tech guide feb 09

7/31/2019 Tech Guide Feb 09

1/16


2/16
http://www.sequenom.com/climbinghttp://www.sequenom.com/


3/16

tal f Cnn

Leer r he Eir 4

Iex Exer 4

Q1: Wh i r ei lr

chice wh? 6

Q2: Hw e le qli

qi? 7

Q3: Wh li l e

cll ri? 8

Q4: Wh cier cceble

clei ccrce re? 9

Q5: Hw rc le? 10

Q6: Wh ierl exerl crl e wh errr re

cier cceble? 11

Li Rerce 14


4/16

Jiang LiDNA GeNotypiNG ScieNtiSt

HaRtWELL CEntER oR

BIoInoRmatICs and BIotECHnoLogy

st JudEs CHILdREns

REsEaRCH HospItaL

Lee MurphylAborAtory mANAGer

RIE CLInICaL REsEaRCH aCILIty

and tHE WELLComE tRust CLInICaL

REsEaRCH aCILIty

unIvERsIty o EdInBuRgH

Mary Lou ShaneSeNior lAb techNiciAN

vERmont CanCER CEntER

dna anaLysIs aCILIty

unIvERsIty o vERmont

Kevin ShiannaDirector

Igsp gEnotypIng aCILIty

dukE unIvERsIty

Lr fr irWith each passing tech-

nical guide on the matter,

it seems that genotyping is

becoming more and morecommonplace you hear

about so many genotyping

companies such that it seems

as if everyone is getting into genotyping. Those

of you in the trenches know that its not as

easy as it sounds. In this latest installment of

Genome Technologys technical guide series,

our stalwart group of experts discusses how

they go about tackling their genotyping

projects. They discuss what platforms they

use and why, as well as how they keep

completion, concordance, and error rates to

acceptable levels, to make calls they can trust.Grab your highlighter. This technical

guide is chock-full of nuggets that youll

want to remember. As always, dont forget

to check out the reference guide in the back

to see where our experts turn when they

themselves get stuck. Many thanks to our

experts for taking the time to contribute to

this technical guide.

Ciara Curtin

Inx f xrGenome Technology would like to thank the following contributors

for taking the time to respond to the questions in this tech guide.

gei4 TEch guidE EBRuaRy 2009

Jenny PansceautechNiciAN/reSeArch ASSociAte

oHIo statE unIvERsIty

Jeremy TaylorprofeSSor

anImaL gEnomICs

unIvERsIty o mIssouRI


5/16
http://info.appliedbiosystems.com/taqmanopenarray


6/16


W p

pf f w?

I r cre cili, e

he le le e-

iciec, we che tqm

aBI dna alzer

thi eqecer cll c

l hi, j e-

qeci I c l snpei re

ize li RLp

hr e ree r cre

cili, [I ] j l

eqeci, b I l

l ei y

ee exr iee

ew eqie y c j

he he e

ie eqeci l-

i ei [I]

er iere l lw-

c l ii

he rjec, ri r

ll rjec he bier

e I er lexible th

wh we che i

Ja L

the Wellce tr Cliicl

Reerch cili rie

eeic r r wie

re cliicl rjec r

r he uk I eleci

r ei lr,

he ir crieri

i ccrc relibili We

l w lr h re

lexible h we c -

r rjec wih re

snp le ize,

well er her erice

ch ee exreiWe crrel e w ier-

e ei lr

h wr well eher, tq-

he alie

Bie 7900Ht he

Illi Besi tq-

i riclrl

lw snp ber lw

hih le ber

oce rjec reqire

re h 25 50 snp,

i i re ecicl e

he Illi lr

Lee Mrp

m reerre ei

lr i lrece-

be cillr elecrh-

rei or cili i eqiewih 3730 dna alzer

(alie Bie) h i

e r lile re,

ch icrellie -

i, dna eqeci, aLp,

ile be exei

, ie snph al-

hh I bie bece

exeriece h bee

liie elecrhrei

e, I eel h CE i cr-

rel he l r r

ceri lie re-

ercher ee re hrh Qeible

bie r hee

lrer-hrh e

re e reiewe c-

ire hrh CE

Je Pasea

We re cre dna li

cili re ble er

ei r iei-

r rie l-

r: ei wih i-

crellie rer, snp

i he snph eh,

aLp r t-RLp le

re r r aBI pri

3100 a gei -

i rel-ie qpCR, ch

hiher-hrh snp e-eci reic e

ei, i e r

aBI pri 7900Ht seqece

deeci se

Mar L Sae

r r rjec reqiriContinued on page 13


7/16

gei EBRuaRy 2009 gEnoME TEchnoLogy 7

hw p

q q?

