Sample Collection and Processing
This section principally presents material supporting conceptualization, design and conduct of sample collections, processing and analysis.
Conceptualization
Please visit the following section:
Design and Conduct
In Theory
General documentation, guidelines and best practices regarding biological samples collection and processing.
Please visit also the following section(s):
Canadian Tumour Repository Network (CTRNet)
This website promotes cancer research by facilitating access to tumour tissues and related clinical information.
Policies and Standard Operating Procedures (SOP)
developed by CTRNet charter members are freely accessible.
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Comparison Chart of Guidelines
This document compares selected referenced guidelines, written by well known organizations. These guidelines cover all biobanking steps, i.e. biological sample collection, labelling, processing, and storage applied to a wide range of sample types. A P3G-prepared document (2008). |
Recommendation for
indicators, international collaboration, protocol and manual of operations for chronic disease risk factor surveys
Part II of this document deals with issues related to defining every step of the survey organization, from the
target population to the recruitment
per se. Part III contains protocols and operational guidelines for individual measurements and biological
samples collection. A European Health Risk Monitoring-written document, the Copyright is reserved for the Finnish
National Public Health Institute (2002).
Best Practice Guidelines for
Biological Resource Centres (OECD)
This document comprises the report on best practice guidelines for Biological Resource Centres (BRCs). Part I outlines
the background and rationale to the project and describes the methodology used for articulating best practice
guidelines and provides general recommendations on implementation and review. Part II describes the best practice
guidelines themselves. Published by the Organisation for Economic Co-operation and Development (OECD) (2007).
Human tissue repositories: Best Practices
for a Biospecimen Resource for the Genomic and Proteomic Era
This document is a blueprint for a high-quality biospecimen network of biological sample banks. It identifies "best practices"
necessary for establishing a national tissue resource and databank to optimize and accelerate genomics- and
proteomics-based research. A RAND Science and Technology-written document (2003).
National
Cancer Institute (NCI) Best Practices for Biospecimen Resources
This document outlines the operational, technical, ethical, legal, and policy best practices for NCI-supported biospecimen resources.
Co-written by NCI, National Institute of Health, and US Department of Health and Human
Services-co-written document (2007).
2008 Best Practices
for Repositories Collection, Storage, Retrieval and Distribution of Biological Materials for Research (ISBER)
This document provides a comprehensive foundation for the guidance of repository activities on the management of human
specimen collections. The recommended practices reflect the most effective approaches to the establishment and
running of specimen collection facilities and are not intended as required practices. They will be reviewed
periodically and will be revised to reflect advances in research and technology. Prepared by the International
Society for Biological and Environmental Repositories (ISBER) (2008).
Australian Biospecimen Network
(ABN) Biorepository Protocols
This document aims to provide information for new biorepositories or biorepositories developing new protocols and to add
to the literature surrounding best practice principles in tissue banking. Prepared by the Australasian Biospecimen
Network (ABN) (2007).
International Network of Biological
Resource Centres (IARC)
This document focuses on developing recommendations towards common minimal technical standards in order to stimulate the
creation, development and networking of Biological Resource Centres (BRCs) at the international level, and, through
their use, enhance and improve cancer research worldwide. Prepared by the International Agency for Research on
Cancer (IARC) (2007).
Quality of
biological resources centres (BRCs) - Management system of a BRC and quality of biological resources from human
or micro-organism origin
This document (available in
English
and
French
) presents quality requirements for biorepositories of biological samples from human as well as micro-organisms. The
document details quality control for many areas such as the biobank infrastructure and apparatus maintenance as well
as sample-derived data management, data transfer, and informatics support. This version is under review/validation.
Co-written document by INSERM, AFNOR and the "Réseau Français des biobanques". (INSERM, AFNOR and Biobanks French
Network) (2007).
In Practice
Real-life examples related to biological samples collection and processing.
Please visit the following section:
Gen2Phen
This website aims to unify human- and model-organism genetic
variation databases towards increasingly holistic views into
Genotype-To-Phenotype (G2P) data, and to link this system into other
biomedical knowledge sources via genome browser functionality. The
GEN2PHEN Knowledge Centre has received funding from the European
Community's Seventh Framework Programme.
onCore UK
This website gives access to a generic patient information sheet and consent form as well as onCoreUK's
patient information sheet and consent form in English and 9 other languages. Furthermore, standard operating
procedures regarding policies, technical procedures (from donor consent and withdrawal to processing and storing
blood and tissue samples), and quality system procedures are available.
