www.agilent.com/genomics/surefish

Latest Innovation and Advancement

in High Resolution Oligo FISH Technology

Nargol Faravashi – Sr. Product Manager, Genomics, Agilent Technologies

Shashikant Kulkarni M.S (Medicine), Ph.D., FACMG

Head of Clinical Genomics

Medical Director Cytogenomics and Molecular Pathology

Associate Professor of Pediatrics, Genetics, Pathology and Immunology

Washington University School of Medicine, St Louis

Overview FISH Technology:

• Method for detection of translocations, inversions, amplifications, deletions and

duplications

• Better detection of low-level mosaicism

• Enables Visualization in intact cellular context

• positional information of aberrations in chromosomal context

Limitations of current technologies:

Clone based methodologies:

bacterial artificial chromosomes (BAC), fosmids, PAC (P1-derived artificial

chromosome), YAC (yeast artificial chromosome), PCR templates

• Resolution limitations (150-300 Kb)

• Not ideal for visualization/verification of smaller genomic regions

• Labor intensive

• Rapid turnaround time

Agilent Industrial Scale Manufacturing: Oligo Library

Synthesis (OLS)

Release

oligonucleotides

from the microarray

substrate

Oligo Library

Synthesis

BioReagent: Gene(ome) synthesis

Gene silencing library

Genome partitioning

OligoFISH

Solution of user-defined oligonucleotides:

“Oligo Library”

Oligos specifically selected to unique sequences

Step 1: Tile region with long oligonucelotides:

Step 2: Remove any non-unique oligos:

Repetitive elements

Segmental duplications

Step 3: Manufacture labeled probes using specifically designed long oligonucleotides

Unique design methodology for specific targets , provides unparalleled resolution with high sensitivity and specificity

Agilent’s SureFISH offerings

SureFISH Probes: 5µl configuration

• ASR manufactured under cGMP/QSR guidelines

General Purpose Reagents: 100µl configuration

• Hybridization buffer • Mounting buffer • Wash buffer1 • Wash buffer2

www.agilent.com/genomics/surefish

Agilent’s SureFISH offerings

Integration with Microarray Data: • Characterization of CGH findings by visualizing the

probe of interest in Agilent CytoGenomics Software • Link from CytoGenomics software to eCommerce

website

http://ft2.genomics.agilent.com/ProductSearch.

aspx?chr=1&PageID=3000

Superior Performance & Key attributes :

Coverage of Most Relevant Targets

Broad menu-Hundreds of relevant probes for constitutional and cancer applications

Streamlined Workflow

• Pre-labeled probes reduce labor time

• Compatible with established FISH procedures and filter sets

• Fast Hybridization time – 4 hours

• No Cot-1 DNA

Flexibility

• Various fluorescent dyes to fit visualization needs

• In silico design methodology to target specific regions

Quality Control

• Probe localization to correct chromosomes demonstrated by FISH hybridization

images. Images provided on the website for both 4, 14 hour, metaphase & interphase

• Each probes is sequence verified to ensure specificity to the region of interest

