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

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

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

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

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

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