# US 12,006,552 B2 · Methylome based analysis and treatment for meningioma

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- Number: US 12,006,552 B2
- Document ID: US12006552B2
- Status: Granted
- Kind: B2
- Application number: 16/503,025
- Filed: 2019-07-03
- Published: 2020-01-09
- Granted: 2024-06-11
- Earliest claimed: 2018-07-04
- Assignees: University Health Network
- Applicants: University Health Network
- Inventors: Gelareh Zadeh; Kenneth Aldape; Farshad Nassiri; Yasheng Maimaitijiang
- Web page: https://patentgrep.com/patent/US12006552B2

## CPC

- C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575)
- C12Q 1/6809: Methods for determination or identification of nucleic acids involving differential detection
- C12Q 1/6816: characterised by the detection means (C12Q1/6804 takes precedence)
- C12Q 1/6827: for detection of mutation or polymorphism
- G06F 17/18: for evaluating statistical data {, e.g. average values, frequency distributions, probability functions, regression analysis (forecasting specially adapted for a specific administrative, business or logistic context G06Q10/04)}
- G16B 20/00: ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B 20/20: Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
- G16B 40/10: Signal processing, e.g. from mass spectrometry [MS] or from PCR
- G16B 40/20: Supervised data analysis
- G16H 50/30: for calculating health indices; for individual health risk assessment
- C12Q 2600/118: Prognosis of disease development
- C12Q 2600/154: Methylation markers
- C12Q 2600/158: Expression markers
- G16B 20/10: Ploidy or copy number detection
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- G06F: ELECTRIC DIGITAL DATA PROCESSING (computer systems based on specific computational models G06N)
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16H: HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA

## Abstract

There is described herein a method of predicting recurrence free survival in a patient with meningioma comprising: (a) determining a tumor DNA methylation profile from a tumor sample from the patient, the tumor DNA methylation profile comprising the methylation status of at least 200 loci represented by the probes set forth in Table 9; and (b) calculating a risk of meningioma recurrence based on comparing the tumor DNA methylation profile and a reference methylation profile comprising the extent to which the methylation status of the at least 200 loci is associated with a risk of recurrence.