ull, he le we

e r here s Je re

cliicl le a l he re

iere i qli, be ril-

l ere lre, r he

l ci We reqire

le 60 r beiwih se wr i

he 10 r [re] r ee

lwer I rer e er

qli he , I he i

50 r th bi

ie r he rjec Ei-

her w, i he cer reqire

lile , lie he w

ierre 600 r 100 snp, we

he whle-ee li-

ci [We e] he aile Bi-

lzer he qici,

qli qici, QC,

he ee re Were i

eer le hrh he

Bilzer bece i c

l We rl che r

le r ech le

Ja L

aer dna exrci, ll -

le re ere r iel -

i icree wih be

le r el he od

ri ere ndr

accre qici

rlizi le i r-

iclrl ir r Illi

glege tqm

re ize i ir r

Illi Ii cheir

hl be le 2 ilbe

while Illi glege tqm c ce wih ch

ller re ize, 200

500 beir

Lee Mrp

the reercher icll i-

cle qli crl i ech

r qi heir le

bere bii he r he

ew ll erice rjec h re

cie i r cili, he le

re qie b reer

r b ri he le

hih-reli re el

beri he b r pCR,

we icle Cere Ee

plrhie Hi -

le w cceri

-ele crl er bch le e he qli

ciec he li-

ci We l icle rl

dna crl() (i

licble), which we icll

bi r he reercher

Je Pasea

sle qli i eerll -

ee i he ndr

thi ie ccre q-

ici dna bewee 27

/l 37 /l We l

r cceble 260:280 r-

i 18 20, 260:230ri reer h 15 view-

i he brbce rce c

hel iei i here re l

r her ci ree

h ih ierere wih w-

re rcee

Mar L Sae

t qi he leel dna i

le, we r he icree r Iire We e

hi i re qli-

ie hi eblih

exc qiie le r

ech le r exle, we

After dNA

extraction

all samples

are measure

for yiel using

picogreen.

L mry

Continued on page 13


8/16


W

v?

I i he aBI 3730-XL

H geemer 40

r re ize li

I eere e he,

e re, lci

b [] ill ee he

e ce wre he ecr li

I j ie he rw

ie cll r snp

ei, I w e-

hize h we lie snp-

h beer h snplex the

re i bece r snp-

h ierre ech

snp, i reqire hree li

snplex, i w li

I che snplex l-

r hi e

ll he li r he c-

, i er exeie, he

lrecel lbele li

m he he be

HpLC-riie al he cli-

e here, we w i be

che ible Ja L

We e he wre h ce

ce wih he e r

tqm hi i he seqece

deeci se eri 23

r Illi i i Besi

eri 313 wih eri 337

he ei le

Lee Mrp

or cili icll rcee

h dna eqeci

re li leer wee the i-eh e-

i li h we rie i

liie rece re

li wih he geemer

wre r alie Bi-

e the geemer rr

i cble eeci ri

rii qli cre r

he ri e eece b

he 3730 dna alzer I -

ii, le , wih

he excei aLp/t-RLp,

re iiill reiewe b

exer eber r cil-

i the geemer wre

ler he reercher -

l che he ize -

r /r e cll e

ri he reiew i rcili We l err c-

i-eh t-RLp li

h we ecicll eie

r iiil reercher

We l eerl e

ere e er-le

ee qli, b he hreh-

l r clli ri i e

ilre he reecie rjec

er we cc exeie

cli wih he reerch-

er B el we err he

ie cerc reer

icle h rel

i le iie the ehi

i lce he reercher

e he l ecii b

llele be cll rc

he ciec w c-

rl le r r r

where licble

Je Pasea

We use genemapper

r lzi icrellie

rer, snp i he aB

snph e aLp

r t-RLp le Rel-

ie li i e wih

sds 22 wre

Mar L Sae

We e he Illi lie

Besi wre r snp

clli r Cnv le, we

e he peCnv wre l-

lwe b il ieci i

Besi gee viewer

Kev Saa



9/16


W

p p

?

