• 43156 Citations
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1986 …2019
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Research Output 1986 2019

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Article
2019
1 Citation (Scopus)

Activation of hedgehog signaling associates with early disease progression in chronic lymphocytic leukemia

HALT Pan-Leukemia Gene Panel Consortium, Jun 20 2019, In : Blood. 133, 25, p. 2651-2663 13 p.

Research output: Contribution to journalArticle

B-Cell Chronic Lymphocytic Leukemia
Disease Progression
Chemical activation
Patient treatment
Gene encoding
2 Citations (Scopus)

Comparative toxicoproteogenomics of mouse and rat liver identifies TCDD-resistance genes

Prokopec, S. D., Lu, A., Lee, S. C. E. S., Yao, C. Q., Sun, R. X., Watson, J. D., Soliymani, R., de Borja, R., Wong, A., Sam, M., Zuzarte, P., McPherson, J. D., Okey, A. B., Pohjanvirta, R. & Boutros, P. C., Oct 1 2019, In : Archives of Toxicology. 93, 10, p. 2961-2978 18 p.

Research output: Contribution to journalArticle

Liver
Rats
Genes
Aryl Hydrocarbon Receptors
Proteomics
1 Citation (Scopus)

Genome-wide germline correlates of the epigenetic landscape of prostate cancer

Houlahan, K. E., Shiah, Y. J., Gusev, A., Yuan, J., Ahmed, M., Shetty, A., Ramanand, S. G., Yao, C. Q., Bell, C., O’Connor, E., Huang, V., Fraser, M., Heisler, L. E., Livingstone, J., Yamaguchi, T. N., Rouette, A., Foucal, A., Espiritu, S. M. G., Sinha, A., Sam, M. & 23 others, Timms, L., Johns, J., Wong, A., Murison, A., Orain, M., Picard, V., Hovington, H., Bergeron, A., Lacombe, L., Lupien, M., Fradet, Y., Têtu, B., McPherson, J. D., Pasaniuc, B., Kislinger, T., Chua, M. L. K., Pomerantz, M. M., van der Kwast, T., Freedman, M. L., Mani, R. S., He, H. H., Bristow, R. G. & Boutros, P. C., Oct 1 2019, In : Nature Medicine. 25, 10, p. 1615-1626 12 p.

Research output: Contribution to journalArticle

Epigenomics
Tumors
Prostatic Neoplasms
Genes
Genome

Identification of distinct prognostic groups: Implications for patient selection to targeted therapies among anti-endocrine therapy–resistant early breast cancers

Bayani, J., Kornaga, E. N., Crozier, C., Jang, G. H., Bathurst, L., Kalatskaya, I., Trinh, Q. M., Yao, C. Q., Livingstone, J., Boutros, P. C., Spears, M., McPherson, J. D., Stein, L. D., Rea, D. & Bartlett, J. M. S., Jan 1 2019, In : JCO Precision Oncology. 3

Research output: Contribution to journalArticle

Patient Selection
Breast Neoplasms
Therapeutics
Cyclin D
Fibroblast Growth Factor Receptors

Next-generation sequencing technologies

McCombie, W. R., McPherson, J. D. & Mardis, E. R., Nov 2019, In : Cold Spring Harbor Perspectives in Medicine. 9, 11, a036798.

Research output: Contribution to journalArticle

Open Access
RNA Sequence Analysis
Genes
Genome
Human Genome
Technology

Regional perturbation of gene transcription is associated with intrachromosomal rearrangements and gene fusion transcripts in high grade ovarian cancer

Krzyzanowski, P. M., Sircoulomb, F., Yousif, F., Normand, J., La Rose, J., E. Francis, K., Suarez, F., Beck, T., Mcpherson, J. D., Stein, L. D. & Rottapel, R. K., Dec 1 2019, In : Scientific Reports. 9, 1, 3590.

Research output: Contribution to journalArticle

Gene Fusion
Ovarian Neoplasms
Transcriptome
Genes
Neoplasms
2018
21 Citations (Scopus)

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

Nattestad, M., Goodwin, S., Ng, K., Baslan, T., Sedlazeck, F. J., Rescheneder, P., Garvin, T., Fang, H., Gurtowski, J., Hutton, E., Tseng, E., Chin, C. S., Beck, T., Sundaravadanam, Y., Kramer, M., Antoniou, E., Mcpherson, J. D., Hicks, J., Richard McCombie, W. & Schatz, M. C., Aug 1 2018, In : Genome Research. 28, 8, p. 1126-1135 10 p.

Research output: Contribution to journalArticle

RNA Sequence Analysis
DNA Sequence Analysis
Oncogenes
Genome
Breast Neoplasms
13 Citations (Scopus)

Diverse EGFR Exon 20 Insertions and Co-Occurring Molecular Alterations Identified by Comprehensive Genomic Profiling of NSCLC

Riess, J., Gandara, D. R., Frampton, G. M., Madison, R., Peled, N., Bufill, J. A., Dy, G. K., Ou, S. H. I., Stephens, P. J., Mcpherson, J. D., Lara, P. N., Burich, R. A., Ross, J. S., Miller, V. A., Ali, S. M., Mack, P. & Schrock, A. B., Oct 1 2018, In : Journal of Thoracic Oncology. 13, 10, p. 1560-1568 9 p.

