Cargando…

STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer

Spatial transcriptomic technologies, such as the Visium platform, measure gene expression in different regions of tissues. Here, we describe new software, STmut, to visualize somatic point mutations, allelic imbalance, and copy number alterations in Visium data. STmut is tested on fresh-frozen Visiu...

Descripción completa

Detalles Bibliográficos
Autores principales:	Chen, Limin, Chang, Darwin, Tandukar, Bishal, Deivendran, Delahny, Pozniak, Joanna, Cruz-Pacheco, Noel, Cho, Raymond J., Cheng, Jeffrey, Yeh, Iwei, Marine, Chris, Bastian, Boris C., Ji, Andrew L., Shain, A. Hunter
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2023
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10688493/ https://www.ncbi.nlm.nih.gov/pubmed/38037084 http://dx.doi.org/10.1186/s13059-023-03121-6

Ejemplares similares

Integrated genomic analyses of acral and mucosal melanomas nominate novel driver genes
por: Wang, Meng, et al.
Publicado: (2022)

The genomic landscapes of individual melanocytes from human skin
por: Tang, Jessica, et al.
Publicado: (2020)

A simple consensus approach improves somatic mutation prediction accuracy
por: Goode, David L, et al.
Publicado: (2013)

Tracing cancer evolution and heterogeneity using Hi-C
por: Erdmann-Pham, Dan Daniel, et al.
Publicado: (2023)

An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data
por: Shiraishi, Yuichi, et al.
Publicado: (2013)

SBSA: an online service for somatic binding sequence annotation
por: Jiang, Limin, et al.
Publicado: (2021)

Unraveling the clonal hierarchy of somatic genomic aberrations
por: Prandi, Davide, et al.
Publicado: (2014)

The genetic evolution of acral melanoma
por: Wang, Meng, et al.
Publicado: (2023)

The landscape of driver mutations in cutaneous squamous cell carcinoma
por: Chang, Darwin, et al.
Publicado: (2021)

Ultradeep analysis of tumor heterogeneity in regions of somatic hypermutation
por: Spence, Janice M, et al.
Publicado: (2015)

Virmid: accurate detection of somatic mutations with sample impurity inference
por: Kim, Sangwoo, et al.
Publicado: (2013)

Explainable multiview framework for dissecting spatial relationships from highly multiplexed data
por: Tanevski, Jovan, et al.
Publicado: (2022)

Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations
por: Patel, Anand, et al.
Publicado: (2014)

Latent feature extraction with a prior-based self-attention framework for spatial transcriptomics
por: Li, Zhen, et al.
Publicado: (2023)

Eruptive Spitz nevus, a striking example of benign metastasis
por: Raghavan, Shyam S., et al.
Publicado: (2020)

DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer
por: Bashashati, Ali, et al.
Publicado: (2012)

Discriminating somatic and germline mutations in tumor DNA samples without matching normals
por: Hiltemann, Saskia, et al.
Publicado: (2015)

MUFFINN: cancer gene discovery via network analysis of somatic mutation data
por: Cho, Ara, et al.
Publicado: (2016)

Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery
por: Köster, Johannes, et al.
Publicado: (2020)

Early embryonic mutations reveal dynamics of somatic and germ cell lineages in mice
por: Uchimura, Arikuni, et al.
Publicado: (2022)

Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing
por: Harismendy, Olivier, et al.
Publicado: (2011)

Assessment of megabase-scale somatic copy number variation using single-cell sequencing
por: Knouse, Kristin A., et al.
Publicado: (2016)

Quantification of somatic mutation flow across individual cell division events by lineage sequencing
por: Brody, Yehuda, et al.
Publicado: (2018)

CRISPR-SONIC: targeted somatic oncogene knock-in enables rapid in vivo cancer modeling
por: Mou, Haiwei, et al.
Publicado: (2019)

Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time
por: Little, Paul, et al.
Publicado: (2019)

A new method for robust quantitative and qualitative analysis of real-time PCR
por: Shain, Eric B., et al.
Publicado: (2008)

MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals
por: Carlson, Keisha D., et al.
Publicado: (2015)

3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets
por: Gao, Jianjiong, et al.
Publicado: (2017)

Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes
por: Przytycki, Pawel F., et al.
Publicado: (2017)

Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection
por: Thirunavukarasu, Deepak, et al.
Publicado: (2021)

A somatic hypermutation–based machine learning model stratifies individuals with Crohn's disease and controls
por: Safra, Modi, et al.
Publicado: (2023)

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing
por: Talevich, Eric, et al.
Publicado: (2016)

Gattaca: Base-Pair Resolution Mutation Tracking for Somatic Evolution Studies using Agent-based Models
por: Schenck, Ryan O., et al.
Publicado: (2022)

GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing
por: Cameron, Daniel L., et al.
Publicado: (2021)

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers
por: Mermel, Craig H, et al.
Publicado: (2011)

Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data with nanomonsv
por: Shiraishi, Yuichi, et al.
Publicado: (2023)

Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers
por: Callari, Maurizio, et al.
Publicado: (2017)

A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence
por: Canisius, Sander, et al.
Publicado: (2016)

Recent advances in molecular genetics of melanoma progression: implications for diagnosis and treatment
por: Yeh, Iwei
Publicado: (2016)

LUMPY: a probabilistic framework for structural variant discovery
por: Layer, Ryan M, et al.
Publicado: (2014)

Cannot write session to /tmp/vufind_sessions/sess_sp865nd3f88u2cqf7ag8gqd2i5