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Items: 31

1.

Primary Biliary Cholangitis in British Columbia First Nations: Clinical features and discovery of novel genetic susceptibility loci.

Asuri S, McIntosh S, Taylor V, Rokeby A, Kelly J, Shumansky K, Field LL, Yoshida EM, Arbour L.

Liver Int. 2018 May;38(5):940-948. doi: 10.1111/liv.13686. Epub 2018 Jan 23.

PMID:
29297981
2.

Engineered in-vitro cell line mixtures and robust evaluation of computational methods for clonal decomposition and longitudinal dynamics in cancer.

Farahani H, de Souza CPE, Billings R, Yap D, Shumansky K, Wan A, Lai D, Mes-Masson AM, Aparicio S, P Shah S.

Sci Rep. 2017 Oct 18;7(1):13467. doi: 10.1038/s41598-017-13338-8.

3.

Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes.

Wang YK, Bashashati A, Anglesio MS, Cochrane DR, Grewal DS, Ha G, McPherson A, Horlings HM, Senz J, Prentice LM, Karnezis AN, Lai D, Aniba MR, Zhang AW, Shumansky K, Siu C, Wan A, McConechy MK, Li-Chang H, Tone A, Provencher D, de Ladurantaye M, Fleury H, Okamoto A, Yanagida S, Yanaihara N, Saito M, Mungall AJ, Moore R, Marra MA, Gilks CB, Mes-Masson AM, McAlpine JN, Aparicio S, Huntsman DG, Shah SP.

Nat Genet. 2017 Jun;49(6):856-865. doi: 10.1038/ng.3849. Epub 2017 Apr 24.

PMID:
28436987
4.

CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor.

Funnell T, Tasaki S, Oloumi A, Araki S, Kong E, Yap D, Nakayama Y, Hughes CS, Cheng SG, Tozaki H, Iwatani M, Sasaki S, Ohashi T, Miyazaki T, Morishita N, Morishita D, Ogasawara-Shimizu M, Ohori M, Nakao S, Karashima M, Sano M, Murai A, Nomura T, Uchiyama N, Kawamoto T, Hara R, Nakanishi O, Shumansky K, Rosner J, Wan A, McKinney S, Morin GB, Nakanishi A, Shah S, Toyoshiba H, Aparicio S.

Nat Commun. 2017 Feb 23;8(1):7. doi: 10.1038/s41467-016-0008-7.

5.

Histological Transformation and Progression in Follicular Lymphoma: A Clonal Evolution Study.

Kridel R, Chan FC, Mottok A, Boyle M, Farinha P, Tan K, Meissner B, Bashashati A, McPherson A, Roth A, Shumansky K, Yap D, Ben-Neriah S, Rosner J, Smith MA, Nielsen C, Giné E, Telenius A, Ennishi D, Mungall A, Moore R, Morin RD, Johnson NA, Sehn LH, Tousseyn T, Dogan A, Connors JM, Scott DW, Steidl C, Marra MA, Gascoyne RD, Shah SP.

PLoS Med. 2016 Dec 13;13(12):e1002197. doi: 10.1371/journal.pmed.1002197. eCollection 2016 Dec.

6.

Scavenging nucleic acid debris to combat autoimmunity and infectious disease.

Holl EK, Shumansky KL, Borst LB, Burnette AD, Sample CJ, Ramsburg EA, Sullenger BA.

Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9728-33. doi: 10.1073/pnas.1607011113. Epub 2016 Aug 15. Erratum in: Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):E6545.

7.

Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer.

McPherson A, Roth A, Laks E, Masud T, Bashashati A, Zhang AW, Ha G, Biele J, Yap D, Wan A, Prentice LM, Khattra J, Smith MA, Nielsen CB, Mullaly SC, Kalloger S, Karnezis A, Shumansky K, Siu C, Rosner J, Chan HL, Ho J, Melnyk N, Senz J, Yang W, Moore R, Mungall AJ, Marra MA, Bouchard-Côté A, Gilks CB, Huntsman DG, McAlpine JN, Aparicio S, Shah SP.

Nat Genet. 2016 Jul;48(7):758-67. doi: 10.1038/ng.3573. Epub 2016 May 16.

PMID:
27182968
8.

Divergent clonal selection dominates medulloblastoma at recurrence.

