The Collaborative Cross at Oak Ridge National Laboratory: Developing a powerful resource for systems genetics

Elissa J. Chesler, Darla R. Miller, Lisa R. Branstetter, Leslie D. Galloway, Barbara L. Jackson, Vivek M. Philip, Brynn H. Voy, Cymbeline T. Culiat, David W. Threadgill, Robert Williams, Gary A. Churchill, Dabney K. Johnson, Kenneth F. Manly

Research output: Contribution to journalReview article

166 Citations (Scopus)

Abstract

Complex traits and disease comorbidity in humans and in model organisms are the result of naturally occurring polymorphisms that interact with each other and with the environment. To ensure the availability of resources needed to investigate biomolecular networks and systems-level phenotypes underlying complex traits, we have initiated breeding of a new genetic reference population of mice, the Collaborative Cross. This population has been designed to optimally support systems genetics analysis. Its novel and important features include a high level of genetic diversity, a large population size to ensure sufficient power in high-dimensional studies, and high mapping precision through accumulation of independent recombination events. Implementation of the Collaborative Cross has been ongoing at the Oak Ridge National Laboratory (ORNL) since May 2005. Production has been systematically managed using a software-assisted breeding program with fully traceable lineages, performed in a controlled environment. Currently, there are 650 lines in production, and close to 200 lines are now beyond their seventh generation of inbreeding. Retired breeders enter a high-throughput phenotyping protocol and DNA samples are banked for analyses of recombination history, allele drift and loss, and population structure. Herein we present a progress report of the Collaborative Cross breeding program at ORNL and a description of the kinds of investigations that this resource will support.

Original languageEnglish (US)
Pages (from-to)382-389
Number of pages8
JournalMammalian Genome
Volume19
Issue number6
DOIs
StatePublished - Jun 1 2008

Fingerprint

Breeding
Genetic Recombination
Controlled Environment
Inbreeding
Population Genetics
Population Density
Population
Comorbidity
Software
Alleles
Phenotype
DNA

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Chesler, E. J., Miller, D. R., Branstetter, L. R., Galloway, L. D., Jackson, B. L., Philip, V. M., ... Manly, K. F. (2008). The Collaborative Cross at Oak Ridge National Laboratory: Developing a powerful resource for systems genetics. Mammalian Genome, 19(6), 382-389. https://doi.org/10.1007/s00335-008-9135-8

The Collaborative Cross at Oak Ridge National Laboratory : Developing a powerful resource for systems genetics. / Chesler, Elissa J.; Miller, Darla R.; Branstetter, Lisa R.; Galloway, Leslie D.; Jackson, Barbara L.; Philip, Vivek M.; Voy, Brynn H.; Culiat, Cymbeline T.; Threadgill, David W.; Williams, Robert; Churchill, Gary A.; Johnson, Dabney K.; Manly, Kenneth F.

In: Mammalian Genome, Vol. 19, No. 6, 01.06.2008, p. 382-389.

Research output: Contribution to journalReview article

Chesler, EJ, Miller, DR, Branstetter, LR, Galloway, LD, Jackson, BL, Philip, VM, Voy, BH, Culiat, CT, Threadgill, DW, Williams, R, Churchill, GA, Johnson, DK & Manly, KF 2008, 'The Collaborative Cross at Oak Ridge National Laboratory: Developing a powerful resource for systems genetics', Mammalian Genome, vol. 19, no. 6, pp. 382-389. https://doi.org/10.1007/s00335-008-9135-8
Chesler EJ, Miller DR, Branstetter LR, Galloway LD, Jackson BL, Philip VM et al. The Collaborative Cross at Oak Ridge National Laboratory: Developing a powerful resource for systems genetics. Mammalian Genome. 2008 Jun 1;19(6):382-389. https://doi.org/10.1007/s00335-008-9135-8
Chesler, Elissa J. ; Miller, Darla R. ; Branstetter, Lisa R. ; Galloway, Leslie D. ; Jackson, Barbara L. ; Philip, Vivek M. ; Voy, Brynn H. ; Culiat, Cymbeline T. ; Threadgill, David W. ; Williams, Robert ; Churchill, Gary A. ; Johnson, Dabney K. ; Manly, Kenneth F. / The Collaborative Cross at Oak Ridge National Laboratory : Developing a powerful resource for systems genetics. In: Mammalian Genome. 2008 ; Vol. 19, No. 6. pp. 382-389.
@article{cc311ac5e9f6480187524b818b394b3c,
title = "The Collaborative Cross at Oak Ridge National Laboratory: Developing a powerful resource for systems genetics",
abstract = "Complex traits and disease comorbidity in humans and in model organisms are the result of naturally occurring polymorphisms that interact with each other and with the environment. To ensure the availability of resources needed to investigate biomolecular networks and systems-level phenotypes underlying complex traits, we have initiated breeding of a new genetic reference population of mice, the Collaborative Cross. This population has been designed to optimally support systems genetics analysis. Its novel and important features include a high level of genetic diversity, a large population size to ensure sufficient power in high-dimensional studies, and high mapping precision through accumulation of independent recombination events. Implementation of the Collaborative Cross has been ongoing at the Oak Ridge National Laboratory (ORNL) since May 2005. Production has been systematically managed using a software-assisted breeding program with fully traceable lineages, performed in a controlled environment. Currently, there are 650 lines in production, and close to 200 lines are now beyond their seventh generation of inbreeding. Retired breeders enter a high-throughput phenotyping protocol and DNA samples are banked for analyses of recombination history, allele drift and loss, and population structure. Herein we present a progress report of the Collaborative Cross breeding program at ORNL and a description of the kinds of investigations that this resource will support.",
author = "Chesler, {Elissa J.} and Miller, {Darla R.} and Branstetter, {Lisa R.} and Galloway, {Leslie D.} and Jackson, {Barbara L.} and Philip, {Vivek M.} and Voy, {Brynn H.} and Culiat, {Cymbeline T.} and Threadgill, {David W.} and Robert Williams and Churchill, {Gary A.} and Johnson, {Dabney K.} and Manly, {Kenneth F.}",
year = "2008",
month = "6",
day = "1",
doi = "10.1007/s00335-008-9135-8",
language = "English (US)",
volume = "19",
pages = "382--389",
journal = "Mammalian Genome",
issn = "0938-8990",
publisher = "Springer New York",
number = "6",

