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MethylMasteR: A Comparison and Customization of Methylation-Based Copy Number Variation Calling Software in Cancers Harboring Large Scale Chromosomal Deletions

DNA methylation-based copy number variation (CNV) calling software offers the advantages of providing both genetic (copy-number) and epigenetic (methylation) state information from a single genomic library. This method is advantageous when looking at large-scale chromosomal rearrangements such as th...

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Autores principales: Mariani, Michael P., Chen, Jennifer A., Zhang, Ze, Pike, Steven C., Salas, Lucas A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9098103/
https://www.ncbi.nlm.nih.gov/pubmed/35573871
http://dx.doi.org/10.3389/fbinf.2022.859828
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author Mariani, Michael P.
Chen, Jennifer A.
Zhang, Ze
Pike, Steven C.
Salas, Lucas A.
author_facet Mariani, Michael P.
Chen, Jennifer A.
Zhang, Ze
Pike, Steven C.
Salas, Lucas A.
author_sort Mariani, Michael P.
collection PubMed
description DNA methylation-based copy number variation (CNV) calling software offers the advantages of providing both genetic (copy-number) and epigenetic (methylation) state information from a single genomic library. This method is advantageous when looking at large-scale chromosomal rearrangements such as the loss of the short arm of chromosome 3 (3p) in renal cell carcinoma and the codeletion of the short arm of chromosome 1 and the long arm of chromosome 19 (1p/19q) commonly seen in histologically defined oligodendrogliomas. Herein, we present MethylMasteR: a software framework that facilitates the standardization and customization of methylation-based CNV calling algorithms in a single R package deployed using the Docker software framework. This framework allows for the easy comparison of the performance and the large-scale CNV event identification capability of four common methylation-based CNV callers. Additionally, we incorporated our custom routine, which was among the best performing routines. We employed the Affymetrix 6.0 SNP Chip results as a gold standard against which to compare large-scale event recall. As there are disparities within the software calling algorithms themselves, no single software is likely to perform best for all samples and all combinations of parameters. The employment of a standardized software framework via creating a Docker image and its subsequent deployment as a Docker container allows researchers to efficiently compare algorithms and lends itself to the development of modified workflows such as the custom workflow we have developed. Researchers can now use the MethylMasteR software for their methylation-based CNV calling needs and follow our software deployment framework. We will continue to refine our methodology in the future with a specific focus on identifying large-scale chromosomal rearrangements in cancer methylation data.
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spelling pubmed-90981032022-05-12 MethylMasteR: A Comparison and Customization of Methylation-Based Copy Number Variation Calling Software in Cancers Harboring Large Scale Chromosomal Deletions Mariani, Michael P. Chen, Jennifer A. Zhang, Ze Pike, Steven C. Salas, Lucas A. Front Bioinform Bioinformatics DNA methylation-based copy number variation (CNV) calling software offers the advantages of providing both genetic (copy-number) and epigenetic (methylation) state information from a single genomic library. This method is advantageous when looking at large-scale chromosomal rearrangements such as the loss of the short arm of chromosome 3 (3p) in renal cell carcinoma and the codeletion of the short arm of chromosome 1 and the long arm of chromosome 19 (1p/19q) commonly seen in histologically defined oligodendrogliomas. Herein, we present MethylMasteR: a software framework that facilitates the standardization and customization of methylation-based CNV calling algorithms in a single R package deployed using the Docker software framework. This framework allows for the easy comparison of the performance and the large-scale CNV event identification capability of four common methylation-based CNV callers. Additionally, we incorporated our custom routine, which was among the best performing routines. We employed the Affymetrix 6.0 SNP Chip results as a gold standard against which to compare large-scale event recall. As there are disparities within the software calling algorithms themselves, no single software is likely to perform best for all samples and all combinations of parameters. The employment of a standardized software framework via creating a Docker image and its subsequent deployment as a Docker container allows researchers to efficiently compare algorithms and lends itself to the development of modified workflows such as the custom workflow we have developed. Researchers can now use the MethylMasteR software for their methylation-based CNV calling needs and follow our software deployment framework. We will continue to refine our methodology in the future with a specific focus on identifying large-scale chromosomal rearrangements in cancer methylation data. Frontiers Media S.A. 2022-04-12 /pmc/articles/PMC9098103/ /pubmed/35573871 http://dx.doi.org/10.3389/fbinf.2022.859828 Text en Copyright © 2022 Mariani, Chen, Zhang, Pike and Salas. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Bioinformatics
Mariani, Michael P.
Chen, Jennifer A.
Zhang, Ze
Pike, Steven C.
Salas, Lucas A.
MethylMasteR: A Comparison and Customization of Methylation-Based Copy Number Variation Calling Software in Cancers Harboring Large Scale Chromosomal Deletions
title MethylMasteR: A Comparison and Customization of Methylation-Based Copy Number Variation Calling Software in Cancers Harboring Large Scale Chromosomal Deletions
title_full MethylMasteR: A Comparison and Customization of Methylation-Based Copy Number Variation Calling Software in Cancers Harboring Large Scale Chromosomal Deletions
title_fullStr MethylMasteR: A Comparison and Customization of Methylation-Based Copy Number Variation Calling Software in Cancers Harboring Large Scale Chromosomal Deletions
title_full_unstemmed MethylMasteR: A Comparison and Customization of Methylation-Based Copy Number Variation Calling Software in Cancers Harboring Large Scale Chromosomal Deletions
title_short MethylMasteR: A Comparison and Customization of Methylation-Based Copy Number Variation Calling Software in Cancers Harboring Large Scale Chromosomal Deletions
title_sort methylmaster: a comparison and customization of methylation-based copy number variation calling software in cancers harboring large scale chromosomal deletions
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9098103/
https://www.ncbi.nlm.nih.gov/pubmed/35573871
http://dx.doi.org/10.3389/fbinf.2022.859828
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