Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes

Lisa M. Maier, Deborah J. Smyth, Adrian Vella, Felicity Payne, Jason D. Cooper, Rebecca Pask, Christopher Lowe, John Hulme, Luc J. Smink, Heather Fraser, Carolyn Moule, Kara M. Hunter, Giselle Chamberlain, Neil Walker, Sarah Nutland, Dag E. Undlien, Kjersti S. Rønningen, Cristian Guja, Constantin Ionescu-Tr̂govişte, David A. Savage & 5 others David P. Strachan, Laurence B. Peterson, John A. Todd, Linda S. Wicker, Rebecca C. Twells

Research output: Contribution to journalArticle

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Abstract

Background: One strategy to help identify susceptibility genes for complex, multifactorial diseases is to map disease loci in a representative animal model of the disorder. The nonobese diabetic (NOD) mouse is a model for human type 1 diabetes. Linkage and congenic strain analyses have identified several NOD mouse Idd (insulin dependent diabetes) loci, which have been mapped to small chromosome intervals, for which the orthologous regions in the human genome can be identified. Here, we have conducted re-sequencing and association analysis of six orthologous genes identified in NOD Idd loci: NRAMP1/SLC11A1 (orthologous to Nramp1/Slc11a1 in Idd5.2), FRAP1 (orthologous to Frap1 in Idd9.2), 4-1BB/CD137/TNFRSF9 (orthologous to 4-1bb/Cd137/ Tnrfrsf9 in Idd9.3), CD101/IGSF2 (orthologous to Cd101/Igsf2 in Idd10), B2M (orthologous to B2m in Idd13) and VAV3 (orthologous to Vav3 in Idd18). Results: Re-sequencing of a total of 110 kb of DNA from 32 or 96 type 1 diabetes cases yielded 220 single nucleotide polymorphisms (SNPs). Sixty-five SNPs, including 54 informative tag SNPs, and a microsatellite were selected and genotyped in up to 1,632 type 1 diabetes families and 1,709 cases and 1,829 controls. Conclusion: None of the candidate regions showed evidence of association with type 1 diabetes (P values > 0.2), indicating that common variation in these key candidate genes does not play a major role in type 1 diabetes susceptibility in the European ancestry populations studied.

Original languageEnglish (US)
JournalBMC Genetics
Volume6
DOIs
StatePublished - Feb 18 2005
Externally publishedYes

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Type 1 Diabetes Mellitus
Single Nucleotide Polymorphism
Inbred NOD Mouse
Genes
Insulin
Human Genome
Microsatellite Repeats
Animal Models
Chromosomes
DNA
Population

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes. / Maier, Lisa M.; Smyth, Deborah J.; Vella, Adrian; Payne, Felicity; Cooper, Jason D.; Pask, Rebecca; Lowe, Christopher; Hulme, John; Smink, Luc J.; Fraser, Heather; Moule, Carolyn; Hunter, Kara M.; Chamberlain, Giselle; Walker, Neil; Nutland, Sarah; Undlien, Dag E.; Rønningen, Kjersti S.; Guja, Cristian; Ionescu-Tr̂govişte, Constantin; Savage, David A.; Strachan, David P.; Peterson, Laurence B.; Todd, John A.; Wicker, Linda S.; Twells, Rebecca C.

In: BMC Genetics, Vol. 6, 18.02.2005.

Research output: Contribution to journalArticle

Maier, LM, Smyth, DJ, Vella, A, Payne, F, Cooper, JD, Pask, R, Lowe, C, Hulme, J, Smink, LJ, Fraser, H, Moule, C, Hunter, KM, Chamberlain, G, Walker, N, Nutland, S, Undlien, DE, Rønningen, KS, Guja, C, Ionescu-Tr̂govişte, C, Savage, DA, Strachan, DP, Peterson, LB, Todd, JA, Wicker, LS & Twells, RC 2005, 'Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes', BMC Genetics, vol. 6. https://doi.org/10.1186/1471-2156-6-9
Maier, Lisa M. ; Smyth, Deborah J. ; Vella, Adrian ; Payne, Felicity ; Cooper, Jason D. ; Pask, Rebecca ; Lowe, Christopher ; Hulme, John ; Smink, Luc J. ; Fraser, Heather ; Moule, Carolyn ; Hunter, Kara M. ; Chamberlain, Giselle ; Walker, Neil ; Nutland, Sarah ; Undlien, Dag E. ; Rønningen, Kjersti S. ; Guja, Cristian ; Ionescu-Tr̂govişte, Constantin ; Savage, David A. ; Strachan, David P. ; Peterson, Laurence B. ; Todd, John A. ; Wicker, Linda S. ; Twells, Rebecca C. / Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes. In: BMC Genetics. 2005 ; Vol. 6.
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abstract = "Background: One strategy to help identify susceptibility genes for complex, multifactorial diseases is to map disease loci in a representative animal model of the disorder. The nonobese diabetic (NOD) mouse is a model for human type 1 diabetes. Linkage and congenic strain analyses have identified several NOD mouse Idd (insulin dependent diabetes) loci, which have been mapped to small chromosome intervals, for which the orthologous regions in the human genome can be identified. Here, we have conducted re-sequencing and association analysis of six orthologous genes identified in NOD Idd loci: NRAMP1/SLC11A1 (orthologous to Nramp1/Slc11a1 in Idd5.2), FRAP1 (orthologous to Frap1 in Idd9.2), 4-1BB/CD137/TNFRSF9 (orthologous to 4-1bb/Cd137/ Tnrfrsf9 in Idd9.3), CD101/IGSF2 (orthologous to Cd101/Igsf2 in Idd10), B2M (orthologous to B2m in Idd13) and VAV3 (orthologous to Vav3 in Idd18). Results: Re-sequencing of a total of 110 kb of DNA from 32 or 96 type 1 diabetes cases yielded 220 single nucleotide polymorphisms (SNPs). Sixty-five SNPs, including 54 informative tag SNPs, and a microsatellite were selected and genotyped in up to 1,632 type 1 diabetes families and 1,709 cases and 1,829 controls. Conclusion: None of the candidate regions showed evidence of association with type 1 diabetes (P values > 0.2), indicating that common variation in these key candidate genes does not play a major role in type 1 diabetes susceptibility in the European ancestry populations studied.",
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T1 - Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes

