A MID-TERM SEMINAR REPORT ON BIOCHIP

SUBMITTED IN PARTIAL FULFILLMENT FOR THE DEGREE OF BACHELOR OF TECHNOLOGY IN (COMPUTER SCIENCE & TECHNOLOGY)

BY ISHA .D. SHENDE LAXMI KEWAT

UNDER THE GUIDANCE OF Mr. NARENDRA GAWAI

USHA MITTAL INSTITUTE OF TECHNOLOGY S.N.D.T. WOMEN'S UNIVERSITY MUMBAI- !! " #!!$-#!!"

CERTIFICATE

This is to certify that M%.I%&' D S&()*( & M%.L'+,- .(/'0 has succesfully completed midterm seminar worj on BIOCHIP in partial fulfilment for the bachelor's degree in C1,230(r S4-()4( & T(4&)15167 during the year 2009-20 0 as prescribed by !"#T $omen's %ni&ersity'

GUIDE

HEAD OF DEPARTMENT

(Mr. N'r()*r' G'/'-)

(Mr.S3,(*& P3)*.'r)

PRINCIPAL (Mr%.K3,3* W'%)-.)

TABLE OF CONTENTS

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LIST OF FIGURES

FIGURE NO. 8.8 ;.8 ;.# >.8 >.#

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ABSTRACT
( biochip is a collection of miniaturi)ed test sites *microarrays+ arranged on a solid substrate that permits many tests to be performed at the same time in order to achie&e higher throughput and speed',i-e a computer chip that can perform millions of mathematical operations in one second. a biochip can perform thousands of biological reactions. such as decoding genes. in a few seconds'/iochips helped to dramatically accelerate the identification of the estimated 00.000 genes in human #"(. an ongoing world-wide research collaboration -nown as the 1uman genome project'#e&eloping a biochip plat-form incorporates electronics for addressing. reading out. sensing and controlling temperature and. in addition. a handheld analy)er capable of multiparameter identification' The biochip platform can be plugged in a peripheric standard bus of the analy)er de&ice or communicate through a wireless channel' /iochip technology has emerged from the fusion of biotechnology and micro2nanofabrication technology' /iochips enable us to reali)e re&olutionary new bioanalysis systems that can directly manipulate and analy)e the micro2nanoscale world of biomolecules. organelles and cells'

CHAPTER 8 8.INTRODUCTION
8.8 W&'0 -% ' C-14&-2D ( biochip is a collection of miniaturi)ed test sites *microarrays+ arranged on a solid substrate that permits many tests to be performed at the same time in order to achie&e higher throughput and speed' Typically. a biochip's surface area is no larger than a fingernail' ,i-e a computer chip that can perform millions of mathematical operations in one second. a biochip can perform thousands of biological reactions. such as decoding genes. in a few seconds'/iochip is a broad term indicating the use of microchip technology in molecular biology and can be defined as arrays of selected biomolecules immobili)ed on a surface' /iochip will also be used in animal and plant breeding. and in the monitoring of foods andthe en&ironment'/iochip is a small-scale de&ice. analogous to an integrated circuit. constructed of or used to analy)e organic molecules associated with li&ing organisms' 3ne type of theoretical biochip is a small de&ice constructed of large organic molecules. such as proteins. and capable of performing the functions *data storage. processing+ of an electronic computer' The other type of biochip is a small de&ice capable of performing rapid. smallscale biochemical reactions for the purpose of identifying gene se4uences. en&ironmental pollutants. airborne to5ins. or other biochemical constituents'

