List of works - Trevor J Pugh

A BAC clone fingerprinting approach to the detection of human genome rearrangements ⬇️

scientific article

A comprehensive assay for CFTR mutational analysis using next-generation sequencing.

scientific article published on 17 June 2013

A distinct innate lymphoid cell population regulates tumor-associated T cells

scientific article published on 6 February 2017

A patient with vertebral, cognitive and behavioural abnormalities and a de novo deletion of NRXN1alpha

scientific article

A shower of second hit events as the cause of multifocal renal cell carcinoma in tuberous sclerosis complex

scientific article

A systematic approach to assessing the clinical significance of genetic variants.

scientific article

Abstracts

article by L. Bie et al published 1 April 2013 in Neuro-Oncology

Activating Mutations Affecting the Dbl Homology Domain of SOS2 Cause Noonan Syndrome

scientific article

Activation of the PD-1 pathway contributes to immune escape in EGFR-driven lung tumors

scientific article published on 27 September 2013

Alternative expression analysis by RNA sequencing

scientific article published on 12 September 2010

An Anaplastic Lymphoma Kinase Immunohistochemistry-Negative but Fluorescence In Situ Hybridization-Positive Lung Adenocarcinoma Is Resistant to Crizotinib

scientific article published on 6 September 2016

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.

scientific article

Brain tumor stem cell dependence on glutaminase reveals a metabolic vulnerability through the amino acid deprivation response pathway

scientific article published on 26 October 2020

CapTCR-seq: hybrid capture for T-cell receptor repertoire profiling

scientific article published on 01 December 2018

Childhood cerebellar tumours mirror conserved fetal transcriptional programs

scientific article published on 01 May 2019

Circulating Tumour DNA for Detecting Minimal Residual Disease in Multiple Myeloma

scientific article published on 01 January 2018

Circulating tumour DNA sequence analysis as an alternative to multiple myeloma bone marrow aspirates

scientific article published on 11 May 2017

Comprehensive diagnostic testing for stereocilin: an approach for analyzing medically important genes with high homology

scientific article published on 23 August 2014

Correlations of EGFR mutations and increases in EGFR and HER2 copy number to gefitinib response in a retrospective analysis of lung cancer patients

scientific article

DNA hypermethylation within TERT promoter upregulates TERT expression in cancer

scientific article

DNA hypermethylation within TERT promoter upregulates TERT expression in cancer

DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts.

scientific article published on August 2015

Data resources for the identification and interpretation of actionable mutations by clinicians.

scientific article

Development and validation of a computational method for assessment of missense variants in hypertrophic cardiomyopathy

scientific article

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

scientific article

Dissecting the genomic complexity underlying medulloblastoma

scientific article

Divergent clonal selection dominates medulloblastoma at recurrence

scientific article published on 13 January 2016

EVOLVE: A Multicenter Open-Label Single-Arm Clinical and Translational Phase II Trial of Cediranib Plus Olaparib for Ovarian Cancer after PARP Inhibition Progression

scientific article published on 22 May 2020

Elevation in viral entry genes and innate immunity compromise underlying increased infectivity and severity of COVID-19 in cancer patients

scientific article published on 25 February 2021

Epidermal growth factor receptor (EGFR) is transcriptionally induced by the Y-box binding protein-1 (YB-1) and can be inhibited with Iressa in basal-like breast cancer, providing a potential target for therapy

scientific article

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy

scientific article

Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors

scientific article

Exome sequencing of pleuropulmonary blastoma reveals frequent biallelic loss of TP53 and two hits in DICER1 resulting in retention of 5p-derived miRNA hairpin loop sequences

scientific article

Facilitated loading of horizontal gels using a capillary comb loader

scientific article published on 01 April 2003

Fate mapping of human glioblastoma reveals an invariant stem cell hierarchy.

