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    ATCC cell lines skbr3 atcc htb30 hek 293h atcc crl 1573 software
    (A) As in the Figure 4A, but assessing the enrichment for loss of the WT allele as the mechanism of mutant allele imbalance. (B) In HR+ HER2− breast cancers, the rate of LOH spanning ESR1 in tumors with or without ESR1 gain-of-function mutations and those acquired before or after endocrine therapy (asterisk, p value = 0.00015, Chi-squared test; numbers in black bars represent the number of affected cases). (C) Luciferase reporter activity (RLU) in HR− <t>SKBr3</t> cells ectopically expressing HA-ERα wild-type (WT) or the specified mutant in proportions equivalent to homozygous mutant (left) to heterozygosity (right) in hormone-depleted medium. Error bars are +/− SD from triplicate experiments. (D) Duration of time of patients with BRAF V600E-mutant metastatic melanomas on vemurafenib therapy as a function of allelic imbalance of V600E and the mechanisms thereof [median PFS is 31.7 months (95% CI, 6-not reached) for patients with loss of WT BRAF versus 6.5 months (4.8-12) in the rest; hazard ratio, 4.4; p value = 0.01]. Complete pathologic responses are indicated in dark blue (p value = 0.01 comparing patients whose tumors lost the WT allele to those whose tumors that do not, two-sided Fisher’s exact test). See also Figure S5.
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    1) Product Images from "Widespread selection for oncogenic mutant allele imbalance in cancer"

    Article Title: Widespread selection for oncogenic mutant allele imbalance in cancer

    Journal: Cancer cell

    doi: 10.1016/j.ccell.2018.10.003

    (A) As in the Figure 4A, but assessing the enrichment for loss of the WT allele as the mechanism of mutant allele imbalance. (B) In HR+ HER2− breast cancers, the rate of LOH spanning ESR1 in tumors with or without ESR1 gain-of-function mutations and those acquired before or after endocrine therapy (asterisk, p value = 0.00015, Chi-squared test; numbers in black bars represent the number of affected cases). (C) Luciferase reporter activity (RLU) in HR− SKBr3 cells ectopically expressing HA-ERα wild-type (WT) or the specified mutant in proportions equivalent to homozygous mutant (left) to heterozygosity (right) in hormone-depleted medium. Error bars are +/− SD from triplicate experiments. (D) Duration of time of patients with BRAF V600E-mutant metastatic melanomas on vemurafenib therapy as a function of allelic imbalance of V600E and the mechanisms thereof [median PFS is 31.7 months (95% CI, 6-not reached) for patients with loss of WT BRAF versus 6.5 months (4.8-12) in the rest; hazard ratio, 4.4; p value = 0.01]. Complete pathologic responses are indicated in dark blue (p value = 0.01 comparing patients whose tumors lost the WT allele to those whose tumors that do not, two-sided Fisher’s exact test). See also Figure S5.
    Figure Legend Snippet: (A) As in the Figure 4A, but assessing the enrichment for loss of the WT allele as the mechanism of mutant allele imbalance. (B) In HR+ HER2− breast cancers, the rate of LOH spanning ESR1 in tumors with or without ESR1 gain-of-function mutations and those acquired before or after endocrine therapy (asterisk, p value = 0.00015, Chi-squared test; numbers in black bars represent the number of affected cases). (C) Luciferase reporter activity (RLU) in HR− SKBr3 cells ectopically expressing HA-ERα wild-type (WT) or the specified mutant in proportions equivalent to homozygous mutant (left) to heterozygosity (right) in hormone-depleted medium. Error bars are +/− SD from triplicate experiments. (D) Duration of time of patients with BRAF V600E-mutant metastatic melanomas on vemurafenib therapy as a function of allelic imbalance of V600E and the mechanisms thereof [median PFS is 31.7 months (95% CI, 6-not reached) for patients with loss of WT BRAF versus 6.5 months (4.8-12) in the rest; hazard ratio, 4.4; p value = 0.01]. Complete pathologic responses are indicated in dark blue (p value = 0.01 comparing patients whose tumors lost the WT allele to those whose tumors that do not, two-sided Fisher’s exact test). See also Figure S5.

    Techniques Used: Mutagenesis, Luciferase, Activity Assay, Expressing

    KEY RESOURCES TABLE
    Figure Legend Snippet: KEY RESOURCES TABLE

    Techniques Used: Recombinant, Luciferase, Plasmid Preparation, Mutagenesis, Transfection, Reporter Assay, DNA Sequencing, Sequencing, Software

    Related Articles

    Recombinant:

