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Lectures and Events

WBBA's Life Science Innovation NW Conference - Washington State Convention Center

July 11-22, 2012

Partners in Personal Oncology Poster Presentation and Abstract

Molecular Medicine Lecture Series - Foege Auditorium S-060* University of Washington

Each Wednesday in May, 2012 11:30am – 12:20pm* (see link for details)

Will Genomics Revolutionize Cancer Therapy? - The Fred Hutchinson/University of Washington Cancer Consortium Symposium

May 23rd, 2012, 9 am - 4:45 pm

Symposium speakers and presentations include:
-Dr. Henry Lynch, Creighton University School of Medicine "Hereditary Cancer Models in the Quest for Genomics Revolutionizing Cancer Therapy"
-Dr. Peter Nelson, Hutchinson Center "Exploiting Cancer Diversity to Deliver Appropriate Therapy"
-Dr. David Solit, Memorial Sloan-Kettering Cancer Center "Genetic Determinants of mTOR Dependence"
-Dr. Samuel Aparicio, University of British Columbia, BC Cancer Agency Research Centre "Clonal and Mutational Spectrum of Breast Cancers"
-Dr. Mary-Claire King, University of Washington "Next Generation Sequencing of Inherited Breast and Ovarian Cancer: Fulfilling a Promise of Personalized Genomic Medicine"
-Dr. Funmi Olopade, The University of Chicago "Making the Case for Data Integration on the Way to Precision Medicine"
-Dr. Timothy Ley, Washington University in St. Louis "The AML Genome"
-Dr. Jerald Radich, Hutchinson Center "The Genetics of Response and Progression in Myeloid Leukemia"
-Dr. Marshall Horwitz, UW (Leading symposium introduction)
Dr. Stephen Friend, president, co-founder and director of Sage Bionetworks (Leading panel discussion)

Registration is required. The symposium is free, but space is limited and registration, which includes lunch, is required. Register and access the agenda here.

Dr. Hartmut Juhl, MD: Standardized tissue collection: A prerequisite for individualization of cancer therapy - Partners in Personal Oncology and P4 Medicine Institute Seminar, November 7, 2011

Brief Event Description
This Seminar aims to introduce local efforts in the areas of personalized medicine and oncology, with a focus on standardizing tissue procurement for research and diagnostic purposes.
Target audience: Individuals and organizations with interests in various aspects of Personalized Health Care, tissue procurement, biobanking, and processing for clinical, diagnostic and research purposes.
This is the era of personalized medicine. In oncology, personalized medicine has the potential to be especially influential in patient treatment due to the complexity and heterogeneity of each form of cancer.
In this era of personalized approach, there is a recognized critical need for:
- Resources, developed and operated under established scientific, technical and ethical standards.
- High quality specimen collection with appropriate clinical annotations
Cancer research using human tumor tissue heavily depends on implementing state of the art procedures for tissue collection. This will be an important driver for the development of an effective and efficient individualized cancer therapy.

C. Anthony Blau, MD & Effie Liakopoulou, MD, PhD, FRCPath: Developing approaches to personalize cancer treatment - ISCRM Stem Cell Club Talk, September 27, 2011


Patient-Centered Educational Activities

Patients with cancer who are "beyond-standard-of-care" are encouraged to enter clinical trials, but often have no rational basis for prioritizing among available options.

We network with oncologists, scientists and research partners to help patients find appropriate clinical trials.

Determining which trial may be best for a patient often requires further testing of the patient's tumor.

We share what we learn through Cancer Commons and other open science initiatives. An example can be found here.

We are currently piloting these services with featured community partners such as Rainier Hematology-Oncology. We will also consider other requests via email.

This is a patient-centered educational activity. PiPO is currently a startup and cannot provide medical care or medical advice at present.


Publications Clinical Publications

Curtin, C. Study Finds Genetic Testing Does Not Lead to Increased Healthcare Use Genome Technology. 2012 July/August.

Lyon GJ. Personalized medicine: Bring clinical standards to human-genetics research Nature. 2012 February 16;482:300–301.

Blau CA. Can Intensive Longitudinal Monitoring of Individuals Advance Cancer Research? Oncologist. 2012 Apr 24.