Morrissy AS, Garzia L, Shih DJ, Zuyderduyn S, Huang X, Skowron P, Remke M, Cavalli FM, Ramaswamy V, Lindsay PE, Jelveh S, Donovan LK, Wang X, Luu B, Zayne K, Li Y, Mayoh C, Thiessen N, Mercier E, Mungall KL, Ma Y, Tse K, Zeng T, Shumansky K, Roth AJ, Shah S, Farooq H, Kijima N, Holgado BL, Lee JJ, Matan-Lithwick S, Liu J, Mack SC, Manno A, Michealraj KA, Nor C, Peacock J, Qin L, Reimand J, Rolider A, Thompson YY, Wu X, Pugh T, Ally A, Bilenky M, Butterfield YS, Carlsen R, Cheng Y, Chuah E, Corbett RD, Dhalla N, He A, Lee D, Li HI, Long W, Mayo M, Plettner P, Qian JQ, Schein JE, Tam A, Wong T, Birol I, Zhao Y, Faria CC, Pimentel J, Nunes S, Shalaby T, Grotzer M, Pollack IF, Hamilton RL, Li XN, Bendel AE, Fults DW, Walter AW, Kumabe T, Tominaga T, Collins VP, Cho YJ, Hoffman C, Lyden D, Wisoff JH, Garvin JH Jr, Stearns DS, Massimi L, Schüller U, Sterba J, Zitterbart K, Puget S, Ayrault O, Dunn SE, Tirapelli DP, Carlotti CG, Wheeler H, Hallahan AR, Ingram W, MacDonald TJ, Olson JJ, Van Meir EG, Lee JY, Wang KC, Kim SK, Cho BK, Pietsch T, Fleischhack G, Tippelt S, Ra YS, Bailey S, Lindsey JC, Clifford SC, Eberhart CG, Cooper MK, Packer RJ, Massimino M, Garre ML, Bartels U, Tabori U, Hawkins CE, Dirks P, Bouffet E, Rutka JT, Wechsler-Reya RJ, Weiss WA, Collier LS, Dupuy AJ, Korshunov A, Jones DT, Kool M, Northcott PA, Pfister SM, Largaespada DA, Mungall AJ, Moore RA, Jabado N, Bader GD, Jones SJ, Malkin D, Marra MA, Taylor MD.

Nature. 2016 Jan 21;529(7586):351-7. doi: 10.1038/nature16478. Epub 2016 Jan 13.

9.

Associations of interleukin-1 gene cluster polymorphisms with C-reactive protein concentration and lung function decline in smoking-induced chronic obstructive pulmonary disease.

Wang Y, Shumansky K, Sin DD, Man SF, Akhabir L, Connett JE, Anthonisen NR, Paré PD, Sandford AJ, He JQ.

Int J Clin Exp Pathol. 2015 Oct 1;8(10):13125-35. eCollection 2015.

10.

Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer.

Murtaza M, Dawson SJ, Pogrebniak K, Rueda OM, Provenzano E, Grant J, Chin SF, Tsui DWY, Marass F, Gale D, Ali HR, Shah P, Contente-Cuomo T, Farahani H, Shumansky K, Kingsbury Z, Humphray S, Bentley D, Shah SP, Wallis M, Rosenfeld N, Caldas C.

Nat Commun. 2015 Nov 4;6:8760. doi: 10.1038/ncomms9760.

11.

The genomic landscape of epithelioid sarcoma cell lines and tumours.

Jamshidi F, Bashashati A, Shumansky K, Dickson B, Gokgoz N, Wunder JS, Andrulis IL, Lazar AJ, Shah SP, Huntsman DG, Nielsen TO.

J Pathol. 2016 Jan;238(1):63-73. doi: 10.1002/path.4636. Epub 2015 Oct 19.

PMID:
26365879
12.

Hereditary Diffuse Gastric Cancer Syndrome: CDH1 Mutations and Beyond.

Hansford S, Kaurah P, Li-Chang H, Woo M, Senz J, Pinheiro H, Schrader KA, Schaeffer DF, Shumansky K, Zogopoulos G, Santos TA, Claro I, Carvalho J, Nielsen C, Padilla S, Lum A, Talhouk A, Baker-Lange K, Richardson S, Lewis I, Lindor NM, Pennell E, MacMillan A, Fernandez B, Keller G, Lynch H, Shah SP, Guilford P, Gallinger S, Corso G, Roviello F, Caldas C, Oliveira C, Pharoah PD, Huntsman DG.

JAMA Oncol. 2015 Apr;1(1):23-32. doi: 10.1001/jamaoncol.2014.168. Erratum in: JAMA Oncol. 2015 Apr;1(1):110.

PMID:
26182300
13.

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution.

