Matthew Mort
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View article: Expanding the utility of variant effect predictions with phenotype-specific models
Expanding the utility of variant effect predictions with phenotype-specific models Open
Current methods for variant effect prediction do not differentiate between pathogenic variants resulting in different disease outcomes and are restricted in application due to a focus on variants with a single molecular consequence. We hav…
View article: Critical assessment of missense variant effect predictors on disease-relevant variant data
Critical assessment of missense variant effect predictors on disease-relevant variant data Open
Regular, systematic, and independent assessments of computational tools that are used to predict the pathogenicity of missense variants are necessary to evaluate their clinical and research utility and guide future improvements. The Critic…
View article: Expanding drug targets for 112 chronic diseases using a machine learning-assisted genetic priority score
Expanding drug targets for 112 chronic diseases using a machine learning-assisted genetic priority score Open
Identifying genetic drivers of chronic diseases is necessary for drug discovery. Here, we develop a machine learning-assisted genetic priority score, which we call ML-GPS, that incorporates genetic associations with predicted disease pheno…
View article: Critical assessment of missense variant effect predictors on disease-relevant variant data
Critical assessment of missense variant effect predictors on disease-relevant variant data Open
Regular, systematic, and independent assessment of computational tools used to predict the pathogenicity of missense variants is necessary to evaluate their clinical and research utility and suggest directions for future improvement. Here,…
View article: Supplementary Table S5 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Supplementary Table S5 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
A VCF file containing putatively pathogenic variants found in 1142 intestinal cancer associated genes in 21 of the duodenal adenomas studied here (see supplementary table 1 for sample details). Full genomic datasets for these samples are a…
View article: Supplementary Table S4 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Supplementary Table S4 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
A VCF file containing putatively pathogenic variants found in 1142 intestinal cancer associated genes in 27 of the duodenal adenomas studied here (see supplementary table 1 for sample details). Full genomic datasets for these samples are a…
View article: Supplementary Figure S5 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Supplementary Figure S5 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
Gene Ontology of DEGs between duodenal adenomas with and without PIGA somatic mutation. Enriched terms are plotted for Biological process(BP), A. Cellular Component (CC), B. and Molecular Function(MF), C. Terms are coloured by Log2-Padj va…
View article: Supplementary Table S3 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Supplementary Table S3 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
Summary statistics for all FAP and MAP patient-derived intestinal samples analysed in this study. Data sets are from two centres, Cardiff University (CU) and MD Anderson Cancer Center (MDACC). Statistically significant P-values < 0.05 are …
View article: Supplementary Figure S1 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Supplementary Figure S1 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
Whole transcriptome sequencing quality control and read distribution for data sets from Cardiff and MD Anderson. A. Sequencing quality assessment, batch aggregates are shown. B. Read distribution across the genome per batch demonstrating t…
View article: Supplementary Figure S3 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Supplementary Figure S3 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
The gating tree was set as follows, shown for an organoid line without a PIGA somatic variant. A: FSC/SSC to isolate cells (represents the distribution of cells in the light scatter based on size and intracellular composition, respectively…
View article: Figure 3 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Figure 3 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
Volcano plot of DEGs of FAP and MAP patients with and without PIGA mutation. Genes have been filtered to remove those with a mean expression ≤10 read counts. Red dots indicate DEGs with Padj ≤ 0.01 at ≥±1.5 LFC. Purple dots indicate genes …
View article: Figure 2 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Figure 2 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
Flow cytometry analysis of FLAER positive cells in 11 FAP duodenal organoids with and without somatic PIGA variants. Fluorescence from FLAER is detected using the FITC-A channel (emission:475–650 nm). A, Abundance of FLAER positive cells d…
View article: Data from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Data from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
The pathogenesis of duodenal tumors in the inherited tumor syndromes familial adenomatous polyposis (FAP) and MUTYH-associated polyposis (MAP) is poorly understood. This study aimed to identify genes that are significantly mutated in these…
View article: Figure 3 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Figure 3 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