F-6 8.8B-14&-2

/iochip26ntroduction

8.#G()(r'0-1)EH-%01r7 The de&elopment of biochips has a long history. starting with early wor- on the underlying sensor technology'/iochip was originally de&eloped in in 907 for monitoring fisheries.the rapid technological ad&ances of the biochemistry and semiconductor fields in the 900s led to the large scale de&elopment of biochips in the 990s' (t this time. it became clear that biochips were largely a 8platform8 technology which consisted of se&eral separate. yet integrated components' Today. a large &ariety of biochip technologies are either in de&elopment or being commerciali)ed' "umerous ad&ancements continue to be made in sensing research that enable new platforms to be de&eloped for new applications' /iochip was in&ented in 9: generation & the de&elopment is still continued. due its &arious applications' /iochips are also continuing to e&ol&e as a collection of assays that pro&ide a technology platform' 3ne interesting de&elopment in this regard is the recent effort to couple so-called representational difference analysis *;#(+ with high-throughput #"( array analysis' The ;#( technology allows the comparison of c#"( from two separate tissue samples simultaneously'6t is important to reali)e that a biochip is not a single product. but rather a family of products that form a technology platform' <any de&elopments o&er the past two decades ha&e contributed to its e&olution'6n a sense. the &ery concept of a biochip was made possible by the worof =red !anger and $alter :ilbert. who were awarded a "obel >ri)e in 900 for their pioneering #"( se4uencing approach that is widely used today' #"( se4uencing chemistry in combination with electric current. as well as micropore agarose gels. laid the foundation for considering miniaturi)ing molecular assays' (nother "obel-pri)e winning disco&ery. ?ary <ullis's polymerase chain reaction *>@;+. first described in 907. continued down this road by allowing researchers to amplify minute amounts of #"( to 4uantities where it could be detected by standard laboratory methods' ( further refinement was pro&ided by ,eroy 1ood's 90A method for fluorescence-based #"( se4uencing. which facilitated the automation of reading #"( se4uence' =urther de&elopments. such as se4uencing by hybridi)ation. gene mar-er identification. and e5pressed se4uence tags. pro&ided the critical technological mass to prompt corporate efforts to de&elop miniaturi)ed and automated &ersions of #"( se4uencing and analysis to increase throughput and decrease costs' 6n the early and mid- 990s. companies such as 1yse4 and (ffymetri5 were formed to de&elop #"( array technologies'
/iochip26ntroduction 2

C&'20(r# H1/ *1(% ' C-14&-2 /1r.D

The 8chip contains a 0 character alphanumeric identification code that is ne&er duplicated' when a scanner is passed o&er the chip. the scanner emits a 'beep' and your ''' number flashes in the scanner's digital display'8 /iochips concentrate thousands of different genetic tests on a surface area of just a few s4uare centimetres so that they can be analysed by computer within a &ery short space of time' 3n the one hand this ma-es the indi&idual genetic tests much cheaper and on the other hand. than-s to the capacity. many more tests can be carried out' /iochips concentrate thousands of different genetic tests on a surface area of just afew s4uare centimetres so that they can be analysed by computer within a &ery shortspace of time' 3n the one hand this ma-es the indi&idual genetic tests much cheaperand on the other hand. many more tests can be carried out'(ffymetri5 in&ented the high-density microarray in 909 and has been selling thisassay since 999 under the name of :ene@hipB *figure +' 6n this conte5t.microarray means that the genetic tests are organised *arrayed+ inmicrometrespacing*micro+'(s it was not pre&iously possible to go below the millimetre range.the description high density is certainly justified' C5periments *e'g' measurement ofgene acti&ity or se4uencing to demonstrate mutations and polymorphisms+ that couldpre&iously only be done indi&idually. one after the other. can now be carried out inlarge numbers at the same time and in a highly automated manner'

/iochip2$hat does /iochip do

C&'20(r ; B-14&-2 Ar4&-0(403r(

The biochip implant system consists of two componentsD a transponder and a reader or scanner' The transponder is the actual biochip implant' The biochip system is a radio fre4uency identification *;=6#+ system. using low-fre4uency radio signals to communicate between the biochip and reader' The reading range or acti&ation range. between reader and biochip is small. normally between 2 and 2 inches' ;.8S-<( The si)e of /iochip is of a si)e of an uncoo-ed rice grain si)e' 6t ranges from 2inches to 2inches'

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/iochip2/iochip (rchitecture

;.#C1,21)()0% The transponderE The transponder is the actual biochip implant' 6t is a passive transponder. meaning it contains no battery or energy of it's own' 6n comparison. an active transponder would pro&ide itFs own energy source. normally a small battery' /ecause the passive biochip contains no battery. or nothing to wear out. it has a &ery long life. up to 99 years. and no maintenance' /eing passive. it's inacti&e until the reader acti&ates it by sending it a low-power electrical charge' The reader 8reads8 or
F-6 ;.# C1,21)()0%