    Article Title: Widespread selection for oncogenic mutant allele imbalance in cancer
    Article Snippet: R code to perform the analyses described here is available with this manuscript ( https://github.com/taylor-lab/AI ) .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal, Phospho-MEK (Ser217/221) Cell Signal Cat#9121; RRID: AB_331649 Rabbit polyclonal, Anti-MEK Cell Signal Cat#9122; RRID: AB_823567 Rabbit polyclonal, Phospho ERK (Thr202/Tyr204) Cell Signal Cat#9109; RRID: AB_331646 Rabbit polyclonal, Anti-ERK Cell Signal Cat#9102; RRID: AB_330744 Rabbit monoclonal, Anti-GFP Cell Signal Cat#2956; RRID: AB_1196615 Rabbit monoclonal, Anti-GAPDH Cell Signal Cat#2118; RRID: AB_561053 Biological Samples MSK-IMPACT Zehir et al. 2017 N/A Chemicals, Peptides, and Recombinant Proteins pEGPF-N1-MEK1 Addgene Cat#14746 3X-ERE-TATA-luciferase reporter Addgene Cat#11354 pRL-TK Renilla luciferase plasmid Promega Cat#E2231 HA-tagged WT ERα This study N/A pcDNA3.1 (EV) Thermo Fisher Cat#V79020 HA-tagged ERα Y537S This study N/A HA-tagged ERα D538G This study N/A Critical Commercial Assays QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat#200521 SuperSignal West Pico Plus Chemiluminescent Thermo Fisher Cat#34577 Lipofectamine 2000 Transfection Reagent Invitrogen Cat#11668027 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Deposited Data Prospective DNA sequencing This study Accession number for the prospective sequencing data reported in this study is EVA: PRJEB28874, https://www.ebi.ac.uk/eva/?eva-study=PRJEB28874 Experimental Models: Cell Lines SKBr3 ATCC HTB30 HEK-293H ATCC CRL-1573 Software and Algorithms R for Statistical Computing R Foundation http://www.r-project.org FACETS Shen, et al. 2016 http://github.com/mskcc/facets FACETS-suite This study http://github.com/mskcc/facets-suite Other BAM files for TCGA exomes TCGA https://cancergenome.nih.gov Open in a separate window KEY RESOURCES TABLE Mutant allele imbalance affects ~half of all oncogenic driver mutations in cancer Positive and negative selection shapes the allelic configuration of mutant oncogenes Mutant dosage gains and stoichiometric changes drive fitness and growth advantages Mutant oncogene zygosity dictates prognosis and enhanced therapeutic sensitivity Bielski et al. describe widespread allele imbalance in cancer, which is selected for via modest dosage increases of gain-of-fitness mutations and can be driven by antecedent oncogenic mutations. ..

    Luciferase:

    Article Title: Widespread selection for oncogenic mutant allele imbalance in cancer
    Article Snippet: R code to perform the analyses described here is available with this manuscript ( https://github.com/taylor-lab/AI ) .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal, Phospho-MEK (Ser217/221) Cell Signal Cat#9121; RRID: AB_331649 Rabbit polyclonal, Anti-MEK Cell Signal Cat#9122; RRID: AB_823567 Rabbit polyclonal, Phospho ERK (Thr202/Tyr204) Cell Signal Cat#9109; RRID: AB_331646 Rabbit polyclonal, Anti-ERK Cell Signal Cat#9102; RRID: AB_330744 Rabbit monoclonal, Anti-GFP Cell Signal Cat#2956; RRID: AB_1196615 Rabbit monoclonal, Anti-GAPDH Cell Signal Cat#2118; RRID: AB_561053 Biological Samples MSK-IMPACT Zehir et al. 2017 N/A Chemicals, Peptides, and Recombinant Proteins pEGPF-N1-MEK1 Addgene Cat#14746 3X-ERE-TATA-luciferase reporter Addgene Cat#11354 pRL-TK Renilla luciferase plasmid Promega Cat#E2231 HA-tagged WT ERα This study N/A pcDNA3.1 (EV) Thermo Fisher Cat#V79020 HA-tagged ERα Y537S This study N/A HA-tagged ERα D538G This study N/A Critical Commercial Assays QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat#200521 SuperSignal West Pico Plus Chemiluminescent Thermo Fisher Cat#34577 Lipofectamine 2000 Transfection Reagent Invitrogen Cat#11668027 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Deposited Data Prospective DNA sequencing This study Accession number for the prospective sequencing data reported in this study is EVA: PRJEB28874, https://www.ebi.ac.uk/eva/?eva-study=PRJEB28874 Experimental Models: Cell Lines SKBr3 ATCC HTB30 HEK-293H ATCC CRL-1573 Software and Algorithms R for Statistical Computing R Foundation http://www.r-project.org FACETS Shen, et al. 2016 http://github.com/mskcc/facets FACETS-suite This study http://github.com/mskcc/facets-suite Other BAM files for TCGA exomes TCGA https://cancergenome.nih.gov Open in a separate window KEY RESOURCES TABLE Mutant allele imbalance affects ~half of all oncogenic driver mutations in cancer Positive and negative selection shapes the allelic configuration of mutant oncogenes Mutant dosage gains and stoichiometric changes drive fitness and growth advantages Mutant oncogene zygosity dictates prognosis and enhanced therapeutic sensitivity Bielski et al. describe widespread allele imbalance in cancer, which is selected for via modest dosage increases of gain-of-fitness mutations and can be driven by antecedent oncogenic mutations. ..