AU - Maier, Lisa M.

AU - Smyth, Deborah J.

AU - Vella, Adrian

AU - Payne, Felicity

AU - Cooper, Jason D.

AU - Pask, Rebecca

AU - Lowe, Christopher

AU - Hulme, John

AU - Smink, Luc J.

AU - Fraser, Heather

AU - Moule, Carolyn

AU - Hunter, Kara M.

AU - Chamberlain, Giselle

AU - Walker, Neil

AU - Nutland, Sarah

AU - Undlien, Dag E.

AU - Rønningen, Kjersti S.

AU - Guja, Cristian

AU - Ionescu-Tr̂govişte, Constantin

AU - Savage, David A.

AU - Strachan, David P.

AU - Peterson, Laurence B.

AU - Todd, John A.

AU - Wicker, Linda S.

AU - Twells, Rebecca C.

PY - 2005/2/18

Y1 - 2005/2/18

N2 - Background: One strategy to help identify susceptibility genes for complex, multifactorial diseases is to map disease loci in a representative animal model of the disorder. The nonobese diabetic (NOD) mouse is a model for human type 1 diabetes. Linkage and congenic strain analyses have identified several NOD mouse Idd (insulin dependent diabetes) loci, which have been mapped to small chromosome intervals, for which the orthologous regions in the human genome can be identified. Here, we have conducted re-sequencing and association analysis of six orthologous genes identified in NOD Idd loci: NRAMP1/SLC11A1 (orthologous to Nramp1/Slc11a1 in Idd5.2), FRAP1 (orthologous to Frap1 in Idd9.2), 4-1BB/CD137/TNFRSF9 (orthologous to 4-1bb/Cd137/ Tnrfrsf9 in Idd9.3), CD101/IGSF2 (orthologous to Cd101/Igsf2 in Idd10), B2M (orthologous to B2m in Idd13) and VAV3 (orthologous to Vav3 in Idd18). Results: Re-sequencing of a total of 110 kb of DNA from 32 or 96 type 1 diabetes cases yielded 220 single nucleotide polymorphisms (SNPs). Sixty-five SNPs, including 54 informative tag SNPs, and a microsatellite were selected and genotyped in up to 1,632 type 1 diabetes families and 1,709 cases and 1,829 controls. Conclusion: None of the candidate regions showed evidence of association with type 1 diabetes (P values > 0.2), indicating that common variation in these key candidate genes does not play a major role in type 1 diabetes susceptibility in the European ancestry populations studied.

AB - Background: One strategy to help identify susceptibility genes for complex, multifactorial diseases is to map disease loci in a representative animal model of the disorder. The nonobese diabetic (NOD) mouse is a model for human type 1 diabetes. Linkage and congenic strain analyses have identified several NOD mouse Idd (insulin dependent diabetes) loci, which have been mapped to small chromosome intervals, for which the orthologous regions in the human genome can be identified. Here, we have conducted re-sequencing and association analysis of six orthologous genes identified in NOD Idd loci: NRAMP1/SLC11A1 (orthologous to Nramp1/Slc11a1 in Idd5.2), FRAP1 (orthologous to Frap1 in Idd9.2), 4-1BB/CD137/TNFRSF9 (orthologous to 4-1bb/Cd137/ Tnrfrsf9 in Idd9.3), CD101/IGSF2 (orthologous to Cd101/Igsf2 in Idd10), B2M (orthologous to B2m in Idd13) and VAV3 (orthologous to Vav3 in Idd18). Results: Re-sequencing of a total of 110 kb of DNA from 32 or 96 type 1 diabetes cases yielded 220 single nucleotide polymorphisms (SNPs). Sixty-five SNPs, including 54 informative tag SNPs, and a microsatellite were selected and genotyped in up to 1,632 type 1 diabetes families and 1,709 cases and 1,829 controls. Conclusion: None of the candidate regions showed evidence of association with type 1 diabetes (P values > 0.2), indicating that common variation in these key candidate genes does not play a major role in type 1 diabetes susceptibility in the European ancestry populations studied.

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