Stanford JL, FitzGerald LM, McDonnell SK, Carlson EE, McIntosh LM, Deutsch K, Hood L, Ostrander EA, Schaid DJ. Dense genome-wide SNP linkage scan in 301 hereditary prostate cancer families identifies multiple regions with suggestive evidence for linkage. Hum Mol Genet. 2009 May 15;18(10):1839-48.

Cook G, Liakopoulou E, Pearce R, Cavet J, Morgan GJ, Kirkland K, Lee J, Davies FE, Hall R, Rahemtulla A, Russell N, Marks DI, on behalf of the British Society of Blood & Marrow Transplantation Clinical Trials Committee. Factors Influencing the Outcome of a Second Autologous Stem Cell Transplant (ASCT) in Relapsed Multiple Myeloma. Biol Blood Marrow Transplant. 2011 Nov;17(11):1638-45.

Craddock C, Nagra S, Peniket A, Brookes C, Buckley L, Nikolousis E, Duncan N, Tauro S, Yin J, Liakopoulou E, Kottaridis P, Snowden J, Milligan D, Cook G, Tholouli E, Littlewood T, Peggs K, Vyas P, Clark F, Cook M, MacKinnon S, Russell N. Factors predicting long-term survival after T-cell depleted reduced intensity allogeneic stem cell transplantation for acute myeloid leukemia. Haematologica. 2010 Jun;95(6):989-95.

Patel B, Kirkland KE, Szydlo R, Pearce RM, Clark RE, Craddock C, Liakopoulou E, Fielding AK, Mackinnon S, Olavarria E, Potter MN, Russell NH, Bronwen E. Shaw, Cook G, Anthony H. Goldstone, Marks DI. Favorable outcomes with alemtuzumab-conditioned unrelated donor stem cell transplantation in adults. Haematologica. 2009 Oct;94(10):1399-406.

Hood L, Friend SH. Predictive, personalized, preventive, participatory (P4) cancer medicine. Nat Rev Clin Oncol. 2011 Mar;8(3):184-7.

Auffray C, Charron D, Hood L. Predictive, preventive, personalized and participatory medicine - back to the future. Genome Med. 2010 Aug 26;2(8):57.

Profile - Lee Hood. Nat Biotechnol. 2011 Mar;29(3):191.

Robinson SP, Sureda A, Canals C, Russell N, Caballero D, Bacigalupo A, Iriondo A, Cook G, Pettitt A, Socie G, Bonifazi F, Bosi A, Michallet M, Liakopoulou E, Maertens J, Passweg J, Clarke F, Martino R, Schmitz N, on behalf of the Lymphoma Working Party of the EBMT. Reduced intensity conditioning allogeneic stem cell transplantation for Hodgkin's lymphoma: identification of prognostic factors predicting outcome. Haematologica. 2009 Feb;94(2):230-8.

Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Čufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, Goldbeter A, Hace N, Henney A, Hood L, Iyengar R, Jackson V, Kallioniemi O, Klingmüller U, Kolar P, Kolch W, Kyriakopoulou C, Laplace F, Lehrach H, Marcus F, Matrisian L, Nolan G, Pelkmans L, Potti A, Sander C, Seljak M, Singer D, Sorger P, Stunnenberg H, Superti-Furga G, Uhlen M, Vidal M, Weinstein J, Wigle D, Williams M, Wolkenhauer O, Zhivotovsky Zinovyev A, Zupan B. Report on EU-USA workshop - how systems biology can advance cancer research (27 October 2008). Mol Oncol. 2009 Feb;3(1):9-17.

Bousquet J, Anto JM, Sterk PJ, Adcock IM, Chung KF, Roca J, Agusti A, Brightling C, Cambon-Thomsen A, Cesario A, Abdelhak S, Antonarakis SE, Avignon A, Ballabio A, Baraldi E, Baranov A, Bieber T, Bockaert J, Brahmachari S, Brambilla C, Bringer J, Dauzat M, Ernberg I, Fabbri L, Froguel P, Galas D, Gojobori T, Hunter P, Jorgensen C, Kauffmann F, Kourilsky P, Kowalski ML, Lancet D, Le Pen C, Mallet J, Mayosi B, Mercier J, Metspalu A, Nadeau JH, Ninot G, Noble D, Öztürk M, Palkonen S, Préfaut C, Rabe K, Renard E, Roberts RG, Samolinski B, Schünemann HJ, Simon H-U, Soares MB, Superti-Furga G, Tegner J, Verjovski-Almeida S, Wellstead P, Wolkenhauer O, Wouters E, Balling R, Brookes AJ, Charron D, Pison C, Chen Z, Hood L, Auffray C. Systems medicine and integrated care to combat chronic noncommunicable diseases. Genome Med. 2011 Jul 6;3(7):43.

