Patient Sample Analysis

Patient Sample Analysis

Resources for supplying and analyzing anonymized patient samples.

Shared Facilities:

Fluorescence Activated Cell Sorting Facility (FACS)

• Description —Full-service sorting and analysis.  Six sorters and four analyzers available.  Consulting on experimental design and data analysis.  Flowjo site license administration.
• Location — Beckman B016
• Questions — Contact Marty Bigos  , (650) 723-6959
• Website — http://facs.stanford.edu/
• Selected References

  Completely phased genome sequencing through chromosome sorting. Yang H, Chen X, Wong WH. Proc Natl Acad Sci U S A. 2011 Jan 4;108(1):12-7. Epub 2010 Dec 15. PubMedID: 21169219

  A polarized epithelium organized by beta- and alpha-catenin predates cadherin and metazoan origins. Dickinson DJ, Nelson WJ, Weis WI. Science. 2011 Mar 11;331(6022):1336-9. PubMedID: 2139354.

  MicroRNA-Mediated Conversion of Human Fibroblasts to Neurons. Yoo AS, Sun AX, Shcheglovito A, Li L, Portmann T, Yulong Li Y, Lee-Messer C, Dolmetsch RE, Tsien RW, Crabtree GR (2011). Nature (in press). PubMedID: 21753754.

Human Immune Monitoring Core (HIMC)

• Description — Analysis of clinical samples by: multiplexed immunoassays (Luminex and MesoScale Discovery); flow cytometry immunophenotyping, phosphoepitope analysis, and intracellular cytokine staining, by fluorescence and mass cytometry (CyTOF); capillary nanoimmunoassay (NanoPro); and genomic assays including microfluidic qPCR (Fluidigm BioMark).
• Location — Fairchild D033 (Immunoassays and Flow Cytometry) and CCSR 0128 (Genomics and NanoPro)
• Questions — Contact Holden Maecker, PhD  , (650) 723-1671
• Website — http://himc.stanford.edu
• Selected References

  Nanofluidic proteomic assay for serial analysis of oncoprotein activation in clinical specimens. Fan AC, Deb-Basu D, Orban MW, Gotlib JR, Natkunam Y, O'Neill R, Padua RA, Xu L, Taketa D, Shirer AE, Beer S, Yee AX, Voehringer DW and Felsher DW. 2009. Nature Medicine 15:566-571. PubMedID: 19363496.

  T helper type 1 and 17 cells determine efficacy of interferon-beta in multiple sclerosis and experimental encephalomyelitis. Axtell RC, de Jong BA, Boniface K, van der Voort LF, Bhat R, De Sarno P, Naves R, Han M, Zhong F, Castellanos JG, Mair R, Christakos A, Kolkowitz I, Katz L, Killestein J, Polman CH, de Waal Malefyt R, Steinman L, and Raman C. 2010. Nature Medicine 16:406-412. PubMedID: 20348925; PMCID: PMC3042885

  Cell type-specific gene expression differences in complex tissues. Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM, and Butte AJ. 2010. Nature Methods 7:287-289. PubMedID: 20208531.

Stanford Blood Center (Part of the Stanford University School of Medicine)

• Description — The Stanford Blood Center provides de-identified blood components and blood byproducts from healthy donors for in vitro investigational use, as well as phlebotomy services. The Stanford Administrative Panel for Human Research has approved these activities.
  
  Depending on your needs, we can collect tubes or whole units of blood from individuals selected by the researcher or recruited by the Stanford Blood Center based on special criteria (e.g. HLA type, CMVsero status, red cell antigen, etc.).
  
  We can provide anything from leukocytes (buffy coat from whole blood, residual leukocytes), plasma (frozen or liquid), platelets, red blood cells, to whole blood. We can also customize your products with irradiation, leukoreduction, or other product manipulation, or by modifying the collection procedure to fit your needs.
• Location — Stanford University, 3373 Hillview Avenue, Palo Alto, CA 94304
• Questions — Contact Department of Special Donations  , (650) 723-6667
• Website — http://bloodcenter.stanford.edu/research/

Stanford Functional Genomics Facility (SFGF)

