1. UCI GENOMICS HIGH THROUGHPUT FACILITY Institute for Genomics and Bioinformatics Review October 11, 2010

2. UCI GENOMICS HIGH THROUGHPUT FACILITY Personnel Director, Suzanne Sandmeyer, Ph.D. Manager, Robert Chadwick, Ph.D. Staff Research Associates Seung Ah Chung, SRAIII Valentina Ciobanu, SRAII Sharmila Mallya, SRAII Co-Director for Bioinformatics, Pierre Baldi, Ph.D. Staff postdoctoral fellow/programmer Christophe Magnan, Ph.D.

3. UCI GENOMICS HIGH THROUGHPUT FACILITY HT Processing and Affymetrix GeneChip Analysis Hybridization Oven 640 Fluidics Station 450 (3 each) GeneArray Scanner 7G ArrayPlex/Beckman FX BioRobot

4. UCI GENOMICS HIGH THROUGHPUT FACILITY Illumina HiSeq Next Gen Sequencer Illumina GAIIX Next Gen Sequencer Cbot cluster Station Paired-end Module MJ Research Tetrad Thermalcycler Agilent Bioanalyzer 2100 Covaris shearer

5. UCI GENOMICS HIGH THROUGHPUT FACILITY Genomics Services Affymetrix microarray analysis Sample preparation and QC Expression analysis SNP and Copy Number Variation Re-sequencing ChIP-Chip Illumina HT DNA sequence analysis Covaris DNA shearing De novo & Re-Sequencing of DNA RNA-seq (Digital Expression) ChIP-seq (Chromatin sequencing) library preparation (coming soon) Sample evaluation Agilent Bioanalyzer RNA and DNA analysis NanoDrop RNA & DNA quantification qPCR of Illumina libraries

6. WEB REDESIGN

7. UCI GENOMICS HIGH THROUGHPUT FACILITY GHTF Analysis Packages Basic consulting on data analysis approaches (free) & perform defined data analysis routines (recharge basis) Recharged access to users on 2 facility computers dedicated for data analysis with the following software: Partek’s Genomic Suite Affymetrix Expression Consol Affymetrix Genotyping Console & Integrated Genome Browser SAS JMP Genomics Various Web-based & Freeware Application Solutions Genomics Workbench from CLC Bio Web based statistical program Cyber-T on Linux Server: http://genomics.biochem.uci.edu/genex/cybert/ Work with the Institute for Genomics and Bioinfomatics: http://www.igb.uci.edu/

8. UCI GENOMICS HIGH THROUGHPUT FACILITY Experimental design consultation Investigator Institute for Genomics and Bioinformatics Pierre Baldi/Christophe Magnan Richard Lathrop Padhraic Smyth Xiaohui Xie UCI Statistical Core Robert Newcombe Hal Stern Rita Petersen CFCCC Bioinformatics Core Chad Garner Jenny Wu Experiment Analysis

9. UCI GENOMICS HIGH THROUGHPUT FACILITY Fixed expenses: Personnel Total recharges $2009-2010: $586,426 2010-2011 (est.): $698,085

10. UCI GENOMICS HIGH THROUGHPUT FACILITY Grants: NIH Shared Instrument Grant $500,000 (SBS PI; PB co-PI) Campus cost sharing: Year 1: $425,000 Year 2: $85,000 salaries Year 3-5 $100,000 salaries plus service contract contribution Stem Cell Center $360,000 toward HiSeq2000 Annual campus support CFCCC: $35,000

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12. UCI GENOMICS HIGH THROUGHPUT FACILITY llumina pipeline software for raw reads, quality scoring, and alignment (ELAND) Genomics Workbench can be found here: http://www.clcbio.com/ MAQ information can be found here: http://maq.sourceforge.net/ VELVET information can be found here: http://www.ebi.ac.uk/~zerbino/velvet/ Bowtie information can be found here: http://bowtie-bio.sourceforge.net/tutorial.shtmlhttp://bowtie-bio.sourceforge.net/tutorial.shtml A discussion comparing some aligners can be found here: http://massgenomics.wordpress.com/2008/05/14/short-read-aligners-maq-eland-and- others/ or http://www.sanger.ac.uk/Users/lh3/NGSalign.shtml

