Evidence map›Paper›PMID 21293453›Full record

ArticleNature protocols2011

Basic statistical analysis in genetic case-control studies.

Geraldine M Clarke, Carl A Anderson, Fredrik H Pettersson, Lon R Cardon, Andrew P Morris, Krina T Zondervan

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature protocols, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 210 papers, 11 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
210citing papers in PubMed, 11 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

210 citing papers in PubMed, 11 syntheses or guidelines pooled it.

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150 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Geraldine M ClarkeGenetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. gclarke@well.ox.ac.uk
Carl A Anderson
Fredrik H Pettersson
Lon R Cardon
Andrew P Morris
Krina T Zondervan

Funding

Wellcome Trust 064890Wellcome Trust 081682Wellcome Trust 085235Wellcome Trust WT91745/Z/10/Z
6 · The paper itself

Abstract

This protocol describes how to perform basic statistical analysis in a population-based genetic association case-control study. The steps described involve the (i) appropriate selection of measures of association and relevance of disease models; (ii) appropriate selection of tests of association; (iii) visualization and interpretation of results; (iv) consideration of appropriate methods to control for multiple testing; and (v) replication strategies. Assuming no previous experience with software such as PLINK, R or Haploview, we describe how to use these popular tools for handling single-nucleotide polymorphism data in order to carry out tests of association and visualize and interpret results. This protocol assumes that data quality assessment and control has been performed, as described in a previous protocol, so that samples and markers deemed to have the potential to introduce bias to the study have been identified and removed. Study design, marker selection and quality control of case-control studies have also been discussed in earlier protocols. The protocol should take ~1 h to complete.

Indexed as

SoftwareCase-Control StudiesData Interpretation, StatisticalGenetic Association StudiesGenetic MarkersGenotypeHumansPolymorphism, Single NucleotideGenetic Markers

Identifiers

PMID21293453
PMCPMC3154648

What OpenQuestion holds

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Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.