van criekinge next_generation_epigenetic_profling_vvumc_uploaded
DESCRIPTION
Next Generation Epigenetic ProfilingTRANSCRIPT
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Next Generation Epigenetic Profiling
Wim Van Criekinge 14th november 2013, Boston (US) 20th november 2013, Amsterdam
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Overview Epigene,cs
– Introduc*on – Methyla*on & Oncology – Biomarkers
MDxHealth – NEXT-‐GENera*on Epigene*c Biomarkers – Methyla*on Based CDx
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Actionable Epigenome
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Outside Oncology ?
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Historically, Cancer Was Considered to be Driven Mostly by Gene,c Changes
Example: Replica,on errors
GENETIC
Altered DNA/mRNA/proteins
Altered DNA sequence
X X
Oncogenesis
Tumor
§ Muta*ons in p53
§ Ac*va*ng muta*ons in RAS
§ Muta*ons or amplifica*ons of the
HER-‐2 gene
§ Chromosomal transloca*ons in
myeloid cells and the genera*on of
the BCR-‐ABL fusion protein
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Epigene,c Changes are Important in Causing Cancer
Example: Replica,on errors
GENETIC EPIGENETIC
Example: Chroma,n modifica,on errors
Altered DNA/mRNA/proteins
Altered DNA sequence
Altered levels of mRNA/proteins
Altered chroma,n structure
X X
Oncogenesis
Tumor
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Source: Schuebel et al 2007
0
20
40
60
80
100
120
Methylated Mutated
76-100 51-75 21-50 1-20
Dx
CDx
Example of Methyla,on vs Muta,on: Colon & Breast Cancer
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MGMT Biology O6 Methyl-Guanine Methyl Transferase
Essential DNA Repair Enzyme Removes alkyl groups from damaged guanine bases Healthy individual:
-‐ MGMT is an essen*al DNA repair enzyme Loss of MGMT ac*vity makes individuals suscep*ble to DNA damage and prone to tumor development
Glioblastoma pa,ent on alkylator chemotherapy: -‐ Pa*ents with MGMT promoter methyla*on show have longer PFS and OS with the use of alkyla*ng agents as chemotherapy
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MGMT Promoter Methylation Predicts Benefit form DNA-Alkylating Chemotherapy
Post-hoc subgroup analysis of Temozolomide Clinical trial with primary glioblastoma patients show benefit for patients with MGMT promoter methylation
0
5
10
15
20
25Median Overall Survival
21.7 months
12.7 months
radiotherapy
plus temozolomide
Methylated MGMT Gene
Non-Methylated MGMT Gene
radiotherapy
Adapted from Hegi et al. NEJM 2005 352(10):1036-‐8. Study with 207 pa*ents
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Clinical Valida,on of MDxHealth assay RTOG 0525 Study
§ MGMT was measured prospec*vely in the RTOG 0525 study § MGMT used to balance the arms of the study as there is an
advantage to overall survival and progression free survival being MGMT methyla*on
§ Physicans goal in this study was to compare current temozolomide schedule (Arm 1) vs a dose-‐dense administra*on of temozolomide(Arm2).
§ The dose dense schedule was hypothesized as being able to overcome the unmethylated MGMT tumors by overwhelming the tumor with alkyla*on.
§ The dose dense schedule did not work.
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Outcomes by MGMT Status-‐ MDxHealth Assay
Ove
rall
Surv
ival
(%)
0
25
50
75
100
Months after Randomization0 12 24 36 48
Patients at RiskMethyUnmethy
244516
168295
104106
3728
66
Dead162433
Total244516
p (2-sided) =< 0.0001HR (95% CI) =1.74 (1.45, 2.08)
MethylatedUnmethylated
Prog
ress
ion-
free
Sur
viva
l (%
)
0
25
50
75
100
Months after Randomization0 12 24 36 48
Patients at RiskMethyUnmethy
244516
99108
5540
1914
34
Dead202486
Total244516
p (2-sided) =< 0.0001HR (95% CI) =1.63 (1.38, 1.92)
MethylatedUnmethylated
ASCO 2011, Mark R. Gilbert, MD 12 Confiden*al
However the study did show that the MDxHealth assay was able to show the benefit to OS and PFS with the MGMT methylated cohort.
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Overview Epigene,cs
– Introduc*on – Methyla*on & Oncology – Biomarkers
MDxHealth – NEXT-‐GENera*on Epigene*c Biomarkers
Can we rediscover MGMT ? What does the epigenome look like ?
