biotech journal

7/27/2019 Biotech Journal

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Extending the Time to Collect DNAin Sexual Assault Casesby Terry Taylor

New research offers hope for extending the timeline for collecting samples suitablefor DNA profiling in sexual assault cases.

DNAprofilingplaysamajorrole

insexualassaultcases,but

ithasasignificantshortcom

ing:UsingthecurrentstandardDNA

profilingmethod,manyjurisdictions

requirethecollectionofevidentiary

sampleswithinthreedaysofthe

assault.Afterthat,itmaybecome

difficulttoobtainausableDNA

profileofthemalesuspect.

Whatifwecouldextendthewindow

oftimeforcollectingevidence?

Weknowthatspermcellsarefound

inthefemalereproductivetract

forsevendaysafterejaculationor

longer.Researchersaretestinga

hypothesisthatmayextendthe

lengthoftimeinwhichDNAprofiling

ispossibleinsexualassaultcases.

Dr.JackBallantyne,professorof

chemistryattheUniversityofCentral

FloridainOrlandoandaninterna

tionallyrecognizedexpertonDNA

profiling,believesthatrealevidence

isbeinglostbecauseofsomejuris

dictionsadherencetothethree-day

window.1Ballantynebelievesthat

newtechniquesmaymakeitpossi

bletocollectsamplesforaslongas

fivetosixdaysafterasexualassault

andstilldoviableanalysis.

ADNAprofileisasetofnumbers

thatrepresentregions,orloci,of

variable,repeatedDNAsequences.

ShortsequencesofDNAthatrepeat

anumberoftimesareknownas

shorttandemrepeats(STRs).The

numberoftimesasequencerepeats

variesfrompersontopersonand,

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NIJ JOURNAL / ISSUE NO. 267

exceptinthecaseofidenticaltwins,

thisvariabilitycanbeusedtotellpeo

pleapart.STRanalysisisaforensic

techniquethatdevelopsanddistin

guishesDNAprofilesbyevaluatingtheseregions.

MostDNAislocatedinthenucleus

ofthecell.Withinthenucleus,

DNAisdividedintolong,tightly

coiledpiecescalledchromosomes.

Humanshave23pairsofchro

mosomes.Ofthese,22pairsare

autosomalchromosomes(orauto

somes),whicharenotinvolvedin

determiningapersonssex.The

otherpairaresex-determining

chromosomes.TherearetwotypesofsexchromosomesXchromo

somesandYchromosomes.Women

havetwoXchromosomes;men

haveoneXchromosomeand

oneYchromosome.(SeeFig.1,

page25.)

STRanalysisistraditionallyper

formedonautosomesbecausethe

mannerinwhichtheyareinherited

resultsinahigherdegreeofvariation

thanYchromosomesandthuspro

ducesprofilesthathavefarstrongerstatisticalpower.2(Seesidebar,

STRAnalysis.)

ThestandardDNAprofilingtechnique

ofusingSTRanalysis,however,

hasshortcomings.One,asmen

tionedabove,isthatitisdifficult

toobtainaDNAprofileusingSTR

analysismorethanthreedaysafter

asexualassault.

Asecondshortcomingofcurrent

DNAprofilingtechniquesisthe

inabilitytogetamaleprofilewhen

inevidencecollectedafteran

allegedsexualassaultfemale

cellsvastlyoutnumbertheavail

ablespermcells.Insuchcases,the

amountofthefemalesDNAisso

greatcomparedtothemalesDNA

thatthefemaleDNAswampsthe

processandlaboratoryanalysisis

extremelydifficult.(Seesidebar,

NewTechnologiesPromiseBetter

FutureResults.)

Anapproachthathasshownpromise

insolvingbothofthesedifficulties

iscalledY-STRanalysis,based

onthemaleYchromosome.An

Using the current

standard DNA

profiling method,

many jurisdictionsrequire the collection

of evidentiary samples

within three days

of the assault. After

that, it may become

difficult to obtain a

usable DNA profile

of the male suspect.

