Aug2014 acro metrix

1. 1
The world leader in serving science
Mona Shahbazian, Staff Scientist
Kara Norman, Head of R&D
AcroMetrix® Brand
Building on the Genome in a Bottle for Oncology

2. 2
NGS Quality Control
CAP Checklist4
•Daily run controls needed
NY State2
•“Low positive control … containing multiple known somatic alterations of each kind”
CDC (Nex-StoCT)3
•Reference material characteristics:
•Complexity and different mutation types
•Most / all of variants
•“Synthetic constructs could be used for routine QC of each NGS run”
•What is needed for robust QC?
1.Dutch Society for Clinical Genetic Laboratory Diagnostics (VKGL): Humu 10.1001/22.368 (2013)
2.New York State Clinical Laboratory Evaluation Program (CLEP) Laboratory Standards.
3.Gargis AS, et al. Nature Biotechnology. 30, 1033–1036 (2012).
4.College of American Pathologists (CAP) Laboratory Accreditation Checklist
VKGL1
•“…a separate SNP control”

3. 3
Reference material for oncology
•Customer needs
•Clinically relevant variants
•Various lengths of indels up to ~40 nt
•Minimize real-estate on chip/flow cell
•High quality/robustness for clinical use

4. 4
Overlapping Variants Problematic for Variant Calling
• 7 KRAS mutant cell lines + 1 WT cell line
• Extracted genomic DNA and mixed at equal conc.
6 or 12%
Expected
Observed
275 280 281 282 283 284 285
T G C C A C C
T A A
G G
T T
A,G (5%) 8 MNVs (5%) T,A,G (3.85%) 7 MNVs (20%) 14 MNVs (19%) G,A,T (55%)
T G C C A C C
A A A C A A
G C G G G G
T T T T T
7 SNVs
29 MNVs
3 SNVs
3.9-55%
Ref
Alt
Ref
Alt

5. 5
AcroMetrix® Oncology Hotspot Control
1 8 I N S
• MegaMix Technology
• Built on Genome in a Bottle material
• GM24385 cell line
• ~550 Common variants
• Low frequencies
• Confirmed by Sanger
• Multiple NGS platforms
• CE-IVD, US-IVD
Length (bp)
0
10
20
30
40
10
0
20
30
40
5 0 4 S N V 2 M N V 2 9 D E L E T I O N S
1 C O M P L E X I N D E L
1 9 I N S
For In Vitro Diagnostic Use

6. 6
Includes Important Cancer Variants
EGFR
L858R
L861Q
E746del
BRAF
V600E
HRAS
Q61R
KRAS
Q61H
G12D
NRAS
Q61R
G12D
PIK3CA
H1047R
E542K
E545K
PTEN
Y68H
AKT1
E17K
ALK
F1174L
R1275Q
CTNNB1
T41A
S45F
KIT
R804W
W853*
IDH1
R132H
IDH2
R140Q
R172K
VHL
G93R
FLT3
D835Y
FGFR3
S249C
FGFR2
S252W
JAK2
V617F
MPL
W515L
NOTCH1
L1600P
PDGFRA
D842V
GNA11
Q209L
GNAS
R201C
GNAQ
T175S
MET
Y1253D
NPM1
W288fs*
RET
M918T
TP53
R273H
R248Q

7. 7
Performance tested at >30 external sites
2 control lots
Ion AmpliSeq™ Cancer Hotspot Panel v2 (CHPv2)
TruSeq® Amplicon Cancer Panel (TSACP)
TruSight® Tumor Panel (TSTP)
Each laboratory is required to establish its own performance specifications