scientific article published on 30 August 2017

GCN2 drives macrophage and MDSC function and immunosuppression in the tumor microenvironment

scientific article published on 01 December 2019

Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition

scientific article

Genomic Profiling of a Large Set of Diverse Pediatric Cancers Identifies Known and Novel Mutations across Tumor Spectra

scientific article published on 9 January 2017

Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion

scientific article published on 04 September 2011

Human Papillomavirus Genotype Association With Survival in Head and Neck Squamous Cell Carcinoma

scientific article published on 24 March 2016

ICGC PedBrain - dissecting the genomic complexity underlying medulloblastoma using whole-genome sequencing.

scientific article

Impact of whole genome amplification on analysis of copy number variants

scientific article

Implementation of serological and molecular tools to inform COVID-19 patient management: protocol for the GENCOV prospective cohort study

publication published on 30 September 2021

Inhibitor-sensitive FGFR2 and FGFR3 mutations in lung squamous cell carcinoma

scientific article published on 20 June 2013

Initial genome sequencing and analysis of multiple myeloma

scientific article

Institutional implementation of clinical tumor profiling on an unselected cancer population

scientific article published on 17 November 2016

Integration of Technical, Bioinformatic, and Variant Assessment Approaches in the Validation of a Targeted Next-Generation Sequencing Panel for Myeloid Malignancies

scientific article published on 9 March 2017

Integration of intra-sample contextual error modeling for improved detection of somatic mutations from deep sequencing

scientific article published on 09 December 2020

Integrative and comparative genomic analysis of HPV-positive and HPV-negative head and neck squamous cell carcinomas

scientific article

Landscape of genomic alterations in cervical carcinomas

scientific article

Loss of CREBBP and KMT2D cooperate to accelerate lymphomagenesis and shape the lymphoma immune microenvironment ⬇️

scientific article published on 3 April 2024

MEDULLOBLASTOMA

Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing

scientific article

Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations

scientific article (publication date: 22 July 2012)

Melanoma genome sequencing reveals frequent PREX2 mutations

scientific article

Minimal Residual Disease in Myeloma: Application for Clinical Care and New Drug Registration

Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer.

scientific article published on 15 August 2016

Molecular profiling of advanced solid tumors and patient outcomes with genotype-matched clinical trials: the Princess Margaret IMPACT/COMPACT trial.

scientific article published on 25 October 2016

Multimodal immunogenomic biomarker analysis of tumors from pediatric patients enrolled to a phase 1-2 study of single-agent atezolizumab

scientific article published in 2023

Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

scientific article (publication date: 8 October 2009)

Mutational heterogeneity in cancer and the search for new cancer-associated genes

scientific article

Mutations in the RAS/MAPK Pathway Drive Replication Repair-Deficient Hypermutated Tumors and Confer Sensitivity to MEK Inhibition

publication published on 09 February 2021

NEURO/MEDICAL ONCOLOGY

Neoadjuvant and Adjuvant Pembrolizumab in Resectable Locally Advanced, Human Papillomavirus-Unrelated Head and Neck Cancer: A Multicenter, Phase 2 Trial

scientific article published on 14 July 2020

Next generation sequencing-based copy number analysis reveals low prevalence of deletions and duplications in 46 genes associated with genetic cardiomyopathies

scientific article published on 16 December 2015

Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer

scientific article published on 23 January 2020

Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer.

scientific article published on 29 August 2016

Novel mRNA isoforms and mutations of uridine monophosphate synthetase and 5-fluorouracil resistance in colorectal cancer

scientific article published on 17 January 2012

Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation

scientific article

Oncotator: cancer variant annotation tool

scientific article published on 16 March 2015

PRMT5 inhibition disrupts splicing and stemness in glioblastoma

scientific article published on 12 February 2021

Patient-Derived Xenografts for Prognostication and Personalized Treatment for Head and Neck Squamous Cell Carcinoma

Personalized oncogenomics.

