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Scott W. Herke Manager, Genomics Facility College of Science Louisiana State University. It’s a BIG topic!. Let’s trim it down. Core DNA Sequencing Facilities Technology & Operational Models for the Future. Scott W. Herke Manager, Genomics Facility College of Science

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Scott W. Herke Manager, Genomics Facility College of Science Louisiana State University


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    scott w herke manager genomics facility college

    Scott W. Herke

    Manager, Genomics Facility

    College of Science

    Louisiana State University

    it s a big topic

    It’s a BIG

    topic!

    Let’s trim it

    down...

    core dna sequencing facilities technology

    Core DNA Sequencing Facilities

    Technology & Operational Models

    for the Future

    Scott W. Herke

    Manager, Genomics Facility

    College of Science

    Louisiana State University

    bench top platforms

    Bench-top

    Platforms

    1Assumes 75% wells occupied by ISPs & 35% loss to filters.

    2 Assumes 75% of Manufacturer’s stated maximum value.

    3 PE run for 200-bp total read; thus, read # is not doubled.

    bench top platforms 1

    Bench-top

    Platforms

    1Assumes 75% wells occupied by ISPs & 35% loss to filters.

    2 Assumes 75% of Manufacturer’s stated maximum value.

    3 PE run for 200-bp total read; thus, read # is not doubled.

    bench top platforms 2

    Bench-top

    Platforms

    1Assumes 75% wells occupied by ISPs & 35% loss to filters.

    2 Assumes 75% of Manufacturer’s stated maximum value.

    3 PE run for 200-bp total read; thus, read # is not doubled.

    bench top platforms 3

    Bench-top

    Platforms

    1Assumes 75% wells occupied by ISPs & 35% loss to filters.

    2 Assumes 75% of Manufacturer’s stated maximum value.

    3 PE run for 200-bp total read; thus, read # is not doubled.

    bench top platforms 4

    Bench-top

    Platforms

    1Assumes 75% wells occupied by ISPs & 35% loss to filters.

    2 Assumes 75% of Manufacturer’s stated maximum value.

    3 PE run for 200-bp total read; thus, read # is not doubled.

    bench top platforms 5

    Bench-top

    Platforms

    1Assumes 75% wells occupied by ISPs & 35% loss to filters.

    2 Assumes 75% of Manufacturer’s stated maximum value.

    3 PE run for 200-bp total read; thus, read # is not doubled.

    bench top platforms 6

    Bench-top

    Platforms

    1Assumes 75% wells occupied by ISPs & 35% loss to filters.

    2 Assumes 75% of Manufacturer’s stated maximum value.

    3 PE run for 200-bp total read; thus, read # is not doubled.

    bench top platforms 7

    Bench-top

    Platforms

    1Assumes 75% wells occupied by ISPs & 35% loss to filters.

    2 Assumes 75% of Manufacturer’s stated maximum value.

    3 PE run for 200-bp total read; thus, read # is not doubled.

    2012 roadmap

    2012

    Roadmap

    1Assumes 75% wells occupied by ISPs & 35% loss to filters.

    2 Assumes 75% of Manufacturer’s stated maximum value.

    3 PE run for 200-bp total read; thus, read # is not doubled.

    ion family 6 month cycle 2

    Ion Family “6-month” Cycle

    • ....Proton IIQ1-2013
    ion proton vs illumina 1

    Ion Proton vs. Illumina

    Let’s first consider...

    ion proton vs illumina 2

    Ion Proton vs. Illumina

    Looking at the near future...

    ion proton vs illumina 3

    Ion Proton vs. Illumina

    And, on the horizon...

    ion proton r d vs illumina

    Ion ProtonR&D vs. Illumina

    1 Assumes no ‘bar codes’; 2 Proton chips; and, 1 Illumina lane for Phi-X control.

    2 Assumes 75% of Illumina’s stated maximum value.

    3PE run with overlapping reads for ~200-bp total; thus, read # is not doubled.

    4 Assumes 30% wells occupied by ISPs & 35% loss to filters (current LifeTech R&D).

    ion proton r d vs illumina 1

    Ion ProtonR&D vs. Illumina

    1 Assumes no ‘bar codes’; 2 Proton chips; and, 1 Illumina lane for Phi-X control.

    2 Assumes 75% of Illumina’s stated maximum value.

    3PE run with overlapping reads for ~200-bp total; thus, read # is not doubled.

    4 Assumes 30% wells occupied by ISPs & 35% loss to filters (current LifeTech R&D).

    ion proton r d vs illumina 2

    Ion ProtonR&D vs. Illumina

    1 Assumes no ‘bar codes’; 2 Proton chips; and, 1 Illumina lane for Phi-X control.

    2 Assumes 75% of Illumina’s stated maximum value.

    3PE run with overlapping reads for ~200-bp total; thus, read # is not doubled.

    4 Assumes 30% wells occupied by ISPs & 35% loss to filters (current LifeTech R&D).

    ion proton r d vs illumina 3

    Ion ProtonR&D vs. Illumina

    1 Assumes no ‘bar codes’; 2 Proton chips; and, 1 Illumina lane for Phi-X control.

    2 Assumes 75% of Illumina’s stated maximum value.

    3PE run with overlapping reads for ~200-bp total; thus, read # is not doubled.

    4 Assumes 30% wells occupied by ISPs & 35% loss to filters (current LifeTech R&D).

    ion proton r d vs illumina 4

    Ion ProtonR&D vs. Illumina

    1 Assumes no ‘bar codes’; 2 Proton chips; and, 1 Illumina lane for Phi-X control.

    2 Assumes 75% of Illumina’s stated maximum value.

    3PE run with overlapping reads for ~200-bp total; thus, read # is not doubled.

