ArticleNature protocols2020
Analysis pipelines for cancer genome sequencing in mice.
Article in Nature protocols, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
27 citing papers in PubMed, 43 citations in OpenAlex.
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- Dissecting cross-lineage tumourigenesis under p53 inactivation through single-cell multi-omics and spatial transcriptomics.Clinical and translational medicine · 2025Article
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- Oxidative stress accelerates intestinal tumorigenesis by enhancing 8-oxoguanine-mediated mutagenesis in MUTYH-deficient mice.Genome research · 2024Article
- An analysis pipeline for understanding 6-thioguanine effects on a mouse tumour genome.Cancer immunology, immunotherapy : CII · 2024Article
- Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification.Nature communications · 2023Article
- Exposure to microbial products followed by loss of Tet2 promotes myelodysplastic syndrome via remodeling HSCs.The Journal of experimental medicine · 2023Article
- Interferon signaling promotes tolerance to chromosomal instability during metastatic evolution in renal cancer.Nature cancer · 2023Article
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- Japanese Regulatory Framework and Approach for Genome-edited Foods Based on Latest Scientific Findings.Food safety (Tokyo, Japan) · 2022Article
- CRISPR somatic genome engineering and cancer modeling in the mouse pancreas and liver.Nature protocols · 2022Review
- Genetic alterations of the SUMO isopeptidase SENP6 drive lymphomagenesis and genetic instability in diffuse large B-cell lymphoma.Nature communications · 2022Article
- Bacterial Genotoxin Accelerates Transient Infection-Driven Murine Colon Tumorigenesis.Cancer discovery · 2022Article
Corrections and comments
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Authors and funding
14 authors at 6 institutions in 4 countries.
Funding
Abstract
Mouse models of human cancer have transformed our ability to link genetics, molecular mechanisms and phenotypes. Both reverse and forward genetics in mice are currently gaining momentum through advances in next-generation sequencing (NGS). Methodologies to analyze sequencing data were, however, developed for humans and hence do not account for species-specific differences in genome structures and experimental setups. Here, we describe standardized computational pipelines specifically tailored to the analysis of mouse genomic data. We present novel tools and workflows for the detection of different alteration types, including single-nucleotide variants (SNVs), small insertions and deletions (indels), copy-number variations (CNVs), loss of heterozygosity (LOH) and complex rearrangements, such as in chromothripsis. Workflows have been extensively validated and cross-compared using multiple methodologies. We also give step-by-step guidance on the execution of individual analysis types, provide advice on data interpretation and make the complete code available online. The protocol takes 2-7 d, depending on the desired analyses.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.