8scans8 the implanted biochip and recei&es bac- data *in this case an identification number+ from the biochip' The communication between biochip and reader is &ia low-fre4uency radio wa&es' The biochip-transponder consists of four partsD computer microchip. antenna coil. capacitor and the glass capsule' C1,230(r M-4r14&-2E The microchip stores a uni4ue identification number from 0 to G digits long' The storage capacity of the current microchips is limited. capable of storing only a single 6# number' (H6# *(merican Heterinary 6dentification #e&ices+. claims their chips. using a nnn-nnnnnn format. has the capability of o&er I0 trillion uni4ue numbers' The uni4ue 6# number is 8etched8 or encoded &ia a laser onto the surface of the microchip before assembly' 3nce the number is encoded it is impossible to alter' The microchip also contains the electronic circuitry necessary to transmit the 6# number to the 8reader8' A)0())' C1-5F This is normally a simple. coil of copper wire around a ferrite or iron core' This tiny. primiti&e. radio antenna 8recei&es and sends8 signals from the reader or scanner' T3)-)6 C'2'4-01rF The capacitor stores the small electrical charge *less than 2 000 of sent by the reader or scanner. which acti&ates the transponder' This 8acti&ation8 allows the transponder to send bac- the 6# number encoded in the computer chip' /ecause 8radio wa&es8 are utili)ed to communicate between the transponder and reader. the capacitor is 8tuned8 to the same fre4uency as the reader'
/iochip2/iochip (rchitecture G

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G5'%% C'2%35(F The glass capsule 8houses8 the microchip. antenna coil and capacitor' 6t is a small

capsule. the smallest measuring

mm in length and 2 mm in diameter. about the si)e of an

uncoo-ed grain of rice' The capsule is made of biocompatible material such as soda lime glass' (fter assembly. the capsule is hermetically *air-tight+ sealed. so no bodily fluids can touch the electronics inside' /ecause the glass is &ery smooth and susceptible to mo&ement. a material such as a polypropylene polymer sheath is attached to one end of the capsule' This sheath pro&ides a compatible surface which the bodily tissue fibers bond or interconnect. resulting in a permanent placement of the biochip'

;.;C1%0F/iochips are not cheap. though the price is falling rapidly' ( year ago. human biochips cost J2.000 per unit' @urrently human biochips cost J .000. while chips for mice. yeast. and fruit flies cost around J900 to JG00' The price for human biochips will probably drop to JG00 this year' 3nce all the human genes are well characteri)ed and all functional human !">s are -nown. manufacture of the chips could concei&ably be standardi)ed' Then. prices for biochips. li-e the prices for computer memory chips. would fall through the floor'

/iochip 2(rchitecture

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.8G()1,-4% :enomics is the study of gene se4uences in li&ing organisms and being able to read and interpret them' The human genome has been the biggest project underta-en to date but there are many research projects around the world trying to map the gene se4uences of other organisms' The use of /iochip facilitateE (utomated genomic analysis including genotyping. gene e5pression #"( isolation from comple5 matrices with aim to increase reco&ery efficiency #"( amplification by optimi)ing the copy number#"( hybridi)ation assays to impro&e speed and stringency ' .#Pr10(1,-4% >roteome analysis or >roteomics is the in&estigation of all the proteins present in a cell. tissue or organism' >roteins. which are responsible for all biochemical wor- within a cell. are often the targets for de&elopment of new drugs' The use of /iochip facilitateE 1igh throughput proteomic analysis <ulti-dimensional microseparations *pre ,@2<!+ to achie&e high plate number Clectro-inetic sample injection for fast. reproducible. samples !tac-ing or other preconcentration methods *as a precursor to biosensors+ to impro&e detection limits ?inetic analysis of interactions between proteins to enable accurate. transport-free -inetics .;C(551,-4% C&ery li&ing creature is made up of cells. the basic building bloc-s of life'' @ells are used widely by for se&eral applications including study of drug cell interactions for drug disco&ery. as well as in biosensing' The use of /iochip facilitateE
/iochip 2(pplications of /iochip I

#esign2de&elop 8lab-in-cell8 platforms handling single or few cells with nanoprobes in carefully controlleden&ironments'

 @ell handling. which in&ol&e sorting and positioning of the cells optimally using #C>. optical traps etc' =ield2reagent based cell lysis. where the contents of the cell are e5pelled out by brea-ing the membrane. or increase the efficiency of transfection using reagents2field 6ntracellular processes to obtain high 4uality safety2to5icity (#<C2T data . B-1*-'6)1%0-4% ')* (N')1) B-1%()%1r% /iodiagnostics or biosensing is the field of sensing biological molecules based on electrochemical. biochemical. optical. luminometric methods' The use of /iochip facilitateE :enetic2/iomar-er #iagnostics. de&elopment of /iowarfare sensors which in&ol&es optimi)ation of the platform. reduction in detection time and impro&ing the signal-to-noise ratio !election of detection platform where different formats such as lateral flow &s' microfluidics are compared for ease2efficiency 6ncorporation of suitablesensing modality by e&aluating tradeoffs and downselect detection modes*color 2 luminometric. electrochemical. biochemical. optical methods+ forspecific need' .> Pr10(-) C&-2% =1r D-'6)1%-% ')* A)'57%-% 1= D-%('%(%