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MBD_Seq
DNA Sheared
Immobilized Methyl Binding Domain
Condensed Chroma*n
DNA Sheared
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Immobilized Methyl binding domain
MgCl2
Next Gen Sequencing GA Illumina: 100 million reads
MBD_Seq
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Confidential Information | ©2013 MDxHealth Inc. All rights reserved.
Quality evalua*on of Methyl Binding Domain based kits for enrichment DNA-‐methyla*on sequencing
De Meyer et al (2013) Plos One
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MBD_Seq MGMT = dual core
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BRCA1, a bidirec,onal promoter
18
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19
Splice variants
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Zooming into Exon 1
20
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Zooming into Exon 1
21
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Zooming into Exon 1
22
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# samples
# markers
MBD_Seq
Genome-‐wide methyla,on …. by next genera,on sequencing
Discovery
1-‐2 million methyla*on
cores
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GCATCGTGACTAGCGACTGATCGATGGATGCTAGCAT
Where is the mC ?
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GCATCGTGACTAGCGACTGATCGATGGATGCTAGCAT
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GCATCGTGACTAGCGACTGATCGATGGATGCTAGCAT
25% 50% 25%
GCATCGTGACTAGCGACTGATCGATGGATGCTAGCAT
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GCATCGTGACTAGCGACTGATCGATGGATGCTAGCAT
25% 50% 25%
GCATCGTGACTAGCGACTGATCGATGGATGCTAGCAT
GCATCGTGACTAGCGACTGATCGATGGATGCTAGCAT
Dense methylated needed for transcrip*onal silencing Are there alleles with all three posi4ons methylated ?
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GCATCGTGACTTACGACTGATCGATGGATGCTAGCAT!
unmethylated alleles
less methyla*on methylated alleles
more methyla*on
Deep Sequencing
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Deep Sequencing MGMT Heterogenic complexity
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Data integra,on with DEEP Sequencing, Infinium, Reac,va,on, (direc,onal) Expression …
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BRCA1
31
1 T47D 2 BT549 3 MCF7 4 MDAMB231 5 HS578T 6 NORMAL 7 NORMAL 8 NORMAL
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9 BI T21 (BRCA1 MUT) 10 BI T22 (BRCA1 MUT) 11 BLC 12 BLC 13 BLC 14 BLC 15 BLC 16 BLC 17 BLC
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13 BLC 14 BLC 15 BLC 16 BLC 17 BLC 18 BLC
19 IVM 20 DKO
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# samples
# markers
MBD_Seq
BT_Seq
Genome-‐wide methyla,on …. by next genera,on sequencing
Discovery
Verifica*on
Valida*on
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Confidential Information | ©2013 MDxHealth Inc. All rights reserved.
Gene,c tes,ng
107 106 105 104 103 102 101 1 108 109
Full genome bp
Whole-genome Bisulphite seq MSP Probes
(450-27K) Enrichment
Targeted Panels
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Gene,c tes,ng
107 106 105 104 103 102 101 1 108 109
Full genome bp
G E N E T I C
Whole-genome sequencing
Enrichment seq (Exome)
PCR Enrichment Targeted Panels
Instrument and Assay providers
CLIA Lab service providers
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Confidential Information | ©2013 MDxHealth Inc. All rights reserved.
Today
107 106 105 104 103 102 101 1 108 109
Full genome bp
Whole-genome Bisulphite seq
RUO sequencing
Clinical PCR
E P I G E N E T I C
Whole-genome sequencing
Enrichment seq (MBD, RRBS)
Enrichment seq (Exome)
MSP Probes (450-27K)
PCR Enrichment Targeted Panels
Enrichment Targeted Panels
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Confidential Information | ©2013 MDxHealth Inc. All rights reserved.
New Methods…
107 106 105 104 103 102 101 1 108 109
Full genome bp
Whole-genome Bisulphite seq
RUO sequencing
Clinical PCR
E P I G E N E T I C
Whole-genome sequencing
Enrichment seq (MBD, RRBS)
Enrichment seq (Exome)
MSP Probes (450-27K)
PCR Enrichment Targeted Panels
Enrichment Targeted Panels
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Confidential Information | ©2013 MDxHealth Inc. All rights reserved.
