Epidemiology and Biostatistics
This section presents material principally supporting conceptualization of epidemiological studies, statistical analysis and dissemination of results.
Conceptualization
Design of Study
In Theory
General documentation and guidelines regarding the conception of epidemiological studies.
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).
Recommendation for
indicators, international collaboration, protocol and manual of operations for chronic disease risk factor surveys
Part I of this document gives a list of recommended population indicators for chronic disease risk factors. 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. A European Health Risk Monitoring-written document, the Copyright is reserved for the
Finnish National Public Health Institute (2002).
HuGENet™
HuGE Review Handbook
This document aims to help biomedical researchers undertaking studies and systematic reviews in human genome
epidemiology to take sensible decisions about methods right through from study design to final analysis.
A HuGENet Systematic Review and Meta-Analysis Working Group handbook (2006).
In Practice
Real-life examples related to conception of specific studies.
Please visit the following section:
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.
UK Biobank: Protocol for a
large-scale prospective epidemiological resource
Part 1 of this document outlines the scientific rationale for
constructing a very large cohort-based biobank in middle aged adults in the UK. It also considers the basic design
of such a study, reviewing and justifying decisions about baseline quetionnaires, physical measures and biological samples.
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).
Power and Sample Size
In Practice
Real-life examples related to power and sample size issues and calculations.
UK Biobank: distribution of incident and prevalent cases of chronic disease and
the statistical power of nested case-control studies
This document explores and describes the incidence rates
anticipated for common chronic diseases in UK Biobank (a cohort of 500 000 adults aged 40-69 years at recruitment).
It also generates and describes the power profiles for nested case-control studies (for direct and interactive effects)
based on the UK Biobank resource. A UK Biobank-commissioned document (2005).
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.
IT Tools
Selected software for power and sample size calculation.
Please visit the following section:
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, TDT and power size calculation (such as
QUANTO,
TDTASP
and PBAT).
A Laboratory of Statistical Genetics-maintained website, based at the Rockefeller University.
STATA power and sample size
STATA is a powerful, flexible, integrated statistical analysis application that provides data management,
data analysis and graphics. Read how
to access external utilities and services to enhance basic use of STATA and how to interface with
the international STATA community. Ado and help files are also available to calculate power and sample size for gene-gene
and gene-environment interactions. A Genetic Epidemiology Division-maintained program, based at the Cancer
Research UK Clinical Centre, University of Leeds. Website maintained by StataCorp, USA.
Power and Sample Size Calculator (PS)
This software performs power and sample size calculations. PS can be used for studies with dichotomous, continuous, or survival
response measures. Developed by Drs W.D. Dupont and W.D. Plummer Jr., Department of Biostatistics, based at the Vanderbilt
University.
Bioconductor
Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.
It is primarily based on the R programming language. Bioconductor and this website are maintained by the Fred Hutchinson Cancer Research Center.
Design and Conduct
Please visit the following sections:
- Samples Collection and Processing
- Data Collection and Processing
-
P3G Study Catalogue
-
P3G Questionnaire Catalogue
-
P3G Physical and Cognitive Measures Catalogue
-
P3G DNA Processing Catalogue
Analysis
In Theory
General documentation and guidelines regarding statistical analysis of genomic and epidemiological data.
Please visit also the following section(s):
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Comparison Chart of Websites for Genetic and Genomic Statistics
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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.
HuGENet™
HuGE Review Handbook
This document aims to help biomedical researchers undertaking studies and systematic reviews in human genome
epidemiology to take sensible decisions about methods right through from study design to final analysis.
A HuGENet Systematic Review and Meta-Analysis Working Group handbook (2006).
In Practice
Real-life examples reporting specific analytic approaches.
National Health and
Nutrition Examination Survey (NHANES)
This document presents analytic and reporting guidelines that should be used for
NHANES data analyses and publications. It represents the latest information from the National Center for Health Statistics on
recommended approaches for analysis of all NHANES data, but with a particular focus on data collected in the continuous
NHANES (since 1999). A US Department of Health and Human Services-written document (2006).
IT Tools
Selected software for statistical analysis.
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.
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.
SAS Software for Distribution
This website lists
SAS macros which you might need while using the SAS statistical software. Provided by the Bonn University and by
the SAS Institute Inc.
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
Unphased,
PDT,
PLINK,
QTDT,
TDT-PC and
FBAT).
A Laboratory of Statistical Genetics-maintained website, based at the Rockefeller University.
R
R is a powerful, flexible, integrated statistical analysis environment
that provides analysis, modelling and graphics for data management. R is a programming language equivalent to S and user defined
functions provide for an open source route to the rich array of specialist statistical methodology usually vehicled by the S language.
StatLib - software and extensions for the S (Splus), and R language
provides access to S, SPlus and R functions across a wide range of specialist areas. It was initially written by Robert
Gentleman and Ross Ihaka of the Statistics Department of the University of Auckland. Website maintained by the R Foundation.
Epi Info™
Epi Info is a versatile software developed for the interface between epidemiology and public health. It can be used to
develop a simple questionnaire or form, customize the data entry process or undertake basic analyses.
The emphasis is on speed and ease of use; it is not a platform for sophisticated
modelling. The software and website are maintained by the Centers for Disease Control and Prevention (CDC) in the United States.
PEDSYS
PEDSYS 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.
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.
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.
STATA power and sample size
STATA is a powerful, flexible, integrated statistical analysis application that provides data management,
data analysis and graphics. Read how
to access external utilities and services to enhance basic use of STATA and how to interface with
the international STATA community. Ado and help files are also available to calculate power and sample size for gene-gene
and gene-environment interactions. A Genetic Epidemiology Division-maintained program, based at the Cancer
Research UK Clinical Centre, University of Leeds. Website maintained by StataCorp, USA.
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.
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.
HuGE Navigator
This website provides access to a continuously updated knowledge base in human genome epidemiology
through three main section. The HuGEpedia,
including Phenopedia and
Genopedia,
is an encyclopedia of human genetic variation in health and disease. HuGEtools allow users to search and
mine the literature in human genome epidemiology (
HuGE Literature Finder,
GWAS Integrator,
HuGE Investigator Browser,
Gene Prospector,
Genotype Prevalence Catalog,
HuGE Watch,
Variant Name Mapper,
HuGE Risk Translator
). A series of HuGE related informatics utilities and projects such as
GAPscreener,
HuGE Track,
and Open Source are available
in the HuGEmix section. Website developed and maintained
by the Human Genome Epidemiology Network (HuGENet™)(2009).
Dissemination
In Theory
General documentation and guidelines regarding dissemination of results.
STrengthening the Reporting of
OBservational studies in Epidemiology (STROBE)
This website provides guidelines to help writing complete and well-planned scientific articles based on observational
studies in epidemiology. STROBE is an initiative (analogous to the CONSORT initiative for randomized trials) involving
an international collaboration of epidemiologists, methodologists, statisticians, researchers and editors involved in the conduct
and dissemination of observational studies, that share the common aim of STrengthening the Reporting of OBservational studies
in Epidemiology. The initiative is currently led from the University of Bern.
Consolidated Standards of Reporting
Trials (CONSORT)
This website provides the CONSORT Statement which is
an evidence-based, minimum set of recommendations for reporting randomized controlled trials. Supported by Family
Health International, Cancer Research UK, Ottawa University and NHS.
In Practice
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.