sice I e snph, I eer

ile , ee i e

icl rei, gC-rich rei,

r be e rei h

lile snp cece -

eher se exei ,

h ifere, ee li

bi he ele I h

re h he snp, he r

ieee re, eie

i icl i exei

there rble r e

Exei , snph,

he pCR, e

li he exei thiechl i er eiie

I erl er,

ele lie pCR-sLp a l

cliici, he bri he

er; he w h

the w j rer-

ce he e here b

ierri e snp I

e ler ie i ie

l ribili th

wh we e he RLp

[re] cie

wih r snph e-

i We eri he

icrrr I e he eri-

ci e snp ieie

b he icrrr We

e rei which c

be erie r e ifere

cll We beliee snph I

we c cr i, I will i-

rec cer beliee

i snph thi i r

bece aferix lr i

hbriizi-be, i be

he cre hbriizi

il which i rible th

ccre eh r e

riclr snp

Ja L

the cceble clei

ccrce re will

ee he ei

l he re he

snp che Icree c-

crc c be chiee b

ei he hrehl r cll-

i ee hih, b hi

c le lw cll re re snp h -

ber hi re icre

c l le irie

iie here ri-

cii c ccr e

-r iferece i

he er ii I

lwer riec i e, he

cll re will be reere

he exee ccrc, le-

i e r erri

snp hwi cii

We wl icll exec

re bewee 90 95erce r Illi gle-

ge, reer h 95 erce

r tqm, hiher h

99 erce r Illi Ii-

We wl exec reer

h 99 erce ccrce

r bh lr

Lee Mrp

a ieir i rcili h cle-

i re hl be hih,

r 98 erce y

l w hih ccr-

ce re, r 97 99

th acceptable

completions an

concorance

rates will

dpnd on the

stuy esign.

L mry



10/16


hw k p?

We he [] hre rerce

ee e, which

i eie b r Hrwell

Ceer iric e I

er er-riel We c rc

le l he clie,

r pI, he c e e heirle wih hi e

Ja L

sle re rce b lbr-

r iri ee

e, which rc le

lci le l r-

ce brce lbel We e

liqi hli rb where

ible lii iee errr

hi i ie b i rb

r eri rcere

, irl, hi well-

rie ie f

Lee Mrp

the le re rce elec-

ricll hrh he LIms

be the be lere re

cce hb r r clie the

icl le w bei whe

he reercher iiie lie

rer the be eere

rer ber r ech bch

le ( 96 er rer)

h he reercher eer r

l i LIms the -

be l eere ere

reqe ber r ech -

le h i r he reecie

rer Ech rer rrie wih

hr c he rer r he le re lbele wih

le w ieier the iei-

er re icll he rer -

ber, reercher l e,

he e the cili rcee

he rer ccril, lze

reiew he , -

l he i LIms

Je Pasea

or cili e Web-be

lr w he uvm

Bide r lci rer

iribi Iei-

r lce heir rer lie

re ie b e-il whe heir

i clee Ieir

c he li heir Bide-

cc wl he le heir w cer

the Bide ii er-

e bc heir

Mar L Sae

We he e ierl

rci e which we cll

l LIms e where

le re rce hrh

eer e he rce thi

i cclihe b i e-

b-e rci hee h we

eele i Excel thi l

e llw cre ll

ecer iri he

rci hee il b i

brce reer

Kev Saa

the eer ieici

cci iri r-

ie wih he le (bree,

eer, ec) i recre i -

be ech le i -

ie r w iqe ix-ii

ierl Id which bece he

rir le ieier Whe

we eere he ei

le hee we e r

iil ii eere

10-ii Id h l ci

bree relice ir-

i th we re ble re

le Id, bree, relice

wihi ile ieer h l

reqire 4 be re i

he be

Jerem Talr


11/16


W x

w

p?

