Somatic variant detection from multi-sampled genomic sequencing data of tumor specimens using the ith.Variant pipeline
Summary: A common technique for uncovering intra-tumor genomic heterogeneity (ITH) is variant detection. However, it can be challenging to reliably characterize ITH given uneven sample quality (e.g., depth of coverage, tumor purity, and subclonality). We describe a protocol for calling point mutatio...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-03-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166722008073 |
| _version_ | 1797961085717839872 |
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| author | Nicole Maeser Aziz Khan Ruping Sun |
| author_facet | Nicole Maeser Aziz Khan Ruping Sun |
| author_sort | Nicole Maeser |
| collection | DOAJ |
| description | Summary: A common technique for uncovering intra-tumor genomic heterogeneity (ITH) is variant detection. However, it can be challenging to reliably characterize ITH given uneven sample quality (e.g., depth of coverage, tumor purity, and subclonality). We describe a protocol for calling point mutations and copy number alterations using sequencing of multiple related clinical patient samples across diverse tissue, optimizing for sensitivity with specificity. The ith.Variant pipeline can be run on single- or multi-region whole-genome and whole-exome sequencing.For complete details on the use and execution of this protocol, please refer to Sun et al. (2017).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-11T00:54:57Z |
| format | Article |
| id | doaj.art-ec2efb838ccb4eeab2bd0efbe10b0b66 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-11T00:54:57Z |
| publishDate | 2023-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-ec2efb838ccb4eeab2bd0efbe10b0b662023-01-05T06:47:42ZengElsevierSTAR Protocols2666-16672023-03-0141101927Somatic variant detection from multi-sampled genomic sequencing data of tumor specimens using the ith.Variant pipelineNicole Maeser0Aziz Khan1Ruping Sun2Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USAStanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USADepartment of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Corresponding authorSummary: A common technique for uncovering intra-tumor genomic heterogeneity (ITH) is variant detection. However, it can be challenging to reliably characterize ITH given uneven sample quality (e.g., depth of coverage, tumor purity, and subclonality). We describe a protocol for calling point mutations and copy number alterations using sequencing of multiple related clinical patient samples across diverse tissue, optimizing for sensitivity with specificity. The ith.Variant pipeline can be run on single- or multi-region whole-genome and whole-exome sequencing.For complete details on the use and execution of this protocol, please refer to Sun et al. (2017).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166722008073BioinformaticsCancerHealth SciencesGenomicsSequencing |
| spellingShingle | Nicole Maeser Aziz Khan Ruping Sun Somatic variant detection from multi-sampled genomic sequencing data of tumor specimens using the ith.Variant pipeline STAR Protocols Bioinformatics Cancer Health Sciences Genomics Sequencing |
| title | Somatic variant detection from multi-sampled genomic sequencing data of tumor specimens using the ith.Variant pipeline |
| title_full | Somatic variant detection from multi-sampled genomic sequencing data of tumor specimens using the ith.Variant pipeline |
| title_fullStr | Somatic variant detection from multi-sampled genomic sequencing data of tumor specimens using the ith.Variant pipeline |
| title_full_unstemmed | Somatic variant detection from multi-sampled genomic sequencing data of tumor specimens using the ith.Variant pipeline |
| title_short | Somatic variant detection from multi-sampled genomic sequencing data of tumor specimens using the ith.Variant pipeline |
| title_sort | somatic variant detection from multi sampled genomic sequencing data of tumor specimens using the ith variant pipeline |
| topic | Bioinformatics Cancer Health Sciences Genomics Sequencing |
| url | http://www.sciencedirect.com/science/article/pii/S2666166722008073 |
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