scientific article

Prediction of acute myeloid leukaemia risk in healthy individuals

scientific article published in Nature

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

scientific article

REFLECTions on Combination Therapies Empowered by Data Sharing

scientific article published in 2022

Rare driver mutations in head and neck squamous cell carcinomas converge on NOTCH signaling

scientific article published on 01 March 2020

Recurrent and functional regulatory mutations in breast cancer

scientific article published on 28 June 2017

Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations

scientific article published on 29 June 2015

Sensitive tumour detection and classification using plasma cell-free DNA methylomes

scientific article published in Nature

Sequence Variant Discovery in DNA Repair Genes from Radiosensitive and Radiotolerant Prostate Brachytherapy Patients

article

Somatic BRCA1/2 Recovery as a Resistance Mechanism After Exceptional Response to Poly (ADP-ribose) Polymerase Inhibition.

scientific article published on 21 February 2017

Somatic mutation of CDKN1B in small intestine neuroendocrine tumors

scientific article published on 3 November 2013

Subgroup-specific prognostic implications of TP53 mutation in medulloblastoma

scientific article published on 08 July 2013

T cell clonality assessment: past, present and future

scientific article published on 21 October 2017

The Role of Minimal Residual Disease Testing in Myeloma Treatment Selection and Drug Development: Current Value and Future Applications

scientific article

The genetic landscape of high-risk neuroblastoma

scientific article published on 20 January 2013

The genomic complexity of primary human prostate cancer

scientific article

The genomic landscape of schwannoma

scientific article published on 10 October 2016

The landscape of genetic variation in dilated cardiomyopathy as surveyed by clinical DNA sequencing

scientific article published on 6 February 2014

Therapeutic radiation for childhood cancer drives structural aberrations of NF2 in meningiomas

scientific article

VisCap: inference and visualization of germ-line copy-number variants from targeted clinical sequencing data

scientific article

WNT activation by lithium abrogates TP53 mutation associated radiation resistance in medulloblastoma

scientific article

Whole Exome Sequencing Identifies TSC1/TSC2 Biallelic Loss as the Primary and Sufficient Driver Event for Renal Angiomyolipoma Development

scientific article

Wnt activation as a therapeutic strategy in medulloblastoma

scientific article published on 28 August 2020

List of works by Trevor J Pugh

A BAC clone fingerprinting approach to the detection of human genome rearrangements ⬇️

A comprehensive assay for CFTR mutational analysis using next-generation sequencing.

A distinct innate lymphoid cell population regulates tumor-associated T cells

A patient with vertebral, cognitive and behavioural abnormalities and a de novo deletion of NRXN1alpha

A shower of second hit events as the cause of multifocal renal cell carcinoma in tuberous sclerosis complex

A systematic approach to assessing the clinical significance of genetic variants.

Abstracts

Activating Mutations Affecting the Dbl Homology Domain of SOS2 Cause Noonan Syndrome

Activation of the PD-1 pathway contributes to immune escape in EGFR-driven lung tumors

Alternative expression analysis by RNA sequencing

An Anaplastic Lymphoma Kinase Immunohistochemistry-Negative but Fluorescence In Situ Hybridization-Positive Lung Adenocarcinoma Is Resistant to Crizotinib

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.

Brain tumor stem cell dependence on glutaminase reveals a metabolic vulnerability through the amino acid deprivation response pathway

CapTCR-seq: hybrid capture for T-cell receptor repertoire profiling

Childhood cerebellar tumours mirror conserved fetal transcriptional programs

Circulating Tumour DNA for Detecting Minimal Residual Disease in Multiple Myeloma

Circulating tumour DNA sequence analysis as an alternative to multiple myeloma bone marrow aspirates

Comprehensive diagnostic testing for stereocilin: an approach for analyzing medically important genes with high homology

Correlations of EGFR mutations and increases in EGFR and HER2 copy number to gefitinib response in a retrospective analysis of lung cancer patients

DNA hypermethylation within TERT promoter upregulates TERT expression in cancer

DNA hypermethylation within TERT promoter upregulates TERT expression in cancer

DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts.

Data resources for the identification and interpretation of actionable mutations by clinicians.