Ierl exerl c-

rl re er ir Ee

hh we re CLIa-ceri-

e, we llw er ri-

e rle, le I Ee-

cill bece here re l

lilexi he reqire hiher

ccrc I eri

he, rbbl j ic

he wr hi r ech i-

iil 96-well le, we ell

r cer, we e w

well r ierl crl

we l he cer

rie heir w crl I

c be blie he w

he ee he

ell We ie he he re-

l le he ecie

wheher i ccre r

or ierl crl i l

eeic crl, bece

he ew snp ee

he cliici, he w

he ee We crie iie crl,

wh we i, we Hr-

Weiber seie we c

eqeci, i were rell

wrrie b i Errr re c-

ll i bi ie b il

re i he cceri r

ei bece l

le be b qli

r be he e

wr r e le Errr

re, I wl rher cier

zer errr re bece

ee ell he I rie99 erce ccrc he

cliici e lie i the

w 100 erce ccrc

Ja L

the crl we r re ee-

e he lr re

e cr he rcl i

wri crrecl Reercher

re ble elec heir w c-

rl eei he

ei, ch lice

le e rercibil-

i errr re il

eber c l be e

chec r meeli ci-

ec I ii, reercher

c elec snp h he rei-

l bee ee bere he e le, b i

ifere lr

r tqm , we

r -ele crl

he r he le hel

eerie he cler

chec r cii thi

l cr he le w

r i he crrec riei

r tqm c ,

we r e le E-

re Clleci Cell Cl-

re dna reercher

dna chec he cleri

Illi he i-

erl qli crl -

r bil i eer rr

e hw well ech e

he ei wrw h

erre geer eie

c l be e chec h

le he bee r i he

crrec rer riei Lee Mrp

the reercher icle ql-

i crl wih ech bch

re--r le bi-

e r re li or

error ra

acually is no

a big issu bu

fail ra is h

mos concrning

for gnoyping.