Volcano plot of DEGs of FAP and MAP patients with and without PIGA mutation. Genes have been filtered to remove those with a mean expression ≤10 read counts. Red dots indicate DEGs with Padj ≤ 0.01 at ≥±1.5 LFC. Purple dots indicate genes …
View article: Figure 2 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Figure 2 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
Flow cytometry analysis of FLAER positive cells in 11 FAP duodenal organoids with and without somatic PIGA variants. Fluorescence from FLAER is detected using the FITC-A channel (emission:475–650 nm). A, Abundance of FLAER positive cells d…
View article: Supplementary Figure S4 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Supplementary Figure S4 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
RNASeq WTS pipeline validation by quantitative RT-PCR (qRT-PCR) and IHC A. Comparison of normalised RNA-Seq read counts (orange) to relative qRT-PCR expression levels (purple) for four top DEGs. Δ CT values are shown, with low values indic…
View article: Supplementary Table S2 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Supplementary Table S2 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
Germline and somatic mutations in FAP patient derived duodenal organoids
View article: Supplementary Figure S5 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Supplementary Figure S5 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
Gene Ontology of DEGs between duodenal adenomas with and without PIGA somatic mutation. Enriched terms are plotted for Biological process(BP), A. Cellular Component (CC), B. and Molecular Function(MF), C. Terms are coloured by Log2-Padj va…
View article: Supplementary Figure S4 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Supplementary Figure S4 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
RNASeq WTS pipeline validation by quantitative RT-PCR (qRT-PCR) and IHC A. Comparison of normalised RNA-Seq read counts (orange) to relative qRT-PCR expression levels (purple) for four top DEGs. Δ CT values are shown, with low values indic…
View article: Supplementary Table S3 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Supplementary Table S3 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
Summary statistics for all FAP and MAP patient-derived intestinal samples analysed in this study. Data sets are from two centres, Cardiff University (CU) and MD Anderson Cancer Center (MDACC). Statistically significant P-values < 0.05 are …
View article: Supplementary Figure S1 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Supplementary Figure S1 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
Whole transcriptome sequencing quality control and read distribution for data sets from Cardiff and MD Anderson. A. Sequencing quality assessment, batch aggregates are shown. B. Read distribution across the genome per batch demonstrating t…
View article: Supplementary Table S1 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Supplementary Table S1 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
Overview of all intestinal samples used in this study. *Sequenced previously (Thomas et al, 2017) and reanalysed here. Somatic mutations in APC, KRAS and PIGA as identified by WES and WTS analysis of CU and MDACC duodenal adenomas. Samples…
View article: Figure 1 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Figure 1 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
A,PIGA mutations identified in 19 duodenal adenomas and two duodenal adenoma patient-derived organoid lines. Relative location in comparison with known protein domains is shown. B, The VAF of four types of somatic mutation (exonic − synony…
View article: Supplementary Table S5 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Supplementary Table S5 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
A VCF file containing putatively pathogenic variants found in 1142 intestinal cancer associated genes in 21 of the duodenal adenomas studied here (see supplementary table 1 for sample details). Full genomic datasets for these samples are a…
View article: Supplementary Figure S3 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Supplementary Figure S3 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
The gating tree was set as follows, shown for an organoid line without a PIGA somatic variant. A: FSC/SSC to isolate cells (represents the distribution of cells in the light scatter based on size and intracellular composition, respectively…
View article: Figure 1 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Figure 1 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
A,PIGA mutations identified in 19 duodenal adenomas and two duodenal adenoma patient-derived organoid lines. Relative location in comparison with known protein domains is shown. B, The VAF of four types of somatic mutation (exonic − synony…
View article: Supplementary Table S2 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Supplementary Table S2 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
Germline and somatic mutations in FAP patient derived duodenal organoids
View article: Supplementary Table S1 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Supplementary Table S1 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis Open
Overview of all intestinal samples used in this study. *Sequenced previously (Thomas et al, 2017) and reanalysed here. Somatic mutations in APC, KRAS and PIGA as identified by WES and WTS analysis of CU and MDACC duodenal adenomas. Samples…