    Plasmid Preparation:

    Article Title: Widespread selection for oncogenic mutant allele imbalance in cancer
    Article Snippet: R code to perform the analyses described here is available with this manuscript ( https://github.com/taylor-lab/AI ) .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal, Phospho-MEK (Ser217/221) Cell Signal Cat#9121; RRID: AB_331649 Rabbit polyclonal, Anti-MEK Cell Signal Cat#9122; RRID: AB_823567 Rabbit polyclonal, Phospho ERK (Thr202/Tyr204) Cell Signal Cat#9109; RRID: AB_331646 Rabbit polyclonal, Anti-ERK Cell Signal Cat#9102; RRID: AB_330744 Rabbit monoclonal, Anti-GFP Cell Signal Cat#2956; RRID: AB_1196615 Rabbit monoclonal, Anti-GAPDH Cell Signal Cat#2118; RRID: AB_561053 Biological Samples MSK-IMPACT Zehir et al. 2017 N/A Chemicals, Peptides, and Recombinant Proteins pEGPF-N1-MEK1 Addgene Cat#14746 3X-ERE-TATA-luciferase reporter Addgene Cat#11354 pRL-TK Renilla luciferase plasmid Promega Cat#E2231 HA-tagged WT ERα This study N/A pcDNA3.1 (EV) Thermo Fisher Cat#V79020 HA-tagged ERα Y537S This study N/A HA-tagged ERα D538G This study N/A Critical Commercial Assays QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat#200521 SuperSignal West Pico Plus Chemiluminescent Thermo Fisher Cat#34577 Lipofectamine 2000 Transfection Reagent Invitrogen Cat#11668027 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Deposited Data Prospective DNA sequencing This study Accession number for the prospective sequencing data reported in this study is EVA: PRJEB28874, https://www.ebi.ac.uk/eva/?eva-study=PRJEB28874 Experimental Models: Cell Lines SKBr3 ATCC HTB30 HEK-293H ATCC CRL-1573 Software and Algorithms R for Statistical Computing R Foundation http://www.r-project.org FACETS Shen, et al. 2016 http://github.com/mskcc/facets FACETS-suite This study http://github.com/mskcc/facets-suite Other BAM files for TCGA exomes TCGA https://cancergenome.nih.gov Open in a separate window KEY RESOURCES TABLE Mutant allele imbalance affects ~half of all oncogenic driver mutations in cancer Positive and negative selection shapes the allelic configuration of mutant oncogenes Mutant dosage gains and stoichiometric changes drive fitness and growth advantages Mutant oncogene zygosity dictates prognosis and enhanced therapeutic sensitivity Bielski et al. describe widespread allele imbalance in cancer, which is selected for via modest dosage increases of gain-of-fitness mutations and can be driven by antecedent oncogenic mutations. ..

    Mutagenesis:

    Article Title: Widespread selection for oncogenic mutant allele imbalance in cancer
    Article Snippet: R code to perform the analyses described here is available with this manuscript ( https://github.com/taylor-lab/AI ) .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal, Phospho-MEK (Ser217/221) Cell Signal Cat#9121; RRID: AB_331649 Rabbit polyclonal, Anti-MEK Cell Signal Cat#9122; RRID: AB_823567 Rabbit polyclonal, Phospho ERK (Thr202/Tyr204) Cell Signal Cat#9109; RRID: AB_331646 Rabbit polyclonal, Anti-ERK Cell Signal Cat#9102; RRID: AB_330744 Rabbit monoclonal, Anti-GFP Cell Signal Cat#2956; RRID: AB_1196615 Rabbit monoclonal, Anti-GAPDH Cell Signal Cat#2118; RRID: AB_561053 Biological Samples MSK-IMPACT Zehir et al. 2017 N/A Chemicals, Peptides, and Recombinant Proteins pEGPF-N1-MEK1 Addgene Cat#14746 3X-ERE-TATA-luciferase reporter Addgene Cat#11354 pRL-TK Renilla luciferase plasmid Promega Cat#E2231 HA-tagged WT ERα This study N/A pcDNA3.1 (EV) Thermo Fisher Cat#V79020 HA-tagged ERα Y537S This study N/A HA-tagged ERα D538G This study N/A Critical Commercial Assays QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat#200521 SuperSignal West Pico Plus Chemiluminescent Thermo Fisher Cat#34577 Lipofectamine 2000 Transfection Reagent Invitrogen Cat#11668027 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Deposited Data Prospective DNA sequencing This study Accession number for the prospective sequencing data reported in this study is EVA: PRJEB28874, https://www.ebi.ac.uk/eva/?eva-study=PRJEB28874 Experimental Models: Cell Lines SKBr3 ATCC HTB30 HEK-293H ATCC CRL-1573 Software and Algorithms R for Statistical Computing R Foundation http://www.r-project.org FACETS Shen, et al. 2016 http://github.com/mskcc/facets FACETS-suite This study http://github.com/mskcc/facets-suite Other BAM files for TCGA exomes TCGA https://cancergenome.nih.gov Open in a separate window KEY RESOURCES TABLE Mutant allele imbalance affects ~half of all oncogenic driver mutations in cancer Positive and negative selection shapes the allelic configuration of mutant oncogenes Mutant dosage gains and stoichiometric changes drive fitness and growth advantages Mutant oncogene zygosity dictates prognosis and enhanced therapeutic sensitivity Bielski et al. describe widespread allele imbalance in cancer, which is selected for via modest dosage increases of gain-of-fitness mutations and can be driven by antecedent oncogenic mutations. ..