8. 8
CHPv2 – 13 sites
Panel
Site 24 22 9 21 11 1
Lot Lot 1 Lot 2 Lot 2 Lot 1 Lot 1 Lot 1 Lot 1 RLX
Run 1 2 1 2 1 1 1 1 1 222234...145 222233...166 22122..373 222334...128 222222...177 222111...378 22342..564 22232..673 222666...136556 1222555...234345 1222122...459127 2222122..69.156 1222113...058169 2222222...178356 1 22122..250 2 222111...457 1 12392..262 2 2022.922 1 22892..225 1222223...136166 2222234...048156 3222011...039557 4222000..67.416 1222334...137115 2222223...357167 3222122...124255 12212..682132 12234..682256 2 2222352...1444 22222233....1233 22221122....4579 22220034....2245 2222232...1173 22220022....1455 22222222....2466 2223332...1344 22222244....22792255 22223345....05594689 22220011....46771227 22220122....01391159 22222222....23443458 22221233..18..6938 1122782...6683 12220348....1399 11221388....1236 11222399....2234 2224462...2586 22220021...123.6127 22222333....11231168 12220090...477.2567 12220008....26682355 22222122.7...1276 12192..1172.6641 22220112....05791458 2220012...1499.2364 22223535..57..6945 22224445....3467 22222344....1235 22221455....5889 12225559....2248 2224442...2452 2221332...1393 2222452...3896 22223444....4568 2222562...6366.3575 2224662...6788.7889 22220444....58883578 22220444...348.3356 22220444....36882445 22221455....03384447 1222382...2293 12221348....4467 12221127....1129 12223348....1349 22222567....2588 22220231...038.2166 22222344....17881369 22222340...169.4559 22220345....24455778 22221345...348.5579 22221133....23391568 221322..2378..3639 2221112...1677.2665 22224556....22491359 12223588....4669 12223467....5688 12222678....2679 12222347....1688 224522..4504 12062..273 22221357....2268 12230038....1129 231412..5788..1635 22222268....57785689 11224789....47892289 12222448....11231188 12221489....24893356 122084..482.2345 1125692...3693 1220392...4794 11230119....1556 1222372...2692 22230026....2345 12221562...235.4337 22212447...239.1268 12221239....04884599 11221399....15891679 12222459....35775699 1222792...2255.2371 122049...28921283 2220162...2156.1191 22220285...388.2225 11223389....2455 2221121...2397 1220082...2660 11222229....1344 2204..79 221.27 2222232...3464 11123899....4467 12222337....02481169 22222336....25551345 1221182...0555.3782 11224489....45571489 12221181...248.2135 12221119....00693459 12220114....1358 11220139....4788 1220242...3672 1119991...2574 221722..5525 12221261...399.8229 12220227....45565578 12221291...166.6255 112990..682.5135 12221139....33351678 12220029....22576668 22220002....44771347 2220112...0177.5685 22221143...011.3116 1225592...1251 22220222....6888 22222245....3679 12220129....5789 22222444....4579 22220112....2667 22222234....3688 22223444....3345 22222377....34685668 2223462...4134.6666 2220332...0689.2789 12221239....16992599 22220255....23571135 222224...12822295 12220239....4599 22222245....2778 22222255....2348 2220032...3394 22330026....2258 22220244...146.9558 12223349....05691345 22221334...247.4268 222011...03423256 22222343...667.9127 2221342...2136.1268 2222222...3588.2781 22220011....16781567 22220412..23..2745 22222233....4459 22223445....1156 22223344....2244 22224455....1479 223522..1955 22221112....2678 22220777....4667 2220672...1497 228922..7933..5956 22222666....45573569 2221242...1128.2565 22224555....01171166 22224445..78..1522 22224566....01371227 22221124....4589 22220466....2558 22223347....1188 12223469....2666 2227893...2250 22224452...347.5169 222266..792.8711 22223564...038.9156 22223234.2...3883 22220566....08991567 2220352...4578.1569 1224582...5589.5578 222333...244179 22225556....16791136 22224445....27781139 21222.1112 22221133....2668 22222334....2577 22221245....1468 22223333....3359 22221222....3678 2220032...5683 12220449....1788 22222277....34995899 22222222....00782468 11223389....03791246 222244...69923443 22222254...112.4114 22221144....02792346 22222233....3479 22220134....4788 22221234....2289 22220034....3788 223722..8844 22221331...127.2357 22222333....45991249 22222331...135.5158 11223399....01244568 22220044....11571357 2220342...0168.4778 11220199....25893558 212.15.45 22224564...012.3155 22224545..67..5826 22221223....1449 22221148....1236 221322..6734 22221222....4666 2233..44 2222..99 11232999....1266 11222399....2368 22224478....00444477 22224455....01272459 222112...139124 22221158....04691568 2201..6923 22223389....11231349 220322..1724 22221233....3789 22220333....1799 1220092...6691 22330111....4568 22221147....33334666 22222368....03572489 22221136....27891239 22210589...135.7357 22221146.2...3996 22220189....02571456 2222222...4578.2255 11222288....88991116 22225669....03894689 2224..0257 22221133....5579 22221223....1446 22222234....2335 22220223....1469 2221332...5572 22220023....1158 11222299....4568 12222239....1468 22221344....13452568 2223442...4126.4562 221122..1145..4655 22221123....05675569 22222222....12571578 22222233....11661249 22221124....1139 2222242...3693 2221222...4573 2220112...4783 22221134....1128 22221222....03474578 22222223....11485579 22221223..15..3816 11120999....12893588 22222223...589.2488 22221122....22592345 2222332...2227.1483 2221122...2188.2889 22222356....14595678 22223343...378.8157 2221222...4681 22223344....1249 2221122...2492 22224455....1128 22142..795 222033...238 2223662...2364 22221133....4489 2322.3312..1494 22223333....11674599 22221112....33683788 22222245....00182355 22221233....23682578 22222244....01132238 22221235....2789 2222222...3472 22221234....2344 22221223....3345 22220133....1558 22221223....56992567 22222333....23481127 22221146....33474588 22220012....66891789 22221255....15692244 22223355....03375689 22221122....15573679 22221122....24772568 22220145....27791166 22223523..00..4812 22220123....3679 22220223....7777 2221222...3332 22221344....3499 2222452...1685 22220133....3579 22222266....1447 22221223....1169 225622..1319..3648 22220336....24883779 22221123....04885789 22221222....01251778 22222231...124.2369 22220123...149.3688 22220123....1256 2221122...5681 22220112....3589 11220199....3588 2225892...2282 22222333...069.9122 22223333....35881779 22223454...688.6269 22221222...448.1167 22221125....11561156 22221344....01271779 2221122...4002.1362 22220122....78994579 22221234....12361158 2234..1766 22220014....5669 1123782...2231 12221159....2457 1221381...2577 2222451...1249 12222226....1247 1224492...2785 12221269....3377 1223492...7158.1563 12220145....00391235 11222368....27881278 12222493...499.1236 11126993...299.2245 22221461...557.1389 2229035....8119 1229258....7239 2228144....9778 229342...1671 12230478....5889 22221246...046.2137 22220244....00283469 22221115..77..2638 22220113....00191469 12223369....38994779 12222458....12292556 1221472...1345.1241 12220229....23442466 12223459....13793446 22221122....1346 22221124....1388 2220122...2681 22223333....2356 222444...245 222222...447 2224442...3454 22221223....2346 22222233....04691225 222234...02925674 2221232...2017.5786 22222223....05781238 122029...14622370 22221142...167.1127 22223455....1349 22220445....1337 12224569....2347 22223556....1559 2224562...1237 22220112....55681335 22221223....00273447 212119.52..8813 11210999...167.4689 22223331...239.8445 2221122...2088.2775 22220011....01894567 222222...55522550 22222445....13892557 24.47 22222222....3589 2224452...1895 22223335....1224 2223332...6676 21.4 23.4 22223446....1255 22222334....4578 22223347....00181148 22222224....22373556 22221112....13665689 22222224...677.4445 22222224....23382344 22223445....03782444 