Development and validation of a computational method for assessment of missense variants in hypertrophic cardiomyopathy

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

Dissecting the genomic complexity underlying medulloblastoma

Divergent clonal selection dominates medulloblastoma at recurrence

EVOLVE: A Multicenter Open-Label Single-Arm Clinical and Translational Phase II Trial of Cediranib Plus Olaparib for Ovarian Cancer after PARP Inhibition Progression

Elevation in viral entry genes and innate immunity compromise underlying increased infectivity and severity of COVID-19 in cancer patients

Epidermal growth factor receptor (EGFR) is transcriptionally induced by the Y-box binding protein-1 (YB-1) and can be inhibited with Iressa in basal-like breast cancer, providing a potential target for therapy

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy

Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors

Exome sequencing of pleuropulmonary blastoma reveals frequent biallelic loss of TP53 and two hits in DICER1 resulting in retention of 5p-derived miRNA hairpin loop sequences

Facilitated loading of horizontal gels using a capillary comb loader

Fate mapping of human glioblastoma reveals an invariant stem cell hierarchy.

GCN2 drives macrophage and MDSC function and immunosuppression in the tumor microenvironment

Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition

Genomic Profiling of a Large Set of Diverse Pediatric Cancers Identifies Known and Novel Mutations across Tumor Spectra

Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion

Human Papillomavirus Genotype Association With Survival in Head and Neck Squamous Cell Carcinoma

ICGC PedBrain - dissecting the genomic complexity underlying medulloblastoma using whole-genome sequencing.

Impact of whole genome amplification on analysis of copy number variants

Implementation of serological and molecular tools to inform COVID-19 patient management: protocol for the GENCOV prospective cohort study

Inhibitor-sensitive FGFR2 and FGFR3 mutations in lung squamous cell carcinoma

Initial genome sequencing and analysis of multiple myeloma

Institutional implementation of clinical tumor profiling on an unselected cancer population

Integration of Technical, Bioinformatic, and Variant Assessment Approaches in the Validation of a Targeted Next-Generation Sequencing Panel for Myeloid Malignancies

Integration of intra-sample contextual error modeling for improved detection of somatic mutations from deep sequencing

Integrative and comparative genomic analysis of HPV-positive and HPV-negative head and neck squamous cell carcinomas

Landscape of genomic alterations in cervical carcinomas

Loss of CREBBP and KMT2D cooperate to accelerate lymphomagenesis and shape the lymphoma immune microenvironment ⬇️

MEDULLOBLASTOMA

Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing

Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations

Melanoma genome sequencing reveals frequent PREX2 mutations

Minimal Residual Disease in Myeloma: Application for Clinical Care and New Drug Registration

Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer.

Molecular profiling of advanced solid tumors and patient outcomes with genotype-matched clinical trials: the Princess Margaret IMPACT/COMPACT trial.

Multimodal immunogenomic biomarker analysis of tumors from pediatric patients enrolled to a phase 1-2 study of single-agent atezolizumab

Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

Mutational heterogeneity in cancer and the search for new cancer-associated genes

Mutations in the RAS/MAPK Pathway Drive Replication Repair-Deficient Hypermutated Tumors and Confer Sensitivity to MEK Inhibition

NEURO/MEDICAL ONCOLOGY

Neoadjuvant and Adjuvant Pembrolizumab in Resectable Locally Advanced, Human Papillomavirus-Unrelated Head and Neck Cancer: A Multicenter, Phase 2 Trial

Next generation sequencing-based copy number analysis reveals low prevalence of deletions and duplications in 46 genes associated with genetic cardiomyopathies

Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer

Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer.

Novel mRNA isoforms and mutations of uridine monophosphate synthetase and 5-fluorouracil resistance in colorectal cancer

Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation

Oncotator: cancer variant annotation tool

PRMT5 inhibition disrupts splicing and stemness in glioblastoma

Patient-Derived Xenografts for Prognostication and Personalized Treatment for Head and Neck Squamous Cell Carcinoma

Personalized oncogenomics.

Prediction of acute myeloid leukaemia risk in healthy individuals

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

REFLECTions on Combination Therapies Empowered by Data Sharing

Rare driver mutations in head and neck squamous cell carcinomas converge on NOTCH signaling

Recurrent and functional regulatory mutations in breast cancer

Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations