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