Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform

<p>Abstract</p> <p>Background</p> <p>Copy number data are routinely being extracted from genome-wide association study chips using a variety of software. We empirically evaluated and compared four freely-available software packages designed for Affymetrix SNP chips to estimate copy number: Affymetrix Power Tools (APT), Aroma.Affymetrix, PennCNV and CRLMM. Our evaluation used 1,418 GENOA samples that were genotyped on the Affymetrix Genome-Wide Human SNP Array 6.0. We compared bias and variance in the locus-level copy number data, the concordance amongst regions of copy number gains/deletions and the false-positive rate amongst deleted segments.</p> <p>Results</p> <p>APT had median locus-level copy numbers closest to a value of two, whereas PennCNV and Aroma.Affymetrix had the smallest variability associated with the median copy number. Of those evaluated, only PennCNV provides copy number specific quality-control metrics and identified 136 poor CNV samples. Regions of copy number variation (CNV) were detected using the hidden Markov models provided within PennCNV and CRLMM/VanillaIce. PennCNV detected more CNVs than CRLMM/VanillaIce; the median number of CNVs detected per sample was 39 and 30, respectively. PennCNV detected most of the regions that CRLMM/VanillaIce did as well as additional CNV regions. The median concordance between PennCNV and CRLMM/VanillaIce was 47.9% for duplications and 51.5% for deletions. The estimated false-positive rate associated with deletions was similar for PennCNV and CRLMM/VanillaIce.</p> <p>Conclusions</p> <p>If the objective is to perform statistical tests on the locus-level copy number data, our empirical results suggest that PennCNV or Aroma.Affymetrix is optimal. If the objective is to perform statistical tests on the summarized segmented data then PennCNV would be preferred over CRLMM/VanillaIce. Specifically, PennCNV allows the analyst to estimate locus-level copy number, perform segmentation and evaluate CNV-specific quality-control metrics within a single software package. PennCNV has relatively small bias, small variability and detects more regions while maintaining a similar estimated false-positive rate as CRLMM/VanillaIce. More generally, we advocate that software developers need to provide guidance with respect to evaluating and choosing optimal settings in order to obtain optimal results for an individual dataset. Until such guidance exists, we recommend trying multiple algorithms, evaluating concordance/discordance and subsequently consider the union of regions for downstream association tests.</p

Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants

<div><p>Genetic variants that modify brain gene expression may also influence risk for human diseases. We measured expression levels of 24,526 transcripts in brain samples from the cerebellum and temporal cortex of autopsied subjects with Alzheimer's disease (AD, cerebellar n = 197, temporal cortex n = 202) and with other brain pathologies (non–AD, cerebellar n = 177, temporal cortex n = 197). We conducted an expression genome-wide association study (eGWAS) using 213,528 <em>cis</em>SNPs within ±100 kb of the tested transcripts. We identified 2,980 cerebellar <em>cis</em>SNP/transcript level associations (2,596 unique <em>cis</em>SNPs) significant in both ADs and non–ADs (q<0.05, p = 7.70×10⁻⁵–1.67×10⁻⁸²). Of these, 2,089 were also significant in the temporal cortex (p = 1.85×10⁻⁵–1.70×10⁻¹⁴¹). The top cerebellar <em>cis</em>SNPs had 2.4-fold enrichment for human disease-associated variants (p<10⁻⁶). We identified novel <em>cis</em>SNP/transcript associations for human disease-associated variants, including progressive supranuclear palsy <em>SLCO1A2</em>/rs11568563, Parkinson's disease (PD) <em>MMRN1</em>/rs6532197, Paget's disease <em>OPTN</em>/rs1561570; and we confirmed others, including PD <em>MAPT</em>/rs242557, systemic lupus erythematosus and ulcerative colitis <em>IRF5</em>/rs4728142, and type 1 diabetes mellitus <em>RPS26</em>/rs1701704. In our eGWAS, there was 2.9–3.3 fold enrichment (p<10⁻⁶) of significant <em>cis</em>SNPs with suggestive AD–risk association (p<10⁻³) in the Alzheimer's Disease Genetics Consortium GWAS. These results demonstrate the significant contributions of genetic factors to human brain gene expression, which are reliably detected across different brain regions and pathologies. The significant enrichment of brain <em>cis</em>SNPs among disease-associated variants advocates gene expression changes as a mechanism for many central nervous system (CNS) and non–CNS diseases. Combined assessment of expression and disease GWAS may provide complementary information in discovery of human disease variants with functional implications. Our findings have implications for the design and interpretation of eGWAS in general and the use of brain expression quantitative trait loci in the study of human disease genetics.</p> </div

Glutathione S-transferase omega genes in Alzheimer and Parkinson disease risk, age-at-diagnosis and brain gene expression: an association study with mechanistic implications