Shaw BE, Apperley JF, Russell NH, Craddock C, Liakopoulou E, Potter MN, Wynn R, Gibson B, Pearce RM, Kirkland K, Lee J, Madrigal JA, Cook G, Byrne JL. Unrelated donor peripheral blood stem cell transplants incorporating pre-transplant in-vivo Alemtuzumab are not associated with any increased risk of significant acute or chronic graft-versus-host disease. Br J Haematol. 2011 Mar 8. doi: 10.1111/j.1365-2141.2011.08615.x.

Cordonnier C, Rovira M, Maertens J, Olavarria E, Faucher C, Bilger K, Pigneux A, Cornely OA, Ullmann AJ, Bofarull RM, de la Cámara R, Weisser M, Liakopoulou E, Abecasis M, Heussel CP, Pineau M, Ljungman P, Einsele H, on behalf of the Voriconazole for Secondary Prophylaxis of Invasive Fungal Infections in Patients With Allogeneic Stem Cell Transplants (VOSIFI) study group and the Infectious Diseases Working Party of the European Group for Blood and Marrow Transplantation (EBMT). Voriconazole for secondary prophylaxis of invasive fungal infections in allogeneic stem cell transplant recipients - results of the VOSIFI study. Haematologica. 2010 Oct;95(10):1762-8.


Scientific Publications

Phimister E, Feero WG, Guttmacher AE. Realizing Genomic Medicine. N Engl J Med. 2012 Feb; 366:757-759

Yan X, Ma L, Yi D, Yoon J, Diercks A, Foltz G, Price ND, Hood LE, Tian Q. A CD133-related gene expression signature identifies an aggressive glioblastoma subtype with excessive mutations. Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1591-6.

Duan Z, Andronescu M, Schutz K, Mcllwain S, Kim YJ, Lee C, Shendure J, Fields S, Blau CA, Noble WS. A Three-Dimensional Model of the Yeast Genome. Nature. 2010 May 20;465(7296):363-7.

Cheng L, Lu W, Kulkarni B, Pejovic T, Yan X, Chiang JH, Hood L, Odunsi K, Lin B. Analysis of chemotherapy response programs in ovarian cancers by the next-generation sequencing technologies. Gynecol Oncol. 2010 May;117(2):159-69.

Roach JC, Glusman G, Smit AFA, Huff CD, Hubley R, Shannon PT, Rowen L, Pant KP, Goodman N, Bamshad M, Shendure J, Drmanac R, Jorde LB, Hood L, Galas DJ. Analysis of Genetic Inheritance in a Family Quartet by Whole Genome Sequencing. Science. 2010 Apr 30;328(5978):636-9.

Panchalingam KM, Paramchuk WJ, Chiang CYK, Shah N, Madan A, Hood L, Foltz G, Behie LA. Bioprocessing of human glioblastoma brain cancer tissue. Tissue Eng Part A. 2010 Apr;16(4):1169-77.

Ideker T, Dutkowski J, Hood L. Boosting signal-to-noise in complex biology - prior knowledge is power. Cell. 2011 Mar 18;144(6):860-3. Review.

Stadler B, Ivanovska I, Mehta K, Song S, Nelson A, Yunbing Tan Y, Mathieu J, Darby C, Blau CA, Ware C, Peters G, Miller DG, Shen L, Cleary MA, Ruohola-Baker H. Characterization of microRNAs Involved in Embryonic Stem Cell States. Stem Cells Dev. 2010 Jul;19(7):935-50.

Shah N, Lin B, Sibenaller Z, Ryken T, Lee H, Yoon JG, Rostad S, Foltz G. Comprehensive Analysis of MGMT Promoter Methylation - Correlation with MGMT Expression and Clinical Response in GBM. PLoS One. 2011 Jan 7;6(1):e16146.

