A framework to link whole genome SNP association studies to systems genetics

Stephen Goodswen; HN Kadarmideen; Cedric Gondro; Julius H Van Der Werf

A framework to link whole genome SNP association studies to systems genetics

Stephen Goodswen
, HN Kadarmideen
, Cedric Gondro
, Julius H Van Der Werf

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

One of the main outcomes from whole genome association studies (WGAS) are statistically significant single nucleotide polymorphisms (SNPs). This outcome would be enhanced if either biological meaning or potential functional roles for these SNPs are revealed. Such knowledge would enhance the process of marker- or gene-assisted selection (MAS/GAS), or at least would provide more understanding of the achieved genetic change. We develop and present an R package called 'FunctSNP', interfaced to a relational database, to add potential functional information to SNPs that have shown to be statistically significant in a WGAS. The approach and developed software has been designed in such away that the database can contain any model species.

Original language	English
Title of host publication	Proceedings of the Association for the Advancement of Animal Breeding and Genetics
Editors	A Safari, B Pattie, B Restall
Place of Publication	Armidale, Australia
Publisher	Association for the Advancement of Animal Breeding and Genetics (AAABG)
Pages	454-457
Volume	18
ISBN (Print)	9780646521039
Publication status	Published - 2009
Event	AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics - Barossa Valley, Australia Duration: 27 Sept 2009 → 2 Oct 2009

Conference

Conference	AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics
City	Barossa Valley, Australia
Period	27/09/09 → 2/10/09

Keywords

Genomics
Bioinformatics Software

Access to Document

https://hdl.handle.net/1959.11/5121

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Cite this

Goodswen, S., Kadarmideen, HN., Gondro, C., & Van Der Werf, J. H. (2009). A framework to link whole genome SNP association studies to systems genetics. In A. Safari, B. Pattie, & B. Restall (Eds.), Proceedings of the Association for the Advancement of Animal Breeding and Genetics (Vol. 18, pp. 454-457). Association for the Advancement of Animal Breeding and Genetics (AAABG). https://hdl.handle.net/1959.11/5121

Goodswen, Stephen ; Kadarmideen, HN ; Gondro, Cedric et al. / A framework to link whole genome SNP association studies to systems genetics. Proceedings of the Association for the Advancement of Animal Breeding and Genetics. editor / A Safari ; B Pattie ; B Restall. Vol. 18 Armidale, Australia : Association for the Advancement of Animal Breeding and Genetics (AAABG), 2009. pp. 454-457

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title = "A framework to link whole genome SNP association studies to systems genetics",

abstract = "One of the main outcomes from whole genome association studies (WGAS) are statistically significant single nucleotide polymorphisms (SNPs). This outcome would be enhanced if either biological meaning or potential functional roles for these SNPs are revealed. Such knowledge would enhance the process of marker- or gene-assisted selection (MAS/GAS), or at least would provide more understanding of the achieved genetic change. We develop and present an R package called 'FunctSNP', interfaced to a relational database, to add potential functional information to SNPs that have shown to be statistically significant in a WGAS. The approach and developed software has been designed in such away that the database can contain any model species.",

keywords = "Genomics, Bioinformatics Software",

author = "Stephen Goodswen and HN Kadarmideen and Cedric Gondro and \{Van Der Werf\}, \{Julius H\}",

year = "2009",

language = "English",

isbn = "9780646521039",

volume = "18",

pages = "454--457",

editor = "A Safari and B Pattie and B Restall",

booktitle = "Proceedings of the Association for the Advancement of Animal Breeding and Genetics",

publisher = "Association for the Advancement of Animal Breeding and Genetics (AAABG)",

note = "AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics ; Conference date: 27-09-2009 Through 02-10-2009",

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Goodswen, S, Kadarmideen, HN, Gondro, C & Van Der Werf, JH 2009, A framework to link whole genome SNP association studies to systems genetics. in A Safari, B Pattie & B Restall (eds), Proceedings of the Association for the Advancement of Animal Breeding and Genetics. vol. 18, Association for the Advancement of Animal Breeding and Genetics (AAABG), Armidale, Australia, pp. 454-457, AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics, Barossa Valley, Australia, 27/09/09. <https://hdl.handle.net/1959.11/5121>

A framework to link whole genome SNP association studies to systems genetics. / Goodswen, Stephen; Kadarmideen, HN; Gondro, Cedric et al.
Proceedings of the Association for the Advancement of Animal Breeding and Genetics. ed. / A Safari; B Pattie; B Restall. Vol. 18 Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG), 2009. p. 454-457.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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T1 - A framework to link whole genome SNP association studies to systems genetics

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AU - Kadarmideen, HN

AU - Gondro, Cedric

AU - Van Der Werf, Julius H

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N2 - One of the main outcomes from whole genome association studies (WGAS) are statistically significant single nucleotide polymorphisms (SNPs). This outcome would be enhanced if either biological meaning or potential functional roles for these SNPs are revealed. Such knowledge would enhance the process of marker- or gene-assisted selection (MAS/GAS), or at least would provide more understanding of the achieved genetic change. We develop and present an R package called 'FunctSNP', interfaced to a relational database, to add potential functional information to SNPs that have shown to be statistically significant in a WGAS. The approach and developed software has been designed in such away that the database can contain any model species.

AB - One of the main outcomes from whole genome association studies (WGAS) are statistically significant single nucleotide polymorphisms (SNPs). This outcome would be enhanced if either biological meaning or potential functional roles for these SNPs are revealed. Such knowledge would enhance the process of marker- or gene-assisted selection (MAS/GAS), or at least would provide more understanding of the achieved genetic change. We develop and present an R package called 'FunctSNP', interfaced to a relational database, to add potential functional information to SNPs that have shown to be statistically significant in a WGAS. The approach and developed software has been designed in such away that the database can contain any model species.

KW - Genomics

KW - Bioinformatics Software

UR - http://web4ftp.it.csiro.au/ftp4goo17a/FunctSNP/FunctSNP_Application.pdf

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M3 - Conference contribution

SN - 9780646521039

VL - 18

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EP - 457

BT - Proceedings of the Association for the Advancement of Animal Breeding and Genetics

A2 - Safari, A

A2 - Pattie, B

A2 - Restall, B

PB - Association for the Advancement of Animal Breeding and Genetics (AAABG)

CY - Armidale, Australia

T2 - AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics

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ER -

Goodswen S, Kadarmideen HN, Gondro C, Van Der Werf JH. A framework to link whole genome SNP association studies to systems genetics. In Safari A, Pattie B, Restall B, editors, Proceedings of the Association for the Advancement of Animal Breeding and Genetics. Vol. 18. Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG). 2009. p. 454-457

A framework to link whole genome SNP association studies to systems genetics

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Keywords

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