Research output: Contribution to journalArticle

Exons
Protein-Tyrosine Kinases
Tumor Burden
Cyclin-Dependent Kinase Inhibitor p15
Cyclin-Dependent Kinase Inhibitor p16
5 Citations (Scopus)
Pigmented Nevus
Nevus
Mutation
Melanoma
Growth

Minimally invasive real-time detection of actionable mutations in patients with metastatic solid tumors using fine-needle and liquid biopsies

Aung, K. L., Bedard, P. L., Yu, C., Boerner, S. L., Zuzarte, P. C., Ghai, S., Berman, H. K., Serra, S., Giesler, A., Ahmed, L., Joshua, A. M., Moore, M. J., Oza, A. M., Amir, E., McPherson, J. D., Zhang, T., Sukhai, M. A., Stockley, T. L., Kamel-Reid, S., Siu, L. L. & 1 others, Hansen, A. R., Jan 1 2018, In : JCO Precision Oncology. 2

Research output: Contribution to journalArticle

Fine Needle Biopsy
Mutation
Large-Core Needle Biopsy
Neoplasms
DNA
94 Citations (Scopus)

Prediction of acute myeloid leukaemia risk in healthy individuals

Abelson, S., Collord, G., Ng, S. W. K., Weissbrod, O., Mendelson Cohen, N., Niemeyer, E., Barda, N., Zuzarte, P. C., Heisler, L., Sundaravadanam, Y., Luben, R., Hayat, S., Wang, T. T., Zhao, Z., Cirlan, I., Pugh, T. J., Soave, D., Ng, K., Latimer, C., Hardy, C. & 55 others, Raine, K., Jones, D., Hoult, D., Britten, A., Mcpherson, J. D., Johansson, M., Mbabaali, F., Eagles, J., Miller, J. K., Pasternack, D., Timms, L., Krzyzanowski, P., Awadalla, P., Costa, R., Segal, E., Bratman, S. V., Beer, P., Behjati, S., Martincorena, I., Wang, J. C. Y., Bowles, K. M., Quirós, J. R., Karakatsani, A., La Vecchia, C., Trichopoulou, A., Salamanca-Fernández, E., Huerta, J. M., Barricarte, A., Travis, R. C., Tumino, R., Masala, G., Boeing, H., Panico, S., Kaaks, R., Krämer, A., Sieri, S., Riboli, E., Vineis, P., Foll, M., McKay, J., Polidoro, S., Sala, N., Khaw, K. T., Vermeulen, R., Campbell, P. J., Papaemmanuil, E., Minden, M. D., Tanay, A., Balicer, R. D., Wareham, N. J., Gerstung, M., Dick, J. E., Brennan, P., Vassiliou, G. S. & Shlush, L. I., Jul 19 2018, In : Nature. 559, 7714, p. 400-404 5 p.

Research output: Contribution to journalArticle

Acute Myeloid Leukemia
Hematopoietic Stem Cells
Hematopoiesis
Mutation
High-Throughput Nucleotide Sequencing
2017
71 Citations (Scopus)

Association of distinct mutational signatures with correlates of increased immune activity in pancreatic ductal adenocarcinoma

Connor, A. A., Denroche, R. E., Jang, G. H., Timms, L., Kalimuthu, S. N., Selander, I., McPherson, T., Wilson, G. W., Chan-Seng-Yue, M. A., Borozan, I., Ferretti, V., Grant, R. C., Lungu, I. M., Costello, E., Greenhalf, W., Palmer, D., Ghaneh, P., Neoptolemos, J. P., Buchler, M., Petersen, G. & 20 others, Thayer, S., Hollingsworth, M. A., Sherker, A., Durocher, D., Dhani, N., Hedley, D., Serra, S., Pollett, A., Roehrl, M. H. A., Bavi, P., Bartlett, J. M. S., Cleary, S., Wilson, J. M., Alexandrov, L. B., Moore, M., Wouters, B. G., Mcpherson, J. D., Notta, F., Stein, L. D. & Gallinger, S., Jun 1 2017, In : JAMA oncology. 3, 6, p. 774-783 10 p.