    Transfection:

    Article Title: Widespread selection for oncogenic mutant allele imbalance in cancer
    Article Snippet: R code to perform the analyses described here is available with this manuscript ( https://github.com/taylor-lab/AI ) .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal, Phospho-MEK (Ser217/221) Cell Signal Cat#9121; RRID: AB_331649 Rabbit polyclonal, Anti-MEK Cell Signal Cat#9122; RRID: AB_823567 Rabbit polyclonal, Phospho ERK (Thr202/Tyr204) Cell Signal Cat#9109; RRID: AB_331646 Rabbit polyclonal, Anti-ERK Cell Signal Cat#9102; RRID: AB_330744 Rabbit monoclonal, Anti-GFP Cell Signal Cat#2956; RRID: AB_1196615 Rabbit monoclonal, Anti-GAPDH Cell Signal Cat#2118; RRID: AB_561053 Biological Samples MSK-IMPACT Zehir et al. 2017 N/A Chemicals, Peptides, and Recombinant Proteins pEGPF-N1-MEK1 Addgene Cat#14746 3X-ERE-TATA-luciferase reporter Addgene Cat#11354 pRL-TK Renilla luciferase plasmid Promega Cat#E2231 HA-tagged WT ERα This study N/A pcDNA3.1 (EV) Thermo Fisher Cat#V79020 HA-tagged ERα Y537S This study N/A HA-tagged ERα D538G This study N/A Critical Commercial Assays QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat#200521 SuperSignal West Pico Plus Chemiluminescent Thermo Fisher Cat#34577 Lipofectamine 2000 Transfection Reagent Invitrogen Cat#11668027 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Deposited Data Prospective DNA sequencing This study Accession number for the prospective sequencing data reported in this study is EVA: PRJEB28874, https://www.ebi.ac.uk/eva/?eva-study=PRJEB28874 Experimental Models: Cell Lines SKBr3 ATCC HTB30 HEK-293H ATCC CRL-1573 Software and Algorithms R for Statistical Computing R Foundation http://www.r-project.org FACETS Shen, et al. 2016 http://github.com/mskcc/facets FACETS-suite This study http://github.com/mskcc/facets-suite Other BAM files for TCGA exomes TCGA https://cancergenome.nih.gov Open in a separate window KEY RESOURCES TABLE Mutant allele imbalance affects ~half of all oncogenic driver mutations in cancer Positive and negative selection shapes the allelic configuration of mutant oncogenes Mutant dosage gains and stoichiometric changes drive fitness and growth advantages Mutant oncogene zygosity dictates prognosis and enhanced therapeutic sensitivity Bielski et al. describe widespread allele imbalance in cancer, which is selected for via modest dosage increases of gain-of-fitness mutations and can be driven by antecedent oncogenic mutations. ..

    Reporter Assay:

    Article Title: Widespread selection for oncogenic mutant allele imbalance in cancer
    Article Snippet: R code to perform the analyses described here is available with this manuscript ( https://github.com/taylor-lab/AI ) .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal, Phospho-MEK (Ser217/221) Cell Signal Cat#9121; RRID: AB_331649 Rabbit polyclonal, Anti-MEK Cell Signal Cat#9122; RRID: AB_823567 Rabbit polyclonal, Phospho ERK (Thr202/Tyr204) Cell Signal Cat#9109; RRID: AB_331646 Rabbit polyclonal, Anti-ERK Cell Signal Cat#9102; RRID: AB_330744 Rabbit monoclonal, Anti-GFP Cell Signal Cat#2956; RRID: AB_1196615 Rabbit monoclonal, Anti-GAPDH Cell Signal Cat#2118; RRID: AB_561053 Biological Samples MSK-IMPACT Zehir et al. 2017 N/A Chemicals, Peptides, and Recombinant Proteins pEGPF-N1-MEK1 Addgene Cat#14746 3X-ERE-TATA-luciferase reporter Addgene Cat#11354 pRL-TK Renilla luciferase plasmid Promega Cat#E2231 HA-tagged WT ERα This study N/A pcDNA3.1 (EV) Thermo Fisher Cat#V79020 HA-tagged ERα Y537S This study N/A HA-tagged ERα D538G This study N/A Critical Commercial Assays QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat#200521 SuperSignal West Pico Plus Chemiluminescent Thermo Fisher Cat#34577 Lipofectamine 2000 Transfection Reagent Invitrogen Cat#11668027 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Deposited Data Prospective DNA sequencing This study Accession number for the prospective sequencing data reported in this study is EVA: PRJEB28874, https://www.ebi.ac.uk/eva/?eva-study=PRJEB28874 Experimental Models: Cell Lines SKBr3 ATCC HTB30 HEK-293H ATCC CRL-1573 Software and Algorithms R for Statistical Computing R Foundation http://www.r-project.org FACETS Shen, et al. 2016 http://github.com/mskcc/facets FACETS-suite This study http://github.com/mskcc/facets-suite Other BAM files for TCGA exomes TCGA https://cancergenome.nih.gov Open in a separate window KEY RESOURCES TABLE Mutant allele imbalance affects ~half of all oncogenic driver mutations in cancer Positive and negative selection shapes the allelic configuration of mutant oncogenes Mutant dosage gains and stoichiometric changes drive fitness and growth advantages Mutant oncogene zygosity dictates prognosis and enhanced therapeutic sensitivity Bielski et al. describe widespread allele imbalance in cancer, which is selected for via modest dosage increases of gain-of-fitness mutations and can be driven by antecedent oncogenic mutations. ..