22222334....1237 22220025....1789 11222599....1167 2221232...1293 22233555....2258 22222262...677.7126 22223335....00181678 11220699....00882246 12220590...068.1359 22221129....07895668 22221229....03484667 22221117....14473789 22220001....11141578 22224585...013.1349 222444...557157 12220489....1189 22232367....2479 2222353...1452 225623..1534 2202..68 23.4 22223369....2378 1225592...1670 22334678....14682668 22220113....25671279 22220336....00283679 22321684...468.3579 22222551...157.9126 22223346....45882356 12220239....1567 12222668....1125 22220455....2579 123712..4939 3336892...1566 22232261...349.8157 22233457....03771347 22232356....25793347 22232235....00892569 22236782...189.6169 2225783...4001.1443 22331256....12992688 12220008....78992458 22224455....05681479 22224457....12691699 12220668....3357 11227799....5889 22221288....2249 22220088....2366 11226677....9999 11227899....1789 22222377....3469 2211..38 2224992...4226.1455 2222552...2034.3892 1227791...9033.2552 11227799....13353367 12215599...789.9245 11225588....13792377 2440111...2359 22440122....1446 22440034....2369 22441156....5568 2251775...1282 22220122....12241569 2233..1615 11227788....06895999 11320889...058.9349 22334444....11995677 23553..6492.6625 23462..4883.5946 11220099....00582378 22222255...999.2345 22225566....4679 22225588....1135 22227888....1146 2225882...6786 2277..13 272.98 22225577....1335 4422..68 22229999....33563455 22225555....44551378 22225566....23572459 22225577....55593368 222588...13621445 22225588....11352377 33440223....1158 33441256....3779 33443455....3678 3340234...2996 3552273...2568 22222245...114.3569 3300..5857 22226677...038.8666 22225995...699.7245 33330045....04991455 3333663...3144.3353 33333356....11581466 1220071...8679.4788 22224446....01771159 11224589....5779 22220055....1233 1221892...5667 22220155....3567 1209..18 192.80 2220062...1266 11343899....4567 2225692...8004.4782 1225591...9888.2368 1224571...6335.4567 11225599....22494789 12220699....02562579 11228888....15666679 1142782...2459 2340222...1681 1144893...1261 22231169....3379 23341278....1558 12220349....22394679 22320129...248.5156 12220569....03571359 22221450...459.9189 22230229....14461579 2123.1303..2472 2232333...3028.3663 115711..8809..7958 22220144....14592456 11117789....6899 12220008....1489 1220181...1447 1121892...2461 11117799....1699 17122.2008 11117899....8899 11115799....1224 2220042...4347.1784 11114799....77891235 1114561...7089.2999 11120578....01293556 11210898...115.1127 11210399...033.4128 11124478....5788 11220669....4689 12220156....1247 12230015....3368 22230679....1256 11210688...012.6156 11221881...279.4126 11220189....03694556 12120808..19..5816 222002...45823155 12220139....07893556 2220042...2079.5675 11116688....13461359 22220011...023.2157 11117778....2367 11220088....1248 1120791...1296 11220089....4556 111788...556 11781..289 1118881...1379 11112499....4589 11119999....02581158 11114477....01682399 11114578....11261346 11114477....22273599 11115899....02341455 11112378....12281677 1114481...5569 11120569....1259 11220046....1269 11220256....1444 22225666....3558 11115588....45791278 122028...00424577 11118999....67795578 11116788...244.5116 11220199....05791167 11220199....66791178 122008...06921891 11116677....02685889 12220009....06891489 111468...229 112159...367 112288...679 112169...289 112169...448 11782..471 1220182...6671 122468...469 222156...55723597 1117991...5237.3799 1120571...5026.1258 12222237....34561589 11127780...348.4369 11115686...178.4146 11120288....2299 12221237....1125 12220236....2778 1223472...3354 22231359....2488 112299...18922478 22221244....12351116 12221283...159.1599 11120788....35781467 22221232...256.9247 22221224....34452469 12223459....08992348 11114446....34772389 12210169...088.7368 19.81 11113336....3456 121511..1455 11114458....2367 11113339....3449 911.800 11121..282 11111128....6668 11111118....4458 1120011...0123.1231 11113337....22696888 1110151...0468.4688 11113337....02471345 11110007....22473347 11110018....13771489 18991....1249 10111.9127 11110118....2578 11110126....2336 11121344....2588 11111119....89991124 11210222...899.8266 11112282...114.2459 11112237....25681277 11122334....08881468 11121333....33351388 1114491...4448.3575 11113336....01131346 11112923..68..4716 11114449....24661268 11113567....2477 11115788....1259 11115689....2669 11113888....3679 111066...123 111277...446 11113356....1248 11120267....3699 11110999....23572245 1114781...7128.2342 115511..2933..8913 11113889....05784889 11110677....66991589 11110898...119.1577 11110456....3357 1114671...2489 11113667....1369 1114581...2684 2223551...2885 11111589....12391157 11222337....11193569 111299...12514256 11113699....24481559 11114599....13671246 1114892...0188.3683 11220157....26771127 111355...356488 11220341...677.2126 15.52 11120888....2378 1120782...4690 1119992...6671 11121899....2469 111599...456 12092..172 1121881...2259 118912..6809 2220132...2055.1561 11220199....02383446 11115578....13571455 11117799....44671466 11220089....35675688 11117779....11561478 11117778....4468 11220199....3678 2220122...1153 11120789....3368 22226778....2258 11120899....67791368 12211298...339.9667 12220007....33671257 11116989..34..5725 22220014....00793579 12220129....11282257 22220114....13671677 11115667....25781246 22221201..24..3627 21.53 11220299....1279 11221999....1478 1220092...1477 22230114....3466 15.6 17.4 2221112...3461 1118882...7894 222144...22721564 2220002...0246.1373 11114777....11555669 11123999....45672556 12220150...016.5668 11120777....23551246 1117882...2385 22221124....2669 1220092...1698 11125889....1478 2225552...2478 12210198...047.8555 22221290...225.7558 11220990...789.3236 12220491...146.5557 22221534..00..4958 22220223....07894566 22220334....16992367 1115561...5288.3388 22220901..27..2216 22221123.0...3466 11222455....1289 22330012....3689 1126882...3468 11334499....2459 19.7 20.2 11221299....2378 1126772...4794 1122992...4256.1266 11220177....03473379 11115567....12231279 11224488....14561456 11210797...246.4556 11221244....35791339 11224567....1258 11220566....3456 11231149....3889 11220556....1238 22223367....2234 11221883...119.1127 13120999..48..6767 22120129..09..7925 222045...05820256 22220303..27..3888 221122..1209..2912 11222399....13662556 1116671...7223.4472 12129989..48..4747 2223..6725 1221151...1586 22220056....4679 11220088....1445 11222299....2367 11222299....2457 1122782...1693 11229999....00175688 1223371...7133.1573 1221251...5257.2571 11225884...124.9156 11223774...259.2259 11220145....12882469 11227788....1289 11224566....2369 1225771...4677 1125672...2238 2223552...5553 11221178....04781459 11227799....55885779 22220606..13..3516 11224499....17995559 22224554...055.1136 22221244....24455556 1129992...9369.5887 1120672...0169.2695 12220595...129.6245 2256..5515 11220144....4456 1123992...5675 11220244....2667 11223377....2345 1221271...3578 11220177....1289 22220077....12262567 11223388....01241357 1221141...4458.4684 11224477....77892788 11224774...224.3666 12210155...468.8159 1124463...1266 1134572...2787 11236777....2338 1234671...1696 11231477....6888 11221288....26673789 22221177....05883568 22223367....35685668 22220405..48..5637 11224555...457.8127 11224778....12591456 11227788....14551478 2200..3626 11224567....02493469 11224667....45791356 1129000....8278 11120001....5567 29911...5650 29992....8892 29991....5671 29992....3558 1129000....5345 27770....3358 2999...3233.17891557 1129.0017...12341378 