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wes-based snvs and snp-based cnvs  (Broad Institute Inc)

 
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    Broad Institute Inc wes-based snvs and snp-based cnvs
    Case studies using tumour phylogenetics
    Wes Based Snvs And Snp Based Cnvs, supplied by Broad Institute Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/wes-based+snvs+and+snp-based+cnvs/pmc05886015-53-0-6?v=Broad+Institute+Inc
    Average 90 stars, based on 1 article reviews
    wes-based snvs and snp-based cnvs - by Bioz Stars, 2026-08
    90/100 stars

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    1) Product Images from "The evolution of tumour phylogenetics: principles and practice"

    Article Title: The evolution of tumour phylogenetics: principles and practice

    Journal: Nature reviews. Genetics

    doi: 10.1038/nrg.2016.170

    Case studies using tumour phylogenetics
    Figure Legend Snippet: Case studies using tumour phylogenetics

    Techniques Used: Sequencing, Methylation, RNA Expression, Clone Assay

    Experimental technologies and data types for tumour phylogenetics
    Figure Legend Snippet: Experimental technologies and data types for tumour phylogenetics

    Techniques Used: Sequencing, Expressing, Marker, DNA Methylation Assay, Methylation Sequencing, Methylation, Gene Expression

    An illustration of a hypothetical scenario described in the main text, in which we seek to infer a phylogenetic history of copy number variant (CNV) events in the progression of a single tumour. Each tree shows the potential evolution of genomic copy number profiles for a set of observed clones (blue lines) and computationally inferred intermediate states (red lines) for a single tumour. a | The hypothetical ‘true’ tree describing the evolution of a set of clones from a diploid root via a series of CNVs: gain or loss of copy number in a localized region, as well as whole-genome duplication, leading to a doubled copy number genome-wide. b | Incorrect inference due to the use of a model designed for single-base changes, leading to a substantially incorrect phylogeny involving various biologically ‘impossible’ evolutionary events, such as partial (non-integer) gain, loss, or whole-genome duplications, leading to fractional copy numbers. c | Improved but still inaccurate inference after correcting to an evolutionary model cognizant of the type of variation occurring with CNVs; this eliminates impossible events and leads to a more accurate tree topology, but still fails to identify the correct tree because the analysis is using an algorithm that identifies biologically plausible but still sub-optimal phylogenies for this kind of evolutionary model. d | Still inaccurate inference after changing to a more sophisticated model and algorithm that are well suited to CNV evolution but make it impractical to use single-cell sequence data; this forces a change to a bulk genomic data type, leading to inadequate sampling of extant clones to capture the rapid mutation process typical of CNV-driven evolution and observed in the true tree.
    Figure Legend Snippet: An illustration of a hypothetical scenario described in the main text, in which we seek to infer a phylogenetic history of copy number variant (CNV) events in the progression of a single tumour. Each tree shows the potential evolution of genomic copy number profiles for a set of observed clones (blue lines) and computationally inferred intermediate states (red lines) for a single tumour. a | The hypothetical ‘true’ tree describing the evolution of a set of clones from a diploid root via a series of CNVs: gain or loss of copy number in a localized region, as well as whole-genome duplication, leading to a doubled copy number genome-wide. b | Incorrect inference due to the use of a model designed for single-base changes, leading to a substantially incorrect phylogeny involving various biologically ‘impossible’ evolutionary events, such as partial (non-integer) gain, loss, or whole-genome duplications, leading to fractional copy numbers. c | Improved but still inaccurate inference after correcting to an evolutionary model cognizant of the type of variation occurring with CNVs; this eliminates impossible events and leads to a more accurate tree topology, but still fails to identify the correct tree because the analysis is using an algorithm that identifies biologically plausible but still sub-optimal phylogenies for this kind of evolutionary model. d | Still inaccurate inference after changing to a more sophisticated model and algorithm that are well suited to CNV evolution but make it impractical to use single-cell sequence data; this forces a change to a bulk genomic data type, leading to inadequate sampling of extant clones to capture the rapid mutation process typical of CNV-driven evolution and observed in the true tree.