    DNA Sequencing:

    Article Title: Widespread selection for oncogenic mutant allele imbalance in cancer
    Article Snippet: R code to perform the analyses described here is available with this manuscript ( https://github.com/taylor-lab/AI ) .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal, Phospho-MEK (Ser217/221) Cell Signal Cat#9121; RRID: AB_331649 Rabbit polyclonal, Anti-MEK Cell Signal Cat#9122; RRID: AB_823567 Rabbit polyclonal, Phospho ERK (Thr202/Tyr204) Cell Signal Cat#9109; RRID: AB_331646 Rabbit polyclonal, Anti-ERK Cell Signal Cat#9102; RRID: AB_330744 Rabbit monoclonal, Anti-GFP Cell Signal Cat#2956; RRID: AB_1196615 Rabbit monoclonal, Anti-GAPDH Cell Signal Cat#2118; RRID: AB_561053 Biological Samples MSK-IMPACT Zehir et al. 2017 N/A Chemicals, Peptides, and Recombinant Proteins pEGPF-N1-MEK1 Addgene Cat#14746 3X-ERE-TATA-luciferase reporter Addgene Cat#11354 pRL-TK Renilla luciferase plasmid Promega Cat#E2231 HA-tagged WT ERα This study N/A pcDNA3.1 (EV) Thermo Fisher Cat#V79020 HA-tagged ERα Y537S This study N/A HA-tagged ERα D538G This study N/A Critical Commercial Assays QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat#200521 SuperSignal West Pico Plus Chemiluminescent Thermo Fisher Cat#34577 Lipofectamine 2000 Transfection Reagent Invitrogen Cat#11668027 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Deposited Data Prospective DNA sequencing This study Accession number for the prospective sequencing data reported in this study is EVA: PRJEB28874, https://www.ebi.ac.uk/eva/?eva-study=PRJEB28874 Experimental Models: Cell Lines SKBr3 ATCC HTB30 HEK-293H ATCC CRL-1573 Software and Algorithms R for Statistical Computing R Foundation http://www.r-project.org FACETS Shen, et al. 2016 http://github.com/mskcc/facets FACETS-suite This study http://github.com/mskcc/facets-suite Other BAM files for TCGA exomes TCGA https://cancergenome.nih.gov Open in a separate window KEY RESOURCES TABLE Mutant allele imbalance affects ~half of all oncogenic driver mutations in cancer Positive and negative selection shapes the allelic configuration of mutant oncogenes Mutant dosage gains and stoichiometric changes drive fitness and growth advantages Mutant oncogene zygosity dictates prognosis and enhanced therapeutic sensitivity Bielski et al. describe widespread allele imbalance in cancer, which is selected for via modest dosage increases of gain-of-fitness mutations and can be driven by antecedent oncogenic mutations. ..

    Sequencing:

    Article Title: Widespread selection for oncogenic mutant allele imbalance in cancer
    Article Snippet: R code to perform the analyses described here is available with this manuscript ( https://github.com/taylor-lab/AI ) .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal, Phospho-MEK (Ser217/221) Cell Signal Cat#9121; RRID: AB_331649 Rabbit polyclonal, Anti-MEK Cell Signal Cat#9122; RRID: AB_823567 Rabbit polyclonal, Phospho ERK (Thr202/Tyr204) Cell Signal Cat#9109; RRID: AB_331646 Rabbit polyclonal, Anti-ERK Cell Signal Cat#9102; RRID: AB_330744 Rabbit monoclonal, Anti-GFP Cell Signal Cat#2956; RRID: AB_1196615 Rabbit monoclonal, Anti-GAPDH Cell Signal Cat#2118; RRID: AB_561053 Biological Samples MSK-IMPACT Zehir et al. 2017 N/A Chemicals, Peptides, and Recombinant Proteins pEGPF-N1-MEK1 Addgene Cat#14746 3X-ERE-TATA-luciferase reporter Addgene Cat#11354 pRL-TK Renilla luciferase plasmid Promega Cat#E2231 HA-tagged WT ERα This study N/A pcDNA3.1 (EV) Thermo Fisher Cat#V79020 HA-tagged ERα Y537S This study N/A HA-tagged ERα D538G This study N/A Critical Commercial Assays QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat#200521 SuperSignal West Pico Plus Chemiluminescent Thermo Fisher Cat#34577 Lipofectamine 2000 Transfection Reagent Invitrogen Cat#11668027 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Deposited Data Prospective DNA sequencing This study Accession number for the prospective sequencing data reported in this study is EVA: PRJEB28874, https://www.ebi.ac.uk/eva/?eva-study=PRJEB28874 Experimental Models: Cell Lines SKBr3 ATCC HTB30 HEK-293H ATCC CRL-1573 Software and Algorithms R for Statistical Computing R Foundation http://www.r-project.org FACETS Shen, et al. 2016 http://github.com/mskcc/facets FACETS-suite This study http://github.com/mskcc/facets-suite Other BAM files for TCGA exomes TCGA https://cancergenome.nih.gov Open in a separate window KEY RESOURCES TABLE Mutant allele imbalance affects ~half of all oncogenic driver mutations in cancer Positive and negative selection shapes the allelic configuration of mutant oncogenes Mutant dosage gains and stoichiometric changes drive fitness and growth advantages Mutant oncogene zygosity dictates prognosis and enhanced therapeutic sensitivity Bielski et al. describe widespread allele imbalance in cancer, which is selected for via modest dosage increases of gain-of-fitness mutations and can be driven by antecedent oncogenic mutations. ..