Research output: Contribution to journalArticle

Adenocarcinoma
DNA Mismatch Repair
Genome
Immunity
Carcinogenesis
159 Citations (Scopus)

Genomic hallmarks of localized, non-indolent prostate cancer

Fraser, M., Sabelnykova, V. Y., Yamaguchi, T. N., Heisler, L. E., Livingstone, J., Huang, V., Shiah, Y. J., Yousif, F., Lin, X., Masella, A. P., Fox, N. S., Xie, M., Prokopec, S. D., Berlin, A., Lalonde, E., Ahmed, M., Trudel, D., Luo, X., Beck, T. A., Meng, A. & 50 others, Zhang, J., D'Costa, A., Denroche, R. E., Kong, H., Espiritu, S. M. G., Chua, M. L. K., Wong, A., Chong, T., Sam, M., Johns, J., Timms, L., Buchner, N. B., Orain, M., Picard, V., Hovington, H., Murison, A., Kron, K., Harding, N. J., P'ng, C., Houlahan, K. E., Chu, K. C., Lo, B., Nguyen, F., Li, C. H., Sun, R. X., de Borja, R., Cooper, C. I., Hopkins, J. F., Govind, S. K., Fung, C., Waggott, D., Green, J., Haider, S., Chan-Seng-Yue, M. A., Jung, E., Wang, Z., Bergeron, A., Pra, A. D., Lacombe, L., Collins, C. C., Sahinalp, C., Lupien, M., Fleshner, N. E., He, H. H., Fradet, Y., Tetu, B., van der Kwast, T., Mcpherson, J. D., Bristow, R. G. & Boutros, P. C., Jan 19 2017, In : Nature. 541, 7637, p. 359-364 6 p.

Research output: Contribution to journalArticle

Prostatic Neoplasms
Prostate
Neoplasms
Exome
DNA Methylation
73 Citations (Scopus)

Germline BRCA2 mutations drive prostate cancers with distinct evolutionary trajectories

Taylor, R. A., Fraser, M., Livingstone, J., Espiritu, S. M. G., Thorne, H., Huang, V., Lo, W., Shiah, Y. J., Yamaguchi, T. N., Sliwinski, A., Horsburgh, S., Meng, A., Heisler, L. E., Yu, N., Yousif, F., Papargiris, M., Lawrence, M. G., Timms, L., Murphy, D. G., Frydenberg, M. & 8 others, Hopkins, J. F., Bolton, D., Clouston, D., Mcpherson, J. D., Van Der Kwast, T., Boutros, P. C., Risbridger, G. P. & Bristow, R. G., Jan 9 2017, In : Nature Communications. 8, 13671.

Research output: Contribution to journalArticle

Germ-Line Mutation
mutations
Prostatic Neoplasms
cancer
Trajectories
11 Citations (Scopus)

Interrogation of Functional Cell-Surface Markers Identifies CD151 Dependency in High-Grade Serous Ovarian Cancer

Medrano, M., Communal, L., Brown, K. R., Iwanicki, M., Normand, J., Paterson, J., Sircoulomb, F., Krzyzanowski, P., Novak, M., Doodnauth, S. A., Saiz, F. S., Cullis, J., Al-awar, R., Neel, B. G., Mcpherson, J. D., Drapkin, R., Ailles, L., Mes-Massons, A. M. & Rottapel, R., Mar 7 2017, In : Cell Reports. 18, 10, p. 2343-2358 16 p.

Research output: Contribution to journalArticle

Ovarian Neoplasms
Tumors
Genes
Cells
Aberrations
17 Citations (Scopus)

ISOWN: Accurate somatic mutation identification in the absence of normal tissue controls

Kalatskaya, I., Trinh, Q. M., Spears, M., Mcpherson, J. D., Bartlett, J. M. S. & Stein, L., Jun 29 2017, In : Genome Medicine. 9, 1, 59.

Research output: Contribution to journalArticle

Mutation
Neoplasms
Genome
Exome
Licensure
43 Citations (Scopus)

Microscopy with ultraviolet surface excitation for rapid slide-free histology

Fereidouni, F., Harmany, Z. T., Tian, M., Todd, A., Kintner, J. A., Mcpherson, J. D., Borowsky, A. D., Bishop, J. W., Lechpammer, M., Demos, S. G. & Levenson, R. M., Dec 1 2017, In : Nature Biomedical Engineering. 1, 12, p. 957-966 10 p.

Research output: Contribution to journalArticle

Ultraviolet Microscopy
Histology
Microscopic examination
Tissue
RNA Sequence Analysis
17 Citations (Scopus)

Mitochondrial mutations drive prostate cancer aggression

Hopkins, J. F., Sabelnykova, V. Y., Weischenfeldt, J., Simon, R., Aguiar, J. A., Alkallas, R., Heisler, L. E., Zhang, J., Watson, J. D., Chua, M. L. K., Fraser, M., Favero, F., Lawerenz, C., Plass, C., Sauter, G., Mcpherson, J. D., Van Der Kwast, T., Korbel, J., Schlomm, T., Bristow, R. G. & 1 others, Boutros, P. C., Dec 1 2017, In : Nature Communications. 8, 1, 656.