Lin B, White JT, Wu J, Lele S, Old LJ, Hood L, Odunsi K. Deep depletion of abundant serum proteins reveals low-abundant proteins as potential biomarkers for human ovarian cancer. Proteomics Clin Appl. 2009 Jul 1;3(7):853-861.

Kutlu B, Burdick D, Baxter D, Rasschaert J, Flamez D, Eizirik DL, Welsh N, Goodman N, Hood L. Detailed transcriptome atlas of the pancreatic beta cell. BMC Med Genomics. 2009 Jan 15;2:3.

del Sol A, Balling R, Hood L, Galas D. Diseases as network perturbations. Curr Opin Biotechnol. 2010 Aug;21(4):566-71.

Foltz G, Yoon J-G, Lee H, Ryken TC, Sibenaller Z, Ehrich M, Hood L, Madan A. DNA methyltransferase-mediated transcriptional silencing in malignant glioma - a combined whole-genome microarray and promoter array analysis. Oncogene. 2009 Jul 23;28(29):2667-77.

Wiseman DH, Das M, Poulton K, Liakopoulou E. Donor cell leukemia following unrelated donor bone marrow transplantation for primary granulocytic sarcoma of the small intestine. Am J Hematol. 2011 Mar;86(3):315-8.

Majetia R, Becker MW, Tian Q, Lee TLM, Yan X, Liu R, Chiang J-H, Hood L, Clarke MF, Weissman IL. Dysregulated gene expression networks in human acute myelogenous leukemia stem cells. Proc Natl Acad Sci USA. 2009 Mar 3;106(9):3396-401.

Yu B, Yang X, Xu Y, Yao G, Shu H, Lin B, Hood L, Wang H, Yang S, Gu J, Fan J, Qin W. Elevated expression of DKK1 is associated with cytoplasmic-nuclear β-catenin accumulation and poor prognosis in hepatocellular carcinomas. J Hepatol. 2009 May;50(5):948-57.

Foltz G, Yoon J-G, Lee H, Ma L, Tian Q, Hood L, Madan A. Epigenetic regulation of wnt pathway antagonists in human glioblastoma multiforme. Genes Cancer. 2010 Jan;1(1):81-90.

Miller CP, Lowe KA, Valliant-Saunders K, Kaiser JF, Mattern D, Urban N, Henke M, Blau CA. Evaluating Erythropoietin-Associated Tumor Progression Using Archival Tissues from a Phase III Clinical Trial. Stem Cells. 2009 Sep;27(9):2353-61.

Etheridge A, Lee I, Hood L, Galas D, Wang K. Extracellular microRNA - A new source of biomarkers. Mutat Res. 2011 Dec 1;717(1-2):85-90.

Mathieu J, Zhang Z, Zhou W, Wang AJ, Heddleston JM, Pinna CMA, Hubaud A, Stadler B, Choi M, Bar M, Tewari M, Liu A, Vessella R, Rostomily R, Born D, Horwitz M, Ware C, Blau CA, Cleary MA, Rich JN, Ruohola-Baker H. HIF Induces Human Embryonic Stem Cell Markers in Cancer Cells. Cancer Res. 2011 Jul 1;71(13):4640-52.

Ware CB, Wang L, Mecham BH, Shen L, Nelson AM, Bar M, Lamba DA, Dauphin DS, Buckingham B, Askari B, Lim R, Tewari M, Gartler SM, Issa JP, Pavlidis P, Duan Z, Blau CA. Histone deacetylase inhibition elicits an evolutionarily conserved self-renewal program in embryonic stem cells. Cell Stem Cell. 2009 Apr 3;4(4):359-69.

Eddy JA, Hood L, Price ND, Geman D. Identifying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC). PLoS Comput Biol. 2010 May 27;6(5):e1000792.

Lin B, Wang J, Hong X, Yan X, Hwang D, Cho JH, Yi D, Utleg AG, Fang X, Schones DE, Zhao K, Omenn GS, Hood L. Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor. PLoS One. 2009 Aug 11;4(8):e6589.

Fang X, Yoon JG, Li L, Tsai YS, Zheng S, Hood L, Goodlett DR, Foltz G, Lin B. Landscape of the SOX2 protein-protein interactome. Proteomics. 2011 Mar;11(5):921-34.

