Schulich School of Medicine & Dentistry The University of Western Ontario
London Regional Genomics Centre
Next Generation Sequencing Meeting
April 1, 2010
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.
Schulich School of Medicine & Dentistry The University of Western Ontario
LRGC Sequencing Facility UseTotal Billings and Sequences Processed per Annum
0
20000
40000
60000
80000
100000
120000
140000
160000
180000
May-03 to Apr-04 May-04 to Apr-05 May-05 to Apr-06 May-06 to Apr-07 May-07 to Apr-08 May-09 to March-10
Sam
ple
s
-
100,000
200,000
300,000
400,000
500,000
600,000
700,000
Am
ou
nt
Bil
led
#of Samples
Amount Billed
Total Billings and Sequences Processed per Annum
0
20000
40000
60000
80000
100000
120000
140000
160000
180000
May-03 to Apr-04 May-04 to Apr-05 May-05 to Apr-06 May-06 to Apr-07 May-07 to Apr-08 May-09 to March-10
Sam
ple
s
-
100,000
200,000
300,000
400,000
500,000
600,000
700,000
Am
ou
nt
Bil
led
#of Samples
Amount Billed
Schulich School of Medicine & Dentistry The University of Western Ontario
Microarray Facility Users
LRGC Users
AAFC5%
UWO33%
Robarts14%
National14%
Provincial15% LHRI
5%LRCP6%
CHRI2%
CPRI1%
LHSC5%
Schulich School of Medicine & Dentistry The University of Western Ontario
Microarray
Amounts Invoiced and Arrays Processed per Annum
0
500
1000
1500
2000
2500
02/03 03/04 04/05 05/06 06/07 07/08 08/09 09/10
Fiscal Year
Arrays
$-
$100,000
$200,000
$300,000
$400,000
$500,000
$600,000
$700,000
$800,000
$ CND
Number of Arrays
Billing
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
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
Schulich School of Medicine & Dentistry The University of Western Ontario
NGS Technology Comparison
ABI SOLiD Illumina GA Roche FLX
Cost SOLiD 4: $495kSOLiD PI: $240k
IIe: $470k IIx: $250kHiSeq: $690k
Titanium: $500k
Quantity of Data per run
SOLiD 4: 100GbSOLiD PI: 50Gb
IIe: 20 - 38 GbIIx: 50 – 95 GbHiSeq: 200Gb +
450 Mb
Run Time 7 Days 4 Days 9 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
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
Schulich School of Medicine & Dentistry The University of Western Ontario
London Regional Genomics Centre
Robarts Research Institute
Survey Monkey Summary Spring 2010
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 email survey 2004: 12/33 (36.45%)
Schulich School of Medicine & Dentistry The University of Western Ontario
Satisfaction
On a scale from 1 to 5 (5 being the highest, 1 being the lowest), how satisfied are you with the service from the London Regional Genomics Centre?
4.00 4.05 4.10 4.15 4.20 4.25 4.30 4.35 4.40 4.45 4.50 4.55
Personal Interaction:
Processing Time:
Data Quality
Data Analysis:
Overall Satisfaction:
Schulich School of Medicine & Dentistry The University of Western Ontario
Satisfaction
Schulich School of Medicine & Dentistry The University of Western Ontario
Financial Support Model
Schulich School of Medicine & Dentistry The University of Western Ontario
Potential New Services
Schulich School of Medicine & Dentistry The University of Western Ontario
Next-Generation Sequencing
Schulich School of Medicine & Dentistry The University of Western Ontario
Next-Generation Sequencing
Schulich School of Medicine & Dentistry The University of Western Ontario
Next-Generation Sequencing
No. Samples/year Response
1 to 20 10
21 to 40
41 to 60 2
61 to80
81 to 100 2
>100 2
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 2010- Announced to be “$50,000”
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
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
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…