    Software:

    Article Title: Widespread selection for oncogenic mutant allele imbalance in cancer
    Article Snippet: R code to perform the analyses described here is available with this manuscript ( https://github.com/taylor-lab/AI ) .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal, Phospho-MEK (Ser217/221) Cell Signal Cat#9121; RRID: AB_331649 Rabbit polyclonal, Anti-MEK Cell Signal Cat#9122; RRID: AB_823567 Rabbit polyclonal, Phospho ERK (Thr202/Tyr204) Cell Signal Cat#9109; RRID: AB_331646 Rabbit polyclonal, Anti-ERK Cell Signal Cat#9102; RRID: AB_330744 Rabbit monoclonal, Anti-GFP Cell Signal Cat#2956; RRID: AB_1196615 Rabbit monoclonal, Anti-GAPDH Cell Signal Cat#2118; RRID: AB_561053 Biological Samples MSK-IMPACT Zehir et al. 2017 N/A Chemicals, Peptides, and Recombinant Proteins pEGPF-N1-MEK1 Addgene Cat#14746 3X-ERE-TATA-luciferase reporter Addgene Cat#11354 pRL-TK Renilla luciferase plasmid Promega Cat#E2231 HA-tagged WT ERα This study N/A pcDNA3.1 (EV) Thermo Fisher Cat#V79020 HA-tagged ERα Y537S This study N/A HA-tagged ERα D538G This study N/A Critical Commercial Assays QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat#200521 SuperSignal West Pico Plus Chemiluminescent Thermo Fisher Cat#34577 Lipofectamine 2000 Transfection Reagent Invitrogen Cat#11668027 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Deposited Data Prospective DNA sequencing This study Accession number for the prospective sequencing data reported in this study is EVA: PRJEB28874, https://www.ebi.ac.uk/eva/?eva-study=PRJEB28874 Experimental Models: Cell Lines SKBr3 ATCC HTB30 HEK-293H ATCC CRL-1573 Software and Algorithms R for Statistical Computing R Foundation http://www.r-project.org FACETS Shen, et al. 2016 http://github.com/mskcc/facets FACETS-suite This study http://github.com/mskcc/facets-suite Other BAM files for TCGA exomes TCGA https://cancergenome.nih.gov Open in a separate window KEY RESOURCES TABLE Mutant allele imbalance affects ~half of all oncogenic driver mutations in cancer Positive and negative selection shapes the allelic configuration of mutant oncogenes Mutant dosage gains and stoichiometric changes drive fitness and growth advantages Mutant oncogene zygosity dictates prognosis and enhanced therapeutic sensitivity Bielski et al. describe widespread allele imbalance in cancer, which is selected for via modest dosage increases of gain-of-fitness mutations and can be driven by antecedent oncogenic mutations. ..

    Selection:

    Article Title: Widespread selection for oncogenic mutant allele imbalance in cancer
    Article Snippet: R code to perform the analyses described here is available with this manuscript ( https://github.com/taylor-lab/AI ) .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal, Phospho-MEK (Ser217/221) Cell Signal Cat#9121; RRID: AB_331649 Rabbit polyclonal, Anti-MEK Cell Signal Cat#9122; RRID: AB_823567 Rabbit polyclonal, Phospho ERK (Thr202/Tyr204) Cell Signal Cat#9109; RRID: AB_331646 Rabbit polyclonal, Anti-ERK Cell Signal Cat#9102; RRID: AB_330744 Rabbit monoclonal, Anti-GFP Cell Signal Cat#2956; RRID: AB_1196615 Rabbit monoclonal, Anti-GAPDH Cell Signal Cat#2118; RRID: AB_561053 Biological Samples MSK-IMPACT Zehir et al. 2017 N/A Chemicals, Peptides, and Recombinant Proteins pEGPF-N1-MEK1 Addgene Cat#14746 3X-ERE-TATA-luciferase reporter Addgene Cat#11354 pRL-TK Renilla luciferase plasmid Promega Cat#E2231 HA-tagged WT ERα This study N/A pcDNA3.1 (EV) Thermo Fisher Cat#V79020 HA-tagged ERα Y537S This study N/A HA-tagged ERα D538G This study N/A Critical Commercial Assays QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat#200521 SuperSignal West Pico Plus Chemiluminescent Thermo Fisher Cat#34577 Lipofectamine 2000 Transfection Reagent Invitrogen Cat#11668027 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Deposited Data Prospective DNA sequencing This study Accession number for the prospective sequencing data reported in this study is EVA: PRJEB28874, https://www.ebi.ac.uk/eva/?eva-study=PRJEB28874 Experimental Models: Cell Lines SKBr3 ATCC HTB30 HEK-293H ATCC CRL-1573 Software and Algorithms R for Statistical Computing R Foundation http://www.r-project.org FACETS Shen, et al. 2016 http://github.com/mskcc/facets FACETS-suite This study http://github.com/mskcc/facets-suite Other BAM files for TCGA exomes TCGA https://cancergenome.nih.gov Open in a separate window KEY RESOURCES TABLE Mutant allele imbalance affects ~half of all oncogenic driver mutations in cancer Positive and negative selection shapes the allelic configuration of mutant oncogenes Mutant dosage gains and stoichiometric changes drive fitness and growth advantages Mutant oncogene zygosity dictates prognosis and enhanced therapeutic sensitivity Bielski et al. describe widespread allele imbalance in cancer, which is selected for via modest dosage increases of gain-of-fitness mutations and can be driven by antecedent oncogenic mutations. ..



