Journal ArticleDOI
Genotyping errors: causes, consequences and solutions.
TLDR
A protocol for estimating error rates is proposed and it is recommended that these measures be systemically reported to attest the reliability of published genotyping studies.Abstract:
Although genotyping errors affect most data and can markedly influence the biological conclusions of a study, they are too often neglected. Errors have various causes, but their occurrence and effect can be limited by considering these causes in the production and analysis of the data. Procedures that have been developed for dealing with errors in linkage studies, forensic analyses and non-invasive genotyping should be applied more broadly to any genetic study. We propose a protocol for estimating error rates and recommend that these measures be systemically reported to attest the reliability of published genotyping studies.read more
Citations
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Journal ArticleDOI
Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment.
TL;DR: This paper showed that the likelihood equations used by versions 1.0 and 2.0 of CERVUS to accommodate genotyping error miscalculate the probability of observing an erroneous genotype.
Journal ArticleDOI
Mendelian randomization: using genes as instruments for making causal inferences in epidemiology.
TL;DR: The use of germline genetic variants that proxy for environmentally modifiable exposures as instruments for these exposures is one form of IV analysis that can be implemented within observational epidemiological studies and can be considered as analogous to randomized controlled trials.
Journal ArticleDOI
Biomarkers of cardiovascular disease: molecular basis and practical considerations.
TL;DR: This review provides an overview of the molecular basis of biomarker discovery and selection and the practical considerations that are a prerequisite to their clinical use.
Journal ArticleDOI
Data quality control in genetic case-control association studies
Carl A. Anderson,Fredrik Pettersson,Geraldine M. Clarke,Lon R. Cardon,Andrew P. Morris,Krina T. Zondervan +5 more
TL;DR: This protocol details the steps for data quality assessment and control that are typically carried out during case-control association studies, including the identification and removal of DNA samples and markers that introduce bias.
Journal ArticleDOI
Who is eating what: diet assessment using next generation sequencing.
François Pompanon,Bruce E. Deagle,Bruce E. Deagle,William Oliver Christian Symondson,David Steven Brown,Simon N. Jarman,Pierre Taberlet +6 more
TL;DR: The power and pitfalls of NGS diet methods are reviewed, the critical factors to take into account when choosing or designing a suitable barcode are presented and the validation of data accuracy including the viability of producing quantitative data is discussed.
References
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Journal ArticleDOI
Micro-Checker: Software for identifying and correcting genotyping errors in microsatellite data
TL;DR: MICRO - CHECKER estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis.
Journal ArticleDOI
Instability and decay of the primary structure of DNA
TL;DR: The spontaneous decay of DNA is likely to be a major factor in mutagenesis, carcinogenesis and ageing, and also sets limits for the recovery of DNA fragments from fossils.
Journal ArticleDOI
Statistical confidence for likelihood-based paternity inference in natural populations
TL;DR: This study derives likelihood ratios for paternity inference with codominant markers taking account of typing error, and defines a statistic Δ for resolving paternity, and demonstrates the method is robust to their presence under commonly encountered conditions.
Journal ArticleDOI
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
Alvis Brazma,Pascal Hingamp,John Quackenbush,Gavin Sherlock,Paul T. Spellman,Chris Stoeckert,John Aach,Wilhelm Ansorge,Catherine A. Ball,Helen C. Causton,Terry Gaasterland,Patrick Glenisson,Frank C. P. Holstege,Irene F. Kim,Victor Markowitz,John C. Matese,Helen Parkinson,Alan J. Robinson,Ugis Sarkans,Steffen Schulze-Kremer,Jason E. Stewart,Ronald C. Taylor,Jaak Vilo,Martin Vingron +23 more
TL;DR: The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools.
Journal ArticleDOI
R/qtl: QTL mapping in experimental crosses
TL;DR: R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTLs) in experimental populations derived from inbred lines and includes functions for estimating genetic maps, identifying genotyping errors, and performing single-QTL and two-dimensional, two- QTL genome scans by multiple methods.
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