Deep Seq
Molecular Unifica,on
107 106 105 104 103 102 101 1 108 109
Full genome bp
Whole-genome Bisulphite seq
E P I G E N E T I C
Whole-genome sequencing
Enrichment seq (MBD, RRBS)
Enrichment seq (Exome)
Probes (450-27K)
Enrichment Targeted Panels
Enrichment Targeted Panels
Ultra Deep
Sequencing RUO Clinical
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Confidential Information | ©2013 MDxHealth Inc. All rights reserved.
Sample MGMTCt MGMTCopies ACTBCt ACTBCopies Ratio Ratio 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 10024052 41.31 0.48 27.57 7307.99 0.07 0.07 0.203461634 0.134093898 0.134207627 0.149994669 0.139766144 0.046749831 0.072289157 0.033080997 0.016988307 0.013341863 0.001741479 0.013412944 0.013420052 0.011507979 0.007207591 0.003937875 0.002423855 0.001229698 0.000767672 0.000305647 7.11E-0524053 38.5 2.79 28.19 4957.3 0.56 0.56 0.268719091 0.096532193 0.118750823 0.138454814 0.094861755 0.106824251 0.052981044 0.033079475 0.024697345 0.015500952 0.002005724 0.012465424 0.012267845 0.009771168 0.006256661 0.00340075 0.001766234 0.000808277 0.000622672 0.000185604 4.79E-0524293 40.67 1.07 29.69 1742.4 0.61 0.61 0.273467629 0.05097645 0.031421802 0.054104784 0.09506031 0.082864938 0.080510995 0.11379954 0.055289448 0.049053294 0.004092476 0.049935382 0.027303684 0.015913473 0.009477312 0.003420653 0.001820588 0.000835932 0.000400016 0.00019488 5.64E-0524279 38.82 4.63 27.98 5541.91 0.83 0.83 0.03197928 0.013280651 0.01213759 0.024922695 0.03955784 0.085590824 0.165737241 0.19406269 0.169959299 0.126747628 0.003951159 0.060727595 0.037760658 0.015507308 0.009547533 0.003838835 0.0022663 0.001387531 0.000568227 0.000356794 0.00011232424265 37.95 3.26 28.69 3351.3 0.97 0.97 0.056994056 0.019769411 0.015913984 0.029030715 0.054868511 0.106125435 0.169261488 0.201250483 0.132483115 0.088697805 0.003478165 0.042676531 0.045901654 0.015725354 0.007733856 0.006063785 0.002222161 0.001016765 0.000478478 0.000253041 5.52E-0524061 37.91 5.12 28.71 3782.94 1.35 1.35 0.081114929 0.042035796 0.069555085 0.034374609 0.086467414 0.109080712 0.141810915 0.143841919 0.066533081 0.084735888 0.005722749 0.035240372 0.055800885 0.025444725 0.008592291 0.005107458 0.002341372 0.001148906 0.000593511 0.000348483 0.00010890124031 35.41 18.98 27.96 5687.55 3.34 3.34 0.22421415 0.061830533 0.024938381 0.0316917 0.021541898 0.025374505 0.046559574 0.086782129 0.098934139 0.095616951 0.008557288 0.137114839 0.060462688 0.037704929 0.017781977 0.013506638 0.00453305 0.001493395 0.000806169 0.00044934 0.00010572724269 35.8 12.59 28.52 3733.97 3.37 3.37 0.273363925 0.058772205 0.046178491 0.014855782 0.011610407 0.013424678 0.008720501 0.007764893 0.009025187 0.012921483 0.002137423 0.017884182 0.028562064 0.022542194 0.033132363 0.069427004 0.136402666 0.142427152 0.072515419 0.017570263 0.00076171724027 36.23 11.44 29.37 2337.17 4.89 4.89 0.343141131 0.136608047 0.115115764 0.04157705 0.022085337 0.016795294 0.029763411 0.023216093 0.047041055 0.088665549 0.003455529 0.054481908 0.044589765 0.014644484 0.008816738 0.004562563 0.00266479 0.001447052 0.000822368 0.000442814 6.33E-0524289 35.94 21.6 28.75 3190.3 6.77 6.77 0.118282761 0.026462975 0.011443727 0.00820412 0.009077907 0.009174766 