A CMOS Imager for DNA Detection

Samir Parikh

MASc Thesis Defense

Dept. of Electrical and Computer Engineering

University of Toronto

24th January, 2007

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Outline

Introduction Motivation and Objectives Design Details Experimental Results Conclusion Future Work

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Introduction: DNA Microarrays

ssDNA FragmentsDNA

Chemical Processing

DNA microarrays used to detect DNA sequence concentration

DNA is split into its two constituent strands One strand is broken into fragments

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Introduction: Using DNA Microarrays

Within a spot multiple identical ssDNA probes are attached Each spot is tailored to match with a particular target ssDNA

sequence target ssDNA is created from Messenger RNA extracted from a cell

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Introduction: DNA Detection

Solution containing target ssDNA+fluorescing dye molecule is introduced to the slide

Spots on the DNA microarray pair/unpair depending on the nucleotide sequence of the probe and target ssDNA

DNA microarray is washed to remove unpaired target ssDNA

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Introduction: DNA Detection

Solution containing target ssDNA+fluorescing dye molecule is introduced to the slide

Spots on the DNA microarray pair/unpair depending on the nucleotide sequence of the probe and target ssDNA

DNA microarray is washed to remove unpaired target ssDNA

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Introduction: Basic Microarray Scanner

Fluorescing dye molecule absorbs energy at λ1nm and emits energy at λ2nm

Light detectors are discussed in the next slide

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Introduction: Existing Light Detectors

Detector Disadvantages

PMT

Bulky Expensive PCB-level integration 10μm resolution → Long scan time

CCD Needs to be cooled Monolithic integration is costly

Commonly used detectors in microarray scanners are: Photomultiplier Tube (PMT) - accurate Charge-Coupled Device (CCD) - fast

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Motivation and Objectives

Determine the feasibility of using standard CMOS technology for light detection and quantification Integrated Smaller Cheaper

Validate the design without the use of cooling Reduce cost related to cooling Reduce power consumption due to cooling equip.

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Design Details: Microarray Scanner

Signal from entire spot captured at once

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Design Details: Microarray Scanner

Signal from entire spot captured at once

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Design Details: Microarray Scanner

Signal from entire spot captured at once

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Design Details: Microarray Scanner

Signal from entire spot captured at once

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Design Details: Microarray Scanner

Signal from entire spot captured at once

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Design Details: Active Pixel Sensor (APS)

photons

5-transistor circuit with pseudo-differential output Pinned photodiode performs the photon-to-electron conversion Circuits has two phases: reset and integration

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Design Details: ΔΣ Modulator

2nd Order Discrete-Time ΔΣ Can be combined with a decimation

filter for a complete ADC Boser-Wooley Architecture Delaying Integrators with 1bit feedback Folded-Cascode Op-amp used

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Design Details: Fabricated Chip

TSMC 1P6M

0.18µm CMOS

Core Area

690×490 μm2

Die Area

1.2×1.4 mm2

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Experimental Results: APS

Photodetector Type P+/n-well/Psubstrate

Sensitivity to low light < 2.6 х 10-2 lux

SNR @ 2.6 х 10-2 lux 16.6dB

Dark-signal@(room temp.) 10mV/sec

Source-Follower non-linearity 0.12%

Photodetector Size 150µm х 150µm

Pixel Size 162.5µm х 154µm

Fill Rate 90%

Dark signal limits the integration time for the APS Low light sensitivity sets the min # of photons detectable

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Experimental Results: ΔΣ Modulator

Simulation includes flicker and thermal noise Close matching between simulation and measured

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Experimental Results: ΔΣ ModulatorDiscrete-Time 2nd Order Single-bit ΔΣ

Power Consumption 26.4 mW

Peak SNDR 75.9 dB

Effective Number of Bits 12 bits

Dynamic Range 74.63 dB

SFDR 85.5 dB

Sampling Rate 3.6 MHz

Nyquist Sampling Rate 14.2 kHz

Commercial microarray scanners have 12 to 16-bits accuracy Sampling rate sets an upper limit on the maximum light level Sampling rate not critical, minimum light level is more important

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Experimental Results: Microarray Scanner Setup

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Experimental Results: Microarray Scanner Setup

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Experimental Results: Microarray Scanner Setup

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Experimental Results: Microarray Scanner Setup

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Experimental Results: Scanner Characterization Slide

Slide contains spots with dilution series Each spot contains fluorescing dye molecules with fixed density Spot density (fluorophores/um2) decreases at a fixed rate

Decreasing dye density

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Experimental Results: Microarray Scanner

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Experimental Results: Commercial Microarray Scanner

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Discussion: Microarray Scanner Portability Potential

Microarray scanner: Smaller, integrated detector w/o cooling Agilent scanner: PMT

Detection Limit Microarray scanner: 4590 fluorophores/um2

Agilent scanner: 4 fluorophores/um2

Resolution and Scan time Microarray scanner: Larger pixel→Entire spot imaged at once Agilent scanner: 10μm resolution→takes longer to image a spot Microarray scanner: Multiple pixels → short scan time Agilent scanner: Single element → long scan time (8 min/slide)

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Discussion: APS

Dark signal of APS not the limiting factor Background of the slide = 1.5 ADU/sample Dark signal of the APS = 0.08 ADU/sample Integration time of the APS is limited by the slide background

Improve the sensitivity of the APS beyond 2.6х10-2 lux Increase its conversion gain Reduce its read noise and reset noise

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Discussion: Optical and Mechanical

Improve optical coupling between

APS ↔ fluorescing spots Use a focusing/collimating element Compensate for slide tilt

Reduce laser noise and drift from 3% to 0.1% Improved power supply Better laser control/feedback

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Conclusion

Standard CMOS technology shows potential to be an alternative to existing PMT/CCD detectors used in microarray scanners

The detection limit of a microarray scanner is determined by: Mechanical and Optical Non-idealities Detector Non-idealities

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Future Work

Improve the conversion gain of the APS Reduce the read noise, and reset noise of the

APS Improve the accuracy of the ADC

Thank You

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