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    ATCC cell lines skbr3 atcc htb30 hek 293h atcc crl 1573 software
    (A) As in the Figure 4A, but assessing the enrichment for loss of the WT allele as the mechanism of mutant allele imbalance. (B) In HR+ HER2− breast cancers, the rate of LOH spanning ESR1 in tumors with or without ESR1 gain-of-function mutations and those acquired before or after endocrine therapy (asterisk, p value = 0.00015, Chi-squared test; numbers in black bars represent the number of affected cases). (C) Luciferase reporter activity (RLU) in HR− <t>SKBr3</t> cells ectopically expressing HA-ERα wild-type (WT) or the specified mutant in proportions equivalent to homozygous mutant (left) to heterozygosity (right) in hormone-depleted medium. Error bars are +/− SD from triplicate experiments. (D) Duration of time of patients with BRAF V600E-mutant metastatic melanomas on vemurafenib therapy as a function of allelic imbalance of V600E and the mechanisms thereof [median PFS is 31.7 months (95% CI, 6-not reached) for patients with loss of WT BRAF versus 6.5 months (4.8-12) in the rest; hazard ratio, 4.4; p value = 0.01]. Complete pathologic responses are indicated in dark blue (p value = 0.01 comparing patients whose tumors lost the WT allele to those whose tumors that do not, two-sided Fisher’s exact test). See also Figure S5.
    Cell Lines Skbr3 Atcc Htb30 Hek 293h Atcc Crl 1573 Software, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    (A) As in the Figure 4A, but assessing the enrichment for loss of the WT allele as the mechanism of mutant allele imbalance. (B) In HR+ HER2− breast cancers, the rate of LOH spanning ESR1 in tumors with or without ESR1 gain-of-function mutations and those acquired before or after endocrine therapy (asterisk, p value = 0.00015, Chi-squared test; numbers in black bars represent the number of affected cases). (C) Luciferase reporter activity (RLU) in HR− SKBr3 cells ectopically expressing HA-ERα wild-type (WT) or the specified mutant in proportions equivalent to homozygous mutant (left) to heterozygosity (right) in hormone-depleted medium. Error bars are +/− SD from triplicate experiments. (D) Duration of time of patients with BRAF V600E-mutant metastatic melanomas on vemurafenib therapy as a function of allelic imbalance of V600E and the mechanisms thereof [median PFS is 31.7 months (95% CI, 6-not reached) for patients with loss of WT BRAF versus 6.5 months (4.8-12) in the rest; hazard ratio, 4.4; p value = 0.01]. Complete pathologic responses are indicated in dark blue (p value = 0.01 comparing patients whose tumors lost the WT allele to those whose tumors that do not, two-sided Fisher’s exact test). See also Figure S5.

    Journal: Cancer cell

    Article Title: Widespread selection for oncogenic mutant allele imbalance in cancer

    doi: 10.1016/j.ccell.2018.10.003

    Figure Lengend Snippet: (A) As in the Figure 4A, but assessing the enrichment for loss of the WT allele as the mechanism of mutant allele imbalance. (B) In HR+ HER2− breast cancers, the rate of LOH spanning ESR1 in tumors with or without ESR1 gain-of-function mutations and those acquired before or after endocrine therapy (asterisk, p value = 0.00015, Chi-squared test; numbers in black bars represent the number of affected cases). (C) Luciferase reporter activity (RLU) in HR− SKBr3 cells ectopically expressing HA-ERα wild-type (WT) or the specified mutant in proportions equivalent to homozygous mutant (left) to heterozygosity (right) in hormone-depleted medium. Error bars are +/− SD from triplicate experiments. (D) Duration of time of patients with BRAF V600E-mutant metastatic melanomas on vemurafenib therapy as a function of allelic imbalance of V600E and the mechanisms thereof [median PFS is 31.7 months (95% CI, 6-not reached) for patients with loss of WT BRAF versus 6.5 months (4.8-12) in the rest; hazard ratio, 4.4; p value = 0.01]. Complete pathologic responses are indicated in dark blue (p value = 0.01 comparing patients whose tumors lost the WT allele to those whose tumors that do not, two-sided Fisher’s exact test). See also Figure S5.

