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The nature and identification of quantitative trait loci: a community's view

Abstract

This white paper by eighty members of the Complex Trait Consortium presents a community's view on the approaches and statistical analyses that are needed for the identification of genetic loci that determine quantitative traits. Quantitative trait loci (QTLs) can be identified in several ways, but is there a definitive test of whether a candidate locus actually corresponds to a specific QTL?

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Author information

Authors and Affiliations

Consortia

Supplementary information

Related links

Related links

Databases

LocusLink

Mtap1a

Tub

OMIM

cystic fibrosis

Further Information

Complex Trait Consortium

Complex Trait Consortium 2003 Meeting

Genetic Mapping Software

Genomics: a global resource

Mouse–Human Homologies

Mouse Nomenclature

Mouse Phenome Database

Neurogenetics at University of Tennessee Health Science Center

R/qtl: a QTL mapping environment

Rat Genome Database

SNPview: SNPs, SSLPs, alleles and haplotypes

Software for QTL data analysis

The Mouse Brain Library

The WebQTL Project

University of Wisconsin-Madison Department of Statistics

Glossary

ADVANCED INTERCROSS LINE

A strain that is derived by producing an F2 generation between any two inbred strains and then intercrossing in each subsequent generation (avoiding matings between closely related individuals).

BACKCROSS

A mating between a member of the F1 generation and a member of one of the parental lines that were used to make the F1.

CONFIDENCE INTERVAL

A statistical estimate of the interval that is likely (usually with 95% confidence) to include the parameter of interest, in this case the quantitative trait locus.

CONGENIC STRAIN

A strain that is produced by repeated backcrosses to an inbred strain with selection for a particular marker or chromosomal region from a donor strain.

CONSOMIC STRAIN

A strain that is produced by repeated backcrosses to an inbred strain, with selection for a whole chromosome from a donor strain.

HETEROGENEOUS STOCK

An outbred stock of mice that is formed from several inbred strains and is maintained by random matings between individuals in each subsequent generation.

INTERCROSS

A mating between two members of the F1 generation, or between two animals that are heterozygous at the same locus.

KNOCKOUT/CONGENIC STRAIN

A congenic strain that is made by repeated backcrossing to an inbred strain and selecting for the ablated target locus at each generation.

LOD THRESHOLD VALUE

The logarithm of the odds (LOD) score that must be reached to obtain highly significant, significant or suggestive statistical status.

MENDELIAN LOCUS

A genetic locus the alleles of which have discrete effects on the phenotype, which obeys Mendel's laws of segregation and independent assortment.

MODIFIER LOCUS

A genetic locus that has quantitative effects on the phenotype controlled by another genetic locus.

NEAR-ISOGENIC LINES

Lines that are identical except at one or a few genetic loci.

PROGENY TESTING

The testing of offspring to confirm the genotypes of the parents.

RECOMBINANT CONGENIC STRAIN

A strain that is made by crossing two inbred strains, followed by a few backcrosses of hybrids to one of the parental strains. Mice are then brother–sister mated until they are inbred.

RECOMBINANT INBRED STRAIN

A strain that is formed by crossing two (or sometimes more) inbred strains, followed by 20 or more consecutive generations of brother–sister matings.

RECOMBINANT INBRED-STRAIN CROSS

A cross that is made between two recombinant inbred lines.

RECOMBINANT QTL-INTROGRESSION STRAIN

A strain that is produced by a small series of repeated backcrosses (or backcrosses–intercrosses) and selection for an extreme phenotype. Mice are then brother–sister mated until they are inbred.

RECOMBINEERING TECHNIQUES

Molecular genetic-engineering techniques that use homologous recombination to manipulate and/or alter DNA.

TYPE I ERROR

The statistical error that is associated with rejecting the null hypothesis when it is true; sometimes referred to as the false-positive rate.

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Members of the Complex Trait Consortium. The nature and identification of quantitative trait loci: a community's view. Nat Rev Genet 4, 911–916 (2003). https://doi.org/10.1038/nrg1206

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