    Techniques Used: Variant Assay, Clone Assay, Genome Wide, Sequencing, Sampling, Mutagenesis



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    wes-based snvs and snp-based cnvs  (Broad Institute Inc)
    90
    Broad Institute Inc wes-based snvs and snp-based cnvs
    Case studies using tumour phylogenetics
    Wes Based Snvs And Snp Based Cnvs, supplied by Broad Institute Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/wes-based+snvs+and+snp-based+cnvs/pmc05886015-53-0-6?v=Broad+Institute+Inc
    Average 90 stars, based on 1 article reviews
    wes-based snvs and snp-based cnvs - by Bioz Stars, 2026-08
    90/100 stars
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    Case studies using tumour phylogenetics

    Journal: Nature reviews. Genetics

    Article Title: The evolution of tumour phylogenetics: principles and practice

    doi: 10.1038/nrg.2016.170

    Figure Lengend Snippet: Case studies using tumour phylogenetics

    Article Snippet: WES-based SNVs and SNP-based CNVs , Broad Institute custom heuristic (parsimony, branch sibling model, and grafting at tips) , 22.

    Techniques: Sequencing, Methylation, RNA Expression, Clone Assay

    Experimental technologies and data types for tumour phylogenetics

    Journal: Nature reviews. Genetics

    Article Title: The evolution of tumour phylogenetics: principles and practice

    doi: 10.1038/nrg.2016.170

    Figure Lengend Snippet: Experimental technologies and data types for tumour phylogenetics

    Article Snippet: WES-based SNVs and SNP-based CNVs , Broad Institute custom heuristic (parsimony, branch sibling model, and grafting at tips) , 22.

    Techniques: Sequencing, Expressing, Marker, DNA Methylation Assay, Methylation Sequencing, Methylation, Gene Expression

    An illustration of a hypothetical scenario described in the main text, in which we seek to infer a phylogenetic history of copy number variant (CNV) events in the progression of a single tumour. Each tree shows the potential evolution of genomic copy number profiles for a set of observed clones (blue lines) and computationally inferred intermediate states (red lines) for a single tumour. a | The hypothetical ‘true’ tree describing the evolution of a set of clones from a diploid root via a series of CNVs: gain or loss of copy number in a localized region, as well as whole-genome duplication, leading to a doubled copy number genome-wide. b | Incorrect inference due to the use of a model designed for single-base changes, leading to a substantially incorrect phylogeny involving various biologically ‘impossible’ evolutionary events, such as partial (non-integer) gain, loss, or whole-genome duplications, leading to fractional copy numbers. c | Improved but still inaccurate inference after correcting to an evolutionary model cognizant of the type of variation occurring with CNVs; this eliminates impossible events and leads to a more accurate tree topology, but still fails to identify the correct tree because the analysis is using an algorithm that identifies biologically plausible but still sub-optimal phylogenies for this kind of evolutionary model. d | Still inaccurate inference after changing to a more sophisticated model and algorithm that are well suited to CNV evolution but make it impractical to use single-cell sequence data; this forces a change to a bulk genomic data type, leading to inadequate sampling of extant clones to capture the rapid mutation process typical of CNV-driven evolution and observed in the true tree.

    Journal: Nature reviews. Genetics

    Article Title: The evolution of tumour phylogenetics: principles and practice

    doi: 10.1038/nrg.2016.170

    Figure Lengend Snippet: An illustration of a hypothetical scenario described in the main text, in which we seek to infer a phylogenetic history of copy number variant (CNV) events in the progression of a single tumour. Each tree shows the potential evolution of genomic copy number profiles for a set of observed clones (blue lines) and computationally inferred intermediate states (red lines) for a single tumour. a | The hypothetical ‘true’ tree describing the evolution of a set of clones from a diploid root via a series of CNVs: gain or loss of copy number in a localized region, as well as whole-genome duplication, leading to a doubled copy number genome-wide. b | Incorrect inference due to the use of a model designed for single-base changes, leading to a substantially incorrect phylogeny involving various biologically ‘impossible’ evolutionary events, such as partial (non-integer) gain, loss, or whole-genome duplications, leading to fractional copy numbers. c | Improved but still inaccurate inference after correcting to an evolutionary model cognizant of the type of variation occurring with CNVs; this eliminates impossible events and leads to a more accurate tree topology, but still fails to identify the correct tree because the analysis is using an algorithm that identifies biologically plausible but still sub-optimal phylogenies for this kind of evolutionary model. d | Still inaccurate inference after changing to a more sophisticated model and algorithm that are well suited to CNV evolution but make it impractical to use single-cell sequence data; this forces a change to a bulk genomic data type, leading to inadequate sampling of extant clones to capture the rapid mutation process typical of CNV-driven evolution and observed in the true tree.

    Article Snippet: WES-based SNVs and SNP-based CNVs , Broad Institute custom heuristic (parsimony, branch sibling model, and grafting at tips) , 22.

    Techniques: Variant Assay, Clone Assay, Genome Wide, Sequencing, Sampling, Mutagenesis