Miller CP, Valliant-Saunders K, Blau CA. Limitations of a Murine Transgenic Breast Cancer Model for Studies of Erythropoietin-Induced Tumor Progression. Transl Oncol. 2010 Jun 1;3(3):176-80.

Okazuka K, Beard BC, Emery DW, Schwarzwaelder K, Spector MR, Sale GE, von Kalle C, Kiem H, Blau CA. Long-term Regulation of Genetically Modified Primary Hematopoietic Cells in Dogs. Mol Ther. 2011 Jul;19(7):1287-94.

Lin B, Madan A, Yoon JG, Fang X, Yan X, Kim TK, Hwang D, Hood L, Foltz G. Massively parallel signature sequencing and bioinformatics analysis identifies up-regulation of TGFBI and SOX4 in human glioblastoma. PLoS One. 2010 Apr 19;5(4):e10210.

Kutlu B, Kayali AG, Jung S, Parnaud G, Baxter D, Glusman G, Goodman N, Behie LA, Hayek A, Hood L. Meta-analysis of gene expression in human pancreatic islets after in vitro expansion. Physiol Genomics. 2009 Sep 9;39(1):72-81.

Blau CA, Spencer DM. Methods of controlling cell differentiation and growth using a fusion protein and a drug

Ouellet E, Lausted C, Lin T, Yang CWT, Hood L, Lagally ET. Parallel microfluidic surface plasmon resonance imaging arrays. Lab Chip. 2010 Mar 7;10(5):581-8.

Gehlenborg N, Yan W, Lee IY, Yoo H, Nieselt K, Hwang D, Aebersold R, Hood L. Prequips--an extensible software platform for integration, visualization and analysis of LC-MS and MS proteomics data. Bioinformatics. 2009 Mar 1;25(5):682-3.

Kim Y, Kim TK, Kim Y, Yoo J, You S, Lee I, Carlson G, Hood L, Choi S, Hwang D. Principal network analysis - identification of subnetworks representing major dynamics using gene expression data. Bioinformatics. 2011 Feb 1;27(3):391-8.

Pan S, Cheng L, White JT, Lu W, Utleg AG, Yan X, Urban ND, Drescher CW, Hood L, Lin B. Quantitative Proteomics Analysis Integrated with Microarray Data Reveals That Extracellular Matrix Proteins, Catenins, and P53 Binding Protein 1 Are Important for Chemotherapy Response in Ovarian Cancers. OMICS. 2009 Aug;13(4):345-54.

Wanga K, Lee I, Carlson G, Hood L, Galas D. Systems biology and the discovery of diagnostic biomarkers. Dis Markers. 2010;28(4):199-207. Review.

Auffray C, Chen Z, Hood L. Systems medicine - the future of medical genomics and healthcare. Genome Med. 2009 Jan 20;1(1):2.

Tu LC, Foltz G, Lin E, Hood L, Tian Q. Targeting stem cells-clinical implications for cancer therapy. Curr Stem Cell Res Ther. 2009 May;4(2):147-53. Review.

Gehlenborg N, Hwang D, Lee IY, Yoo H, Baxter D, Petritis B, Pitstick R, Marzolf B, DeArmond SJ, Carlson GA, Hood L. The Prion Disease Database - a comprehensive transcriptome resource for systems biology research in prion diseases. Database (Oxford). 2009;2009:bap011.

Fang X, Yoon JG, Li L, Yu W, Shao J, Hua D, Zheng S, Hood L, Goodlett DR, Foltz G, Lin B. The SOX2 response program in glioblastoma multiforme - an integrated ChIP-seq, expression microarray, and microRNA analysis. BMC Genomics. 2011 Jan 6;12:11.

Ao R, Galas D, Hood L, Yin L, Zhu XM. Towards predictive stochastic dynamical modeling of cancer genesis and progression. Interdiscip Sci. 2010 Jun;2(2):140-4.

Mo F, Mo Q, Chen Y, Goodlett DR, Hood L, Omenn GS, Li S, Lin B. WaveletQuant, an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis. BMC Bioinformatics. 2010 Apr 29;11:219.



Rattray K, Liakopoulou E, Lee SI, Foltz G, Blau CA. Accelerating Innovation from Bench to Bedside - Personalizing Treatment for Cancer, July 2011


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