Jiang Li


12/16


cili r i-he qli

crl le r dna e-

qeci, b hi i el

ecer r re l-

i e he liie ce

r cili ilee

i he jri re

li rjec Bece we

he rcee -

le reqiri ifere e

le (icrellie,

snph, ec), we e hi

rereeiel e

he relie qli rer-

cibili ech r r bch le We he reree-

ie r ifere e-

cie, ie, cleic i-

li echiqe, which

iece he execc

ee qli cce

re bjecie bi I

ii, he iic -

erce he ize r

wihi he elecrherr

re e cie ierl

qli crl ere

Je Pasea

the e crl e

will ee he e

ei bei erre,

b wl eerll icle

le r ech ee,

-ele crl,

-lici crl

sle h ll ie

he cler c be eqece

r eerie he e-

e all le r he

3100 a he ierl

ize r e sle

re icll reee i

here i rble wih he

ize r micrellie

re eerll r wih crl

dna h h w reize a ieir i he

cili l r errr re

r e w erce

Mar L Sae

Whe we r re hih-

hrh rcei, we

e e Cere dEe

plrhie Hi ri

crl l wih e erce

lice er 96 well le

Hweer, we qicl lere

h he Illi e-

i were er rb

rercible crl

were eee lie he

ei

t cr h -

le he bee ixe r-

i rcei, we r le

hree tq i

he ieicl le le

r he riil exerie

thee tq ch

snp h exi he e-

i BeChi I he c-

crce i 100 erce

he we re (

10) rc ie Kev Saa

We he ierl

crl r he e-

i wrw i ccere

the rir ie h we

wch r i whe re h

e le er chi r e-

ire chi il ri ei

i Besi thi i ll

iicie le hli

ie r l chi (which re

er rre) i he ce eire

chi ilre mii re

re qie ll r exle i

ee-wie cii l-

i erre 1,720 iii-

l r he a bree, we

lere snp wih ir llele

reqecie le h 5 erce

lei 41,028 lci; he reli

e h le h 13 er-ce ii o he her

h, ei errr re

re icl eie bece

he reqire h w he

re ee Hweer, we

he eerl ler l-

eri h we l

exrci wih he r -

ll bei le cll re le 90 erce aer h we

eerll chec r meeli

iherice whe we he e-

e re /r fri

he le iiil Wih

he Biesnp50 BeChi

we h crrec re-

chil relihi will he le

h 05 erce icr

ee while icrrec

relihi will icll he

2 7 erce icrce re

Whe he icrrec

eiree relihi i ic

lie re hb

Jerem Talr


13/16


hih-hrh ei,

we e he Illi e-

i echlie (gle-

ge, verce, Ii

Hd) the i re r hichice w he qli re-

rcibili he

Kev Saa

We e he Illi B-

iesnp50 BeChi Iii-

r ll r hih-

ei snp ei

i cle the Besi

cer i lce i he ui-

eri miri dna Cre

where i i brl e r

ei exreili or lb i e-

ber he iBmaC (Illi,

usda aRs Belille, uier-

i miri, uieri

alber, usda aRs Cl

Ceer) cri h

erre he snp ic-

er exerie

ei rjec h le

he rci he Bie

snp50 BeChi We che

Illi cre he

bece he i-lici heir cheir, r-

be he Iii -

, er hih qli

rce ee bh i

er cleee

lw errr re

Jerem Talr

Q1:Continued from page 6

he eblihe cce-

ble hrehl relie -

rece i whe i he

icree I le

i be hi hrehl he

i i re r ei I

le i belw he hrehl

we will e ccere

i I cceri he le

e wr, he he le

will be rcee

We ciel e

le qli the i re-

r hi i he ie c

i el iri

i ecii he qli

le I hih-hrh

lb, i i cll re c

efecie he lihl el-

ee ilre leel h i i

e he efr e

qli eer le

Kev Saa

We he r er 12,000 -

le hi dna w

exrce r ee, bl,

l wb, cle all

he exrci were qi-

e wih eiher uv r ndr

ecrheer we

icll h r he 260/280

ri be bewee 18 20

or exeriece wih he I-

i e h i i

ch re eiie er-

li h er-li dna

sice le re

ll rble r , we

icll e 300 r

(200 r rece-

e) dna er le llw

r he ibili errr i he

eii dna ccer-

i bece we h rrbe, i i beer he

re h lile dna thi

rce wr er well r

we er rrel ee ile re-

ci e lw cll re

Jerem Talr


Besi excliel Becewe cribe he eel-

e he Biesnp50

we eele r w i-he

c cler le r clli

ee be er 8,000

le ee r ri-

bree Bos tauruscle

thi h llwe he be cler le h err

er well cr he

cle bree h we ee

or cler le w eele

r bree h riie r

he erile Crece we he

h we c iicl

ire r ee cll re

qli r bree rii-i he Ii bcie

b eeli cler le e-

cicll r hee bree thi i

qie bi wr, b i ece-

r i w ere he

hihe-qli ee

Jerem Talr



14/16


Li f rrcHere are some articles and websites to turn to when

you have further questions.

pubLICAtIoNs

e Ber pIW, yele R, peer I, gbriel

sB, dl mJ, alhler d (2005) Efe

a pwer eet assat stes

nture geetics 37: 1217-1223

Chc sJ, mli t, Behe m, Ber-

wile E, Her dJ, th g, HirchhrJm, abeci g, alhler d, Bile-Wil

JE, Br Ld, Cr LR, dl m, dell

p, rei,Jr J, reier nB, gerhr ds,

ger C, gcher aE, ger ms, Hrri

EL, Hh J, Her R, k Ca, meri

kR, mr CC, pler LJ, phiier Eg,

Rice Jp, Rber J, Rii C, tcer ma, v-

kJ, Wchler s, Wij Em, Wi dm,

Clli s r nCI-nHgRI Wri gr

Relici i acii sie (2007)

Replat etpepetpe assa-ts nture 447: 655-660

mcCrh mI, abeci gR, Cr LR, gl-

ei dB, Lile J, Iii Jpa, Hirchhr

Jn (2008) geme-we assat

stes r mplex trats: sess, -

ertat a allees nture Reviews

geetics 9: 356-369

pcer BR, yeer m, Bre L, Welch R,

Beer m, Qi L, sice H, s B, ach-

r m, Crehw a, Ecer a, pri v, gerhr

ds, Chc sJ (2006) SnP500caer:

a pbl resre r seqee vala-

t, assa evelpmet, a reqe

aalss r eet varat a-

ate ees nucleic acids Reserch 34:

d617-d621

Wlle dC, tri BE, s yC, Wlle kR, teb-b sJ (2006) MAcgT: mlt-mesal

atmate lster etp tl r

aalss mrarra-base m-seqe-

ata Bioifortics 22(9):1147-1149

y y, Li ss, Chie J, ariee J, Zh Lp

(2008) A sstemat sear r SnPs/

apltpes assate wt sease pe-

tpes s a apltpe-base step-

wse prere BmC geetics 9:90

websItesgeeWw:

h://eewiwciih/Welce

SnP500caer:

h://500ccerciih/

TaZlla:

h://zillciih/

erce, b he will eer

be erec

Mar L Sae

a le ilre re beweee hree erce cr

lre rjec i cceble We

eerie ccrce

re r lice il er

ric cri le qli-

he snp therere,

he lice ccrce re

i lw r 999999 er-

ce I iei he snp

h re icr, i i l

lw bece snp r e

he le i he lice

ir i bei clle rher

h bei iclle

Kev Saa

I eerl, we he

clei ec h we

h r I he b 12,000

cle le h we he

r he ere cll re h

bee 9886 erce l

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The broader your view,the more associations youll find.

Get the solutions that bring SNPs and CNPs together for the first time.Affymetrix genotyping products allow you to study more variation, providing you with the most complete view of

the genome. By combining SNPs and copy number polymorphisms (CNPs), the Affymetrix platform not only gives

you a competitive advantage, but also helps advance our understanding of many common diseases. With open

software and instrument platforms, and a unique view of SNPs and CNPs, youll make more relevant discoveries.

To learn more about our genotyping solutions for association studies, visitwww.affymetrix.com/snp6
http://www.affymetrix.com/snp6http://www.affymetrix.com/snp6http://www.affymetrix.com/snp6

tech guide feb 09

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