11112226....14891679 11110118....12592234 1299..0279..00451589 1129.0117...01445788 991..1699 19991...3770 118909....5822 11120111....2238 1233..16 7278.7..0066.5596 11210140...127.5125 29.3089.04..7956 29.0099.05..1379 11210121...459.8166 11121123....33481556 11120003....48891557 1888...8689.16665889 11120011....03666667 22.15 8889....2368 118801....1839 1890...2329 8899....1114 688...679 799...355 7899....2677 6788....1558 1778...0122.00011144 7899....044927995569 69..9286.043.3825 1166..0034..44561378 788...0699015.3482 7799....004556892345 79..1278 789...4897 889...2237 8891...1261 78..196707..1467 1177..0019..04585578 187.089..905.9545 119018...122.8515 191.1791.26..8215 19.010.9159..5922 118.119..0232399 6699....348823493778 1188.009...70265168 111011...9455.5666 991..5709 1118011....7177 9991...3560 1118001....4248 888...3449 889...3479 119900....4547 8889....2688 888...8588.24564465 1889...0557.12474578 1789...1188.15674444 1781..0590.079.2119 79..237803..6779 897..178.047.9967 7888....3578 8899....2479 8999....7788 118111...9120 14.8 1788..039..30185238 1999..023..33455169 9988..34..57065545 1119.0000...00595567 1991..0291.689.1445 1119.0018...15672579 1110019....14776675 889...9345.05828898 1199..0155..06795559 189.08..956169 19990....4778 1119001....9159 1119000....6358 19901...8871 8888....5566 8899....2388 19990....8994 8888....2557 1110019....02991574 11110000....22453668 888...9899.23821495 9999..58..77475738 9989..37..99141549 8898...339.34662367 119900....3537 9991...4451 1119001....8577 1110011...2370 151.53 7889..19..22145827 8999....333500054555 11800...9044957 8919..69.0805.5558 11110000....56995567 111111...9014.5577 1119.0002...14672567 7788....566612332589 11110102..17..5927 1101.3.96 1119000....7115 119001...8110 11110001....1668 119001...7240 77..117 9.299 1110121...2882 7789....3589 1999...0569.01283477 1889...0299.02771356 1999...0677.33682589 1118.0011...24552456 7797...079.70361335 1889...0055.12452479 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577..466.478.5536 8957..24..89175528 178..0814..02604787 6788....114400012346 6777....226913892359 788...1597456.8996 7888....1338 8888....2259 6778....5779 1117000....5258 5778....2569 116001...7460 6778....2489 6777....1235 88..7358.558.4425 777...7566.35592686 677...7678.67921994 7778....224707893488 8886...033.72381147 7888....345667991677 7888....1778 888...278 115901....6911 8889....3578 778...1357014.5244 778...3467555.8448 77.477.86..7955 777..777.855.6548 888...3577015.7447 88..8949..15564756 778...6223.05584475 6777....669927992477 9999.1...12255559 777...6687 8888....3567 778...1388 1780...2858 67..7888 8888....4557 8888....5667 6667....2778 788...8346.05524795 1799...0667.02362447 677...7568.12651385 7777....278835882358 778...0037055.4493 6777...336.36693147 5667....1777 6677....1247 6667....1139 6778....2367 1118000....75775339 7777....577944592789 6888...029.01597137 1116000....81115237 999...9997147.5123 888...3468247.3796 118.0015..0223.1332 6777....678855792788 998..12.9400.5597 52.10 179..86 1476...199 1454...355 173..25 189..56 171..16 161..88 158..524.238124 157..3519..13881895 16.26.0239 1336...1356.34781237 147..029.016347 1456...2056.01343449 1550...3755 349...458 49..785 1560...693 1453..309..92694679 14.51.2535 138..103.148148 146..328.347389 1551..0442.059.6255 144..499.9137.3485 1459...1017.22891225 78..576979 155..2956 11111999....5788 1118881...7785 11113777 11114448....5778 11110333....2459 11114899....2229 1118111....8345 11110111....8888 115611..2516..1337 1118.3337...13672678 1111129....07901595 1118.1228...13673445 111010..817..6598 1119.1226...02794468 8991...6680 8999....2366 118801....2728 118001...8451 11110234....01783567 11110555..45..5568 1118.0000...05893688 1119.3347...02885999 1118222....73475135 114411..0424..9918 1110011...0277.4679 777...7466.05642366 11113565...148.6137 1116111....9888 118441...7565 117331...8123 1117888....7467 1116000....3789 1117444....9123 888...7776 11001..7861 116.1114..1349.1131 6888....566724591227 789...0489257.7772 7888....078922785799 1699...0226.12451345 5999....677857772238 788...2577 6889....2337 49..2689 1590...6769 1117.0009...07881168 1110060..55..7628 589...0198000.4348 5999...457.70125146 7999...058.32665344 6899....117906892456 1118.0004...55671667 777...6577.05892355 1161.2353..357.7136 8.691 5667....2227 678...1587 666...6677 677...3788 57..337 69..349 667...2666 566...5896 677...7247.35567895 6777....556756791466 56..6646..02442414 7777....012504572447 6666..67..45011533 5557...455.83691445 066...2556 667...148 566...167 6678....2349 6767..27..18155534 566...0587006.1339 666...2245567339 6666..33..28015533 887..488.526.2535 7778....045702554488 5668....145900356678 666...6177.12366886 6768..13..02585537 7778....2399 8899....2348 6777....3467 677...1238 5667....2378 688...2688 5677....3358 4788....2268 688...2347555.1684 668...6668.01965678 5666....236701384478 7777...017.60122256 567...0596005.6776 6667....245633791356 588...1338 4667....5788 578...1237 79..1259 5675...469.80005334 577...0175005.7344 5666....000800053399 666..016.555.1533 1177..0079..01251445 79..9468.164.4545 888...0557578.2449 5666....007800147899 6787...259.61555134 65.0.8559 7788....2567 8899....2345 6677....3788 7799....2279 66..886 88..688 5577....2368 7788....2233 7788....124401464899 6667....266934882288 6677....457833892489 6788....134906791458 666...6776155.3457 6666...357.60281369 778...5667 677...1447 678...239 7789....1237 666..786.406.5528 6767..67..67091523 5666....1467 666...0235000.2139 189..0298.016.5455 799...7024.15555595 668...8345.03446686 6666....004412381139 6778..26..03055547 56.8.6601..5557 788...2458 8899....1223 6788....1139 7799....4677 5.9688 799...3498 5567....4467 6777....1349 78..7813..05594645 7777....001314565579 67..8696.554.1331 8867..01..28175569 5667....356900251449 6677...248.70365478 5677....1157 6677....1359 6677....5889 567...1598 6677...389.30455127 77..46615.5878 6.25565...2793 66..34834.1658 888..038.900.2548 7.6647..055.4655 55..89748.1668 6677....234425783678 7788....1567 556...6389.5557 6777....2259 8888....4448 788...2338 7777....6667 888...1998 19901...4491 777...3358 677...2377 889...9067.55667991 7777....012302331334 55..6689..68575655 788...1787058.4583 677..45.7256.5576 667...0440771147 677...4476 6777....3358 566...2667 677...1466 776..567.401.2589 66.167.91..1258 667..25.0015727 666..116.615.4538 78..078957..3544 77..7126.570.4555 99..7138.153.4535 777...7113.25625788 88..458801..4724 677...4677006.1383 7888....1128 7788....2459 88..6888 7788....4667 8889....1449 19911...8911 6688....3389 7788....2334 8889....068904553445 788...7122.12325899 5688....133800794569 8888....457901475568 76.5.6740..5825 6996...134.52674156 678...367 678...589 667...234 677...2688 6767..56..57055547 66.867.95..1953 5676...056.40005334 666.26..270.9553 87.378.01..7952 778...2477056.3442 8.8999..019.4155 777...7122.04615897 888...0358005.4485 678..69.3005477 7788....1467 7788....2679 8888....2577 788...4998 888...3678 9999....5568 18890....5782 7778....3679 89..8968..24894955 889...8129.12523795 8889....014702772278 7788....135612582579 667...2582554776 9999...115.72474155 666...1298 6777....1456 6667....2479 6778....2244 666...7897557.4137 667...0895577134 77..015501..6748 7767..33..55561545 778...0270667146 778...4598255.4441 8889....347802564589 667...7089.68922682 8888....023501582447 6666...778.80165477 477...258 5577....2389 448...3668 5588....2289 88..13 99..23 6799....2689 77..46 