Comprehensive SureFISH Probe Menu Telomere

dLOC100130417,SAM

D11,NOC2L,KLHL17,

PLEKHN1,C1orf170,H

ES4,ISG15,AGRN,RN

F223,C1orf159,LOC25

4099,MIR200B,MIR20

0A,MIR429,TTLL10,

SKI,MORN1,LOC1001

29534,RER1,PEX10,P

LCH2,PANK4,HES5,L

OC115110,LOC10013

3445,TNFRSF14,

AJAP1,

AMPD1,NRAS,CSDE1

,SIKE1, NOTCH2,

Centromere

RNF115,CD160,PDZK

1,, BCL9,,

GJA5,GJA8,,

ANXA9,CERS2,FAM6

3A,PRUNE,SETDB1,

ISG20L2,RRNAD1,M

RPL24,HDGF,PRCC,

SH2D2A,NTRK1,INSR

R,PEAR1,LRRC71,AR

HGEF11,MIR765,,

RALGPS2,FAM20B,T

OR3A,ABL2,, DISP1,,

FH,KMO,,

SDCCAG8,AKT3,AKT

3,AKT3,

SH3BP5L,MIR3124,Z

NF672,ZNF692,PGB2

Telomere

Telomere

FAM110C,SH3YL1,ACP1

,FAM150B,

MYCNOS,MYCN,

NCOA1, LBH,YPEL5,,

ABHD12,GINS1,NANP,N

INL,PYGB,ZNF337,

EML4,COX7A2L,,

VRK2,FANCL,, BCL11A,,

FLJ16341,REL,PUS10

KIAA1841,LOC339803,C

2orf74,AHSA2,USP4

MALL,NPHP1,LINC0011

6, MBD5,,

HOXD13,HOXD12,HOXD

11,HOXD10,HOXD9,HO

XD8,LOC100506783,MIR

10B,HOXD4,HOXD3,LO

C401022,HOXD1,LOC40

1022,,

OSGEPL1,ORMDL1,PM

S1,, PAX3,, CCDC140,,

HDAC4,MIR4440,MIR44

41,,

HDAC4,MIR4440,MIR44

41,MGC16025,MIR4269,

MIR2467,,

ING5,D2HGDH,GAL3ST

2,NEU4,PDCD1,C2orf85,

Telomere

Telomere

CHL1,, CNTN4,,

SYN2,TIMP4,PPARG

,,

TSEN2,LOC1001294

80,MKRN2,,

CEP19,FBXO45,LRR

C33,PIGX,WDR53,,

FOXL2,C3orf72,,

NULL,, MECOM,,

BDH1,,

PIK3CA,KCNMB3,,

SOX2-OT,SOX2,,

SST,RTP2,LOC1001

31635,BCL6,,

CWH43,FRYL,OCIA

D1,OCIAD2,SLC10A

4,ZAR1,,

PIGX,PAK2,SENP5,

NCBP2,LOC152217,

PIGZ,MFI2,MFI2-

AS1,DLG1,MIR4797,

LOC100507086,,

LOC100505806,LOC

285692,SEMA5A,SN

ORD123,TAS2R1,,

KIAA0226,KIAA0226,

MIR922,FYTTD1,LR

CH3,IQCG,RPL35A,L

MLN,

Telomere

Telomere

ZNF721,PIGG,PDE6B,

ATP5I,MYL5,MFSD7,P

CGF3,LOC100129917,

CPLX1,,

FAM53A,SLBP,TMEM

129,TACC3,FGFR3,LE

TM1,WHSC1,

RPL21P44,CHIC2,GS

X2,, PDGFRA, KIT,,

TET2,TET2,,,

Telomere

Telomere

PLEKHG4B,LRRC14B,C

CDC127,SDHA, TERT,

KHDRBS2,

DCBLD1,ROS1,VGLL2,R

OS1, APC,

KDM3B,REEP2,EGR1,E

TF1,

PDE6A,SLC26A2,TIGD6,

HMGXB3,CSF1RTCOF1,

CD74,

RANBP17,TLX3,MIR391

2,NPM1,FGF18MIR3912,

NPM1,FGF18,

CNOT6,SCGB3A1,FLT4,

BTNL8,BTNL3,BTNL9,O

R2V2,TRIM7,MIR4638,T

RIM41,GNB2L1,SNORD9

6A,SNORD95,TRIM52.