Atherosclerosis Risk in Communities (ARIC)
This is the website of the American ARIC study. It displays biochemical procedures such as Blood Collection and
Processing, Lipid and Lipoprotein Determinations, Hemostasis Determination and Clinical Chemistry Determinations
that were used during the recruitment and the follow up. A Collaborative Studies Coordinating Center-maintained
website, based at the University of North Carolina.
UK Biobank: Protocol for a large-scale
prospective epidemiological resource
Part 2 of this document details the overall implementation strategy for UK Biobank, and provides detailed protocols
for recruiting participants and for obtaining, processing and maintaining data and samples both at recruitment and
as the biobank matures. Prepared by UK biobank (2007).
UK Biobank: Report of the integrated
pilot phase
This document reports on, and provides recommendations based on, the results obtained from the pilot phase of UK Biobank.
The pilot phase was conducted between February and June 2006, in order to assess the basic design of the study and
the approaches to data and sample collection. Prepared by UK Biobank (2006).
UK DNA Banking Network (UDBN)
This website describes services to manage DNA samples in a standardized way for academic laboratories and commercial
facilities. UDBN manages samples collected from 13 common complex diseases funded by the Medical Research Council
(MRC). UDBN is also coordinating an international project to harmonize DNA measurements. The aim is to facilitate
the movement of samples between labs by ensuring compatibility of results obtained in quantity and quality
measurements. An MRC-funded network, based at the University of Manchester.
The National
Children's Study
This website displays the "Reviews and Analytic Reports" section of the website of the National Children's Study (NCS). It offers
access to a wide variety of literature reviews and "white papers" on study design and conduct relevant to the
construction of a large (approx 100 000 live births) national birth cohort. Other sections of the website deal with
issues specific to the NCS itself (e.g. study hypotheses). The website is cosupported by the U.S. Environmental
Protection Agency, U.S. Department of Health and Human Services and USA.gov Agency.
Bancoadn™ (BNADN)
This is the website of the Spanish blood-based National DNA Bank. This DNA bank processes and stores DNA, plasma and cell
samples from voluntary donors along with relevant information on health and lifestyle habits. It provides procedures
for DNA extraction, separation of mononuclear cells, cellular immortalization and offers these three services to
outside laboratories. A University of Salamanca-maintained website.
National Health and
Nutrition Examination Survey (NHANES)
This website of the American survey displays all serum/plasma collection and biochemistry procedures, from cholesterol to
heavy metals, electrolytes, metabolic enzymes. It also provides among others questionnaire administration methods
and individual physical and cognitive measurements. US Department of Health and Human Services-maintained website
(2006).
IT Tools
SAIL
is an open source system designed to hold phenotype availability
information and meta data about samples, experiments and phenotypes,
submitted by data owners or databases that contain actual measurement
data. This can apply for epidemiological data as well as biosamples.
SAIL is produced by SIMBioMS itself powered by EBI, IMCS and FIMM.
Advanced Tissue Management (ATiM)
This website is a web-based software designed for the operations of a tissue bank. It
consists of 2 key modules for Clinical Annotation and Laboratory Inventory Management System. Other user tools
included are the ad-hoc query, batch manager, order management, and form manager. ATiM was designed and developed by
CTRNet in conjunction with Canadian tissue banks.
Analysis
In Theory
General documentation and guidelines regarding genotyping and sample analysis.
GeneStat
This website presents a series of tutorials on the design, analysis and interpretation of empirical studies involving
genetic data. Aimed at geneticists, epidemiologists and molecular scientists working within the field of functional
genomics, it includes links to other relevant internet-sites and computer programs for analyzing genetics data. A
Wiki-conceived webpage, maintained by the Medical Epidemiology and Biostatistics and based at the Karolinska
Institute .
IT Tools
Selected software and databases for genotyping and analysis.
Please visit also the following section(s):
Genomics
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Comparison Chart of Websites for Managing and Interpreting Genomic Data
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HapMap
This website presents this project which has undertaken a global analysis of polymorphism patterns and of linkage
disequilibrium across the human genome. Based on informatics tools including the
genome browser,
this information has many uses - for example, it can be used to guide selection of tag SNPs across the entire
human genome. HapMap is based on an international partnership of scientists and funding agencies from Canada, China,
Japan, Nigeria, the United Kingdom and the United States.