0.01706152 0.022743197 0.028058049 0.05531444 0.004791404 0.163839223 0.175639472 0.123544031 0.111226517 0.044787777 0.028004468 0.014716308 0.003837245 0.023301679 0.00048841424177 36.48 12.24 30.26 1402.59 8.72 8.72 0.584283402 0.079453886 0.030287836 0.105659946 0.016766952 0.010978571 0.011251276 0.010477146 0.011541574 0.011585559 0.002058482 0.014945987 0.015843274 0.014242232 0.019027763 0.01140962 0.03199444 0.014470953 0.002946972 0.000624582 0.00014954824274 34.37 74.97 28.13 5042.56 14.87 14.87 0.444145473 0.082331479 0.031013551 0.017166966 0.023866926 0.018942859 0.029124646 0.02636394 0.032584947 0.027090441 0.002862955 0.04430046 0.036895524 0.039849964 0.058437645 0.022069507 0.032084468 0.011710131 0.016166008 0.002819903 0.00017220824168 35.33 24.62 30.09 1563.27 15.75 15.75 0.232961742 0.094066234 0.077658094 0.0182452 0.011580373 0.009423552 0.011962832 0.013448782 0.018332978 0.03469723 0.004576975 0.092003461 0.163498313 0.062735902 0.035023261 0.02299773 0.030540334 0.015198064 0.049287121 0.001573727 0.00018809524022 33.31 68.96 28.62 3762.21 18.33 18.33 0.032670856 0.011702993 0.004962808 0.00493684 0.004977235 0.004654075 0.006145803 0.008583926 0.013093734 0.019877199 0.003416258 0.034393412 0.060494319 0.080189741 0.169465459 0.230265626 0.210561547 0.079791562 0.017923815 0.00158983 0.00030296224042 33.21 78.19 28.72 3533.77 22.13 22.13 0.153857528 0.038000887 0.017214709 0.007148625 0.006335377 0.008968482 0.006102208 0.006170452 0.008081302 0.012050865 0.00196772 0.017004288 0.032717615 0.028657059 0.043830116 0.03318964 0.091425062 0.134407807 0.211023783 0.124262105 0.01758436724201 28.82 1015.04 27.72 6244.94 162.54 162.54 0.029623825 0.010316194 0.004583096 0.003917899 0.004859322 0.003838977 0.005067901 0.00550197 0.006973296 0.01071644 0.001871572 0.016274783 0.019876995 0.02168092 0.022904206 0.023343913 0.043993213 0.086594021 0.250666607 0.335214301 0.0921805524297 33.46 104.52 31.32 608.72 171.71 171.71 0.09853738 0.023217538 0.007607208 0.007109487 0.004270217 0.003602819 0.004688755 0.005011142 0.006459057 0.009699897 0.001532753 0.014411276 0.018890762 0.020152031 0.021181408 0.021763967 0.034625522 0.130431094 0.304921779 0.197702567 0.06418334224167 31.32 283.22 30.87 952.56 297.32 297.32 0.100591975 0.035233834 0.011751911 0.009642406 0.010474529 0.006226323 0.006890561 0.007459908 0.00916795 0.012109577 0.001956219 0.017197206 0.020992854 0.024073168 0.029270287 0.087110125 0.100146716 0.267279323 0.184081636 0.054847116 0.003496376
HT29 0.753566786 0.096042826 0.036705396 0.01508264 0.01079523 0.008066144 0.008954308 0.00800155 0.007460578 0.008704007 0.001711734 0.0105853 0.011715691 0.00939839 0.00650782 0.0031005 0.00185707 0.00088009 0.000524824 0.000201855 0.000137262
24025 Undetermined 0 28.34 4471.4 0 0 0.418789899 0.179009196 0.096823939 0.055595242 0.042328582 0.013686204 0.047079634 0.010675693 0.009400052 0.010692701 0.001916295 0.013516118 0.014462927 0.012359538 0.00860632 0.004921137 0.004546949 0.003974328 0.00454128 0.042322913 0.00475105224026 Undetermined 0 29.66 1944.13 0 0 0.516916773 0.202731325 0.059880115 0.046417299 0.037086771 0.021069827 0.012320727 0.011109419 0.011386289 0.012902154 0.002242649 0.015214021 0.0156847 0.013234398 0.009607398 0.004962899 0.003460878 0.002131901 0.00106595 0.000498366 7.61E-0524034 Undetermined 0 29.71 1879.44 0 0 0.383378528 0.21459944 0.178158129 0.094466966 0.033571401 0.01313284 0.011757902 0.00994102 0.008135049 0.008718852 0.001374938 0.010252017 0.010497542 0.008326013 0.006099923 0.002853542 0.00177869 0.000987555 0.000660188 0.000583803 0.000725662