Eirew P, Steif A, Khattra J, Ha G, Yap D, Farahani H, Gelmon K, Chia S, Mar C, Wan A, Laks E, Biele J, Shumansky K, Rosner J, McPherson A, Nielsen C, Roth AJ, Lefebvre C, Bashashati A, de Souza C, Siu C, Aniba R, Brimhall J, Oloumi A, Osako T, Bruna A, Sandoval JL, Algara T, Greenwood W, Leung K, Cheng H, Xue H, Wang Y, Lin D, Mungall AJ, Moore R, Zhao Y, Lorette J, Nguyen L, Huntsman D, Eaves CJ, Hansen C, Marra MA, Caldas C, Shah SP, Aparicio S.

Nature. 2015 Feb 19;518(7539):422-6. doi: 10.1038/nature13952. Epub 2014 Nov 26.

14.

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data.

Ha G, Roth A, Khattra J, Ho J, Yap D, Prentice LM, Melnyk N, McPherson A, Bashashati A, Laks E, Biele J, Ding J, Le A, Rosner J, Shumansky K, Marra MA, Gilks CB, Huntsman DG, McAlpine JN, Aparicio S, Shah SP.

Genome Res. 2014 Nov;24(11):1881-93. doi: 10.1101/gr.180281.114. Epub 2014 Jul 24.

15.

Mutational context and diverse clonal development in early and late bladder cancer.

Nordentoft I, Lamy P, Birkenkamp-Demtröder K, Shumansky K, Vang S, Hornshøj H, Juul M, Villesen P, Hedegaard J, Roth A, Thorsen K, Høyer S, Borre M, Reinert T, Fristrup N, Dyrskjøt L, Shah S, Pedersen JS, Ørntoft TF.

Cell Rep. 2014 Jun 12;7(5):1649-1663. doi: 10.1016/j.celrep.2014.04.038. Epub 2014 May 15.

16.

Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4.

Ramos P, Karnezis AN, Craig DW, Sekulic A, Russell ML, Hendricks WP, Corneveaux JJ, Barrett MT, Shumansky K, Yang Y, Shah SP, Prentice LM, Marra MA, Kiefer J, Zismann VL, McEachron TA, Salhia B, Prat J, D'Angelo E, Clarke BA, Pressey JG, Farley JH, Anthony SP, Roden RB, Cunliffe HE, Huntsman DG, Trent JM.

Nat Genet. 2014 May;46(5):427-9. doi: 10.1038/ng.2928. Epub 2014 Mar 23.

17.

Correction: Type-Specific Cell Line Models for Type-Specific Ovarian Cancer Research.

Anglesio MS, Wiegand KC, Melnyk N, Chow C, Salamanca C, Prentice LM, Senz J, Yang W, Spillman MA, Cochrane DR, Shumansky K, Shah SP, Kalloger SE, Huntsman DG.

PLoS One. 2013 Sep 27;8(9). doi: 10.1371/annotation/ffcaf179-872f-470b-8bb6-f06d8ba6d03a. eCollection 2013.

18.

Type-specific cell line models for type-specific ovarian cancer research.

Anglesio MS, Wiegand KC, Melnyk N, Chow C, Salamanca C, Prentice LM, Senz J, Yang W, Spillman MA, Cochrane DR, Shumansky K, Shah SP, Kalloger SE, Huntsman DG.

PLoS One. 2013 Sep 4;8(9):e72162. doi: 10.1371/journal.pone.0072162. eCollection 2013. Erratum in: PLoS One. 2013;8(10). doi:10.1371/annotation/856f0890-9d85-4719-8e54-c27530ac94f4. PLoS One. 2013;8(9). doi:10.1371/annotation/ffcaf179-872f-470b-8bb6-f06d8ba6d03a.

19.

Nucleic acid scavenging polymers inhibit extracellular DNA-mediated innate immune activation without inhibiting anti-viral responses.

Holl EK, Shumansky KL, Pitoc G, Ramsburg E, Sullenger BA.

PLoS One. 2013 Jul 23;8(7):e69413. doi: 10.1371/journal.pone.0069413. Print 2013.

20.

Alveolar macrophage proteinase/antiproteinase expression in lung function and emphysema.

Ishii T, Abboud RT, Wallace AM, English JC, Coxson HO, Finley RJ, Shumansky K, Paré PD, Sandford AJ.

Eur Respir J. 2014 Jan;43(1):82-91. doi: 10.1183/09031936.00174612. Epub 2013 Jul 30.

21.

Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling.

Bashashati A, Ha G, Tone A, Ding J, Prentice LM, Roth A, Rosner J, Shumansky K, Kalloger S, Senz J, Yang W, McConechy M, Melnyk N, Anglesio M, Luk MT, Tse K, Zeng T, Moore R, Zhao Y, Marra MA, Gilks B, Yip S, Huntsman DG, McAlpine JN, Shah SP.

