Angela N. Brooks
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View article: STEM-26. COMPREHENSIVE FUNCTIONAL GENOMIC SCREENS REVEAL HUMAN TRANSCRIPTION FACTORS REQUIRED TO MAINTAIN GLIOBLASTOMA OLIGODENDROCYTE PROGENITOR CELL-LIKE IDENTITY
STEM-26. COMPREHENSIVE FUNCTIONAL GENOMIC SCREENS REVEAL HUMAN TRANSCRIPTION FACTORS REQUIRED TO MAINTAIN GLIOBLASTOMA OLIGODENDROCYTE PROGENITOR CELL-LIKE IDENTITY Open
For glioblastoma (GBM), like other solid tumors, intratumoral heterogeneity is likely a critical factor in promoting tumor growth, homeostasis, and therapeutic response. Recent applications of single-cell genomics techniques have revealed …
View article: SMAdd-seq: probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing
SMAdd-seq: probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing Open
Studies of in vivo chromatin organization have relied on the accessibility of the underlying DNA to nucleases or methyltransferases, which is limited by their requirement for purified nuclei and enzymatic treatment. Here, we introduce a na…
View article: A novel splice site variant in<i>DEGS1</i>leads to aberrant splicing and loss of DEGS1 enzyme activity, a VUS resolved
A novel splice site variant in<i>DEGS1</i>leads to aberrant splicing and loss of DEGS1 enzyme activity, a VUS resolved Open
Purpose Pathogenic DEGS1 variants have been reported in individuals with autosomal recessive hypomyelinating leukodystrophy 18 (HLD18; MIM# 618404). We sought to resolve a 5′ +4/+5 splice site variant of uncertain significance found in thr…
View article: <i>U2AF1 S34F</i>enhances tumorigenic potential of lung cells by exhibiting synergy with<i>KRAS</i>mutation and altering response to environmental stress
<i>U2AF1 S34F</i>enhances tumorigenic potential of lung cells by exhibiting synergy with<i>KRAS</i>mutation and altering response to environmental stress Open
SUMMARY Although U2AF1 S34F is a recurrent splicing factor mutation in lung adenocarcinoma (ADC), U2AF1 S34F alone is insufficient for producing tumors in previous models. Because lung ADCs with U2AF1 S34F frequently have co-occurring KRAS…
View article: Detecting haplotype-specific transcript variation in long reads with FLAIR2
Detecting haplotype-specific transcript variation in long reads with FLAIR2 Open
Background RNA-seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these RNA variants in a variety of diseases. Aberrant splicing and single nucleotide variants (SNVs) in RNA have been demonst…
View article: SMAdd-seq: Probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing
SMAdd-seq: Probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing Open
Studies of in vivo chromatin organization have relied on the accessibility of the underlying DNA to nucleases or methyltransferases, which is limited by their requirement for purified nuclei and enzymatic treatment. Here, we introduce a na…
View article: MET exon 14 skipping is overexpressed in an allele-specific manner in lung adenocarcinoma primary samples
MET exon 14 skipping is overexpressed in an allele-specific manner in lung adenocarcinoma primary samples Open
MET exon 14 skipping (METΔ14) is a well-characterized oncogene in the Ras-MAPK pathway driving lung adenocarcinoma (LUAD). Previous studies on METΔ14 revealed this aberrantly spliced oncogene is expressed in LUAD primary samples and is ass…
View article: Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification Open
The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from …
View article: Full-length transcript alterations in human bronchial epithelial cells with<i>U2AF1</i>S34F mutations
Full-length transcript alterations in human bronchial epithelial cells with<i>U2AF1</i>S34F mutations Open
U2AF1 is one of the most recurrently mutated splicing factors in lung adenocarcinoma and has been shown to cause transcriptome-wide pre-mRNA splicing alterations; however, the full-length altered mRNA isoforms associated with the mutation …
View article: Detecting haplotype-specific transcript variation in long reads with FLAIR2
Detecting haplotype-specific transcript variation in long reads with FLAIR2 Open
Background RNA-Seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these RNA variants in a variety of diseases. Aberrant splicing and single nucleotide variants in RNA have been demonstrated t…
View article: DeepSea is an efficient deep-learning model for single-cell segmentation and tracking in time-lapse microscopy
DeepSea is an efficient deep-learning model for single-cell segmentation and tracking in time-lapse microscopy Open
Time-lapse microscopy is the only method that can directly capture the dynamics and heterogeneity of fundamental cellular processes at the single-cell level with high temporal resolution. Successful application of single-cell time-lapse mi…
View article: Supplementary Methods from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma
Supplementary Methods from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma Open
Supplementary Methods
View article: Conflict of Interest Form from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma
Conflict of Interest Form from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma Open
Conflict of Interest Form
View article: Conflict of Interest Form from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma
Conflict of Interest Form from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma Open
Conflict of Interest Form
View article: Conflict of Interest Form from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma
Conflict of Interest Form from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma Open
Conflict of Interest Form
View article: Data from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma
Data from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma Open
Targeting somatically activated oncogenes has revolutionized the treatment of non–small cell lung cancer (NSCLC). Mutations in the gene mesenchymal–epithelial transition (MET) near the exon 14 splice sites are recurrent in lung adenocarcin…
View article: Data from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma
Data from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma Open
Targeting somatically activated oncogenes has revolutionized the treatment of non–small cell lung cancer (NSCLC). Mutations in the gene mesenchymal–epithelial transition (MET) near the exon 14 splice sites are recurrent in lung adenocarcin…
View article: Supplementary Figure Legends from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma
Supplementary Figure Legends from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma Open
Supplementary Figure Legends
View article: supplementary figures 1-5 from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma
supplementary figures 1-5 from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma Open
Supplementary Figure 1: A survey of MET mutations and expression across TCGA datasets from diverse cancer types. Supplementary figure 2, MET exon 14 status and trypsin assay Supplementary Figure 3 MET half-life assay results Supplementary …
View article: Supplementary Figure Legends from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma
Supplementary Figure Legends from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma Open
Supplementary Figure Legends
View article: Supplementary Tables 1 and 2 from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma
Supplementary Tables 1 and 2 from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma Open
Supplementary Tables 1 and 2
View article: Supplementary Methods from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma
Supplementary Methods from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma Open
Supplementary Methods
View article: Conflict of Interest Form from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma
Conflict of Interest Form from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma Open
Conflict of Interest Form
View article: Supplementary Tables 1 and 2 from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma
Supplementary Tables 1 and 2 from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma Open
Supplementary Tables 1 and 2
View article: supplementary figures 1-5 from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma
supplementary figures 1-5 from <i>MET</i> Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma Open
Supplementary Figure 1: A survey of MET mutations and expression across TCGA datasets from diverse cancer types. Supplementary figure 2, MET exon 14 status and trypsin assay Supplementary Figure 3 MET half-life assay results Supplementary …
View article: Author Correction: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations
Author Correction: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations Open
In the published version of this paper, the members of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortiumwere listed in the Supplementary Information; however, these members shouldhave been included in themainpaper.The originalArt…