Research output: Contribution to journalArticle

mutations
Aggression
Prostatic Neoplasms
Genes
cancer
22 Citations (Scopus)

Molecular heterogeneity of non-small cell lung carcinoma patient-derived xenografts closely reflect their primary tumors

Wang, D., Pham, N. A., Tong, J., Sakashita, S., Allo, G., Kim, L., Yanagawa, N., Raghavan, V., Wei, Y., To, C., Trinh, Q. M., Starmans, M. H. W., Chan-Seng-Yue, M. A., Chadwick, D., Li, L., Zhu, C. Q., Liu, N., Li, M., Lee, S., Ignatchenko, V. & 13 others, Strumpf, D., Taylor, P., Moghal, N., Liu, G., Boutros, P. C., Kislinger, T., Pintilie, M., Jurisica, I., Shepherd, F. A., Mcpherson, J. D., Muthuswamy, L., Moran, M. F. & Tsao, M. S., Feb 1 2017, In : International Journal of Cancer. 140, 3, p. 662-673 12 p.

Research output: Contribution to journalArticle

Heterografts
Non-Small Cell Lung Carcinoma
Neoplasms
Lung Neoplasms
Inbred NOD Mouse
21 Citations (Scopus)

Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma

Feigin, M. E., Garvin, T., Bailey, P., Waddell, N., Chang, D. K., Kelley, D. R., Shuai, S., Gallinger, S., Mcpherson, J. D., Grimmond, S. M., Khurana, E., Stein, L. D., Biankin, A. V., Schatz, M. C. & Tuveson, D. A., Jun 1 2017, In : Nature Genetics. 49, 6, p. 825-833 9 p.

Research output: Contribution to journalArticle

Adenocarcinoma
Mutation
Homeobox Genes
Nucleic Acid Regulatory Sequences
Protein Binding

TMPRSS2-ERG fusions unexpectedly identified in men initially diagnosed with nonprostatic malignancies

Lara, P. N., Heilmann, A. M., Elvin, J. A., Parikh, M., White, R. D. V., Gandour-Edwards, R., Evans, C. P., Pan, C. X., Schrock, A. B., Erlich, R., Ross, J. S., Stephens, P. J., McPherson, J., Miller, V. A. & Ali, S. M., Jan 1 2017, In : JCO Precision Oncology. 2017, 1, p. 1-6 6 p.

Research output: Contribution to journalArticle

Prostatic Neoplasms
Neoplasms
Squamous Cell Carcinoma
Adenocarcinoma
Gene Fusion
108 Citations (Scopus)

Tracing the origins of relapse in acute myeloid leukaemia to stem cells

Shlush, L. I., Mitchell, A., Heisler, L., Abelson, S., Ng, S. W. K., Trotman-Grant, A., Medeiros, J. J. F., Rao-Bhatia, A., Jaciw-Zurakowsky, I., Marke, R., McLeod, J. L., Doedens, M., Bader, G., Voisin, V., Xu, C., Mcpherson, J. D., Hudson, T. J., Wang, J. C. Y., Minden, M. D. & Dick, J. E., Jul 6 2017, In : Nature. 547, 7661, p. 104-108 5 p.

Research output: Contribution to journalArticle

Acute Myeloid Leukemia
Stem Cells
Recurrence
Leukemia
Hematopoietic Stem Cells
2016
167 Citations (Scopus)

A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns

Notta, F., Chan-Seng-Yue, M., Lemire, M., Li, Y., Wilson, G. W., Connor, A. A., Denroche, R. E., Liang, S. B., Brown, A. M. K., Kim, J. C., Wang, T., Simpson, J. T., Beck, T., Borgida, A., Buchner, N., Chadwick, D., Hafezi-Bakhtiari, S., Dick, J. E., Heisler, L., Hollingsworth, M. A. & 26 others, Ibrahimov, E., Jang, G. H., Johns, J., Jorgensen, L. G. T., Law, C., Ludkovski, O., Lungu, I., Ng, K., Pasternack, D., Petersen, G. M., Shlush, L. I., Timms, L., Tsao, M. S., Wilson, J. M., Yung, C. K., Zogopoulos, G., Bartlett, J. M. S., Alexandrov, L. B., Real, F. X., Cleary, S. P., Roehrl, M. H., Mcpherson, J. D., Stein, L. D., Hudson, T. J., Campbell, P. J. & Gallinger, S., 2016, In : Nature. 538, 7625, p. 378-382 5 p.

Research output: Contribution to journalArticle

Pancreatic Neoplasms
Neoplasms
Carcinogenesis
DNA Copy Number Variations
Informatics
19 Citations (Scopus)

Candidate DNA repair susceptibility genes identified by exome sequencing in high-risk pancreatic cancer

Smith, A. L., Alirezaie, N., Connor, A., Chan-Seng-Yue, M., Grant, R., Selander, I., Bascuñana, C., Borgida, A., Hall, A., Whelan, T., Holter, S., McPherson, T., Cleary, S., Petersen, G. M., Omeroglu, A., Saloustros, E., Mcpherson, J. D., Stein, L. D., Foulkes, W. D., Majewski, J. & 2 others, Gallinger, S. & Zogopoulos, G., Jan 28 2016, In : Cancer Letters. 370, 2, p. 302-312 11 p.

