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…