• Description — The Stanford Functional Genomics Facility (SFGF) provides microarrays and microarray services to researchers within the Stanford community and beyond. The facility also provides 24/7 access to instruments, equipment and software utilized within the microarray field. We support all arrays based on a microscope slide format including Agilent, Illumina, Nimblegen, and arrays produced by SFGF. Besides printing cDNA and oligonucliotide microarrays, the facility can also print arrays of your material in a high throughput fashion, including proteins, peptides, antibodies, cell lysates, siRNAs, etc.
• Location — Center for Clinical Sciences Research (CCSR), 0120
• Questions — Contact John Coller, PhD  , (650) 736-2434
• Website — http://www.microarray.org/sfgf/
• Selected References

  The essential genome of a bacterium. Christen B, Abeliuk E, Collier JM, Kalogeraki VS, Passarelli B, Coller JA, Fero MJ, McAdams HH, Shapiro L. Mol Syst Biol. 2011 Aug 30;7:528. PubMedID: 21878915; PMCID: PMC3202797.

  Single-molecule sequencing of an individual human genome. Pushkarev D, Neff NF, Quake SR. Nat. Biotechnol. 2009 Sep;27(9):847-50. Epub 2009 Aug 10. PubMedID: 19668243.

  Direct lineage conversion of terminally differentiated hepatocytes to functional neurons. Marro S, Pang ZP, Yang N, Tsai MC, Qu K, Chang HY, Südhof TC, Wernig M. Cell Stem Cell. 2011 Oct 4;9(4):374-82. PubMedID: 21962918.

Tissue Bank (Pathology Tissue Bank)

• Description — Activities and services include collecting and banking freshly-frozen tissue specimens for viable cell studies, processing and banking blood components, maintaining a tissue database and coordinating patient consent and assuring regulatory compliance.
• Location — SIM1 G0815
• Questions — Contact Danielle Leuenberger , (650) 724-9121
• Website — http://tissuebank.stanford.edu/
• Selected References

  Cancer stem cells from human breast tumors are involved in spontaneous metastases in orthotopic mouse models. Liu H, Patel MR, Prescher JA, Patsialou A, Qian D, Lin J, Wen S, Chang YF, Bachmann MH, Shimono Y, Dalerba P, Adorno M, Lobo N, Bueno J, Dirbas FM, Goswami S, Somlo G, Condeelis J, Contag CH, Gambhir SS, Clarke MF. Proc Natl Acad Sci U S A. 2010 Oct 19;107(42):18115-20. PubMedID: 20921380; PMID: 20921380

  Single-cell dissection of transcriptional heterogeneity in human colon tumors. Dalerba P, Kalisky T, Sahoo D, Rajendran PS, Rothenberg ME, Leyrat AA, Sim S, Okamoto J, Johnston DM, Qian D, Zabala M, Bueno J, Neff NF, Wang J, Shelton AA, Visser B, Hisamori S, Shimono Y, van de Wetering M, Clevers H, Clarke MF, Quake SR. Nat Biotechnol. 2011 Nov 13;29(12):1120-7. PubMedID: 22081019.

  Recurrent deletion of CHD1 in prostate cancer with relevance to cell invasiveness. Huang S, Gulzar ZG, Salari K, Lapointe J, Brooks JD, Pollack JR. Oncogene. 2011 Dec 19. doi: 10.1038/onc.2011.590. [Epub ahead of print]. PubMedID: 22179824.

Translational Applications Service Center (TASC)

• Description — The Translational Applications Service Center (TASC) Program is designed to focus on removing barriers and communication gaps between scientists and the clinicians. Our initiatives include research facilities and pilot grants that support translational projects of faculty, clinical fellows and students. The program also fosters education by organizing a series of seminars, symposia and an annual retreat.
  
  Our program is interested in all phases of translational research, as well as both directions of translation (from bench to bedside and from bedside to bench) and also in the extension to the population level. TASC provides:
        –  Clinical Specimen Processing
        –  Sample Preparation
        –  Tissue Banking and Clinical Sample Storage
        –  Cell Culture Facility
        –  Laboratory Bench Space Use
        –  Methods and Assay Development
        –  Data Analysis and Consulting
  
• Location — Grant S107
• Questions — Contact Joanna Liliental, PhD  , (650) 736-1285
• Website — http://tram.stanford.edu/