Telomere

Telomere

FOXC1,GMDS,

C6orf15,PSORS1C1,C

DSN,PSORS1C2,CCH

CR1,TCF19,POU5F1,P

SORS1C3,

SUPT3H,RUNX2,,

MTRNR2L9,KHDRBS2,

,

CEBPD,KIAA0146,LOC

100287846,, MYB,

MLLT4,,

FAM120B,MIR4644,PS

MB1,TBP,PDCD2

Telomere

Telomere

FAM20C,,

LOC100133311,HOX

A5,HOXA6,HOXA7,H

OXA10-

HOXA9,HOXA9,MIR1

96B,HOXA10,HOXA1

1,HOXA11-

AS1,HOXA13,

IKZF1,FIGNL1,DDC,

EGFR, VOPP1, HIP1,

LOC100506136,SHF

M1, TES, MET, BRAF,

MRPS33,LOC100507

421, EPHB6,TRPV6,

GALNT11,MLL3,

RBM33,SHH, VIPR2

Telomere

Telomere

RPL23AP53,ZNF596,

GATA4,NEIL2,,

PNOC,ZNF395,,

DDHD2,PPAPDC1B,

WHSC1L1,LETM2,FG

FR1,C8orf86,,

CEBPD,LOC1002878

46,KIAA0146,, CHD7,

RUNX1T1, TRPS1,,

EXT1, NULL,,

MYC,PVT1,MIR1204,,

PVT1,MIR1204,,

ZNF251,ZNF34,RPL8,

ZNF517,ZNF7,COMM

D5,ZNF250,ZNF16,ZN

F252,TMED10P1,C8o

rf77,C8orf33

Telomere

Telomere

C9orf66,DOCK8,KAN

K1,, DMRT1,DMRT3,,

RCL1,MIR101-

2,JAK2,

C9orf46,CD274,,

PAX5,MIR4540,MIR44

76,,

PTCH1,LOC10050734

6, LMX1B,,

ASS1,LOC100272217

,FUBP3,PRDM12,EX

OSC2,ABL1,QRFP,FI

BCD1,,

NOTCH1,MIR4673,MI

R4674,,

EHMT1,FLJ40292,MI

R602

Telomere

Telomere

ZMYND11,DIP2C,FLJ

45983,GATA3,

C10orf114,MIR1915,C

10orf140,MLLT10,DN

AJC1,, NULL,, RET,,

BMPR1A,,

ACTA2,FAS,FAS-

AS1, DPCD,FBXW4,

CALY,PRAP1,C10orf1

25,ECHS1,MIR3944,P

AOX,MTG1,SPRN,LO

C619207,CYP2E1,SY

CE1,SPRNP1

Telomere

Telomere

INS-

IGF2,IGF2,MIR483,IGF2-

AS,INS,TH,MIR4686,

KCNQ1, WT1,WT1-AS,

EXT2,, NULL,

CCND1,ORAOV1,FGF19

, ORAOV1,FGF19,

FGF4,FGF3,

YAP1,BIRC3,BIRC2,TME

M123, NPAT,ATM,

ZBTB16,

CD3E,CD3D,CD3G,UBE

4A,ATP5L,MLL,

CD3D,CD3G,UBE4A,AT

P5L,MLL,TTC36,TMEM2

5,IFT46,ARCN1,PHLDB1

,

MLL,TTC36,TMEM25,IFT

46,ARCN1,PHLDB1,TRE

H, SNX19,

JAM3,NCAPD3,VPS26B,

THYN1,ACAD8,, NULL

Telomere

Telomere

IQSEC3,LOC574538,S

LC6A12,SLC6A13,

A2M,C12orf33,LOC144

571,PZP,

CASC1,LYRM5,KRAS,

R3HDM2,INHBC,INHB

E,GLI1,ARHGAP9,MAR

S,

MBD6,DCTN2,KIF5A,PI

P4K2C,DTX3,ARHGEF

25,SLC26A10,B4GALN

T1, 9-

Mar,AGAP2,CDK4,CYP

27B1,LOC100130776,

METTL1,METTL21B,T

SFM,TSPAN31,

RPSAP52,HMGA2,

RAP1B,SNORA70G,LO

C100507250,NUP107,

SLC35E3,MDM2,CPM,

RPL6,PTPN11,,

TBX5,LOC255480,

WDR66,BCL7A,MLXIP

Telomere

Centromere

MPHOSPH8,PSPC1T,

TTL,, ELF1,WBP4,

DLEU2,TRIM13,KCNRG,

MIR16-

1,MIR15A,DLEU1,

DLEU7, ZIC5,ZIC2,

PCID2,CUL4A,LAMP1,G

RTP1, RASA3,CDC16

Telomere

Centromere

FOXG1,C14orf23,

METTL21D,SOS2,L2HG

DH,ATP5S,CDKL1, NIN,

PTGDR,PTGER2,

SAMD4A,

C14orf33,KTN1,

RAD51B,

DICER1,MIR3173,DICE

R1-AS, TCL6,TCL1B

NULL,

Telomere

Centromere

SNRPN,SNURF,SNURF,

SNORD107,PAR-

SN,PAR5,SNORD64,SN

ORD108, UBE3A,

OCA2,, OTUD7A,

CHRNA7,

ANKRD26P1,C16orf87,D

NAJA2,GPT2,MYLK3,NE

TO2,ORC6,SHCBP1,VP

S35, SMAD6,

CYP1A1,CYP1A2,CSK,M

IR4513,LMAN1L,CPLX3,

ULK3,SCAMP2,

LOC100507217,CHD2,MI

R3175,

IGF1R,MIR4714,PGPEP

1L

Telomere

Telomere

TRAP1,CREBBP, RBFOX1,

TNFRSF17,SNX29,

C16orf45,KIAA0430,NDE1,

MIR484,MYH11,

FOPNL,ABCC1,ABCC6,,

C16orf52,VWA3A,

ATXN2L,TUFM,MIR4721,S

H2B1,ATP2A1,RABEP2,CD