Abstract Background Glutathione S-transferase omega-1 and 2 genes (GSTO1, GSTO2), residing within an Alzheimer and Parkinson disease (AD and PD) linkage region, have diverse functions including mitigation of oxidative stress and may underlie the pathophysiology of both diseases. GSTO polymorphisms were previously reported to associate with risk and age-at-onset of these diseases, although inconsistent follow-up study designs make interpretation of results difficult. We assessed two previously reported SNPs, GSTO1 rs4925 and GSTO2 rs156697, in AD (3,493 ADs vs. 4,617 controls) and PD (678 PDs vs. 712 controls) for association with disease risk (case-controls), age-at-diagnosis (cases) and brain gene expression levels (autopsied subjects). Results We found that rs156697 minor allele associates with significantly increased risk (odds ratio = 1.14, p = 0.038) in the older ADs with age-at-diagnosis > 80 years. The minor allele of GSTO1 rs4925 associates with decreased risk in familial PD (odds ratio = 0.78, p = 0.034). There was no other association with disease risk or age-at-diagnosis. The minor alleles of both GSTO SNPs associate with lower brain levels of GSTO2 (p = 4.7 × 10-11-1.9 × 10-27), but not GSTO1. Pathway analysis of significant genes in our brain expression GWAS, identified significant enrichment for glutathione metabolism genes (p = 0.003). Conclusion These results suggest that GSTO locus variants may lower brain GSTO2 levels and consequently confer AD risk in older age. Other glutathione metabolism genes should be assessed for their effects on AD and other chronic, neurologic diseases.</p

Novel late-onset Alzheimer disease loci variants associate with brain gene expression

OBJECTIVE: Recent genome-wide association studies (GWAS) of late-onset Alzheimer disease (LOAD) identified 9 novel risk loci. Discovery of functional variants within genes at these loci is required to confirm their role in Alzheimer disease (AD). Single nucleotide polymorphisms that influence gene expression (eSNPs) constitute an important class of functional variants. We therefore investigated the influence of the novel LOAD risk loci on human brain gene expression. METHODS: We measured gene expression levels in the cerebellum and temporal cortex of autopsied AD subjects and those with other brain pathologies (∼400 total subjects). To determine whether any of the novel LOAD risk variants are eSNPs, we tested their cis-association with expression of 6 nearby LOAD candidate genes detectable in human brain (ABCA7, BIN1, CLU, MS4A4A, MS4A6A, PICALM) and an additional 13 genes ±100 kb of these SNPs. To identify additional eSNPs that influence brain gene expression levels of the novel candidate LOAD genes, we identified SNPs ±100 kb of their location and tested for cis-associations. RESULTS: CLU rs11136000 (p = 7.81 × 10(−4)) and MS4A4A rs2304933/rs2304935 (p = 1.48 × 10(−4)–1.86 × 10(−4)) significantly influence temporal cortex expression levels of these genes. The LOAD-protective CLU and risky MS4A4A locus alleles associate with higher brain levels of these genes. There are other cis-variants that significantly influence brain expression of CLU and ABCA7 (p = 4.01 × 10(−5)–9.09 × 10(−9)), some of which also associate with AD risk (p = 2.64 × 10(−2)–6.25 × 10(−5)). CONCLUSIONS: CLU and MS4A4A eSNPs may at least partly explain the LOAD risk association at these loci. CLU and ABCA7 may harbor additional strong eSNPs. These results have implications in the search for functional variants at the novel LOAD risk loci

Validation of top cerebellar <i>cis</i>SNP/transcript associations in the temporal cortex.

<p>Of the 2,980 top <i>cis</i>SNP/transcript associations, 2,685 existed in the temporal cortex replication study. Some of these top associations are shown. Only one <i>cis</i>SNP/transcript pair is selected for depiction. The chromosome (CHR), SNP, Probe, Gene Symbol (SYMBOL) of these associations are depicted. The uncorrected (P), genome-wide (P_Bonf) and study-wide Bonferroni-corrected (P_Bonf-study) P values, Beta coefficient of association are shown for the combined (All) analyses in the cerebellar eGWAS and the temporal cortex replication study. Regression coefficients are based on the SNP minor allele using an additive model.</p

Summary of brain eGWAS and human disease associations.

<p>Summary of brain eGWAS and human disease associations.</p

Examples of top cerebellar eGWAS <i>cis</i>SNP/transcript associations.

<p>There are 2,980 cerebellar <i>cis</i>SNP/transcript associations with q<0.05 both in the ADs and non–ADs. Some of these top associations are shown. Only one <i>cis</i>SNP/transcript pair is selected for depiction. The chromosome (CHR), SNP, Probe, Gene Symbol (SYMBOL) of these associations are depicted. The uncorrected (P), Bonferroni-corrected (P_Bonf) P, q values, and Beta coefficients of association are shown for the Non–ADs, ADs and combined (All) analyses. Regression coefficients are based on the SNP minor allele using an additive model.</p

Examples of top cerebellar eGWAS <i>cis</i>SNPs also associated with complex diseases/traits.

<p>The top 2,980 cerebellar eGWAS <i>cis</i>SNPs were compared to the “Catalog of Published GWAS” (<a href="http://www.genome.gov/gwastudies" target="_blank">www.genome.gov/gwastudies</a>). Some of the resulting 60 common associations are reported. The chromosome (CHR), SNP, eGWAS Minor Allele, Probe, Gene Symbol (SYMBOL) of these associations are depicted. The uncorrected (P) and Beta coefficient of associations are shown for the combined (All) analyses of the cerebellar eGWAS. Regression coefficients are based on the SNP minor allele using an additive model. The information for the complex disease/trait GWAS was downloaded from their website accessed on 04/23/2011. The disease/trait associated SNPs shown are the strongest SNPs depicted in the disease/trait GWAS. The associating allele (Strongest SNP-Risk Allele), p-value, OR or beta for the strongest disease/trait SNPs are shown.</p