We are aiming to build a collaborative and translational genomics research program in order to link knowledge of cancer genome alterations to clinical outcome, monitor shifts in cancer and immune cell populations during treatment and enable the use of cancer genome analysis as a routine clinical test. We have established a clinical genomics platform in order to extract genomic, epigenomic and transcriptomic data, invented new technologies for targeted sequencing of cell-free DNA and developed software for secure data sharing between clinical and basic research teams.
Assessing genome-wide copy number aberrations and copy-neutral loss-of-heterozygosity as best practice: An evidence-based review from the Cancer Genomics Consortium working group for plasma cell disorders.
Pugh TJ, Fink JM, Lu X, Mathew S, Murata-Collins J, Willem P, Fang M.
Cancer genetics. 2018; 228-229:184-196. PubMed [journal]PMID: 30393007
Landscape of genomic alterations in high-grade serous ovarian cancer from exceptional long- and short-term survivors.
Yang SYC, Lheureux S, Karakasis K, Burnier JV, Bruce JP, Clouthier DL, Danesh A, Quevedo R, Dowar M, Hanna Y, Li T, Lu L, Xu W, Clarke BA, Ohashi PS, Shaw PA, Pugh TJ, Oza AM.
Genome medicine. 2018; 10(1):81. PubMed [journal]PMID: 30382883 PMCID: PMC6208125
Patient-Derived Xenografts for Prognostication and Personalized Treatment for Head and Neck Squamous Cell Carcinoma.
Karamboulas C, Bruce JP, Hope AJ, Meens J, Huang SH, Erdmann N, Hyatt E, Pereira K, Goldstein DP, Weinreb I, Su J, O’Sullivan B, Tiedemann R, Liu FF, Pugh TJ, Bratman SV, Xu W, Ailles L.
Cell reports. 2018; 25(5):1318-1331.e4. PubMed [journal]PMID: 30380421
Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.
Samadian S, Bruce JP, Pugh TJ.
PLoS computational biology. 2018; 14(3):e1006080. PubMed [journal]PMID: 29590101 PMCID: PMC5891060
Somatic BRCA1/2 Recovery as a Resistance Mechanism After Exceptional Response to Poly (ADP-ribose) Polymerase Inhibition.
Lheureux S, Bruce JP, Burnier JV, Karakasis K, Shaw PA, Clarke BA, Yang SY, Quevedo R, Li T, Dowar M, Bowering V, Pugh TJ, Oza AM.
Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 2017; 35(11):1240-1249. PubMed [journal]PMID: 28221868
Data resources for the identification and interpretation of actionable mutations by clinicians.
Prawira A, Pugh TJ, Stockley TL, Siu LL.
Annals of oncology : official journal of the European Society for Medical Oncology. 2017; 28(5):946-957. PubMed [journal]PMID: 28327901
VisCap: inference and visualization of germ-line copy-number variants from targeted clinical sequencing data.
Pugh TJ, Amr SS, Bowser MJ, Gowrisankar S, Hynes E, Mahanta LM, Rehm HL, Funke B, Lebo MS.
Genetics in medicine : official journal of the American College of Medical Genetics. 2016; 18(7):712-9. PubMed [journal]PMID: 26681316 PMCID: PMC4940431
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.
Pugh TJ, Yu W, Yang J, Field AL, Ambrogio L, Carter SL, Cibulskis K, Giannikopoulos P, Kiezun A, Kim J, McKenna A, Nickerson E, Getz G, Hoffher S, Messinger YH, Dehner LP, Roberts CW, Rodriguez-Galindo C, Williams GM, Rossi CT, Meyerson M, Hill DA.
Oncogene. 2014; 33(45):5295-302. NIHMSID: NIHMS586233. PubMed [journal]PMID: 24909177 PMCID: PMC4224628
The landscape of genetic variation in dilated cardiomyopathy as surveyed by clinical DNA sequencing.
Pugh TJ, Kelly MA, Gowrisankar S, Hynes E, Seidman MA, Baxter SM, Bowser M, Harrison B, Aaron D, Mahanta LM, Lakdawala NK, McDermott G, White ET, Rehm HL, Lebo M, Funke BH.
Genetics in medicine : official journal of the American College of Medical Genetics. 2014; 16(8):601-8. PubMed [journal]PMID: 24503780