Correlation -0.378717418 0.749526573 0.817780411 0.715954841 0.721224123 0.725933015 0.871789771 0.95567526 0.930713611 0.913277334 0.73018162 0.80233553 0.819357467 0.852443607 0.831785309 0.853097602 0.922340853 0.663535204 0.755785968 0.866175664 0.975660054
0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100ivm dko 78.19% 6.71% 2.65% 1.45% 1.16% 0.90% 0.97% 0.91% 0.93% 0.95% 0.17% 1.15% 1.22% 1.02% 0.69% 0.34% 0.24% 0.16% 0.09% 0.06% 0.03%dko 0.07 20.35% 13.41% 13.42% 15.00% 13.98% 4.67% 7.23% 3.31% 1.70% 1.33% 0.17% 1.34% 1.34% 1.15% 0.72% 0.39% 0.24% 0.12% 0.08% 0.03% 0.01%
24052 41.31 0.48 27.57 7307.99 0.07 0.56 26.87% 9.65% 11.88% 13.85% 9.49% 10.68% 5.30% 3.31% 2.47% 1.55% 0.20% 1.25% 1.23% 0.98% 0.63% 0.34% 0.18% 0.08% 0.06% 0.02% 0.00%0.61 27.35% 5.10% 3.14% 5.41% 9.51% 8.29% 8.05% 11.38% 5.53% 4.91% 0.41% 4.99% 2.73% 1.59% 0.95% 0.34% 0.18% 0.08% 0.04% 0.02% 0.01%0.83 3.20% 1.33% 1.21% 2.49% 3.96% 8.56% 16.57% 19.41% 17.00% 12.67% 0.40% 6.07% 3.78% 1.55% 0.95% 0.38% 0.23% 0.14% 0.06% 0.04% 0.01%0.97 5.70% 1.98% 1.59% 2.90% 5.49% 10.61% 16.93% 20.13% 13.25% 8.87% 0.35% 4.27% 4.59% 1.57% 0.77% 0.61% 0.22% 0.10% 0.05% 0.03% 0.01%1.35 8.11% 4.20% 6.96% 3.44% 8.65% 10.91% 14.18% 14.38% 6.65% 8.47% 0.57% 3.52% 5.58% 2.54% 0.86% 0.51% 0.23% 0.11% 0.06% 0.03% 0.01%3.34 22.42% 6.18% 2.49% 3.17% 2.15% 2.54% 4.66% 8.68% 9.89% 9.56% 0.86% 13.71% 6.05% 3.77% 1.78% 1.35% 0.45% 0.15% 0.08% 0.04% 0.01%3.37 27.34% 5.88% 4.62% 1.49% 1.16% 1.34% 0.87% 0.78% 0.90% 1.29% 0.21% 1.79% 2.86% 2.25% 3.31% 6.94% 13.64% 14.24% 7.25% 1.76% 0.08%4.89 34.31% 13.66% 11.51% 4.16% 2.21% 1.68% 2.98% 2.32% 4.70% 8.87% 0.35% 5.45% 4.46% 1.46% 0.88% 0.46% 0.27% 0.14% 0.08% 0.04% 0.01%6.77 11.83% 2.65% 1.14% 0.82% 0.91% 0.92% 1.71% 2.27% 2.81% 5.53% 0.48% 16.38% 17.56% 12.35% 11.12% 4.48% 2.80% 1.47% 0.38% 2.33% 0.05%8.72 58.43% 7.95% 3.03% 10.57% 1.68% 1.10% 1.13% 1.05% 1.15% 1.16% 0.21% 1.49% 1.58% 1.42% 1.90% 1.14% 3.20% 1.45% 0.29% 0.06% 0.01%
14.87 44.41% 8.23% 3.10% 1.72% 2.39% 1.89% 2.91% 2.64% 3.26% 2.71% 0.29% 4.43% 3.69% 3.98% 5.84% 2.21% 3.21% 1.17% 1.62% 0.28% 0.02%15.75 23.30% 9.41% 7.77% 1.82% 1.16% 0.94% 1.20% 1.34% 1.83% 3.47% 0.46% 9.20% 16.35% 6.27% 3.50% 2.30% 3.05% 1.52% 4.93% 0.16% 0.02%18.33 3.27% 1.17% 0.50% 0.49% 0.50% 0.47% 0.61% 0.86% 1.31% 1.99% 0.34% 3.44% 6.05% 8.02% 16.95% 23.03% 21.06% 7.98% 1.79% 0.16% 0.03%22.13 15.39% 3.80% 1.72% 0.71% 0.63% 0.90% 0.61% 0.62% 0.81% 1.21% 0.20% 1.70% 3.27% 2.87% 4.38% 3.32% 9.14% 13.44% 21.10% 12.43% 1.76%
162.54 2.96% 1.03% 0.46% 0.39% 0.49% 0.38% 0.51% 0.55% 0.70% 1.07% 0.19% 1.63% 1.99% 2.17% 2.29% 2.33% 4.40% 8.66% 25.07% 33.52% 9.22%171.71 9.85% 2.32% 0.76% 0.71% 0.43% 0.36% 0.47% 0.50% 0.65% 0.97% 0.15% 1.44% 1.89% 2.02% 2.12% 2.18% 3.46% 13.04% 30.49% 19.77% 6.42%297.32 10.06% 3.52% 1.18% 0.96% 1.05% 0.62% 0.69% 0.75% 0.92% 1.21% 0.20% 1.72% 2.10% 2.41% 2.93% 8.71% 10.01% 26.73% 18.41% 5.48% 0.35%