NIJ-fundedpilotstudyofY-STR

DNAprofilingbyBallantyneandhis

colleaguesofferedhopeforasolu

tiontotheproblemofanalyzing

postcoitalsamplescollectedmore

thanthreedaysaftertheincident. 3

Histeamwasabletoobtaincom

pleteY-STRprofilesonsamples

collectedasmanyasfivedays

aftercoitusandapartialprofile

atsixdays.

Y-STRanalysisalsohelpssolve

theswampingproblembecause

itisselectiveforYchromosome

DNA,whichhaslittleoverlapwith

femaleDNA.Aslongasthequan

tityofmaleDNAissufficient,the

amountoffemaleDNApresentis

notaproblem.

Ballantyneisquicktocautionthat

Y-STRprofilingcannotsupplant

autosomalDNAprofiling.Y-STR

profilesdonothavethestatistical

powerofautosomalSTRprofiles

andthereforedonotcarrythesame

powertodiscriminateamongindi

viduals.Inmanycases,scientistsare

unabletoobtainaDNAprofilebased

onYchromosomeDNA,andonly

afewY-STRsystemsarecurrently

availableforuse.4

Thelikelihoodofobtaininganautoso

malDNAprofile,however,issmallin

severalsituations:

n Whenasamplecontainsbothmaleandfemalebodyfluidsotherthan

semen(e.g.,saliva-saliva,saliva-

vaginalfluids,fingernailscrapings).

n Whenthenumberofspermislow,ortheyareinafragilestate.

n Whenthereismorethanonesemendonor,asincasesof

multipleperpetratorrape.

Ballantyneandhiscolleaguescon

tinuetheirworktoincreasethe

numberofY-STRsystems,butother

thanaddingmoreY-STRlocitothe

analysis,littlecanbedonetochange

YchromosomeDNAsrelativelack

ofpowertodistinguishindividuals

thegreatestweaknessofthistype

ofDNAprofiling.

Still,Y-STRprofilingissometimes

theonlyoptionavailable. 5

Becausetheirpilotstudyinvolved

collectionofpostcoitalsamplesfrom

onlythreeconsentingmale-female

couples,Ballantyneandhisteam

Extending the Time to Collect DNA in Sexual Assault Cases | 23


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24 | Extending the Time to Collect DNA in Sexual Assault Cases


STR Analysis

ThemostcommontypeofDNAprofilingtodayforcriminalcasesandothertypes

offorensicusesiscalledSTR

(shorttandemrepeat)analysis.

UsingDNAtodistinguishbetween

twoindividualsisatrickymat

ter,becausecloseto99.9per

centofourDNAisthesameas

everybodyelsesDNA.1DNAthat

actuallycodesforproteinscan

notvarymuchwithoutrenderingtheproteinsineffective.Thefour

nucleotidebasesthatmakeup

thebackboneofDNAprovide

instructionsforassemblingthe

aminoacidsinproteinsbybeing

inaprecisesequence,witheach

three-basegroupcodingfora

specificaminoacid.IfthatDNA

basesequenceisaltered(or

mutated,asscientistsgenerally

say),thesequenceofaminoacids

intheresultingproteincanalso

bealtered.Asaresult,becauseproteinfunctionderivesfroma

specificaminoacidsequence,

theproteinmaynotwork.

ThinkofDNAastheblueprint

forahouseandproteinsasthe

steel,timber,bricksandmortar,

fromwhichthehousewillbebuilt.

Abrickthatismostlysandinstead

ofclaywillcrumble,andmortar

withthewrongratioofcement

plantoaddstatisticalpowerto

theirexperimentalevidencewith

anewNIJ-fundedstudythatwill

include150consentingmale-female

couples.Hisco-principalinvestiga

torisDr.PatriciaM.Speck,associate

toaggregatewillfail.Likewise,

aproteinwiththewrongsequence

ofaminoacidsoftenwontfunction.

(Thisanalogyfailstocapturethe

complexityoftheDNA-proteinsys

tem,however,becauseproteinsare

notonlythebricksandtimber.

Somereadtheblueprintand

supervisethebuilding,othersare

thebricklayersandcarpenters,

andstillothersmaintainandkeep

thehousefunctioningafteritisbuilt.)

