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A noise-reduction GWAS analysis implicates altered regulation of neurite outgrowth and guidance in autism

John P Hussman1, Ren-Hua Chung2, Anthony J Griswold2, James M Jaworski2, Daria Salyakina2, Deqiong Ma2, Ioanna Konidari2, Patrice L Whitehead2, Jeffery M Vance2, Eden R Martin2, Michael L Cuccaro2, John R Gilbert2, Jonathan L Haines3 and Margaret A Pericak-Vance2*

Author Affiliations

1 Hussman Foundation, Ellicott City, MD, USA

2 John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, Miami, FL 33136, USA

3 Vanderbilt Center for Human Genetics Research, Vanderbilt University, Nashville, TN, USA

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Molecular Autism 2011, 2:1 doi:10.1186/2040-2392-2-1

Published: 19 January 2011

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Additional File 1:

Appendix

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Additional File 2:

Table S7: Haplotype configuration Association configuration for the power simulations.

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Additional File 3:

Comparative classification rates for genome-wide association studies - noise reduction (GWAS-NR), Joint analysis and Fisher's Test. GWAS-NR has an area under the curve (AUC) of 0.679 and the joint and Fisher's tests have AUC of 0.624 and 0.604, respectively, for the recessive model. Also GWAS-NR has AUC of 0.855 and the joint and Fisher's tests have AUC of 0.781 and 0.751, respectively, for the multiplicative model. For the dominant model, AUC for GWAS-NR, the joint and Fisher's tests are 0.964, 0.871 and 0.853, respectively. For the additive model, AUC for GWAS-NR, the joint and Fisher's tests are 0.893, 0.806 and 0.771, respectively.

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Flow Chart: GWAS-NR analysis workflow in autism datasets. A flow chart demonstrating the data analysis and candidate gene selection of the autism datasets presented. HIHG: Hussman Institute for Human Genomics dataset, AGRE: Autism Genetic Resource Exchange dataset, APL: Association in the Presence of Linkage, GWAS-NR: Genome-wide Association Study - Noise Reduction, DAVID: Database for Annotation, Visualization and Integrated Discovery.

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Additional File 5:

Table S1: linkage disequilibrium (LD) blocks identified by Genome-wide Association Study - Noise Reduction (GWAS-NR). Every LD block identified by GWAS-NR and haplotype analysis with a P-value < 0.05 is listed with the chromosome start and stop position, the length in basepairs of the LD block, and the minimum GWAS-NR P-value of the block.

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Additional File 6:

Table S2: RefSeq genes overlapping linkage disequilibrium (LD) blocks identified by Genome-wide Association Study - Noise Reduction (GWAS-NR). Every LD block identified by GWAS-NR and haplotype analysis with a P-value < 0.05 and that overlaps a gene in the RefSeq database is listed with the chromosome start and stop position, the length in basepairs of the LD block, the minimum GWAS-NR P-value of the block, and the RefSeq name of the gene(s) that overlap the block.

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Additional File 7:

Table S3: RefSeq genes nearest to linkage disequilibrium (LD) blocks identified by Genome-wide Association Study - Noise Reduction (GWAS-NR). Every LD block identified by GWAS-NR and haplotype analysis with a P-value < 0.05 that does not overlap with a gene in the reference sequence (RefSeq) database is listed with the chromosome start and stop position, the length in basepairs of the LD block, the minimum GWAS-NR P-value of the block and the RefSeq name of the gene(s) that is nearest to the block.

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Additional File 8:

Table S4: Autism candidate genes identified by Genome-wide Association Study - Noise Reduction (GWAS-NR). A complete list of reference sequence (RefSeq) genes either overlapping or nearest to every LD blocks with the P-value of either the overlapping or nearest block.

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Additional File 9:

Table S5: Autism candidate genes [Genome-wide Association Study - Noise Reduction (GWAS-NR)] having known roles in neurite outgrowth and guidance. A list of autism candidate genes with known roles in neurite outgrowth and axon guidance followed by a comment on molecular function and PubMed identifications of supporting literature.

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Additional File 10:

Table S6: autism candidate genes [Genome-wide Association Study - Noise Reduction (GWAS-NR)] having suggestive roles in neurite outgrowth and guidance. A list of autism candidate genes with presumptive roles in neurite outgrowth and axon guidance followed by a comment on molecular function and PubMed identifications of supporting literature.

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