    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal, Phospho-MEK (Ser217/221) Cell Signal Cat#9121; RRID: AB_331649 Rabbit polyclonal, Anti-MEK Cell Signal Cat#9122; RRID: AB_823567 Rabbit polyclonal, Phospho ERK (Thr202/Tyr204) Cell Signal Cat#9109; RRID: AB_331646 Rabbit polyclonal, Anti-ERK Cell Signal Cat#9102; RRID: AB_330744 Rabbit monoclonal, Anti-GFP Cell Signal Cat#2956; RRID: AB_1196615 Rabbit monoclonal, Anti-GAPDH Cell Signal Cat#2118; RRID: AB_561053 Biological Samples MSK-IMPACT Zehir et al. 2017 N/A Chemicals, Peptides, and Recombinant Proteins pEGPF-N1-MEK1 Addgene Cat#14746 3X-ERE-TATA-luciferase reporter Addgene Cat#11354 pRL-TK Renilla luciferase plasmid Promega Cat#E2231 HA-tagged WT ERα This study N/A pcDNA3.1 (EV) Thermo Fisher Cat#V79020 HA-tagged ERα Y537S This study N/A HA-tagged ERα D538G This study N/A Critical Commercial Assays QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat#200521 SuperSignal West Pico Plus Chemiluminescent Thermo Fisher Cat#34577 Lipofectamine 2000 Transfection Reagent Invitrogen Cat#11668027 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Deposited Data Prospective DNA sequencing This study Accession number for the prospective sequencing data reported in this study is EVA: PRJEB28874, https://www.ebi.ac.uk/eva/?eva-study=PRJEB28874 Experimental Models: Cell Lines SKBr3 ATCC HTB30 HEK-293H ATCC CRL-1573 Software and Algorithms R for Statistical Computing R Foundation http://www.r-project.org FACETS Shen, et al. 2016 http://github.com/mskcc/facets FACETS-suite This study http://github.com/mskcc/facets-suite Other BAM files for TCGA exomes TCGA https://cancergenome.nih.gov Open in a separate window KEY RESOURCES TABLE Mutant allele imbalance affects ~half of all oncogenic driver mutations in cancer Positive and negative selection shapes the allelic configuration of mutant oncogenes Mutant dosage gains and stoichiometric changes drive fitness and growth advantages Mutant oncogene zygosity dictates prognosis and enhanced therapeutic sensitivity Bielski et al. describe widespread allele imbalance in cancer, which is selected for via modest dosage increases of gain-of-fitness mutations and can be driven by antecedent oncogenic mutations.

    Techniques: Mutagenesis, Luciferase, Activity Assay, Expressing

    KEY RESOURCES TABLE

    Journal: Cancer cell

    Article Title: Widespread selection for oncogenic mutant allele imbalance in cancer

    doi: 10.1016/j.ccell.2018.10.003

    Figure Lengend Snippet: KEY RESOURCES TABLE

    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal, Phospho-MEK (Ser217/221) Cell Signal Cat#9121; RRID: AB_331649 Rabbit polyclonal, Anti-MEK Cell Signal Cat#9122; RRID: AB_823567 Rabbit polyclonal, Phospho ERK (Thr202/Tyr204) Cell Signal Cat#9109; RRID: AB_331646 Rabbit polyclonal, Anti-ERK Cell Signal Cat#9102; RRID: AB_330744 Rabbit monoclonal, Anti-GFP Cell Signal Cat#2956; RRID: AB_1196615 Rabbit monoclonal, Anti-GAPDH Cell Signal Cat#2118; RRID: AB_561053 Biological Samples MSK-IMPACT Zehir et al. 2017 N/A Chemicals, Peptides, and Recombinant Proteins pEGPF-N1-MEK1 Addgene Cat#14746 3X-ERE-TATA-luciferase reporter Addgene Cat#11354 pRL-TK Renilla luciferase plasmid Promega Cat#E2231 HA-tagged WT ERα This study N/A pcDNA3.1 (EV) Thermo Fisher Cat#V79020 HA-tagged ERα Y537S This study N/A HA-tagged ERα D538G This study N/A Critical Commercial Assays QuikChange II XL Site-Directed Mutagenesis Kit Stratagene Cat#200521 SuperSignal West Pico Plus Chemiluminescent Thermo Fisher Cat#34577 Lipofectamine 2000 Transfection Reagent Invitrogen Cat#11668027 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Deposited Data Prospective DNA sequencing This study Accession number for the prospective sequencing data reported in this study is EVA: PRJEB28874, https://www.ebi.ac.uk/eva/?eva-study=PRJEB28874 Experimental Models: Cell Lines SKBr3 ATCC HTB30 HEK-293H ATCC CRL-1573 Software and Algorithms R for Statistical Computing R Foundation http://www.r-project.org FACETS Shen, et al. 2016 http://github.com/mskcc/facets FACETS-suite This study http://github.com/mskcc/facets-suite Other BAM files for TCGA exomes TCGA https://cancergenome.nih.gov Open in a separate window KEY RESOURCES TABLE Mutant allele imbalance affects ~half of all oncogenic driver mutations in cancer Positive and negative selection shapes the allelic configuration of mutant oncogenes Mutant dosage gains and stoichiometric changes drive fitness and growth advantages Mutant oncogene zygosity dictates prognosis and enhanced therapeutic sensitivity Bielski et al. describe widespread allele imbalance in cancer, which is selected for via modest dosage increases of gain-of-fitness mutations and can be driven by antecedent oncogenic mutations.

    Techniques: Recombinant, Luciferase, Plasmid Preparation, Mutagenesis, Transfection, Reporter Assay, DNA Sequencing, Sequencing, Software