Research output: Contribution to journalArticle

Exome
Pancreatic Neoplasms
DNA Repair
Adenocarcinoma
Genes
250 Citations (Scopus)

Distinct routes of lineage development reshape the human blood hierarchy across ontogeny

Notta, F., Zandi, S., Takayama, N., Dobson, S., Gan, O. I., Wilson, G., Kaufmann, K. B., McLeod, J., Laurenti, E., Dunant, C. F., Mcpherson, J. D., Stein, L. D., Dror, Y. & Dick, J. E., Jan 8 2016, In : Science. 351, 6269, aab2116.

Research output: Contribution to journalArticle

Human Development
Hematopoiesis
Multipotent Stem Cells
Cell Lineage
Blood Cells
21 Citations (Scopus)

Fine mapping of chromosome 5p15.33 based on a targeted deep sequencing and high density genotyping identifies novel lung cancer susceptibility loci

Kachuri, L., Amos, C. I., McKay, J. D., Johansson, M., Vineis, P., Bueno-de-Mesquita, H. B., Boutron-Ruault, M. C., Johansson, M., Quirós, J. R., Sieri, S., Travis, R. C., Weiderpass, E., Le Marchand, L., Henderson, B. E., Wilkens, L., Goodman, G. E., Chen, C., Doherty, J. A., Christiani, D. C., Wei, Y. & 24 others, Su, L., Tworoger, S., Zhang, X., Kraft, P., Zaridze, D., Field, J. K., Marcus, M. W., Davies, M. P. A., Hyde, R., Caporaso, N. E., Landi, M. T., Severi, G., Giles, G. G., Liu, G., McLaughlin, J. R., Li, Y., Xiao, X., Fehringer, G., Zong, X., Denroche, R. E., Zuzarte, P. C., Mcpherson, J. D., Brennan, P. & Hung, R. J., Jan 1 2016, In : Carcinogenesis. 37, 1, p. 96-105 10 p.

Research output: Contribution to journalArticle

High-Throughput Nucleotide Sequencing
Chromosome Mapping
Telomere
Lung Neoplasms
Single Nucleotide Polymorphism
52 Citations (Scopus)

Truncating Erythropoietin Receptor Rearrangements in Acute Lymphoblastic Leukemia

Iacobucci, I., Li, Y., Roberts, K. G., Dobson, S. M., Kim, J. C., Payne-Turner, D., Harvey, R. C., Valentine, M., McCastlain, K., Easton, J., Yergeau, D., Janke, L. J., Shao, Y., Chen, I. M. L., Rusch, M., Zandi, S., Kornblau, S. M., Konopleva, M., Jabbour, E., Paietta, E. M. & 17 others, Rowe, J. M., Pui, C. H., Gastier-Foster, J., Gu, Z., Reshmi, S., Loh, M. L., Racevskis, J., Tallman, M. S., Wiernik, P. H., Litzow, M. R., Willman, C. L., Mcpherson, J. D., Downing, J. R., Zhang, J., Dick, J. E., Hunger, S. P. & Mullighan, C. G., Feb 8 2016, In : Cancer Cell. 29, 2, p. 186-200 15 p.

Research output: Contribution to journalArticle

Erythropoietin Receptors
Precursor Cell Lymphoblastic Leukemia-Lymphoma
Philadelphia Chromosome
Erythropoietin
B-Lymphoid Precursor Cells
2015
6 Citations (Scopus)

A cancer cell-line titration series for evaluating somatic classification

Denroche, R. E., Mullen, L., Timms, L., Beck, T., Yung, C. K., Stein, L., Mcpherson, J. D. & Brown, A. M. K., Dec 26 2015, In : BMC Research Notes. 8, 1, 1803.

Research output: Contribution to journalArticle

Titration
Tumors
Cells
Cell Line
Pipelines
124 Citations (Scopus)

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing

Alioto, T. S., Buchhalter, I., Derdak, S., Hutter, B., Eldridge, M. D., Hovig, E., Heisler, L. E., Beck, T. A., Simpson, J. T., Tonon, L., Sertier, A. S., Patch, A. M., Jäger, N., Ginsbach, P., Drews, R., Paramasivam, N., Kabbe, R., Chotewutmontri, S., Diessl, N., Previti, C. & 63 others, Schmidt, S., Brors, B., Feuerbach, L., Heinold, M., Gröbner, S., Korshunov, A., Tarpey, P. S., Butler, A. P., Hinton, J., Jones, D., Menzies, A., Raine, K., Shepherd, R., Stebbings, L., Teague, J. W., Ribeca, P., Giner, F. C., Beltran, S., Raineri, E., Dabad, M., Heath, S. C., Gut, M., Denroche, R. E., Harding, N. J., Yamaguchi, T. N., Fujimoto, A., Nakagawa, H., Quesada, V., Valdés-Mas, R., Nakken, S., Vodák, D., Bower, L., Lynch, A. G., Anderson, C. L., Waddell, N., Pearson, J. V., Grimmond, S. M., Peto, M., Spellman, P., He, M., Kandoth, C., Lee, S., Zhang, J., Létourneau, L., Ma, S., Seth, S., Torrents, D., Xi, L., Wheeler, D. A., López-Otín, C., Campo, E., Campbell, P. J., Boutros, P. C., Puente, X. S., Gerhard, D. S., Pfister, S. M., Mcpherson, J. D., Hudson, T. J., Schlesner, M., Lichter, P., Eils, R., Jones, D. T. W. & Gut, I. G., Dec 9 2015, In : Nature Communications. 6, 10001.