SeattleSNPs
This website presents protocols and software for identifying, genotyping, and modeling the associations between single
nucleotide polymorphisms (SNPs) in candidate genes and pathways that underlie inflammatory responses in humans.
Funded as part of the National Heart Lung and Blood Institute's (NHLBI) Programs for Genomic Applications (PGA).
University of California Santa Cruz (UCSC) Genome
Bioinformatics
This website contains the reference sequence and working draft assemblies for a large collection of genomes and several
tools are available such as
In Silico PCR,
Proteome and
Genome Browsers. It also provides a portal to the
ENCODE project. A University of California Santa Cruz-maintained website.
American National Center for Biotechnology Information
(NCBI)
This website provides access to public databases and bioinformatic tools. NCBI conducts research in computational
biology, develops software tools for analyzing genome data, and disseminates biomedical information. Co-supported by
National Institute of Health, US Department of Health and Human Services and USA.gov.
European Bioinformatics Institute (EBI)
This website provides access to public databases and bioinformatic tools. The resource includes data on nucleic acid and
protein sequences and macromolecular structures. EBI is a centre for research and services in bioinformatics and an
outstation of the European Molecular Biology Laboratory (EMBL).
Genetic Association Database (GAD)
This website displays an archive of the results of genetic association studies of complex human diseases and disorders.
This updatable database uses standardized nomenclature to allow the user to search on the basis of disease, genetic
variant or other criterion, to rapidly identify clinically relevant genetic associations from the huge volume of
polymorphism and mutational data that exist. A National Institute of Health-maintained website.
Broad Institute Software
This website displays a wide spectrum of software tools (such as
Arachne,
Argo,
Conrad,
PLINK,
EIGENSTRAT,
Haploview,
Locusview,
Sweep,
Tagger,
GeneHunter,
MapMaker3,
GenePattern,
GSEA,
GeneCruiser,
ConnectivityMap)
for the analysis of genomic and genetic datasets: genome sequence, genetic variation, linkage analysis,
high-throughput image analysis and expression analysis. Website maintained by the Broad Institute, a collaborative
effort involving the MIT, Harvard and its affiliated hospitals, and the Whitehead Institute.
CLC Free Workbench
CLC Free Workbench is an open source software environment enabling users to undertake a large number of bioinformatic analyses,
combined with smooth data management, graphical viewing and output options with a focus on applications in '-omics'.
It provides access to integrated research tools (creating and editing alignments, interactive restriction site
analysis, phylogenetics, advanced DNA to protein translation etc). The software and website are maintained by
CLC-bio.
Bioconductor
Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.
BioConductor is primarily based on the R programming language. Bioconductor and this website are maintained by the
Fred Hutchinson Cancer Research Center.
ACCE
This website presents the ACCE Model Process for Evaluating Genetic Tests, which includes 1) Analytic
validity of the test; 2) Clinical validity of the test; 3) Clinical utility of the test to improve patient
outcomes; 4) Ethical, legal, and social issues that may arise in the context of using the test. These
issues are being addressed in a 44-question assessment. A model project established and supported by
CDC's Office of Public Health Genomics (OPHG) (2000-2004).
EGAPP™
This website presents the EGAPP™ (Evaluation of Genomic Applications in Practice and Prevention) project
whose main goal is to establish and test a systematic, evidence-based process for evaluating genetic
tests and other applications of genomic technology that are in transition from research to clinical and
public health practice. EGAPP is an initiative launched by the Centers for
Disease Control and Prevention in 2004.
Genetic Statistics
Please visit also the following section(s):
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Comparison Chart of Websites for Genetic and Genomic Statistics
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HapMap
This website presents this project which has undertaken a global analysis of polymorphism patterns and of linkage
disequilibrium across the human genome. Based on informatics tools including the
genome browser,
this information has many uses - for example, it can be used to guide selection of tag SNPs across the entire
human genome. HapMap is based on an international partnership of scientists and funding agencies from Canada, China,
Japan, Nigeria, the United Kingdom and the United States.
SeattleSNPs
This website presents protocols and software for identifying, genotyping, and modeling the associations between single
nucleotide polymorphisms (SNPs) in candidate genes and pathways that underlie inflammatory responses in humans.
Funded as part of the National Heart Lung and Blood Institute's (NHLBI) Programs for Genomic Applications (PGA).