5599....056712784459 1188..1179..01111445 669...8056.16744596 7777...003.20174168 467...1160276794 7799...144.71468358 55..4978 66..137 55..665 577...234 5567....245902574779 556...1387555.6345 4467....066700052379 3376...278.71585247 6688....124444561288 667...8898018.1448 5588....578901231377 6666....579912584678 5858..35..34075513 445...7896055.2373 5777....2347 567...2797 78..2857 6779....2789 77..33 88..77 6678....2389 16880....2899 678...7798049.4475 1199..1212..16783467 689...4558025.4797 777...3557025.2345 6775...013.10057347 777...1487056.6448 567...235 4677....7899 456...3888 4788....5678 12.8 777..587.514.7588 6688...699.01675349 566..276.403.7533 568...5688078.1148 777.48..485.6554 8.880..1687459 778...7026.05957995 6777....045966891245 677..59.8608.5497 5556...179.20065367 7778....3578 19990....5891 7779....1257 679...4497 555...346 777...678 16660....1892 679...1897 66..6249.332.2475 6669....234815671899 55..578.038997 6669....000255681157 455...249047489 5559..38..67795718 6779....1289 6678....5688 789...1337 59..1767 57..095500..5858 16055..14..2851 373..11.605524 83.04.95.8554 48..27425.4429 48..4264.025.2965 8.4433.82..4565 667...6399.13595693 1780...7016.5515 5586...122.40155235 18891....2343 16890....5582 1790...2879 18992....3459 777...789 6.977 11110002....2348 19990....1689 199..2869..04595585 1999...0899.12231117 1110019....15991585 199.02..9314.5244 11110012....00332556 1110029...036.7127 118801....2816 1890...3778 1110021...3340 19901...4420 17807...495.1555 899..269.408.3557 6866..46..05045539 18.0288.56..3945 788.89..275.4554 8.8788.07..4175 17.088.8.565.2415 7777....122906783579 119.009..9125.1258 78..846.553 7788....5778 7888....1338 788...8999 7788....3578 7888....2348 77..2788 6999....1236 888...6899 1119.0001...01351466 118.0014..0225.1462 1118.1118...22331245 1888...0678.02571347 1899...0279.12564558 8899....069906784789 778...3468 17801...2720 899...2669 8889....2234 878.98..380.7554 111800.0..957.5668 787..188.606.1546 991..789046..4145 899...0249015.5445 199..0839..05571555 88..368855..4917 7777....588813462355 111001...8269.1469 899..17.8217.5245 8888....1456 889...1168 8899....1228 7778....3568 6678....1689 6777....5578 7999....5779 7778....2467 11110001....33771267 8899....015635583358 188..0988..04823573 1888...0334.00562457 181.070.361.3360 1798..009..70299145 7779....6788 181..4299 8889....2899 8889....2589 777.6..3655584 1199.015...50275256 7899...679.20055458 899..469.855.3559 8899..79..29051544 889...1448006.3499 9.9299.01..5285 777...7688.26762391 189.07..9804.6141 788...4555557 7788....1478 8889....1248 889...4578 88..4688 77..148 77..187 19990....5575 789...2498 1199..0146..11174679 188..1867..01965776 1119.0017...01281566 788..88.7455349 8991...0271006.2445 1777..059..80557445 7778....6669 891..2608 11800...1128 7811..2700 8897...268.50035144 1188..0046..01783468 79..57768.3825 88..798825..1525 1118.0007...12571457 188..128.8015.4495 1119.0001...00164558 7778....244602563566 11990..0.895.5663 777...1147000.4478 77..7777 7888....2348 6899....1349 7888....3555 777...155 677...789 117900....2823 6888....2788 1110011...0189.1456 1178..1109..01441135 1188..0068..16794578 7777....899935591478 171.040.927..8253 178..057.01612390 789...1389 688...4558 118900....4547 7889....1389 7997...366.00555459 1199.006...21685144 6799....666701563345 8889..67..01362539 1110080..36..4758 119.0190...06804595 999...2789129.3496 6788....022304571455 18.08.9904..4558 779...2260057897 16770....1187 16770....2399 777...2687 17770....5684 79..157 69..487 8889....3579 18883....1237 1110001...1779.6665 1678...0179.22893455 1999...8022.02261123 1888...1003.12781349 7717..69.2835.4923 888...0146026.5457 881..1480 799...4579 8999....1139 7889....5788 6778....167700134577 1119.0003...00124669 666.89..685.5153 8888...289.80165229 899...5789015.7459 8888....255815584589 89..9913..07782518 6669....123601892379 1888..027..11455269 788...288001348 118800....1769 1118001....7239 17992....2882 117802....1324 9.5 99..34 1890...5818 1103..78 1177..1357..01231468 1119.0027...02233479 1112381...2016.2695 1671..1492.033.6178 1199..2344..24661169 61.6610..559 11011..220 11802...516 1119333....5577 11912...349 1668...0125.23675579 1177..0188..11491249 177..0489.138.3236 7889...488.54996566 1789...0189.25691489 88..856.44213913 1118.0013...13481489 1119.0337...27882569 1189..0178..12571235 178..137.058144 114800....2658 118802....2829 114822....1516 1921..6282 17790....4699 111011...2368 1790...8819 115801....1877 1118.0029...27991355 1789...2379.04443367 118.2312..0456.1189 1179..1214..56791499 1119.0341...12494444 1118.1129...16992347 115801....3458 11612...113 115902....2478 116912....4437 1178..0134..24454679 11110220...111.2234 1189.000...43375356 7889....018801681144 1199..1212..11784467 119.1214..2117.4677 1168..1357..13461778 1188..0246..15783678 1159.229...53695258 1112.4.11 6778....1227 7888....2589 7899....1235 8899....5799 777...5678 8888....1345 8889....4599 5678....2457 110099....02371757 8889....235701472568 1889...1038.00052244 6888...135.43575367 88.3.9992..5158 1997..047..41675247 779...2338 788...277 8889....6669 7888....3578 999..138.538.2525 179..1259.015.4557 7887...678.81455145 777..357.715.5559 79..689988..6857 9999....039900164558 99..9247.558.8956 7888....256678991347 889..79.8015.5393 456...4896 4679....1558 5889....2234 469...1399 68..248 888...112 8899....3335 666...467 189..068.1194784 788...6129.15951689 199..022.4336.2499 788...5784344.2573 8848..69..99465537 1795..067..61145249 579...278 477...245 578...169 779...159 9958..38..12015559 1859.06...25135659 5899...245.10585239 7578.7...15665552 1186.007...00275225 39..9969..08571457 699...9118.05653585 788...128149455 184.09..9401.5147 491670..2404 4914560...8590 3868..364 4914670...7280 47.5 44.1 4918340...5190 491550..390 449.5551..15502290 69.245.545.665 449.4881..04402280 49441..4880.7740 941.4104.8068 495561...42705350 4936..165 49408...813 49425...415 491270..6850 491490..260 459.4531..44503990 449.4751..02402550 459.3511..04703460 495615..010.5450 469.4501..04701390 49451..4010.5740 49561..5190.6770 499359...358389 94515.40.590 94.58 44515680...4590 41650.590 451450..240 51240.550 2418..79 224237...166 4160.50 46612370...1990 3452551...45502340 45451..030770 34271..090170 46051..560370 42618.00.940 469448...588259 46339..459 461350..180 461660..290 4664799...2479 45610890...1490 45581..040190 45691..880570 45881..240790 4650615..570.4470 461470..370 4563451...13707880 4662451...89901780 51.11 45561..790280 44591123....1148 33591489....4558 34590138....1578 33591678....1458 60.6 52.4 451449..6802 4492263...6888 34591338....57891349 4490025...0237.3887 442659..2506..2848 34591193...036.7189 33592891...147.6456 45930346...016.2455 3490285...6795 33592279....2678 33592278....7799 33591267....3449 3594563...2586 35931297...004.6145 34590239....01165599 34590493...178.8158 43590348.9...1561 33590299....06894557 33591288....34591458 3351999...3457.1351 345128...24897793 35396824..24..1417 36.57 848.49 8908..77 8913..88 8919..16 89.3 89.1 898.59 6856..48 8878..6935 8869..4745 8806..1435 8879..7917 8877..6768 9913.3.43 8911..17 7908..45 7906..39 898.20 8848..39 8919..2547 8899..4556 9900..2667 9920.3.97 8909..4648 8915..4959 8906..6658 92.9 7858..1949 81.17
Lot 1 Lot 2 Lot 1 Lot 1 Lot 1
33
CHPv2
SNV
15-35%
5-15%
genomic
Lot 1 Lot 2 Lot 1 Lot 2
1111 3 4 2 26 20
397
Run-to-run variation
Library prep issue?
Difficult variants?
Bioinformatics?
Detected
Not Detected
Runs
Variants