    4 Assumes 30% wells occupied by ISPs & 35% loss to filters (current LifeTech R&D).

    ion proton r d vs illumina 5

    Ion ProtonR&D vs. Illumina

    1 Assumes no ‘bar codes’; 2 Proton chips; and, 1 Illumina lane for Phi-X control.

    2 Assumes 75% of Illumina’s stated maximum value.

    3PE run with overlapping reads for ~200-bp total; thus, read # is not doubled.

    4 Assumes 30% wells occupied by ISPs & 35% loss to filters (current LifeTech R&D).

    ion proton pgm vs illumina

    Ion ProtonPGM vs. Illumina

    1 Assumes no ‘bar codes’; 2 Proton chips; and, 1 Illumina lane for Phi-X control.

    2 Assumes 75% of Illumina’s stated maximum value.

    3PE run with overlapping reads for ~200-bp total; thus, read # is not doubled.

    4 Assumes 75% wells occupied by ISPs & 35% loss to filters (based on PGM history).

    ion proton pgm vs illumina 1

    Ion ProtonPGM vs. Illumina

    1 Assumes no ‘bar codes’; 2 Proton chips; and, 1 Illumina lane for Phi-X control.

    2 Assumes 75% of Illumina’s stated maximum value.

    3PE run with overlapping reads for ~200-bp total; thus, read # is not doubled.

    4 Assumes 75%wells occupied by ISPs & 35% loss to filters (based on PGM history) .

    ion proton pgm vs illumina 2

    Ion ProtonPGM vs. Illumina

    1 Assumes no ‘bar codes’; 2 Proton chips; and, 1 Illumina lane for Phi-X control.

    2 Assumes 75% of Illumina’s stated maximum value.

    3PE run with overlapping reads for ~200-bp total; thus, read # is not doubled.

    4 Assumes 75%wells occupied by ISPs & 35% loss to filters (based on PGM history) .

    today

    Today

    Tomorrow?

    tomorrow s bench top world

    Tomorrow’s Bench-top World

    • Semi-conductor
    • 400-bp Reads
    • ~4 Gb/day
    • ~$2,000/run
    • Scanning Camera
    • 2X250-bp Reads
    • ~4 Gb/day
    • ~3,000/run
    today s high throughput world

    Today’s “High-Throughput” World

    • Pay-per-Lane
    • 75X35-bp Reads
    • ~8 Gb/day
    • <7 Day runs
    today s high throughput world 1

    Today’s “High-Throughput” World

    • Pay-per-Lane
    • 75X35-bp Reads
    • ~8 Gb/day
    • <7 Day runs
    • Gb or Speed
    • 2X100-bp Reads
    • ~30 Gb/day
    • <10 Day runs
    today s high throughput world 2

    Today’s “High-Throughput” World

    • Pay-per-Lane
    • 75X35-bp Reads
    • ~8 Gb/day
    • <7 Day runs
    • Gb or Speed
    • 2X100-bp Reads
    • ~30 Gb/day
    • <10 Day runs
    • Regular runs
    • Up to ~800-bp
    • ~0.5 Gb/day
    • ~1 Day runs
    tomorrow s high throughput world

    Tomorrow’s “High-Throughput” World

    • Gb – & – Speed
    • Ave. 200-bp reads
    • ~30 Gb/dayProton 1
    • ~1 Day runs
    tomorrow s high throughput world 1

    Tomorrow’s “High-Throughput” World

    • Gb – & – Speed
    • Ave. 200-bp reads
    • ~30 Gb/dayProton 1
    • ~1 Day runs
    • Gb – or – Speed
    • 2X100-bp reads
    • ~30 Gb/day
    • <10 Day runs
    ohs platforms over the horizon

    ‘OHS’ Platforms (over the horizon)?

    Single-molecule, long read systems

    Camera detects clipped Phosphate-linked nts

    DNA bound to Polymerase bound

    Quantum dots to SMRTcells

    bench tops semiconductors altering the deployment

    Bench-tops & Semiconductors

    ... altering the Deployment Landscape?

    Fading away

    institutional core models

    Institutional Core Models

    Level of Institutional Support Required

    Cost of Data to PI

    institutional core models 1

    Institutional Core Models

    Level of Institutional Support Required

    Cost of Data to PI

    institutional core models 2

    Institutional Core Models

    Level of Institutional Support Required

    Cost of Data to PI

    institutional core models 3

    Institutional Core Models

    Level of Institutional Support Required

    Cost of Data to PI

    institutional core models 4

    Institutional Core Models

    Level of Institutional Support Required

    Cost of Data to PI

    institutional core models 5

    Institutional Core Models

    Level of Institutional Support Required

    Cost of Data to PI

    institutional core models 6

    Institutional Core Models

    Level of Institutional Support Required

    Cost of Data to PI

    institutional core models 7

    Institutional Core Models

    Level of Institutional Support Required

    Cost of Data to PI

    institutional core models 8

    Institutional Core Models

    Level of Institutional Support Required

    Cost of Data to PI

    institutional core models 9

    Institutional Core Models

    Level of Institutional Support Required

    Cost of Data to PI

    institutional core models 10

    Institutional Core Models

    Level of Institutional Support Required

    Cost of Data to PI

    institutional core models 11

    Institutional Core Models

    Level of Institutional Support Required

    Cost of Data to PI

    with the mind boggling pace of change

    With the Mind-Boggling Pace of Change,

    only one thing is for certain...