Non-functionalormissingproteinsarethebasisformanygeneticdis

eases.UsefuldifferencesintheDNA

mustbefoundintheremainingone-

tenthofonepercent,whichisnot

knowntocodeforanythingspecific.

BecausethissectionoftheDNAs

precisesequenceisnotsoimpor

tant,itisquitevariable,whichmakes

itpossibletouseDNAtodistinguish

betweenindividuals.

Amongthe3millionorsoDNA

basesthatdonotcodeforproteinsareregionswithmultiplecopiesof

shortrepeatingsequencesofthese

bases,whichmakeuptheDNA

backbone(forexample,TATT).*

Thesesequencesrepeatavariable

numberoftimesindifferentindividu

als.Suchregionsarecalledvariable

numbershorttandemrepeats,and

theyarethebasisofSTRanalysis.A

collectionofthesecangivenearly

irrefutableevidencestatisticallyof

professorofnursingattheUniversity

ofTennesseeHealthScienceCenter

CollegeofNursinginMemphis.

Giventhevariablesinthecollec

tionofsamples,wedontknow

apersonsidentitybecausethe

likelihoodoftwounrelatedpeople

havingthesamenumberofrepeated

sequencesintheseregionsbecomes

increasinglysmallasmoreregions

areanalyzed.

Autosomalchromosomesarethose

notinvolvedindeterminingaper

sonsgender,andSTRsonthese

chromosomesarecalledautosomal

STRs.OtherSTRsusedforforensic

purposesarecalledY-STRs,whicharederivedsolelyfromthemalesex-

determiningYchromosome.Profiles

basedonautosomalSTRsprovidefar

strongerstatisticalpowerthanpro

filesbasedonY-STRs,becauseauto

somalDNAisrandomlyexchanged

betweenmatchedpairsofchromo

somesintheprocessofmakingegg

andspermcells.Thatshow,with

billionsofhumansontheplanet,

notwopeoplewhoarenotidenti

caltwinsareexactlyalike.Profiles

basedonY-STRsarestatisticallyweakerbecauseonlymaleshave

aYchromosomeandallmalesget

theirsfromtheirfathers,soallmales

inanypaternallinehavenearlyidenti

calYchromosomes.Givenenough

Y-STRs,whichscientistscallloci,

aY-STRprofilecanoffersubstan

tialpowertodiscriminatebetween

individuals,butthistypeofprofile

iscertainlynotaspowerfulasan

autosomalSTRprofile.

whatwecandoandwithwhom,

Speckexplained.Thelargestudy

aimstoexpandknowledgeabout

thelimitsofDNAprofilinginsexual

assaultcases.Thestudywillexam

inetheimpactofanumberoffactors


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IntheUnitedStates,13autosomal

STRlociarenowacceptedasthe

systemusedforforensicpurposes.2

GivenarobustcrimesceneDNA

samplewithgooddataforall13

STRs,thelikelihoodofaperson

unrelatedtotheactualperpetrator

havingaperfectmatchforall13is

typicallyaround1in1billion.Bycon

trast,experimentalworkwithavery

robustsetof30Y-STRlocishowed

aprobabilityofabout1in50,000for

aperfectmatch.

3

* TATTstandsforaspecificstringof

nucleotidebases,thymine-adenine

thymine-thymine.Thymineandade

ninearetwoofthefourbases

frequentlyfoundinDNA.Theother

twoarecytosine(C)andguanine(G).

Notes

1. BasicsofDNATyping.http://dna.gov/basics/(accessedJuly7,2010).

2. Norrgard,K.,Forensics,DNAFingerprinting,andCODIS,NatureEducation1(1)(2008):http://www.nature.com/scitable/topicpage/forensics-dna-fingerprinting-andcodis-736.

3. Hanson,E.,andJ.Ballantyne,AHighlyDiscriminating21LocusY-STRMegaplexSystemDesignedtoAugmenttheMinimalHaplotypeLociforForensicCasework,Journalof Forensic Sciences49(January2004):1-12.

fromsamplingtimelinetomen

struationcycleontheabilityof

investigatorstoobtainaDNAprofile.