9. 9
Control highlights bioinformatics issues
Panel
Site 11 11
Lot Lot 1 Lot 1
Run 221892..522 122682..197 2224462...6258 22222445....3569 22222567....2588 22224668....1139 22230026....2345 12220789....2238 221722..2555 12222339....1227 22330026....2258 2330022...1394 2227893...0225 2227782...2368 223722..4488 22223346....1288 22330111....4568 22222267....1133 22221134....1128 22221235....1558 22220133....1558 22221244....2899 2225892...2228 22221156....1458 12230478....5889 1225882...1337 2224562...7123 2223552...3396 22233555....2258 22233334....3569 3336892...6156 23334678....2367 2251775...2128 22551177....3488 3552273...8256 3351775...4782 23341278....1558 33340016....1788 22230679....1256 22331236....2589 22225666....3558 22225667....1248 22231359....2488 2231163...4692 11121344....2588 11121444....8899 2223551...5288 12223455....1229 22226778....2258 22224669....2456 2225552...8247 22226668....1135 22223367....2234 226722..3944 2223552...3555 22223455....1379 11231477....6888 222067...237 1233..16 1121271...2362 119912....4616 14.8 11110124....1159 151.35 11112333....1277 11113333....2345 1145..55 1114551...1225 1112241...8884 15521...4762 5667....3568 7777....1356 4446....1677 4566....1157 4556....3569 5567....2334 6666....3445 4556....1279 12.8 14561....5782 13 1115111....93561711..7561 18891....2774 119901....6722 889...1589 18990....4695 14.5 11806...8569 151.48 1119028....5237 1891...4818 7799....3678 18880....5688 6899....4589 1560...3417 7889....2568 7999....3456 17.1 17897....2474 7811..3800 999...6799 7799....1478 8888....7888 18890....4598 11110000....2456 17770....2253 6778....1559 6789....4558 788...2467 6668....7788 13352....1584 1119222....9134 6991...2380 4777....1267 4589....1558 888...3489 8888....7888 889...289911800...8999 11110000....1179 1100..11 12.8 7789....2455 8889....2266 18991....2296 1110111...5551 18891....2441 889...157 7889....2379 17782....1683 11110112....1358 119922....3516 1110121...2251 117911....2446 491490..026 4789..314 45610890...0149 4160.20 3594563...6258 33593558....3669 8848..39 8857..25
SNV
CHPv2
15-35%
5-15%
genomic
Germline
Somatic
Lot 1 Lot 2 Lot 1 Lot 2
NextGENe TS 4.0.2
SNV
15-35%
5-15%
genomic

