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7/31/2019 Tech Guide Feb 09
1/16
7/31/2019 Tech Guide Feb 09
2/16
http://www.sequenom.com/climbinghttp://www.sequenom.com/7/31/2019 Tech Guide Feb 09
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
7/31/2019 Tech Guide Feb 09
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
7/31/2019 Tech Guide Feb 09
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http://info.appliedbiosystems.com/taqmanopenarray7/31/2019 Tech Guide Feb 09
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gei6 TEch guidE EBRuaRy 2009
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
7/31/2019 Tech Guide Feb 09
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
7/31/2019 Tech Guide Feb 09
8/16
gei8 TEch guidE EBRuaRy 2009
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
Continued on page 13
7/31/2019 Tech Guide Feb 09
9/16
gei EBRuaRy 2009 gEnoME TEchnoLogy 9
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
Continued on page 14
7/31/2019 Tech Guide Feb 09
10/16
gei10 TEch guidE EBRuaRy 2009
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
7/31/2019 Tech Guide Feb 09
11/16
gei EBRuaRy 2009 gEnoME TEchnoLogy 11
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
7/31/2019 Tech Guide Feb 09
12/16
gei12 TEch guidE EBRuaRy 2009
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
7/31/2019 Tech Guide Feb 09
13/16
gei EBRuaRy 2009 gEnoME TEchnoLogy 13
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
Q2:Continued from page 7
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
Q3:Continued from page 8
7/31/2019 Tech Guide Feb 09
14/16
gei14 TEch guidE EBRuaRy 2009
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/
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http://genewindow.nci.nih.gov/Welcomehttp://genewindow.nci.nih.gov/Welcomehttp://genewindow.nci.nih.gov/Welcomehttp://snp500cancer.nci.nih.gov/http://snp500cancer.nci.nih.gov/http://snp500cancer.nci.nih.gov/http://tagzilla.nci.nih.gov/http://tagzilla.nci.nih.gov/http://tagzilla.nci.nih.gov/http://tagzilla.nci.nih.gov/http://snp500cancer.nci.nih.gov/http://genewindow.nci.nih.gov/Welcome7/31/2019 Tech Guide Feb 09
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The broader your view,the more associations youll find.
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