Toensurerigorous,uniformmeth

ods,qualifiedforensicnurseswill

collectallsamples.Afterthecouples

1 2 3 54

6 7 8 10 11 129

13 14 15 17 1816

19 20 21 22 X Y Humans have 23 pairs of chromosomes 22 pairs of autosomes and one pair

of chromosomes that determine gender (the X and Y chromosomes).

Figure 1. Human Chromosomes

haveabstainedfromsexualinter-

coursefor10days,theywillengage

inunprotectedintercourse,andvagi-

nalsampleswillbecollectedat4,7

and9days,witheachcollectionfol-

lowinganewunprotectedcoitus

episode.Thecollectionprocess

willalsoincludeacervicalsample

becausespermcellslivelongerin

thecervixthaninthevagina,where

theyarequicklyeliminated.

http://dna.gov/basics/http://dna.gov/basics/http://www.nature.com/scitable/topicpage/forensics-dna-fingerprinting-and-codis-736http://www.nature.com/scitable/topicpage/forensics-dna-fingerprinting-and-codis-736http://www.nature.com/scitable/topicpage/forensics-dna-fingerprinting-and-codis-736http://www.nature.com/scitable/topicpage/forensics-dna-fingerprinting-and-codis-736http://www.nature.com/scitable/topicpage/forensics-dna-fingerprinting-and-codis-736http://www.nature.com/scitable/topicpage/forensics-dna-fingerprinting-and-codis-736http://www.nature.com/scitable/topicpage/forensics-dna-fingerprinting-and-codis-736http://www.nature.com/scitable/topicpage/forensics-dna-fingerprinting-and-codis-736http://dna.gov/basics/http://dna.gov/basics/


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26 | Extending the Time to Collect DNA in Sexual Assault Cases


New Technologies Promise Better Future Results

Aroutinedifficultyencounteredinproducingautoso

malDNAprofilesinrapecasesis

obtainingenoughspermcellsfor

theanalysis.Cellscanbedam

agedordegradedduetotime,

orsimplystucktoepithelialcells

(thosethatlinethecavitiesand

structuresofthebody,suchas

thevagina),makingitdifficultto

carryoutastandardautosomal

STRanalysis.

Asessionatthe2010NIJAnnualConferencehighlightedtwoprom

isingtechnologiesforenhancing

theseparationofspermcells

fromothercellsinamixedsam

ple.GaryStacey,vicepresident

oftechnologyatHaemonetics

Corporation,presentedatech

niquecalledholographicopti

caltrapping(HOT).HOTisan

automatedsystemnowcom

merciallyavailablefromArryx,a

Haemoneticssubsidiary.Thissys

temallowssmallparticles,such

asspermcellsorcellfragments,

tobedirectlymanipulatedusing

acomputer-controlledhologram

array.Staceyshowedvideoand

presenteddataofferingevidence

thatHOTcanseparatesperm

Participantsinthestudywillalso

beaskedquestionsabouttheir

menstrualcycle,generalhealthbackgroundandvarioussocialindica

tors.Tohelpanswerquestionsabout

theeffectsofmenstruationonDNA

cellsfromfemaleepithelialcells

(orothercontaminants)beforemicro-dissectiontoobtainDNA,

enhancingtheresultingSTRanaly

ses.Thesystemissimpletouse,

providesvisualconfirmationofthe

processasitproceedsandallows

videodatatracking.

HenryK.Lin,amemberofthe

BiosciencesDivision,oftheOak

RidgeNationalLaboratory,discussed

amicrofabricatedfiltertechnology

originallydevelopedtoseparatemet

astaticcancercellsfromtheblood.

