Bai, H

Constandinou, TG

Garner, DM

Georgiou, P

Lim, KT

Reed, S

Shepherd, LM

Toumazou, C

Wong, W

Spiral - Imperial College Digital Repository

492 •  2010 IEEE International Solid-State Circuits ConferenceISSCC 2010 / SESSION 27 / DIRECTIONS IN HEALTH, ENERGY & RF / 27.427.4 A Multichannel DNA SoC for Rapid Point-of-Care Gene DetectionDavid M Garner, Hua Bai, Pantelis Georgiou, Tim G Constandinou,Samuel Reed, Leila M Shepherd, Winston Wong Jr, K.T. Lim, Christofer ToumazouDNA Electronics, London, United KingdomPoint-of-care diagnostics for detection of genetic sequences require biosensingplatforms that are sensitive to the target sequence, and are also fast, mass-man-ufacturable, and – ideally – disposable. Conventional lab-based methods ofdetecting DNA sequences rely on optical methods, typically by the addition offluorescent tags to the target DNA that in turn latches onto a DNA probesequence only if there is a match between the two. These techniques are cum-bersome as they require upfront tagging of the DNA with expensive reagents andlaboratory equipment to detect the optical signals. Recently, developments havebeen made in transferring these optical methods to inexpensive CMOS ICs [1],although the requirement for tagging remains. Magnetic beads offer an alterna-tive means of tagging the DNA and their presence can be detected by the shift inresonant frequency of an on-chip LC tank [2]. There have also been attemptsbased on “label-free” electrochemical detection using FETs [3,4], but none ofthese have been implemented in unmodified standard CMOS.We have developed a pioneering all-electrical approach that does not require tag-ging of DNA. The principle of label-free electrochemical DNA detection using anion-sensitive field effect transistor (ISFET) was originally described in [5].However, this prior art used a custom (non-CMOS) FET with an exposed Al2O3gate insulator, a macroscopic reference electrode, and a heat bath with controlunit to control the temperature of the reagents; furthermore, it was only able todetect a single DNA sequence, which has limited application. The SOC for DNAdetection presented herein integrates the discrete laboratory apparatus of [5]into a single IC while using standard CMOS manufacturing (unlike the all-elec-trical approach in [6]), and moreover has scalability to the detection of multipleDNA sequences by use of multiple on-chip ISFET sensors, temperature sensorsand heaters along with ADCs and digital IO.  This single-chip solution can beincorporated into disposable cartridges that are interchangeable depending onthe DNA sequences to be detected. The structure of the cartridge is shown in Fig.27.4.1 and consists of the IC embedded within a microfluidic assembly in whichthere are microchambers with access channels for the delivery of reagents. TheISFETs are implemented as unmodified floating-gate pMOS devices [7].When there is a match between target DNA from a sample and the on-chip DNAprobes, H+ ions are released, changing the pH of the reagents inside themicrochamber in which the match took place (Fig. 27.4.1). ISFETs are sensitiveto the pH of liquids on the passivation interface above their floating gates andthis manifests itself as a shift in the Vt of the ISFET where Vt is the threshold volt-age referred to a reference electrode that sets the potential of the electrolyte [8].Hence, the IC can detect whether a reaction has taken place in any of the cham-bers by monitoring the Vt of the ISFETs beneath those chambers. There are manyways to do this, one of which is to pass the drain current through weak-inver-sion signal processing circuits for the optimum balance of sensitivity anddynamic range [9]. The architecture of the SOC is shown in Fig. 27.4.2. The IC consists of a bank of40 ISFETs with associated readout circuitry that allows one of the 40 ISFETs tobe used as a reference ISFET (termed a REFET). Thus all ISFET readout signalsare outputted differentially as (VISFET-VREFET): this means that all common-modenoise (including electrochemical noise in the reaction chambers, allowing aquasi-reference electrode to be used) is rejected and this, together with up-frontgain, gives an input-referred noise voltage of only 25µV over the bandwidth ofinterest. Floating-gate transistors have different levels of as-deposited chargewhich cause large variations in the output voltage: these variations are cancelledusing individual 10-bit DACs as shown in Fig. 27.4.3, thus preventing saturationof the instrumentation circuitry which is designed to resolve small signals.Therefore this architecture overcomes the two common performance issueswith standard CMOS ISFETs: electrochemical drift and Vt offsets due to charge[8].Because biochemical reactions are highly sensitive to the temperature ofenzymes and reagents, the system controls temperature to an accuracy of 0.5°Cwith an inter-chamber precision of 0.1°C. This is done with an array of 10 tem-perature sensors distributed across the chip outputting the differential signal(VPTAT-VCTAT). These sensors are trimmed using individual 8-bit current-steeringDACs fed from registers sitting within an OTP block. Figure 27.4.3 shows thereported temperature from the IC under isothermal conditions before and aftertrimming showing that the required precision is obtained. The ISFET and temperature signals are filtered by 50 Gm-C anti-aliasing LPFswith a low f3dB of 8 Hz. The filtered signals are passed through 50 2nd-order