Research output: Contribution to journalArticle

sequencing
genome
mutations
Genes
cancer
35 Citations (Scopus)

GLI2 inhibition abrogates human leukemia stem cell dormancy

Sadarangani, A., Pineda, G., Lennon, K. M., Chun, H. J., Shih, A., Schairer, A. E., Court, A. C., Goff, D. J., Prashad, S. L., Geron, I., Wall, R., Mcpherson, J. D., Moore, R. A., Pu, M., Bao, L., Jackson-Fisher, A., Munchhof, M., VanArsdale, T., Reya, T., Morris, S. R. & 6 others, Minden, M. D., Messer, K., Mikkola, H. K. A., Marra, M. A., Hudson, T. J. & Jamieson, C. H. M., Dec 12 2015, In : Journal of Translational Medicine. 13, 1, p. 1 1 p., 98.

Research output: Contribution to journalArticle

Stem cells
Leukemia
Stem Cells
Blast Crisis
Cell Cycle
42 Citations (Scopus)

Optimization of miRNA-seq data preprocessing

Tam, S., Tsao, M. S. & Mcpherson, J. D., Feb 6 2015, In : Briefings in Bioinformatics. 16, 6, p. 950-963 14 p., bbv019.

Research output: Contribution to journalArticle

RNA
MicroRNAs
Biomarkers
Linear regression
Dilution
208 Citations (Scopus)

Spatial genomic heterogeneity within localized, multifocal prostate cancer

Boutros, P. C., Fraser, M., Harding, N. J., De Borja, R., Trudel, D., Lalonde, E., Meng, A., Hennings-Yeomans, P. H., McPherson, A., Sabelnykova, V. Y., Zia, A., Fox, N. S., Livingstone, J., Shiah, Y. J., Wang, J., Beck, T. A., Have, C. L., Chong, T., Sam, M., Johns, J. & 45 others, Timms, L., Buchner, N., Wong, A., Watson, J. D., Simmons, T. T., P'ng, C., Zafarana, G., Nguyen, F., Luo, X., Chu, K. C., Prokopec, S. D., Sykes, J., Pra, A. D., Berlin, A., Brown, A., Chan-Seng-Yue, M. A., Yousif, F., Denroche, R. E., Chong, L. C., Chen, G. M., Jung, E., Fung, C., Starmans, M. H. W., Chen, H., Govind, S. K., Hawley, J., D'Costa, A., Pintilie, M., Waggott, D., Hach, F., Lambin, P., Muthuswamy, L. B., Cooper, C., Eeles, R., Neal, D., Tetu, B., Sahinalp, C., Stein, L. D., Fleshner, N., Shah, S. P., Collins, C. C., Hudson, T. J., Mcpherson, J. D., Van Der Kwast, T. & Bristow, R. G., Jun 26 2015, In : Nature Genetics. 47, 7, p. 736-745 10 p.

Research output: Contribution to journalArticle

Prostatic Neoplasms
Neoplasms
Spatial Analysis
Neoplasm Grading
Genomics
2014
17 Citations (Scopus)

A defining decade in DNA sequencing

Mcpherson, J. D., Jan 1 2014, In : Nature Methods. 11, 10, p. 1003-1005 3 p.

Research output: Contribution to journalArticle

Animals
Genes
DNA
Genomics
39 Citations (Scopus)

Antioxidant supplementation reduces genomic aberrations in human induced pluripotent stem cells

Ji, J., Sharma, V., Qi, S., Guarch, M. E., Zhao, P., Luo, Z., Fan, W., Wang, Y., Mbabaali, F., Neculai, D., Esteban, M. A., Mcpherson, J. D. & Batada, N. N., Jan 14 2014, In : Stem Cell Reports. 2, 1, p. 44-51 8 p.

Research output: Contribution to journalArticle

Induced Pluripotent Stem Cells
Stem cells
Aberrations
Antioxidants
Genomic Instability
8 Citations (Scopus)

A two-dimensional pooling strategy for rare variant detection on next-generation sequencing platforms

Zuzarte, P. C., Denroche, R. E., Fehringer, G., Katzov-Eckert, H., Hung, R. J. & Mcpherson, J. D., Apr 11 2014, In : PLoS One. 9, 4, e93455.

Research output: Contribution to journalArticle

DNA
sampling
Genome-Wide Association Study
lung neoplasms
DNA Sequence Analysis
40 Citations (Scopus)

Genomic support for a moa-tinamou clade and adaptive morphological convergence in flightless ratites

Baker, A. J., Haddrath, O., Mcpherson, J. D. & Cloutier, A., 2014, In : Molecular Biology and Evolution. 31, 7, p. 1686-1696 11 p.