Dr David Reich's Laboratory
Dr David Reich's Laboratory does both theoretical and experimental work in human population genetics. The website provides access to a variety
of software including ANCESTRYMAP, EIGENSOFT and EIGENSTRAT. The software that are available address a range of key
issues in population genetics including admixture mapping, and the exploration, detection and correction for
population stratification (ancestral substructure) in genetic association studies. A Harvard University-maintained
website.
Dr David Clayton's website
This website contains the C and C++ source files for
SPLINK,
TRANSMIT,
PED2SPL,
GH2STAT
and
SNPHAP.
It also displays packages for analysis of genetic association studies for the STATA statistical system together
with some exercises, and some miscellaneous programs in the R language. A Cambridge Institute for Medical
Research-maintained website.
Tagzilla
This software computes an optimal array of tag SNPs to capture a set of SNPs of scientific interest, based on pairwise
linkage disequilibrium that takes into account practical needs and constraints faced by investigators. A
collaboration of the National Institute of Health, NCI and US Department of Health and Human Services.
GeneStat
This website presents a series of tutorials on the design, analysis and interpretation of empirical studies involving
genetic data. Aimed at geneticists, epidemiologists and molecular scientists working within the field of functional
genomics, it includes links to other relevant internet-sites and computer programs for analyzing genetics data. A
Wiki-conceived webpage, maintained by the Medical Epidemiology and Biostatistics and based at the Karolinska
Institute.
Matthews Stephens's
website
This website provides information about, and access to software for, applications in Bayesian and computational
statistics particularly in population genetics. This includes association analyses for genome scans and candidate
genes (see BIMBAM), estimating haplotypes from population genotype data (see PHASE) and developing statistical
models for patterns of linkage disequilibrium across multiple loci, and using these patterns to identify
recombination hotspots. A University of Chicago-maintained website.
The Obiba Project
This website provides a free, complete, secure and high-performance open source information management system for
biobanks that can be used as is or be adapted. This information system will support a wide range of biobank
activities and will integrate data collected or produced through those activities. Obiba will be compliant with high
security standards and will include data exchange interfaces to facilitate sharing between different installations.
A collaboration of Genome Quebec; Estonian Genome Project, University of Tartu; Institute for Molecular Medicine
Finland, University of Helsinki; Instituto Nacional de Medicina Genomica, Mexico.
Rockefeller University Linkage
Software
This website is a repository of software dealing with: genetic linkage analysis for human pedigree data, QTL analysis for
animal/plant breeding data, genetic marker ordering, genetic association analysis, haplotype construction, pedigree
drawing, population genetics and TDT (such as
Tagger,
Haploview,
ldSelect,
PLINK,
Structure).
A Laboratory of Statistical Genetics-maintained website, based at the Rockefeller University.
Gonçalo's website
This website, from Gonçalo Abecasis' research group, emphases on developing computational and statistical software
required for understanding human genetic variation, with a particular focus on complex human disease and
encompassing both linkage and association analysis. The website provides access to a number of packages widely used
by genetic epidemiologists including Merlin, QTDT and Gold. Website maintained by the University of Michigan.
Genetic Power
Calculator
This website provides access to automated analysis of statistical power for variance components (VC), quantitative trait
locis (QTL) linkage and association tests in sibships, and other common tests. Constructed by Shaun Purcell based on
work by himself and Pak Sham originally carried out at the Institute of Psychiatry (London), and maintained by the
Psychiatric and Neurodevelopmental Genetics Unit at Harvard University.
PEDSYS
PEDESYS is a database system developed to provide a software environment in which to manage and analyse genetic and
demographic data, particularly in relation to pedigree (family-based) data. The system supports integrated
collection, management and analysis of constantly evolving data sets. The software and website are supported by the
Southwest Foundation For Biomedical Research.
Dissemination
In Theory
NHMRC Biobanks Information Paper
The aim of this paper is to provide information relevant for the
establishment, management and governance of biobanks in Australia.
National and international documentation, as well as other relevant case
studies are used to identify best practices with regard to
standardization of biobank policies, practices and procedures. Prepared
by the NHMRC (2010).
In Practice
Websites displaying genotype results and databases.
Gen2Phen
This website aims to unify human- and model-organism genetic
variation databases towards increasingly holistic views into
Genotype-To-Phenotype (G2P) data, and to link this system into other
biomedical knowledge sources via genome browser functionality. The
GEN2PHEN Knowledge Centre has received funding from the European
Community's Seventh Framework Programme.