ivm 0.30% 0.27% 0.29% 0.36% 0.34% 0.47% 0.71% 1.01% 1.16% 1.45% 0.18% 1.56% 1.84% 1.92% 1.87% 1.73% 2.33% 3.56% 7.80% 22.58% 48.27%
0%
20.00%
40.00%
60.00%
80.00%
Amount
0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 9095
100
Percentage Methylation
IVM
DKO0.07
0.560.61
0.83
1.350.97
3.343.374.89
6.778.7214.8715.7518.3322.13162.54171.71
297.32
MSP M
GMT Cop
ies / A
CTB C
opies
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Confidential Information | ©2013 MDxHealth Inc. All rights reserved.
Deep Seq
Molecular Unifica,on
107 106 105 104 103 102 101 1 108 109
Full genome bp
Whole-genome Bisulphite seq
E P I G E N E T I C
Whole-genome sequencing
Enrichment seq (MBD, RRBS)
Enrichment seq (Exome)
Probes (450-27K)
Enrichment Targeted Panels
Enrichment Targeted Panels
Ultra Deep
Sequencing RUO Clinical
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Epi-‐health: comprehensive epigene,c profiling
§ Key genes
– For all know epigene*c genes – For all important gene classes (CT genes, immune-‐response)
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Confidential Information | ©2013 MDxHealth Inc. All rights reserved.
440 cancer-‐related genes genes are known to be epigene*cally altered in human solid cancers based on recent scien*fic and clinical literature.
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44
Heyn, H. H. & Esteller, M. M. DNA methylation profiling in the clinic: applications and challenges. Nat. Rev. Genet. 13, 679–692 (2012).
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Epigenetic Alterations Associated with Cancer Therapy Response
PCFT – folate transport (MTX)
WRN
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Kinases, CT genes ….
46
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Epi-‐health: comprehensive epigene,c profiling
§ Key genes
– For all know epigene*c genes – For all important gene classes (CT genes, immune-‐response)
§ Key regions – Iden*fied by mining epigenomes
![Page 48: Van criekinge next_generation_epigenetic_profling_vvumc_uploaded](https://reader034.vdocuments.mx/reader034/viewer/2022052619/55501b8fb4c905af648b4f7a/html5/thumbnails/48.jpg)
Data integra,on Correla,on tracks
methylation methylation
expression expression
Corr =-1 Corr = 1
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Correla,on track in GBM @ MGMT
+1
-1
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Epi-‐health: comprehensive epigene,c profiling
§ Key genes
– For all know epigene*c genes – For all important gene classes (CT genes, immune-‐response)
§ Key regions – Iden*fied by mining epigenomes
§ Approach – Acceptable amounts of clinical material – TAT/cost
§ Analysis – Ac*onable interpreta*on – Get gene*c data as a bonus
![Page 51: Van criekinge next_generation_epigenetic_profling_vvumc_uploaded](https://reader034.vdocuments.mx/reader034/viewer/2022052619/55501b8fb4c905af648b4f7a/html5/thumbnails/51.jpg)
Sequencing
Deep Seq
Molecular Unifica,on
107 106 105 104 103 102 101 1 108 109
Full genome bp
Whole-genome Bisulphite seq
RUO Clinical
E P I G E N E T I C
Whole-genome sequencing
Enrichment seq (MBD, RRBS)
Enrichment seq (Exome)
Probes (450-27K)
Enrichment Targeted Panels
Enrichment Targeted Panels
Ultra Deep