Becausespermcellsaresubstantially

smallerthanthefemaleepithelial

cellswithwhichtheyarelikelytobe

mixedinrapecases,thistwo-tier

filtrationprocessfirstselectsout

thelargercells,allowingthesperm

collection,participantswillbedivided

betweenwomenwhosesamplecol

lectioncomesbeforemenstruationandwomenwhosemenstruationhas

startedbetweentheepisodeofinter

courseandthesamplecollection.

cellstopassthroughand

bedrawnoffseparately.Experimentstestingthisapplica

tionofthesystemhavesuccess

fullyseparatedspermcellsin

mixtureswheretheywereout

numbered25to1,withahigher

DNArecoveryrateandcleaner

STRprofilesthanareobtained

withstandardmethods.The

investigatorsintendtocontinue

thisresearchwithepithelialcell-to

spermcellratiosupto100to1.

Ballantyneexplainedtheimpor

tanceofsuchresearch:Ifwecan

separatespermcellsaccurately

andefficientlyinchallengingsam

ples,itwillpermitstandardautoso

malDNAanalysisinmorecases.

Thiswillbeagreatmoveforward.

Thevariablesarecomplexand

potentiallyconfounding,Specksaid.

Anopenquestioniswhetherestrogenprotectsfrominjury.Knowing

thiscouldbeimportanttotestimony

aboutinjuryinasexualassaultcase


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becausewherethewomanisinher

menstrualcycleatthetimeofthe

eventcouldplayaroleinwhether

sheisphysicallyinjured.

AccordingtoBallantyne,another

possibleaimofthestudywillbe

todocumentexactlywhenautoso

malDNAanalysisfails.Atseven

orninedays,thecurrentconsensus

isthatthereisnohopeforanautoso

malSTRprofile.Ifwesuccessfully

obtainaY-STRprofilewithasam

plecollectedsevenorninedays

later,wecanperhapsusetheexper

tisewehavegainedtoalsotease

outanautosomalprofile,Ballantyne

explains.Wellbemorecertainwhetherornotitshouldbearoutine

mattertocollectsamplesmore

thanafewdaysaftertheassault.

Forexample,ifthestudyshows

thatmorethan50percentofthe

samplesyieldareportableDNA

profileafterfourdays,itwould

haveimportantpolicyimplications.

Itwontbejustareportinascientificjournal.

Speckagrees:Thisstudycould

havetheeffectofchangingthe

timeframeforbringingvictimsin,

oritcouldconfirmcuttingoffsam

plecollectionearlier.Theimportant

thingistodevelopinterventions

thatwillhelpvictims.Thebottom

lineis,shesaid,wewanttotake

rapistsoffthestreet.

Terry Taylor is a senior science writer

and editor at Palladian Partners, Inc.

NCJ233285

The important thing

is to develop

interventions thatwill help victims.

The bottom line is,

we want to take

rapists off the street.

Notes

1. Thethree-daywindowmaybeinpart

duetothejurisdictionsprotocol,thelaboratorysprotocolorboth.

2. Foreachoftheir22pairsofautosomes,childreninheritoneautosomalchromosomefromeachparent.Theautosomesthechildreceives,however,arenotidenticaltotheirparentsautosomesbeforeaparentpassesonhisorherautosomes,eachpairgoesthroughaprocesscalledrecombination,whichrandomlyshufflesthatpair.Themixedautosomeproducedbythatprocessiswhatgetspassedontothechild

fromtheparent.Inthemother,theX

chromosomepairalsogoesthroughrecombination,justlikeautosomes,andthemixedXchromosomeispassedontothesonordaughter.BecausemenonlyhaveoneXchromosome,recombinationdoesnotoccurandtheypasstheirXchromosomeonunchangedtotheirdaughters.Similarly,becausemenonlyhaveoneYchromosome,itispassedunchangedtotheirsons.

3. Mayntz-Press,K.,L.Sims,A.Hall,andJ.Ballantyne,Y-STRProfilinginExtendedInterval(3Days)

PostcoitalCervicovaginalSamples,

Journal of Forensic Sciences53(March2008):342-348.

4. AcollectionofY-STRmarkersorY-STRloci(seesidebar,STRAnalysis)mustbediscoveredandvalidatedasusefulbeforeitcanbeusedasaY-STRsystem forDNAprofiling.

5. Inadditiontoitsusefulnessinsexualassaultcases,investigatorsmightbeabletoidentifyadisastervictimusingtheY-STRprofileofaclosemalerelative.


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