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Schulich School of Medicine & Dentistry The University of Western Ontario London Regional Genomics Centre Next Generation Sequencing Meeting April 1, 2010.

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Presentation on theme: "Schulich School of Medicine & Dentistry The University of Western Ontario London Regional Genomics Centre Next Generation Sequencing Meeting April 1, 2010."— Presentation transcript:

1 Schulich School of Medicine & Dentistry The University of Western Ontario London Regional Genomics Centre Next Generation Sequencing Meeting April 1, 2010

2 Schulich School of Medicine & Dentistry The University of Western Ontario DNA Sequencing Facility User Base The LRGC Sequencing Facility has worked with over 400 labs across Canada.

3 Schulich School of Medicine & Dentistry The University of Western Ontario LRGC Sequencing Facility Use

4

5 Schulich School of Medicine & Dentistry The University of Western Ontario Microarray Facility Users

6 Schulich School of Medicine & Dentistry The University of Western Ontario Microarray

7 Schulich School of Medicine & Dentistry The University of Western Ontario NGS Applications Targeted resequencing (SNP, Indel, CNV) De novo genome sequencing Whole transcriptome seq Small RNAseq Epigenomics eg. ChIP seq

8 Schulich School of Medicine & Dentistry The University of Western Ontario NGS Technologies Next Generation Platforms now… –Illumina Solexa –Roche 454 –Applied Biosystems SOLid Single molecule sequencing coming… –Pacific BioSciences –Helicos –Ion Torrent

9 Schulich School of Medicine & Dentistry The University of Western Ontario NGS Technology Comparison ABI SOLiDIllumina GARoche FLX Cost SOLiD 4: $495k SOLiD PI: $240k IIe: $470k IIx: $250k HiSeq: $690k Titanium: $500k Quantity of Data per run SOLiD 4: 100Gb SOLiD PI: 50Gb IIe: Gb IIx: 50 – 95 Gb HiSeq: 200Gb Mb Run Time 7 Days4 Days9 Hours Pros Low error rate due to dibase probes Most widely used NGS platform. Requires least DNA Short run time. Long reads better for de novo sequencing Cons Long run times. Has been demonstrated certain reads don’t match reference Least multiplexing capability of the 3. Poor coverage of AT rich regions Expensive reagent cost. Difficulty reading homopolymer regions

10 Schulich School of Medicine & Dentistry The University of Western Ontario Needs Assessment Does the London Scientific Community need/want local access to NGS technology at a core lab? Recruitment tool? Survey users regarding which applications are required from NGS? –RNA-Seq, DNA-Seq, ChIP-Seq Other infrastructure –Data storage, bioinformatics, sequence capture device

11 Schulich School of Medicine & Dentistry The University of Western Ontario London Regional Genomics Centre Robarts Research Institute Survey Monkey Summary Spring 2010

12 Schulich School of Medicine & Dentistry The University of Western Ontario Survey Monkey Statistics Survey: 8 questions Recipients: 172 Total Started Survey: 60 (34.9%) Total Completed Survey: 54 (31.4%) Last survey 2004: 12/33 (36.45%)

13 Schulich School of Medicine & Dentistry The University of Western Ontario Satisfaction

14 Schulich School of Medicine & Dentistry The University of Western Ontario Satisfaction

15 Schulich School of Medicine & Dentistry The University of Western Ontario Financial Support Model

16 Schulich School of Medicine & Dentistry The University of Western Ontario Potential New Services

17 Schulich School of Medicine & Dentistry The University of Western Ontario Next-Generation Sequencing

18 Schulich School of Medicine & Dentistry The University of Western Ontario Next-Generation Sequencing

19 Schulich School of Medicine & Dentistry The University of Western Ontario Next-Generation Sequencing No. Samples/yearResponse 1 to to to to80 81 to 1002 >1002

20 Schulich School of Medicine & Dentistry The University of Western Ontario Single Molecule Real Time Sequencing Removes misrepresentation of template introduced during preparation 3 Platforms: Helicos - hardware cost $999,000 Pacific Bioscience - Expected platform late 2010/early 2011 Ion Torrent - Recently announced on March 2nd Announced to be “$50,000”

21 Schulich School of Medicine & Dentistry The University of Western Ontario Funding Plan Strategies to fund the initial purchase Granting agencies Trans-faculty; trans-department Funding for ongoing costs –salaries, software, service contracts

22 Schulich School of Medicine & Dentistry The University of Western Ontario Outcomes for today Agree on need for NGS Process for platform selection Sub-committee involvement –Bioinformatics –Capital –Governance –Ongoing operation

23 Schulich School of Medicine & Dentistry The University of Western Ontario Future Directions De-briefing from today’s meeting Timelines for –Software –Hardware –Funding User and Governance committees Next meeting…


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