J Pathol. 2013 Sep;231(1):21-34. doi: 10.1002/path.4230.

22.

Dense-map genome scan for dyslexia supports loci at 4q13, 16p12, 17q22; suggests novel locus at 7q36.

Field LL, Shumansky K, Ryan J, Truong D, Swiergala E, Kaplan BJ.

Genes Brain Behav. 2013 Feb;12(1):56-69. doi: 10.1111/gbb.12003. Epub 2012 Dec 7.

23.

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer.

Ha G, Roth A, Lai D, Bashashati A, Ding J, Goya R, Giuliany R, Rosner J, Oloumi A, Shumansky K, Chin SF, Turashvili G, Hirst M, Caldas C, Marra MA, Aparicio S, Shah SP.

Genome Res. 2012 Oct;22(10):1995-2007. doi: 10.1101/gr.137570.112. Epub 2012 May 25.

24.

The clonal and mutational evolution spectrum of primary triple-negative breast cancers.

Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, Turashvili G, Ding J, Tse K, Haffari G, Bashashati A, Prentice LM, Khattra J, Burleigh A, Yap D, Bernard V, McPherson A, Shumansky K, Crisan A, Giuliany R, Heravi-Moussavi A, Rosner J, Lai D, Birol I, Varhol R, Tam A, Dhalla N, Zeng T, Ma K, Chan SK, Griffith M, Moradian A, Cheng SW, Morin GB, Watson P, Gelmon K, Chia S, Chin SF, Curtis C, Rueda OM, Pharoah PD, Damaraju S, Mackey J, Hoon K, Harkins T, Tadigotla V, Sigaroudinia M, Gascard P, Tlsty T, Costello JF, Meyer IM, Eaves CJ, Wasserman WW, Jones S, Huntsman D, Hirst M, Caldas C, Marra MA, Aparicio S.

Nature. 2012 Apr 4;486(7403):395-9. doi: 10.1038/nature10933.

25.

Effect of heme oxygenase-1 polymorphisms on lung function and gene expression.

Tanaka G, Aminuddin F, Akhabir L, He JQ, Shumansky K, Connett JE, Anthonisen NR, Abboud RT, Paré PD, Sandford AJ.

BMC Med Genet. 2011 Sep 8;12:117. doi: 10.1186/1471-2350-12-117.

26.

Cystic fibrosis modifier genes related to Pseudomonas aeruginosa infection.

Park JE, Yung R, Stefanowicz D, Shumansky K, Akhabir L, Durie PR, Corey M, Zielenski J, Dorfman R, Daley D, Sandford AJ.

Genes Immun. 2011 Jul;12(5):370-7. doi: 10.1038/gene.2011.5. Epub 2011 Jan 27.

PMID:
21270830
27.

Associations of IL6 polymorphisms with lung function decline and COPD.

He JQ, Foreman MG, Shumansky K, Zhang X, Akhabir L, Sin DD, Man SF, DeMeo DL, Litonjua AA, Silverman EK, Connett JE, Anthonisen NR, Wise RA, Paré PD, Sandford AJ.

Thorax. 2009 Aug;64(8):698-704. doi: 10.1136/thx.2008.111278. Epub 2009 Apr 8.

28.

Association of genetic variations in the CSF2 and CSF3 genes with lung function in smoking-induced COPD.

He JQ, Shumansky K, Connett JE, Anthonisen NR, Paré PD, Sandford AJ.

Eur Respir J. 2008 Jul;32(1):25-34. doi: 10.1183/09031936.00040307. Epub 2008 Mar 19.

29.

Genetic variation in H2AFX contributes to risk of non-Hodgkin lymphoma.

Novik KL, Spinelli JJ, Macarthur AC, Shumansky K, Sipahimalani P, Leach S, Lai A, Connors JM, Gascoyne RD, Gallagher RP, Brooks-Wilson AR.

Cancer Epidemiol Biomarkers Prev. 2007 Jun;16(6):1098-106.

30.

Polymorphisms of interleukin-10 and its receptor and lung function in COPD.

He JQ, Shumansky K, Zhang X, Connett JE, Anthonisen NR, Sandford AJ.

Eur Respir J. 2007 Jun;29(6):1120-6. Epub 2007 Mar 1.

31.

Analysis of multiple biomarkers shows that lymphoma-associated macrophage (LAM) content is an independent predictor of survival in follicular lymphoma (FL).

Farinha P, Masoudi H, Skinnider BF, Shumansky K, Spinelli JJ, Gill K, Klasa R, Voss N, Connors JM, Gascoyne RD.

Blood. 2005 Sep 15;106(6):2169-74. Epub 2005 Jun 2.

PMID:
15933054

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