Research output: Contribution to journalArticle

Palaeognathae
ratites
topology
genomics
phylogenetics
36 Citations (Scopus)

Genomic testing in cancer: Patient knowledge, attitudes, and expectations

Blanchette, P. S., Spreafico, A., Miller, F. A., Chan, K., Bytautas, J., Kang, S., Bedard, P. L., Eisen, A., Potanina, L., Holland, J., Kamel-Reid, S., Mcpherson, J. D., Razak, A. R. & Siu, L. L., 2014, In : Cancer. 120, 19, p. 3066-3073 8 p.

Research output: Contribution to journalArticle

Neoplasms
Clinical Trials, Phase I
Aptitude
Germ-Line Mutation
Neoplasm Genes
111 Citations (Scopus)

Hotspot activating PRKD1 somatic mutations in polymorphous low-grade adenocarcinomas of the salivary glands

Weinreb, I., Piscuoglio, S., Martelotto, L. G., Waggott, D., Ng, C. K. Y., Perez-Ordonez, B., Harding, N. J., Alfaro, J., Chu, K. C., Viale, A., Fusco, N., Da Cruz Paula, A., Marchio, C., Sakr, R. A., Lim, R., Thompson, L. D. R., Chiosea, S. I., Seethala, R. R., Skalova, A., Stelow, E. B. & 22 others, Fonseca, I., Assaad, A., How, C., Wang, J., De Borja, R., Chan-Seng-Yue, M., Howlett, C. J., Nichols, A. C., Wen, Y. H., Katabi, N., Buchner, N., Mullen, L., Kislinger, T., Wouters, B. G., Liu, F. F., Norton, L., Mcpherson, J. D., Rubin, B. P., Clarke, B. A., Weigelt, B., Boutros, P. C. & Reis-Filho, J. S., Nov 5 2014, In : Nature Genetics. 46, 11, p. 1166-1169 4 p.

Research output: Contribution to journalArticle

Salivary Glands
Adenocarcinoma
Minor Salivary Glands
Mutation
Glandular and Epithelial Neoplasms
20 Citations (Scopus)

Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants

Peltekova, V. D., Lemire, M., Qazi, A. M., Zaidi, S. H. E., Trinh, Q. M., Bielecki, R., Rogers, M., Hodgson, L., Wang, M., D'Souza, D. J. A., Zandi, S., Chong, T., Kwan, J. Y. Y., Kozak, K., De Borja, R., Timms, L., Rangrej, J., Volar, M., Chan-Seng-Yue, M., Beck, T. & 12 others, Ash, C., Lee, S., Wang, J., Boutros, P. C., Stein, L. D., Dick, J. E., Gryfe, R., Mcpherson, J. D., Zanke, B. W., Pollett, A., Gallinger, S. & Hudson, T. J., May 15 2014, In : International Journal of Cancer. 134, 10, p. 2330-2341 12 p.

Research output: Contribution to journalArticle

Colorectal Neoplasms
Colon
Mucous Membrane
Genes
Tissue Array Analysis
717 Citations (Scopus)

Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia

Shlush, L. I., Zandi, S., Mitchell, A., Chen, W. C., Brandwein, J. M., Gupta, V., Kennedy, J. A., Schimmer, A. D., Schuh, A. C., Yee, K. W., McLeod, J. L., Doedens, M., Medeiros, J. J. F., Marke, R., Kim, H. J., Lee, K., Mcpherson, J. D., Hudson, T. J., Brown, A. M. K., Trinh, Q. M. & 4 others, Stein, L. D., Minden, M. D., Wang, J. C. Y. & Dick, J. E., 2014, In : Nature. 506, 7488, p. 328-333 6 p.

Research output: Contribution to journalArticle

Hematopoietic Stem Cells
Acute Myeloid Leukemia
Leukemia
Mutation
Heterografts
87 Citations (Scopus)

Next-generation sequencing identifies rare variants associated with Noonan syndrome

Chen, P. C., Yin, J., Yu, H. W., Yuan, T., Fernandez, M., Yung, C. K., Trinh, Q. M., Peltekova, V. D., Reid, J. G., Tworog-Dube, E., Morgan, M. B., Muzny, D. M., Stein, L., Mcpherson, J. D., Roberts, A. E., Gibbs, R. A., Neel, B. G. & Kucherlapati, R., Aug 5 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 31, p. 11473-11478 6 p.

Research output: Contribution to journalArticle

Noonan Syndrome
Nonsense Codon
Alleles
Coffin-Lowry Syndrome
MAP Kinase Kinase 1
74 Citations (Scopus)

Robust global microRNA expression profiling using next-generation sequencing technologies

Tam, S., De Borja, R., Tsao, M. S. & Mcpherson, J. D., Mar 2014, In : Laboratory Investigation. 94, 3, p. 350-358 9 p.