10. 10
3 sites – TruSight® Tumor Panel
• Good
performance
in H0007
(custom
bioinformatics
solution)
• Library prep
differences (A
and B)
• Run-to-run
differences
Panel
Site
Lot Lot 1 Lot 2
Run 111A001...189 111B000...466 111A444...224 111B333...667 1115515..36.423 1117771...778579 1110001...899244 1112222...001178 1110003...335137 9994...456358 1112221...003178 1115552...345478 1112223...012468 1112224...457478 1114481...3456 115611..4879 11117788....2357 11123455....2799 11118928..08..1236 11113778....33442789 1112241...2113.5695 11112335....56793578 11111123....35891235 11112343...346.3158 11116667....02484568 11114456....26786899 11115567....48991688 11114455....22223666 11114499....5667 11116688....7889 1115991...3586 11222255....4588 11115899....02572449 11115799....03671279 11112333....15663599 11112344...335.6349 11111333...567.5127 11113334....02671288 11115777....33471469 11112577....11691569 11115777....03451355 11113565...249.9449 11221349....1239 11223568....2889 220212..3546 11222266....1488 11117779....06991268 11122589....26793579 11112334....22294689 11112345....06673678 11111343...689.2117 11113345....03353348 1116891...5469.1282 11112667....34791299 11115689....01592778 11113676...124.4137 12282456....2289 12272246....2259 12294477....3467 12270034....2368 11120689....35581499 11122799....16773667 1110331...3269.5775 11111454...478.9358 11111234....04482399 11111445....03441255 11115788....89995778 1116771...2129.2387 11120688....00661288 11112677....00882559 122006...115 111699...677 111799...235 11381..789 11221168....23341189 122019...44922255 11110222....11471558 11114661...347.4789 111122...235459 11112450...678.7278 11115578....34691167 11112566....06992799 111585..26.819 11112345....57784799 267..98 1189..46 23.28 1219..79 11113378....02591333 1129.0398...22493789 1111141...2255.5562 11110447....45771566 11111116....36793469 11110224....01491577 11113457....14583457 11111679....05781359 11114583...038.4588 11111335....05782558 11222277....1588 1112991...1242 11222222....4677 11220044....3445 22220123....01576679 22221441...267.1889 1166..0927 11113377....04562479 1178..4913 1166..1622 191.88.27 11114499....23484899 1199..2525 1167..3913 11112233....3399 11111266....3459 11112233....4689 11114488....2347 22220011....11691689 122019...29920269 11113334....14591337 1114441...4267.2582 1222791...7893 11232669....3335 11223367....1149 11226888....2346 12221292...077.4799 22210028...066.4126 1167..0468 11113367....27891488 1167.7.65 1156..5715 2211..0323 11114489....05682445 2201..3656 1189..3823 2223342...1285 22222225....4579 2222472...1124 1224492...5895 111599...128236 2106.92.318 11110445....11581567 11115555....23892568 11110444....46673799 11112455....00783399 1113892...1027.5786 1114791...6028.3349 11211288...058.5599 11112668....24491339 124612..6925 1221221...3488 2220221...1333 1120392...1560 11116677...034.3446 11115669....06683588 111011...469147 1119156....10782589 111011...258229 111133...346279 111446...122238 1111551...4118.2499 111346...019156 111345...047257 11111223....2359 11111117....3448 1113331...3673 11113345....1689 11117779....34791458 11120999....02232668 1994...9121.5765 11111115....13671239 1113337....1246 1118777....6244 1113331...3460 11110555....4779 11120699....04891599 12220007....23361345 9.42 11934...729366 9.36 10.16 13.03 111155...357577 13.15 11.92 15777....1567 1885...9919 119051...9340 11110116....1149 11114567....24582449 11116677....06992559 11018...338261 1990...9990.3889 1110.92..152 11129..14.815 11451..206.358 11111112....44474999 111245...168234 111242..28.856 11111115....4448 12111.2225 19995....7796 11111116....1124 11114444....55682467 11111115....56797788 8.78 18880....44705695 9.12 9.68 12.75 1299.9..647.5549 12.69 12.58 1111229....6887 111233...259 11110044....3557 111145...156 1116.1345...13671669 1114134....82275236 78..0929 5888....02351178 77..3334 488..03.318 11005...236697 11015..9.190.7865 11600...123344 11400...056166 112299....2288 1188..25 1110041...1564 1167..19 11111122...178.5146 11110045....01463457 66..2979 559...9004.5675 56..7869 4478....45664689 6678....01691134 111155....01004689 668...1882449 4498...455.5159 12 16678....2893 14 1666...6467 1133..1448 1122..3756 566...0053447 111111...9011.1354 5666....44671468 8998...778.4138 8899....67992239 11110000....00182459 118900....49331434 7889....46781245 9999....1134 7777....5789 9999....3466 11111122....07882299 11111212..68..1967 7889....02494456 8889....01251357 8888....3455 8888....3566 9999....6778 111122...16711482 11111223....36893477 5566....01663346 6666....45563677 5555....33792288 5576...299.6278 10889....44678149 8888....66782358 1890...8233.6644 8889....22596667 10999....1226 11110003....3456 1111221...1282 11113334....1236 11111125....03341288 11112233....02991579 5666....44676699 111900.0..524.3657 5555....44671457 8888....45572338 8888...357.8247 11110001....23442346 7789....01993669 8988..56..6728 1100..12 1133..668 11822...415 111044...359 111555...022688 111225...799188 3556....06692688 7799....35782224 555...4179.1593 6788...045.4356 10689....30297367 111178....36594848 6999....00123789 7899....14791478 7.78 88..14 1100..69 45..092923 55..455869 44..0219 3377....13452779 4.46.45 3366...014.5238 4466....45562234 5588...014.4367 446...6114.2386 4477....23782569 7.4 7.9 6667....344724592355 7787...045.54497256 4.51 3334....11281237 4.54 4.77 3445....02991179 5555....67792389 3335....99991134 4446....22253467 88..56 77..56 6777...557.53674247 6688....567915674899 444...3012.3899 34..1888 55..0119 4455....34785689 5.40.16 55..2359 79..18 888...158 8.1 778...279 6678....057934564699 5678....347917996778 67..1447 4467....01287789 66..2717 67..1949 77.2.91 4557....05781278 78..0128 57..2523 11007...138 778...339 78..23 7789....1347 6778....357936793347 7789....067856681578 4455...349.2166 5566....00591378 4555....11342348 5565...007.8168 6667....34692335 5675...058.8159 667...1361457 5557....00893358 88..11 99..14 678...4498039.4673 7778....006826661344 3446....14881344 55..5757..3514 3455....35582357 4557....14463456 6675...467.9156 5676...047.6445 5667....01793666 4566....12482789 888...455 777...578 5565...178.81355245 6778....347758991229 6.03 5.4550...9129 6.08 4.57 5.65 4445....23332345 5.66 5.1 8.6 7.6 3667....023866792677 3677..66..15275668 55..5579 4556....24571359 55..5649 56..1359 57..1314 4664...236.7337 57..1837 56..5937 46.4.666.327 666...456689339 3344....36994568 3355....56772679 444...118249 344...567128 3445..19..1958 4455....00121569 444...227267 334...055356 13.6 25.1 34.5 19.9 6666..01..16483411 5666....001606782467 344...667236 345...3557.4587 44..400.582 334...455788 344...339589 4444....33894889 44..414.795 344...344158 1133..45 27742...5585 3344..45 1199..56 5556....668805895689 4566...018.42595348 34..5815 445...1231265 44..1849 34..7924 44.9.21 4455....24561789 45..0449 34..5847 11 8.3 777...388 5567...399.23584245 6666...011.40896146 4445....23482239 5555....01674578 4445....45771799 4555....24454577 4555....01672677 5655..36..3425 455...5078.2691 4556....12373679 77..59 191..52 88..22 79..38 676..59.247913 347...029008157 335...136115 45..448.295 334...009245 33..22466 336...129123 446...446459 6.73 336...556244 777...678 88..238 56.5.0385 34..362748 333...016445 44..3303..3589 3.05 33.0.61 3344....13492489 4444....23552677 334...089445 3333...568.8356 77..77 7799....3555 89..18 7788....2288 6666...145.03459289 5566....125625781468 3333....11123559 3344....77891456 33..328.399 3344....34593679 4456....16672569 3445....11893346 4456....05684455 4455....22251358 7.5 7.5 4577....689902681468 4588....024601177788 34..0829 355...3556.1227 4.68 353..46.867 454..68.934 3455....78894557 46..434.285 455...134346 89..13 170..91 77..798 78..38 6787...357.32898357 7789.7...11815793 4457....06893479 456...6569.1262 4567....01261469 4566....22684678 5677....34681589 5577....16783377 5677....33473449 5857..09..1528 8.2 777...667 7777....2779 677...267236347 778...139359888 4445....02263677 5577....13693578 445...4223.2454 5566...278.6256 5565...578.8147 5566....11581123 5566....33486899 5555....47781669 8.2 4458...477.00222113 5667....034623563358 5.31 5.85 4.98 6.99 445...444167 353..15.428 445...559449 335...224689 4455...156.90028159 4555....123445573578 3334....45664568 334...235468 333...3599.2286 343..24.544 4455....01692456 3334....13455678 4445....26793456 33..5955 5555....033303464559 5555....111234591228 3333....48991239 34..4459..3856 334...3069.1247 334...0695584 4545..47..2811 4444....19992258 4555....12465677 3444...457.2258 444...889266358 3.738.99 3333....44893459 33..3415 44.2.47 444..02.4664 44..6735 44..4559 4455....777816881346 5533..55..79023913 3.85 333..29.249 5566....025700582779 4555....158934591224 33..0158 44..2338 33..3339 33.8.99 55..5534 3344....25781159 55..3426 44..2216 4455...129.80573459 3553...446.71143277 33.7.83 3344....66891478 33..8817 44..0069 55..1215 3444...049.5116 44..9924 33..9927 4455....011317782399 3344....346701354677 334...4588.5687 4444....45991255 5566....004738884457 4467....033514692239 334...268279 3444....77891445 6655..56..47287837 6666....148803471246 2277..4824 3377....45795779 55..345924 66..224724 22377...616723 377..66.726 3344....445702591367 3345....158902591159 333...033389 3333...445.5278 4445...899.41233125 3333...568.52236344 3333...113.1367 5666....111902675689 5666....012811382899 33..1114 3333....12344569 788...2789 788...7798 889...5679 11009...4519 5577...266.21284147 6677....136711662458 3344...347.9568 444...4666.1255 3344....89994679 4444....55562345 4455....56992778 4445....08991679 5566....00121589 4444....67774589 88..46 88..78 88..55 466...347289239 466..48.434734 4455...129.9456 4555....03392359 4455....12441255 4455...112.4277 4555....13592346 4455....11675999 4455....00891189 4455....33563688 79..66 78..15 889...122 88..269 5666...367.56884367 7786...035.21463288 4454...247.3679 345...4346.2238 3444....45781258 3445....22782456 456..89.8576 4456....01255688 567...249245 3456....03591377 4497894...4567 44493569....2247 4494794...4897 44493579....6789 88.96 88.25 99.74 99.7 99.77 99.69 99.86 99.78 99.74 99.8 44440588....4789 3440784...1660 44441489....1356 3445784...1260 144789...278133 4489..582112 444035...344279 443678..59.999 444034...166238 344678...249349 44564..345.486 444556...368899 444466...012135 444566...159137 35993478....1588 45990246....2334 5993483...2559 45990346....2568 26.43 27.42 5906..56 5906..6956 4969..5636 5906..6815 5905..0657 5916..1415 5905..6938 5906..5618 95.2 92.7 95.2 91.4
Lot 2
TSTP
H0006 H0007 H1111
Lot 1 Lot 2 Lot 1
SNV
15-35%
5-15%
genomic
244
MiSeq® Custom
system
VariantStudio
No intronic variants