Human Specimens for Research
This website discusses 3 main issues. First, it helps in locating tumor specimens and related data of interest.
Legal and ethical issues are addressed and a model informed consent and patient information sheet are available.
Finally, issues relating to the establishment and management of a tissue bank are discussed. The website is
maintained by the Cancer diagnosis program of the National Cancer Institute (NCI).
Biospecimen Research Network
This website was initiated to address the impact of specific specimen handling variables on molecular testing of
human tissues. The BRN database can be surveyed by biospecimen type or by experimental factor. The website is
supported by the Office of Biorepositories and Biospecimen Research of the National Cancer Institute (NCI).
Catalog of Genome-Wide Association Studies
This website presents a list of publications in which studies assayed at least 100,000 single nucleotide
polymorphisms (SNPs) in the initial stage. Publications can be searched by journal, first author, disease/trait or
multiple diseases, chromosomal refion, gene, SNP, or p-value. This website is maintained by the Office of Population
Genomics of The National Human Genome Research Institute (NHGRI).
GeneSNPs Environmental Genome
Project
This website displays information on the integration of gene, sequence and polymorphism data into individually annotated
gene models. The human genes on this site are related to DNA repair, cell cycle control, cell signaling, cell
division, homeostasis and metabolism, and are thought to play a role in susceptibility to environmental exposure.
Sponsored by National Institute of Environmental Health Sciences, and developed by the Genome center, based at the
University of Utah.
The SeattleSNPs project
This area of the website provides information about obtaining access to data. Funded as part of the National Heart
Lung and Blood Institute's (NHLBI) Programs for Genomic Applications (PGA).
Genetic Association Database (GAD)
This website displays an archive of the results of genetic association studies of complex human diseases and disorders.
This updatable database uses standardized nomenclature to allow the user to search on the basis of disease, genetic
variant or other criterion, to rapidly identify clinically relevant genetic associations from the huge volume of
polymorphism and mutational data that exist. A National Institute of Health-maintained website.
Broad Institute
This area of the website provides information about obtaining access to data. Website maintained by the Broad
Institute, a collaborative effort involving the MIT, Harvard and its affiliated hospitals, and the Whitehead
Institute.
UK DNA Banking Network
This area of the website provides information about obtaining access to data/samples. An MRC-funded network, based
at the University of Manchester.
HapMap
This area of the website provides information about obtaining access to data. HapMap is based on an international
partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United
States.
HapMap- The Encode Project
This website displays the HapMap ENCODE resequencing and genotyping project which aims to produce a dense set of
genotypes across large genomic regions. Ten 500-kilobase regions of the genome were resequenced in 48 unrelated DNA
samples. These regions serve as the foundation on which to test and evaluate the effectiveness and efficiency of a
diverse set of methods and technologies for finding various functional elements in human DNA.
GAPPNET
This organization aims to accelerate and streamline effective and responsible use of validated and
useful genomic knowledge and applications. GAPPNET has 4 functions: knowledge synthesis and dissemination,
evidence-based recommendations development, translational research and translational programs;
for which some tools have been developed such as ACCE,
EGAPP,
USPSTF.
GAPPNet was formed by CDC's Office of Public Health Genomics, NCI's Division of Cancer Control and
Population Sciences, and other stakeholders in 2009.
IT Tools
ORCID
This website aims
to solve the author/contributor name ambiguity problem in scholarly
communications by creating a central registry of unique identifiers for
individual researchers and an open and transparent linking mechanism
between ORCID and other current author ID schemes. ORCID is an
independent organization.
ACCE
This website presents the ACCE Model Process for Evaluating Genetic Tests, which includes 1) Analytic
validity of the test; 2) Clinical validity of the test; 3) Clinical utility of the test to improve patient
outcomes; 4) Ethical, legal, and social issues that may arise in the context of using the test. These
issues are being addressed in a 44-question assessment. A model project established and supported by
CDC's Office of Public Health Genomics (OPHG) (2000-2004).
EGAPP™
This website presents the EGAPP™ (Evaluation of Genomic Applications in Practice and Prevention) project
whose main goal is to establish and test a systematic, evidence-based process for evaluating genetic
tests and other applications of genomic technology that are in transition from research to clinical and
public health practice. EGAPP is an initiative launched by the Centers for
Disease Control and Prevention in 2004.