Research output: Contribution to journalArticle

MicroRNAs
Technology
Paraffin
Formaldehyde
Real-Time Polymerase Chain Reaction
6 Citations (Scopus)

SeqControl: Process control for DNA sequencing

Chong, L. C., Albuquerque, M. A., Harding, N. J., Caloian, C., Chan-Seng-Yue, M., De Borja, R., Fraser, M., Denroche, R. E., Beck, T. A., Van Der Kwast, T., Bristow, R. G., Mcpherson, J. D. & Boutros, P. C., Jan 1 2014, In : Nature Methods. 11, 10, p. 1071-1075 5 p.

Research output: Contribution to journalArticle

DNA Sequence Analysis
Area Under Curve
Process control
Throughput
DNA
34 Citations (Scopus)

ShatterProof: Operational detection and quantification of chromothripsis

Govind, S. K., Zia, A., Hennings-Yeomans, P. H., Watson, J. D., Fraser, M., Anghel, C., Wyatt, A. W., van der Kwast, T., Collins, C. C., Mcpherson, J. D., Bristow, R. G. & Boutros, P. C., Mar 19 2014, In : BMC Bioinformatics. 15, 1, 78.

Research output: Contribution to journalArticle

Statistical tests
Quantification
Bone
Pipelines
Throughput
11 Citations (Scopus)

Use of sequenom sample ID plus® SNP genotyping in identification of FFPE tumor samples

Miller, J. K., Buchner, N., Timms, L., Tam, S., Luo, X., Brown, A. M. K., Pasternack, D., Bristow, R. G., Fraser, M., Boutros, P. C. & Mcpherson, J. D., Feb 13 2014, In : PLoS One. 9, 2, e88163.

Research output: Contribution to journalArticle

formalin
Paraffin
Microsatellite Repeats
alkanes
Formaldehyde
9 Citations (Scopus)

WaveCNV: Allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing

Holt, C., Losic, B., Pai, D., Zhao, Z., Trinh, Q., Syam, S., Arshadi, N., Jang, G. H., Ali, J., Beck, T., Mcpherson, J. D. & Muthuswamy, L. B., Mar 2014, In : Bioinformatics. 30, 6, p. 768-774 7 p.

Research output: Contribution to journalArticle

Heterografts
Sequencing
Tumors
Tumor
Genes
2013
17 Citations (Scopus)

Exome sequencing identifies nonsegregating nonsense ATM and PALB2 variants in familial pancreatic cancer

Grant, R. C., Al-Sukhni, W., Borgida, A. E., Holter, S., Kanji, Z. S., McPherson, T., Whelan, E., Serra, S., Trinh, Q. M., Peltekova, V., Stein, L. D., Mcpherson, J. D. & Gallinger, S., 2013, In : Human Genomics. 7, 1, 11.

Research output: Contribution to journalArticle

Exome
Pancreatic Neoplasms
Alleles
Neoplasms
70 Citations (Scopus)

Feasibility of real time next generation sequencing of cancer genes linked to drug response: Results from a clinical trial

Tran, B., Brown, A. M. K., Bedard, P. L., Winquist, E., Goss, G. D., Hotte, S. J., Welch, S. A., Hirte, H. W., Zhang, T., Stein, L. D., Ferretti, V., Watt, S., Jiao, W., Ng, K., Ghai, S., Shaw, P., Petrocelli, T., Hudson, T. J., Neel, B. G., Onetto, N. & 4 others, Siu, L. L., Mcpherson, J. D., Kamel-Reid, S. & Dancey, J. E., Apr 1 2013, In : International Journal of Cancer. 132, 7, p. 1547-1555 9 p.

Research output: Contribution to journalArticle

Neoplasm Genes
Clinical Trials
Technology
Pharmaceutical Preparations
Mutation
405 Citations (Scopus)

Variable clonal repopulation dynamics influence chemotherapy response in colorectal cancer

Kreso, A., O'Brien, C. A., Van Galen, P., Gan, O. I., Notta, F., Brown, A. M. K., Ng, K., Jing, M., Wienholds, E., Dunant, C., Pollett, A., Gallinger, S., Mcpherson, J. D., Mullighan, C. G., Shibata, D. & Dick, J. E., Feb 1 2013, In : Science. 339, 6119, p. 543-548 6 p.

Research output: Contribution to journalArticle

Colorectal Neoplasms
Clone Cells
Drug Therapy
Neoplasms
Serial Passage
2012
109 Citations (Scopus)

Elevated coding mutation rate during the reprogramming of human somatic cells into induced pluripotent stem cells

Ji, J., Ng, S., Sharma, V., Neculai, D., Hussein, S., Sam, M., Trinh, Q., Church, G. M., Mcpherson, J. D., Nagy, A. & Batada, N. N., Mar 2012, In : Stem Cells. 30, 3, p. 435-440 6 p.

Research output: Contribution to journalArticle

Induced Pluripotent Stem Cells
Mutation Rate
Mutation
Exome
Foreskin