The >rotein chip is a micro-chip with its surface modified to detect &arious disease causing proteins simultaneously in order to help find a cure for them' /io-chemical materials such as antibodies responding to proteins. receptors. and nucleic acids are to be fi5ed to separate and analy)e protein'

/iochip 2(pplication of /iochip

C&'20(r> H3,') -)0(r='4( 01 B-14&-2

/iochips pro&ide interfaces between li&ing systems and electro-mechanical and computational de&ices' These chips may be used in such &aried applications as artificial sensors. prosthesis. portable2disposable laboratories or e&en as implantable de&ices to enhance human life' /iochips promise dramatic changes in future medical science and human life in general' $ith the ad&ances of bio and nano technologies two strong paradigms of integrated electronic and life are emerging' /iosensor chips can pro&ide the construction of sophisticated human sensing systems such as nose and ears' The second paradigm is chips for sensing biology that will pro&ide for interactions with li&ing bodies and build new diagnosis tools *such as diabetes glucose meters+ or new medicines *such as a bio-assay chip+' ( tiny microchip. the si)e of a grain of rice. is simply placed under the s-in' 6t is so designed as to be injected simultaneously with a &accination or alone'8 The biochip is inserted into the subject with a hypodermic syringe' 6njection is safe and simple. comparable to common &accines' (nesthesia is not re4uired nor recommended' 6n dogs and cats. the biochip is usually injected behind the nec- between the shoulder blades' Tro&an. ,td'. mar-ets an implant. featuring a patented 8)ip 4uill8. which you simply press in. no syringe is needed' (ccording to (H6# 83nce implanted. the identity tag is &irtually impossible to retrie&e' ' ' The number can ne&er be altered'8

=iG' 1uman interfacing of /iochip

/iochip 21uman interface to biochip 9

The syringe used is of a normal si)e seringe & the chip can be placed below the s-in layer &ery easily'

=ig G'2 !yringe to implant /iochip

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3n <ay 0 2002. three members of a family in =lorida *8medical pioneers.8 according to a fawning report on the @/! C&ening "ews+ became the first people to recei&e the implants' Cach de&ice. made of silicon and called a Heri@hipK. is a small radio transmitter about the si)e of a piece of rice that is injected under a person's s-in' 6t transmits a uni4ue personal 6# number whene&er it is within a few feet of a special recei&er unit' Heri@hip's ma-er describes it as 8a miniaturi)ed. implantable. radio fre4uency identification de&ice *;=6#+ that can be used in a &ariety of security. emergency and healthcare applications'

/iochip 21uman interface to biochip

CHAPTER? ADVANTAGES & DISADVANTAGES

A*@')0'6(% 'The ability to detect multiple &iral agents in parallel e'g' differential diagnosis of agents from other diseases that cause similar clinical symptoms. or the recognition of comple5 mi5tures of agents' '@larification of syndromes of un-nown aetiology '6ncrease speed of diagnosis of un-nown pathogens *8future proofed8 sur&eillance tools+' 'Hiral typing *(6H. =<#H. ;abies+ '#ri&e policy for diagnostics and disease control' 'Cpidemiological tracing '6nteragency collaboration' The consortium consists of "ational. C% and 36C referencelaboratories and has access to real sample material from a wide selection of hosts and &iruses' D-%'*@')0'6(% 'These methods ha&e problems that a #"( chip cannot be fabricated at high density and mass production is limited' Thus. these methods are applicable to fabrication of a #"( chip for study' '<eanwhile. the #"( chip and the #"( microarray ha&e different fabrication methods but are similar in that different oligonucleotides are aligned on a s4uare spot ha&ing a certain si)e in a chec- pattern'