13. UCI GENOMICS HIGH THROUGHPUT FACILITY Financial Support Affymetrix Use Illumina Use

14. UCI GENOMICS HIGH THROUGHPUT FACILITY Leadership Suzanne Sandmeyer, Ph.D., Biological Chemistry, Director Robert Chadwick, Ph.D., Manager GHTF Pierre Baldi, Ph.D., Computer Science, Co-Director for Bioinformatics GHTF Chad Garner, Ph.D., Director CFC Cancer Center Bioinformatics Advisory Board Dan Mercola, M.D., Pathology, Director CFCCC Personal Genomics Hung Fan, Ph.D., Director, Cancer Research Institute, Dept. Molecular Biology and Biochemistry Anthony Long, Ph.D., Dept. Ecology and Evolutionary Biology Padhraic Smyth, Ph.D., Dept. Computer Sciences Bogi Andersen, M.D., Dept. Medicine, Div. of Endocrinology Robert Newcomb, Ph.D., Dept. Statistics Peter Donovan, Ph.D., Director, Stem Cell Center Lisa Dahm, Ph.D., Director, Clinical Informatics Kyoko Yokomori, Ph.D., Dept. Biological Chemistry

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17. UCI GENOMICS HIGH THROUGHPUT FACILITY Reduced Cluster Density Variability Using cBot vs Cluster Station

18. UCI GENOMICS HIGH THROUGHPUT FACILITY Improved Library Quantitation by qPCR Reduces Cluster Generation Variability

19. UCI GENOMICS HIGH THROUGHPUT FACILITY GAIIX versus HiSeq 2000 at the Broad Institute

20. UCI GENOMICS HIGH THROUGHPUT FACILITY Accuracy of HiSeq 2000 at the Broad Institute

21. UCI GENOMICS HIGH THROUGHPUT FACILITY NEBNext paired-end genomic library$350 for 10 libraries (primers not included) NuGen Encore paired-end genomic library$680 for 8 libraries Epicentre Nextera paired-end genomic library $625 for 5 libraries Illumina RNA-Seq library$3500 for 8 libraries (Superscript not included) Ambion/NuGen RNA-Seq library$1480 for 8 libraries Epicentre ScriptSeq RNA-Seq library$1200 for 6 libraries In process NuGen Barcoded RNA-Seq Libraries$3200 for 4 libraries (8 barcodes x 4 RNA) Epicentre Barcoded ScriptSeq Libraries$1400 for 4 libraries (12 barcodes x for Paired End Genomic Libraries take 4 to 6 hours to make RNA-Seq Libraries take 6 hours (Epicentre) to 3 partial days (Illumina) to make RNA Library Methods Tested in the GHTF

22. UCI GENOMICS HIGH THROUGHPUT FACILITY Standard Curve : Standards from KAPA Library qPCR Kit Efficiency of the standard qPCR reaction is 98%

23. UCI GENOMICS HIGH THROUGHPUT FACILITY SampleNanodrop QPCR ng/ul Nugen DNA lib: SM65.81 48.77 Nugen DNA lib :VC60.8 33.66 PhiX control 3.12 RNA seq Illumina35.51 0.00007 RNA seq 1 Ambion_Nugen Lib kit9.67 1.2 RNA seq 2 Ambion Second cycle cDNA_Nugen lib kit27.22 18.99 Comparison Between Nanodrop and qPCR Quantification Note that by Nanodrop the Illumina RNA-Seq library gives a good yield but by qPCR the yield was very poor indicating the library is mostly primer artifacts.

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34. * Whole genome re-sequencing and targeted re-sequencing of genomes of any size and type – from bacteria and viral to humans * De novo assembly of an unlimited number of reads, for genomes up to human size (3 billion bp) * SNP/DIP detection and identification of genomic rearrangements * Digital Gene Expression based on RNA-Seq, including a wide range of downstream gene expression analyses * Discovery of novel transcripts/exons * Ability to work with Expression Arrays and RNA-seq results at the same time, enabling comparison of results * Interactive views of assemblies and derived gene expression data * Small RNA-seq * Tag Profiling, including SAGE screen analyses * Chromatin immunoprecipitation sequencing (ChIP-seq) analysis * Peak finding and peak refinement * Graph and table of background distribution and false discovery rate * Peak table and annotations Genomics Workbench (CLC Bio)

35. The Broadcom Distributed Unified Cluster (BDUC) is, as the name suggests, a distributed group of clusters unified by running under a single Sun Grid Engine (SGE) Resource Manager. BDUC consists of 2 subclusters of 40 2core AMD64 Opteron252/2.6GHz nodes running 64bit/CentOS 5. One group of 40 nodes is in the NACS Academic Data Center and another of 40 nodes is in the ICS data center, for a total of 80 nodes / 160 cores. The nodes are interconnected with 1Gb ethernet and have the MPICH and MPICH2 environments for parallel jobs. BDUC

36. Sequence Capture Microarrays Can Be Used to Enrich Genomic DNA for Specific Regions of the Genome Following enrichment and DNA amplification, the enriched DNA regions can be directly sequenced using next-gen sequencers. This can greatly expedite the discovery of causative genes in genetic linkage association studies.