19,NFATC2IP,MIR4517,SP

NS1,LAT,

ZNF668,ZNF646,PRSS53,V

KORC1,BCKDK,KAT8,PRS

S8,PRSS36, MAF,

LOC400550,FOXF1,MTHFS

D,FLJ30679,FOXC2,FOXL1

Telomere

Telomere

YWHAE,CRK,MYO1C

PAFAH1B1,KIAA0664,

SHBG,SAT2,ATP1B2,T

P53,WRAP53,EFNB3,D

NAH2,

ALOX15B,ALOX12B,MI

R4314,ALOXE3,HES7,

PER1,VAMP2,TMEM10

7,MIR4521,MIR3676,C1

7orf59,AURKB,LINC003

24,CTC1,PFAS,

PMP22,PMP22,PMP22,

MIR4731,, TEKT3,

CDRT4,FAM18B2-

CDRT4,FAM18B2,

RAI1,SMCR5,SREBF1,

MIR33B, SPECC1,

MIR4733,NF1,OMG,EVI

2B,EVI2A,RAB11FIP4,

ACACA,

PGAP3,ERBB2,MIR472

8,MIEN1,GRB7,,

DHX8,ETV4,

CRHR1,LOC100128977

,IMP5,MAPT,LOC10013

0148,STH,KIAA1267,

MKS1,LPO,MPO,BZRA

P1,LOC100506779,MIR

142,MIR4736, SOX9,

ASPSCR1,STRA13,LR

RC45

Telomere

Telomere

USP14,THOC1,COLE

C12, SS18,, TCF4,

BCL2,KDSR,,

BCL2,KDSR,VPS4B,

HSBP1L1,TXNL4A,RB

FA,ADNP2,LOC10013

0522,PARD6G

Telomere

Telomere

PPAP2C,MIER2,THE

G,C2CD4C,SHC2,OD

F3L2,MADCAM1,C19

orf20,CDC34,GZMM,

POLRMT,FGF22,RNF

126,FSTL3,PRSS57,

STK11,C19orf26,ATP

5D,MIDN,C19orf23,CI

RBP,C19orf24,

LYPD4,DMRTC2,RPS

19,CD79A,ARHGEF1,

KLC3,ERCC2,PPP1R

13L,CD3EAP,ERCC1,

FOSB,

Telomere

Telomere

JAG1,

DNMT3B,MA

PRE1,

PTPRT

ABCC13,HSP

A13,LIPI,RBM

11,SAMSN1,

C20orf108,AU

RKA,CSTF1,

CASS4,

LSM14B,PSM

A7,SS18L1,G

TPBP5,

IL17RA,GAB4

,CECR7,CEC

R6,CECR5-

AS1,CECR5,

CECR3,CEC

R2,CECR1,

Telomere

Centromere

CLIC6,LINC001

60,LOC1005063

85,RUNX1,

LINC00114,LIN

C00114,LINC00

114,ETS2,PSM

G1,BRWD1,

LINC00323,MIR

3197,BACE2,PL

AC4,FAM3B,MX

2,MX1Telomere

Centromere

CLTCL1, HIRA,,

TBX1,GNB1L,,

TXNRD2,COMT,MI

R4761,ARVCF

CRKL,AIFM3,LZTR

1,THAP7,FLJ39582,

MIR650,IGLL5,

IGLL5,RTDR1,GNA

Z,RAB36,BCR,FBX

W4P1,CES5AP1,ZD

HHC8P1,IGLL1,C22

orf43,GUSBP11,RG

L4,ZNF70,VPREB3,

C22orf15,CHCHD10

,MMP11,SMARCB1,

DERL3,SLC2A11,L

OC284889,MIF,GST

T2,GSTT2B,DDTL,

DDT,GSTT2,GSTTP

1,LOC391322,GSTT

1,GSTTP2,CABIN1,

KREMEN1,EMID1,R

HBDD3,EWSR1,GA

S2L1,RASL10A,AP1

B1,MIR3653,SNOR

D125EWSR1,GAS2

L1,RASL10A,AP1B1

,MIR3653,SNORD1

25SOX10,MIR4534,

PICK1PPP6R2,SBF

1,ADM2,MIOX,LMF

2,NCAPH2,SCO2,T

YMP,ODF3B,KLHD

C7B,SYCE3,CHKB-

CPT1B,CPT1B,CHK

B,LOC100144603S

HANK3,

Telomere

STS, CDKL5,RS1,

DMD, RP2,PHF16,,

SLC38A5,FTSJ1,P

ORCN,EBP,TBC1D

25,

GLOD5,GATA1,HD

AC6,ERAS,PCSK1

N,

BCYRN1,GJB1,ZM

YM3,NONO,ITGB1

BP2, TSIX,XIST,

PLP1,RAB9B,,

COL4A6,

KCNE1L,ACSL4,

DCX,, ATP2B3,

AVPR2,ARHGAP4,

NAA10,RENBP,HC

FC1, MECP2,,

ATP6AP1,GDI1,FA

M50A,PLXNA3,LA

GE3,UBL4A,SLC10

A3,

GAB3,DKC1,SNOR

A36A,SNORA56,M

PP1,

MPP1,CXorf68,F8,

H2AFB3,H2AFB1,F

8A1,F8A3,F8A2,MI

R1184-3,MIR1184-

2,MIR1184-

1,FUNDC2,

FUNDC2,MTCP1N

B,MTCP1,BRCC3

BCORP1,T

XLNG2P,T

XLNG2P,T

XLNG2P,C

Yorf15B,K

DM5DTelo

mere

Summary

Comprehensive line of probes available now as FDA Class I Analyte Specific Reagents

Simplified workflow with flexible hybridization times ranging from 4 to 14 hours

Unique range of sizes from <50kb to >200kb

Complementary to CGH microarrays

www.agilent.com/genomics/surefish