ΣΔMswith a peak SNR of 80 dB. The resulting bitstreams are gathered by control logicwhich implements an SPI interface for full-duplex communication with an exter-nal handheld analyser which also does decimation filtering. The IC as it current-ly stands can detect up to 39 different genetic letters (allowing for one channelto be used for the reference chamber). Scalability is a key aspect to the designof the IC because as research into genetics advances, applications will be foundthat require the identification of more and more genetic letters. To that end, theIC is both scalable internally in that the architecture allows more ISFETs and tem-perature sensors to be easily added, and the SPI interface is implemented suchthat multiple ICs can be daisy-chained together. A table of key performancespecifications is given in Fig. 27.4.4 in which all values are exact or typicalunless otherwise stated. The sensitivity of the IC to pH of liquids in themicrochambers is shown in Fig. 27.4.5; the output signal has a square-lawdependence on pH and the dotted line is a 2nd-order polynomial least squaresbest fit. Deviations from this best fit are due to the difficulty of precisely settingthe pH of buffers as shown by the error bars, and do not represent a limitationof the IC itself.This platform can be applied to many different kinds of genetic testing. Oneapplication is the identification of single nucleotide polymorphisms (SNPs),which are a change in a single letter of the genetic code. The IC has sufficientISFETs to be able to identify up to 19 SNPs but for demonstration purposes inthis paper only one SNP was detected, utilising only 3 of the ISFETs: one as aREFET described above, and the other two beneath chambers containingreagents suitable for identifying a SNP which reveals information about a per-son’s drug metabolism. This SNP can take the letter A or C only and so each oftwo chambers was loaded with a different DNA detection “probes” suitable forcapturing the target region of the DNA and detecting these two letters. In thiscase, a reaction is deemed to have occurred when the output signal from eitheror both chambers crosses a preset threshold: if this happens, there is a matchbetween the patient’s DNA and the letter of interest. The time-to-result of 29 dif-ferent reactions with DNA in which a match was verified to have occurred usingoptical lab apparatus is shown as a histogram in Fig. 27.4.6 (“Inf” refers to reac-tions that failed to pass the detection threshold; this occurred due to non-opti-mised reaction chemistry in those cases). This Figure shows the speed of thison-chip DNA detection method and good agreement with conventional opticalmethods.The die is shown in Fig. 27.4.7. In a 0.35µm process, it has an area of 26 mm2.References:[1] Byungchul Jang et al., “A CMOS Fluorescent-Based Biosensor Microarray,”ISSCC Dig. Tech. Papers, pp. 436-437, Feb. 2009.[2] Hua Wang et al., “A Frequency-Shift CMOS Magnetic Biosensor Array withSingle-Bead Sensitivity and No External Magnet,” ISSCC Dig. Tech. Papers, pp.438-439, Feb. 2009.[3] T. Sakurai and Y. Husimi, “Real-Time Monitoring of DNA PolymeraseReactions by a Micro ISFET pH Sensor,” Anal. Chem., Vol. 64, pp. 1996-1997,Apr. 1992.[4] T. Sakata and Y. Miyahara, “Direct Detection of Single-Base ExtensionReaction using Genetic Field Effect Transistor,” Proc 3rd Ann. Int. IEEE EMBSSpecial Topic Conf. On Microtechnologies in Medicine and Biology, pp. 219-222,May 2005.[5] S. Purushothaman, C. Toumazou, C.P. Ou, “Protons and Single NucleotidePolymorphism Detection: A Simple Use for the Ion Sensitive Field EffectTransistor,” Sensor Actuat B-Chem, Vol. 114, pp. 964-968, Nov 2005.[6] R. Thews et al., “Sensor Arrays for Fully-Electronic DNA Detection onCMOS,” ISSCC Dig. Tech. Papers, pp. 350-473, Feb. 2002.[7] J. Bausells et al., “Ion-sensitive Field-effect Transistors Fabricated in aCommercial CMOS Technology,” Sens. Actuators B, Vol. 57, pp 56-61, Sep.1999.[8] P.A. Hammond and D.R.S. Cumming, “Performance and System-on-ChipIntegration of an Unmodified CMOS ISFET, Sensor Actuat B-Chem, Vol. 111, pp.254-258, Feb. 2005.[9] C. Toumazou, L. Shepherd, “Using Transistors to Linearise Biochemistry,”Electronics Letters, Vol. 43, pp. 65-67, Jan. 2007.978-1-4244-6034-2/10/$26.00 ©2010 IEEE493DIGEST OF TECHNICAL PAPERS  •ISSCC 2010 / February 10, 2010 / 3:15 PMFigure 27.4.1: Cross-section through the cartridge containing the IC and themicrofluidic assembly. Figure 27.4.2: Architecture of the SOC.Figure 27.4.3: Cancellation of offsets in the ISFETs and trimming of the tem-perature sensors to a precision of 0.1C.Figure 27.4.5: ADC decimation filter output as the pH of the liquid in a reac-tion chamber is varied.Figure 27.4.6: The time taken to identify a match between probe and targetwhen using the SOC for SNP detection.Figure 27.4.4: Key performance metrics of the DNA detection system incorpo-rating the SOC.27•  2010 IEEE International Solid-State Circuits Conference 978-1-4244-6034-2/10/$26.00 ©2010 IEEEISSCC 2010 PAPER CONTINUATIONSFigure 27.4.7: Micrograph of the manufactured IC. The die size is 5.5x4.7mm.

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A Multichannel DNA SoC for Rapid Point-of-Care Gene Detection

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A multichannel DNA SoC for rapid point-of-care gene detection

A Multichannel DNA SoC for Rapid Point-of-Care Gene Detection

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