}

TY - JOUR

T1 - The Collaborative Cross at Oak Ridge National Laboratory

T2 - Developing a powerful resource for systems genetics

AU - Chesler, Elissa J.

AU - Miller, Darla R.

AU - Branstetter, Lisa R.

AU - Galloway, Leslie D.

AU - Jackson, Barbara L.

AU - Philip, Vivek M.

AU - Voy, Brynn H.

AU - Culiat, Cymbeline T.

AU - Threadgill, David W.

AU - Williams, Robert

AU - Churchill, Gary A.

AU - Johnson, Dabney K.

AU - Manly, Kenneth F.

PY - 2008/6/1

Y1 - 2008/6/1

N2 - Complex traits and disease comorbidity in humans and in model organisms are the result of naturally occurring polymorphisms that interact with each other and with the environment. To ensure the availability of resources needed to investigate biomolecular networks and systems-level phenotypes underlying complex traits, we have initiated breeding of a new genetic reference population of mice, the Collaborative Cross. This population has been designed to optimally support systems genetics analysis. Its novel and important features include a high level of genetic diversity, a large population size to ensure sufficient power in high-dimensional studies, and high mapping precision through accumulation of independent recombination events. Implementation of the Collaborative Cross has been ongoing at the Oak Ridge National Laboratory (ORNL) since May 2005. Production has been systematically managed using a software-assisted breeding program with fully traceable lineages, performed in a controlled environment. Currently, there are 650 lines in production, and close to 200 lines are now beyond their seventh generation of inbreeding. Retired breeders enter a high-throughput phenotyping protocol and DNA samples are banked for analyses of recombination history, allele drift and loss, and population structure. Herein we present a progress report of the Collaborative Cross breeding program at ORNL and a description of the kinds of investigations that this resource will support.

AB - Complex traits and disease comorbidity in humans and in model organisms are the result of naturally occurring polymorphisms that interact with each other and with the environment. To ensure the availability of resources needed to investigate biomolecular networks and systems-level phenotypes underlying complex traits, we have initiated breeding of a new genetic reference population of mice, the Collaborative Cross. This population has been designed to optimally support systems genetics analysis. Its novel and important features include a high level of genetic diversity, a large population size to ensure sufficient power in high-dimensional studies, and high mapping precision through accumulation of independent recombination events. Implementation of the Collaborative Cross has been ongoing at the Oak Ridge National Laboratory (ORNL) since May 2005. Production has been systematically managed using a software-assisted breeding program with fully traceable lineages, performed in a controlled environment. Currently, there are 650 lines in production, and close to 200 lines are now beyond their seventh generation of inbreeding. Retired breeders enter a high-throughput phenotyping protocol and DNA samples are banked for analyses of recombination history, allele drift and loss, and population structure. Herein we present a progress report of the Collaborative Cross breeding program at ORNL and a description of the kinds of investigations that this resource will support.

UR - http://www.scopus.com/inward/record.url?scp=52549103273&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=52549103273&partnerID=8YFLogxK

U2 - 10.1007/s00335-008-9135-8

DO - 10.1007/s00335-008-9135-8

M3 - Review article

C2 - 18716833

AN - SCOPUS:52549103273

VL - 19

SP - 382

EP - 389

JO - Mammalian Genome

JF - Mammalian Genome

SN - 0938-8990

IS - 6

ER -