1 SNPTrack Quick Start National Center for Toxicological Research U.S. Food and Drug Administration 3900 NCTR Road Jefferson, AR 72079

2 SNPTrack Overview Mission – To support the FDA’s research in pharmacogenetics and regulation of personalized medicine (8 out of 40 VGDS submissions contain SNP data) What is SNPTrack? – An integrated system for SNP (Single Nucleotide Polymorphism) and GWAS (Genome-wide Association Studies) data management, analysis and interpretation.

3 SNPTrack - An integrated system for SNP data Oracle Relational Database Hosting – Phenotype data (study information) Including sample ID, sex, age, race, family history, and etc. Plus demographic and phenotypic information – Genotype data (genotype results) Genotype calls results (SNP chip assay results or individual genotype results, usually calls generated from software provided by the manufacture) – SNP panel (a list of SNP that is typed. Or SNP chip from Affymatrix or Illumina). Affymatrix (SNP 6.0, SNP 5.0, Mapping 500K, Mapping 100K, Mapping10K, DMET 2K) Illumina BeadChips (100K, 300K, 550K and 1 million) – SNP Library and other Libraries from ArrayTrack

4 Association analysis – SNP filtering by the Hardy-Weinberg equilibrium – PLINK (Allelic association, Genotypic association, Linear/logistic regression etc.) – Haploview (table view, correlation plot, LD plot, Haplotype block view, combination of p value filter, FDR, and combining and merging tables). SNPTrack - An integrated system for SNP data

5 Links of SNP Library for data interpretation – dbSNP, HapMap, Ensemble and UCSC Browser – Gene library for extended annotation and other library inter-links, such as protein Library, Orthologene Library, EntrezGene, GenBank, Gene Card, SwissPort, OMIM, Chromosomal map etc. – GOFFA and Pathway analysis for gene ontology, pathway and disease information SNPTrack - An integrated system for SNP data

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7 Microarray DB Libraries SNP data analysis SNPTrack for Genetic Data Management, Analysis and Interpretation

8 SNP DB Exp Owner Data is organized in a tree structure : Exp Name SNP List Study Dataset Input Data Formatted Data

9 Exploring DB SNP Panel (a list of SNP that is typed) Phenotype (study information) Genotype data (genotype results from SNP array or sequencing)

10 Exploring DB ( Creating a SNP Exp, data security, sharing and data importing)

11 Searching SNP Library

12 Analysis Tools

13 Analysis Tools Allelic Association SNPs are taken one by one. For every SNP, a 2x2 contingency table is built by counting the number of times each possible allele SNP appears in a case or control sample. Test results output F_A: Minor Allele freq in cases F_U: Minor Allele freq in controls CHISQ: Allelic test chi-square P: Fisher’s exact test OR: Odds Ratio

14 Analysis Tools Genotypic Association Test Results (Full Model Association Tests) One may perform tests of association between a disease and a variant other than the basic allelic test (which compares frequencies of alleles in cases versus controls), In addition to the basic allelic test: Cochran-Armitage trend test (additive) Genotypic (2 df) test – 2x3 contingency table) Dominant gene action test Recessive gene action test Results: ALLELIC, TREND, GENO, DOM or REC test with CHISQ, DF and corresponding P values. AAABBB Ctrl Case

15 Analysis Tools Linear /Logistic regression (Quantitative trait association) Quantitative traits can be tested for association also, using either asymptotic (likelihood ratio test and Wald test) or empirical significance values. If the chosen phenotype is quantitative (i.e. contains values other than 1, 2, 0 or missing) then PLINK will automatically treat the analysis as a quantitative trait analysis. That is, the same command as for disease-trait association BETA Regression coefficient SE Standard error R2 Regression r-squared T Wald test (based on t-distribution) P Wald test asymptotic p-value

16 SNP List Create Display Import Export Delete

17 SNP List – Venn Diagram Comm and unique SNP

18 Study Case1- CFS (Chronic Fatigue syndrome) collaborating with CDC It is part of the Wichita CFS Surveillance Study. Microarray Data (MWG 20K Human) was generated from167 participants and genotype data was generated from 80 participants by Affymatrix GeneChip (Mapping 100K). There are 62 participants are common for both platforms, in which 35 CFS and 27 non_CFS 175 genes have been identify as significant (P 4) and 65 SNPs are indentified as significant in Allelic association tests (P<0.01). Two genes are common (NPAS2_rs356653, and GRIK2 _rs & rs )

19 LD plot ( linkage disequilibrium)( they can be exchangeable) Gene_GRIK2 HapMap view:rs and rs are at intron (glutamate receptor, ionotropic, kainate)

20 UCSC browser on NPAS2_rs (neuronal PAS domain protein 2) Raj did one SNP at a time for 65 SNPs, we Show aTable for SNP information from UCSC using SNP Track by one click!!!)

21 UCSC browser on NPAS2_rs (a closer view)

22 Hapmap View Gene_NPAS2NPAS2_rs is closer to exon LD plot ( linkage disequilibrium)

23 NPAS2_rs HapMap view LD plot ( linkage disequilibrium)

24 Study Case2- Parkinson Disease _SNPTrack live demo ( Hon-Chung Fung etl. Laboratory of Nerogenetics, The Lancet Neurology, Vol. 6 No. 5 pp , May 2007) 273 Parkinson’s disease samples and 275 controls, total of 548 samples. SNP 100K (Illumina Infinium I) and HumanHap 300K are used, total of 400K SNP have been typed

25 Interpretation Link SNPs to various libraries for data interpretation

26 Interpretation (continued) KEGG – Kyoto Encyclopedia of Genes and Genomes KEGG is a suite of databases and associated software. KEGG Pathway database provides the information of metabolic, regulatory and disease pathways; Most of them are metabolic pathways.

27 Interpretation (continued) HumanRatMouse Kegg PathArt PathArt (Jubilant) – a pathway database The Pathways (over 600 mammalian disease and signaling) The Pathways is a collection of manually curated information from literature and public domain databases. In ArrayTrack

28 Interpretation (continued) PathArt GenesPathwaysPhysiology/diseaseStatistical significance of the pathway

29 Accessing SNPTrack and Support Currently SNPTrack is only available to FDA internally: SNPTrack is developed by the U.S. Food and Drug Administration, National Center for Toxicological Research (FDA/NCTR). FDA/NCTR reserves all rights for the software.

30 Thank you! National Center for Toxicological Research U.S. Food and Drug Administration