1_latest...latest innovation and advancement in high resolution oligo fish technology nargol...
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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