Supplemental Table 1: an overview of technical guidelines for biospecimen handling guidelines available as Jan 1, 2010.
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1 Supplemental Table 1: an overview of technical guidelines for biospecimen handling guidelines available as Jan 1, This table compiles documents available either as publications in referenced journals or books or downloadable through websites. The search method to identify these documents included extensive PubMed and Google searches using keywords such as genomics, transcriptomics, proteomics, epigenetics, metabolomics/metabonomics, blood specimens, tissue specimens, bodily fluids, urine, saliva and extraction of documents pertaining to standards, protocols, guidelines, recommendations. The compilation exclusively addresses technical standards. For references to ethical, legal, societal and regulatory issues users may refer to the HumGen Database of Law and Policies, University of Montreal: This table is divided in two parts. Part 1 lists general guidelines applicable to different aspects of biorepository activities. Part 2 is divided in specific categories of biomarker applications and provides references to the guidelines available for different types of biospecimens (blood and derivatives, tissues, bodily fluids, exfoliated cells). This list has been complied as part of the review of existing guidelines in the framework of the Work Package 3 of the FP7 BBMRI program of the European Union. Readers and users should be aware that electronic links to documents may change rapidly. This table is certified as accurate as Jan but several weblinks may become obsolete in a matter of weeks. 1
2 PART 1: GENERAL BIOREPOSITORY GUIDELINES processing: IARC p ISBER J8.300, J OCED p ABN p13, NCI p3-4 Storage: IARC p ISBER D1.000-D OECD p41, ABN p NCI p Farkas DH, Arch Pathol Lab Med Jun;120(6):591-6 General Guidelines for Biospecimen Resources Shipping: IARC p ISBER I1.000-I OECD p93-94, ABN p NCI p6-7 Biosafety: IARC p ISBER F OECD p35, 87-88, 91, NCI p Quality control and Standard Operating Procedures: IARC p ISBER E1.000-E OECD p40, 43, 91, ABN p NCI p
3 PART 2: SPECIFIC BIOMARKER GUIDELINES Biomarker type Genome Genetics Epigenome Methylation Chromatin Transcriptome mrna microrna Proteome Proteins Post-translational modifications Metabolome Metabolites Enzymes Vitamins oligoelements lipids Living materials* Primary cells Organotypic cultures Stem cells Xenografts General Guidelines and protocols Protocols (Epigenome Network of excellence e- noe.net/researchtools /protocols.php) Processing and storage Farkas DH, Arch Pathol Lab Med Jun;120(6):591-6 Quantity and quality control (ABN BN_SOPs_Review_Mar07_fi nal.pdf + Schroeder A, BMC Mol Biol Jan 31;7:3) Protocols Methods in Molecular Biology, vol.358: Metabolomics:Met hods and Protocols, edited by W.Weckwerth (no free access to all book) Blood and blood products* - WBC - plasma - serum - red blood cells Collection and processing (IARC p13 ublications/pdfsonline/wrk/wrk2/stand ards_protocolsbrc.p df + ABN p12 DNA methylation (Wong IH, Cancer Res Jan 1;59(1):71-3) PBMC collection (Marteau JB, Clin Chem Jul;51(7):1250-2) RNA Isolation ( m/support/technical/techn otes/blood_technote.pdf) processing (ABN p OPs_Review_Mar07_final.pdf + Proteomics of human Body Fluids book Methods in Molecular Biology, vol.358: Metabolomics:Met hods and Protocols, edited by W.Weckwerth. Chapter 1, Establishment of cell lines (ABN p /ABN_SOPs_Review_Mar 07_final.pdf) + Louie LG Am J Hum Genet Mar;48(3):
4 pdf/abn_sops_revie w_mar07_final.pdf + Yokota M J Clin Lab Anal. 1999;13(3):133-40) Storage (OECD p99 dataoecd/7/13/ pdf) DNA storage Farkas DH, Diagn Mol Pathol Dec;5(4): Visvikis S Clin Chem Lab Med Aug;36(8): Farkas DH, Arch Pathol Lab Med Jun;120(6):591-6 Quality control (OECD p98 dataoecd/7/13/ pdf) DNA Extraction (ABN p pdf/abn_sops_revie w_mar07_final.pdf leucocytes preparation (Pérez IA, Genet Mol Res May 11;6(2): ) 6SkzhODYFxQC&pg=PR5&dq= Proteomics+of+human+Body+Fl uids+book&sig=acfu3u1wnxsh NQHKK4iK_moveYAHwWeYdw + The Proteomics Protocols Handbook hl=en&id=1enfskpkv2mc&dq= The+Proteomics+Protocols+Ha ndbook&printsec=frontcover&so urce=web&ots=wxj2byenuo&si g=cvy868grgh4cxfuqig5ossd E_wc&sa=X&oi=book_result&re snum=7&ct=result#ppa52,m1 + Lundblad RL, Internet J of Genomics and Proteomics, vol1, N 2, ex.php?xmlprinter=true&xmlfile Path=journals/ijgp/vol1n2/plas ma.xml + Boyanton BL, Clin Chem Dec;48(12): Preissner CM, Clin Chem Jul;50(7):1245-7) + Biorepository Protocols wer.aspx?id=4 Storage (Lundblad RL, Internet J of Genomics and Proteomics, vol1, N 2, ex.php?xmlprinter=true&xmlfile Path=journals/ijgp/vol1n2/plas ma.xml + Evans MJ, Clin Biochem Mar;34(2):107-12) Metabolite Profiling in Blood Plasma, by O.Fiehn and T.Kind ols.com/abstract/doi/ / _1 Storage (ABN p54 /ABN_SOPs_Review_Mar 07_final.pdf, ISBER J BestPractices2008.pdf) 4
5 Tissues (surgery; biopsy; autopsy/ necropsy) Collection and processing RAND p36,44-46,78-81, t.nci.nih.gov/docs/03 RAND.pdf+ Farkas DH, Arch Pathol Lab Med Jun;120(6):591-6 Quantity and quality control ( Dumur CI, Clin Chem Nov;50(11): Epub 2004 Sep 13) processing (RAND p36,44-46,78-81, ov/docs/03rand.pdf) Storage (RAND p66-68,81-82, ov/docs/03rand.pdf) Storage (RAND p66-68, t.nci.nih.gov/docs/03 RAND.pdf) Quality control (RAND p41-44,47-48,55-56,72-74, ov/docs/03rand.pdf) Bodily Fluids (urine, saliva, semen) Quality control (RAND t.nci.nih.gov/docs/03 RAND.pdf) Collection and processing Collection for RNA extraction (Li Y, Clin Cancer Res Dec 15;10(24): ) processing (UCLA Human Salivary 5
6 (IARC p ublications/pdfsonline/wrk/wrk2/stand ards_protocolsbrc.p df + ISBER J8.4000, J bs/bestpractices2008.pd f + ABN p15,31 pdf/abn_sops_revie w_mar07_final.pdf) Proteome Annex no free access at + Biorepository protocols wer.aspx?id=4 + Proteomics of human Body Fluids book 6SkzhODYFxQC&pg=PR5&dq= Proteomics+of+human+Body+Fl uids+book&sig=acfu3u1wnxsh NQHKK4iK_moveYAHwWeYdw + Navazesh M Ann N Y Acad Sci Sep 20;694:72-7) Storage (UCLA Human Salivary Proteome Section 2 no free access at Shipping (UCLA Human Salivary Proteome Section 5 no free access at 6
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