/iochip2(d&antages & #isad&antage

CHAPTERA D(@(512,()0% & Pr1B(40%

V-(/ 1= 0&( F303r( The immediate prospects for biochip technology depend on a range of technologic and economic issues' 3ne is the 4uestion of chip reusability' @urrent biochips are of necessity disposable. in part because the current de&ices are not physically robust' =or e5ample. nucleic acid probes tend to brea- away from a supporting glass plate' ( decade from now. this problem may ha&e been better addressed. ma-ing the chips more reusable. and perhaps at the same time permitting probes with longer spans of genetic data than are feasible today' 6n this way. a manufacturing impro&ement might facilitate more powerful forms of genetic analysis' 3n the other hand. it may be better to manufacture biochips so ine5pensi&e that they can be used once and then discarded' (nother issue is biochip &ersatility' @urrent biochips are single-purpose. hardwired de&ices' C&en if future biochips do not become programmable. in the fashion of computer chips. they may become usable for multiple purposes. such as the analysis of a tissue sample for numerous pathogens' (n o&erarching issue is standardi)ation' =or diagnostic purposes. any medical test should be administered. and its results interpreted. in a standardi)ed way' /eyond that. it seems desirable for biochips performing different tests to ha&e an output detectable by the same readout de&ice' 1ence. a race is underway to create a biochip platform or motherboard capable of handling a wide range of biochips. irrespecti&e of the internal details of a gi&en chip's function' 6n particular. two companies. (ffymetri5 and <olecular #ynamics. ha&e formed the :enetic (nalysis Technology @onsortium. or :(T@ *a name that also represents the four nucleotides that carry genetic code in #"(+' The hope is to establish industry-wide standards for the reading of biochips'

/iochip2#e&elopments & >rojects

R(%('r4& C7 Willson ;esearch :roup

The %ni&ersity of Te5as at (ustin <ost biochips are 2# arrays of sensors placed carefully in a grid arrangement' The position of the sensor on the chip determines its function' =or e5ample. a sensor at the 5-y coordinate *9.G+ might sense the antibody for 16H. while the sensor at *I.7+ might sense the antibody for an influen)a &irus' To place the sensors in precise coordinates. sophisticated and e5pensi&e microdeposition techni4ues are used' The sensors are essentially placed one at a time. or serially. on the chip' Thus. throughput and yield tend to be low' Theyare de&eloping a biochip that inde5es sensor function to its shape. instead of its position on the chip' Thus. the sensors can be placed anywhere' 6mage recognition software can then then used to read the chip' The shaped sensors are made &ia a no&el contact lithography' The benefits of this approach are multifoldE The sensors can be batch produced and then assembled together in parallel. pro&iding high throughput and high yield' The sensors can be pac-ed &ery tightly together. unli-e those deposited with microdeposition systems' The sensors are 7# in nature. and thus pro&ide a higher signal than 2# sensors of other chips' (lmost any chemistry can be incorporated into the sensors' <ost biochips use only one type of chemistry' /ecause the sensors are produced offline and assembled later. they can be custom tailoredfor their specific application'

/iochip2#e&elpment & projects

CHAPTER$ CONCLUSION
/iochips are fast. accurate. miniaturi)ed. and can be e5pected to become economically ad&antageous attributes that ma-e them analogous to a computer chip' 3ne e5pects to see an accelerated trend of ultraminiaturi)ation. perhaps in&ol&ing entirely no&el media. and an increased ability to analy)e not only genetic material but also other types of biologic molecules' 3ne e5pects. too. an e&entual harmoni)ation of technologies. so that dominant fabrication strategies will emerge. at least for certain types of applications. including a fa&ored format for genetic analysis and another for antibodies and other proteins' !ince the potential applications are &ast. both for research and for clinical use. the potential mar-ets for biochips will be huge. a powerful dri&ing force for their continued de&elopment '

/iochip2@onclusion

CHAPTER" ;C=C;C"@C!

' <arshall.('. 1odgson. L'. #"( chipsE (n array of possibilities. "ature /iotechnology. 990. AE 2I' 2' ?richa. ,'L'. <iniaturi)ation of analytical systems. @linical @hemistry. 990. 99 E 2000' 7' Hahid /emanian. =rMydis #' /lystad. ,i&e /ruseth. :unn (' 1ildrestrand. ,ise 1olden. Cndre ?jNrland. >Ol >unter&oll. 1anne ;a&neberg and <orten ;uud. 8$hat is /ioethicsP8 #ec 990' 9' =an et al' *2009+' 8Two-#imensional Clectrophoresis in a @hip8' Lab-on-a-Chip Technology: Biomolecular Separation and Analysis' @aister (cademic' G' 1erold. ?CD ;asooly. ( *editor+ *2009+' Lab-on-a-Chip Technology: Fabrication and Microfluidics

/iochip2;eferences