11. 11
Run controls are important in QC monitoring
•High coverage does not guarantee variant detection
•Routine use of standardized material helps track run performance
Mean Depth
9k
47k
32k
29k

12. 12
How else can this technology assist labs with quality assurance?

13. 13
Massively parallel LOD study
3%
1
2
1
2
1
2
1
2
1
2
1
2
dPCR assigned value
Run #
550 Variants
Samples
ND
0.5%
70%
5%
11%
18%
30%
48%
Frequency
•Variants drop out at different levels
•Multiplexing minimizes runs/preps
•12 libraries (versus hundreds)

14. 14
Standardized controls allow users to track performance
•Variant context affects performance
•Important to test variants in regions of interest rather than generic variants
•Bioinformatics/post-VCF filtering impact results

15. 15
Acknowledgments
R&D
Nakul Nataraj
Aron Lau
Kara Norman
Product Mgmt
Patty Chiang
Quality Assurance
Lorenzo Sapinoso
Program Mgmt
Susan Ewald
Regulatory
Erin Kipperman
Operations
Anjali Gupta
© 2014 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. TruSight, TruSeq, and MiSeq are trademarks of Illumina, Inc.

16. 16
Appendix

17. 17
Stability - AcroMetrix® Oncology Hotspot Control
•-20C or below for 18 months
•Stable through five freeze-thaw cycles
•4C for 6 days (open vial stability)

18. 18
Hotspot Control Summary
•Variant Distribution
5-15%
15-35%
genomic
Complex
0
1
0
DEL
15
14
0
INS
9
8
2*
MNV
0
2
0
SNV
317
155
32*
•Subset of variants covered by different panels
* genomic variants supported by whole genome sequencing data (Complete Genomics)

19. 19
Significant pooling and libraries needed for LOD study
pooling
10 @ 5%
10 @ 5%
10 @ 5%
40 @1.3%
20 @ 2.5%
20 @ 2.5%
10 @ 5%
40 @ 50%
40
@ 5%
40 @ 2.5%
40 @1.3%
141 LIBRARIES
12
LIBRARIES
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
Sensitivity study for 40 variants
50%
5%
2.5%
1.3%
40
4
2
1
# Libraries Needed
1
1
1
1
Freq.
3 reps