## Claims

### Claim 1

An array consisting of probes for detecting CpG methylation at all 2332 loci represented by the following 2332 probes:
cg00015770, cg00018128, cg00025981, cg00028678, cg00035316, cg00036347, cg00048759, cg00055679, cg00060304, cg00063471, cg00073003, cg00099393, cg00117172, cg00123478, cg00130808, cg00143249, cg00155423, cg00155526, cg00158122, cg00168835, cg00182639, cg00184452, cg00204465, cg00204782, cg00222472, cg00237475, cg00247571, cg00254681, cg00255368, cg00262621, cg00286125, cg00298065, cg00299047, cg00299972, cg00306311, cg00323305, cg00337466, cg00360794, cg00384539, cg00407546, cg00418216, cg00425918, cg00431187, cg00434010, cg00435063, cg00445405, cg00463767, cg00487737, cg00490421, cg00495775, cg00499700, cg00503840, cg00504902, cg00505979, cg00506343, cg00507727, cg00513205, cg00553149, cg00556112, cg00567703, cg00574563, cg00585714, cg00599564, cg00616687, cg00629427, cg00663077, cg00667789, cg00673290, cg00674304, cg00687252, cg00714725, cg00716277, cg00733728, cg00756451, cg00762160, cg00767496, cg00779924, cg00790395, cg00795248, cg00806704, cg00838919, cg00840332, cg00864474, cg00867835, cg00877329, cg00882235, cg00887814, cg00905524, cg00913949, cg00926215, cg00928397, cg00947782, cg00949753, cg00963169, cg00970313, cg00982919, cg00982984, cg00983437, cg00985729, cg00989853, cg01003803, cg01031400, cg01040654, cg01054755, cg01078824, cg01141459, cg01156550, cg01163842, cg01172183, cg01174140, cg01177854, cg01182865, cg01229452, cg01243879, cg01258751, cg01277331, cg01277372, cg01285501, cg01286685, cg01287476, cg01295203, cg01323777, cg01351315, cg01371072, cg01402735, cg01405040, cg01405445, cg01438365, cg01449663, cg01456368, cg01460436, cg01463565, cg01467266, cg01484487, cg01494454, cg01499197, cg01530101, cg01533258, cg01550148, cg01564135, cg01587682, cg01602621, cg01622304, cg01627823, cg01631162, cg01645998, cg01655831, cg01658421, cg01665555, cg01673674, cg01693350, cg01708273, cg01713701, cg01727145, cg01739725, cg01789499, cg01803928, cg01811325, cg01815671, cg01819512, cg01821018, cg01824969, cg01832036, cg01850449, cg01853561, cg01882880, cg01896761, cg01904410, cg01913455, cg01921432, cg01926269, cg01934626, cg01939477, cg01942863, cg01946451, cg01961447, cg01972418, cg02005600, cg02006615, cg02022733, cg02032558, cg02037307, cg02051616, cg02055963, cg02058624, cg02069715, cg02086801, cg02100373, cg02102424, cg02108033, cg02109484, cg02115599, cg02120658, cg02132714, cg02145932, cg02150354, cg02151625, cg02154252, cg02188185, cg02194789, cg02213684, cg02233197, cg02250594, cg02281208, cg02283931, cg02285920, cg02286091, cg02330683, cg02335804, cg02346492, cg02348751, cg02360980, cg02364236, cg02367696, cg02428056, cg02435495, cg02439266, cg02458062, cg02468250, cg02483701, cg02487130, cg02495310, cg02497558, cg02511456, cg02524946, cg02530022, cg02552311, cg02553516, cg02569236, cg02585702, cg02595832, cg02596153, cg02599464, cg02611848, cg02623050, cg02624770, cg02628823, cg02633371, cg02642123, cg02642822, cg02646491, cg02655630, cg02660440, cg02688752, cg02694427, cg02700894, cg02701080, cg02703870, cg02741882, cg02760031, cg02767242, cg02768694, cg02770983, cg02771142, cg02781618, cg02798576, cg02800607, cg02803914, cg02865068, cg02873421, cg02874942, cg02878244, cg02885007, cg02886033, cg02906407, cg02907064, cg02916932, cg02948476, cg02964031, cg02971322, cg03001942, cg03011535, cg03020554, cg03024760, cg03036592, cg03045635, cg03086235, cg03091551, cg03099728, cg03102494, cg03129884, cg03133868, cg03144922, cg03148184, cg03171465, cg03177551, cg03181248, cg03219282, cg03219968, cg03242698, cg03276408, cg03293507, cg03301582, cg03323462, cg03325664, cg03343571, cg03347590, cg03350299, cg03356900, cg03405909, cg03405983, cg03431846, cg03465861, cg03491584, cg03522132, cg03529432, cg03562044, cg03572772, cg03583111, cg03596280, cg03609639, cg03636532, cg03637815, cg03640756, cg03650674, cg03655683, cg03656099, cg03660500, cg03669298, cg03672342, cg03692563, cg03694713, cg03695236, cg03711485, cg03733219, cg03733760, cg03735496, cg03744440, cg03744763, cg03771840, cg03774463, cg03780851, cg03826976, cg03851159, cg03854796, cg03867465, cg03885037, cg03905867, cg03927133, cg03945700, cg03947464, cg03951833, cg03958979, cg03959515, cg03960072, cg03964958, cg03970615, cg03975235, cg03981954, cg03989480, cg04022561, cg04025675, cg04046669, cg04047221, cg04052466, cg04059568, cg04065086, cg04079760, cg04080041, cg04080282, cg04091063, cg04131898, cg04134048, cg04136369, cg04142323, cg04158367, cg04178316, cg04180086, cg04193970, cg04198914, cg04203646, cg04213746, cg04236178, cg04251368, cg04255230, cg04265576, cg04290346, cg04328477, cg04342594, cg04360793, cg04366687, cg04369341, cg04378886, cg04403809, cg04407470, cg04415176, cg04415798, cg04418091, cg04446345, cg04450456, cg04456238, cg04461228, cg04467589, cg04469219, cg04489012, cg04504066, cg04513006, cg04514123, cg04515001, cg04521510, cg04543413, cg04552206, cg04554928, cg04558175, cg04566159, cg04574034, cg04586579, cg04597433, cg04597449, cg04598774, cg04617948, cg04623837, cg04630292, cg04636269, cg04648480, cg04654530, cg04673825, cg04685170, cg04688051, cg04728480, cg04729913, cg04730685, cg04738888, cg04739647, cg04765277, cg04775710, cg04787024, cg04796181, cg04809787, cg04821708, cg04850999, cg04854328, cg04856858, cg04864199, cg04886060, cg04887494, cg04904318, cg04916091, cg04937416, cg04938549, cg04956913, cg04959815, cg04972566, cg04972745, cg04996219, cg05001964, cg05009601, cg05027336, cg05029822, cg05031521, cg05065507, cg05072100, cg05140806, cg05142617, cg05142765, cg05158615, cg05165940, cg05167251, cg05180443, cg05193369, cg05196969, cg05210501, cg05222924, cg05236677, cg05256269, cg05290058, cg05301866, cg05317714, cg05345154, cg05347898, cg05351827, cg05368740, cg05376374, cg05377576, cg05380821, cg05387167, cg05408649, cg05449136, cg05457563, cg05470554, cg05475934, cg05477444, cg05488632, cg05490659, cg05498007, cg05500840, cg05501996, cg05520409, cg05522011, cg05527530, cg05529506, cg05555207, cg05578840, cg05592035, cg05603881, cg05604079, cg05635754, cg05639205, cg05656180, cg05658487, cg05667348, cg05678749, cg05690644, cg05697849, cg05724997, cg05736768, cg05744332, cg05766510, cg05787556, cg05818685, cg05822926, cg05835105, cg05839235, cg05853632, cg05890484, cg05896902, cg05899618, cg05905176, cg05915293, cg05921905, cg05922610, cg05924583, cg05925327, cg05928186, cg05929882, cg05937630, cg05942128, cg05974274, cg05975410, cg05976500, cg05977669, cg05990544, cg06005695, cg06023345, cg06049868, cg06055873, cg06060135, cg06102419, cg06133205, cg06142537, cg06146234, cg06148812, cg06150468, cg06157318, cg06159394, cg06166809, cg06178563, cg06198398, cg06226156, cg06226630, cg06230848, cg06238409, cg06239355, cg06249604, cg06254440, cg06255601, cg06262436, cg06272038, cg06274159, cg06287951, cg06303875, cg06312283, cg06323023, cg06367117, cg06367311, cg06375967, cg06376715, cg06382344, cg06382559, cg06386307, cg06390536, cg06410191, cg06410537, cg06428620, cg06440348, cg06451900, cg06488443, cg06490225, cg06497848, cg06520675, cg06535993, cg06554090, cg06571387, cg06579271, cg06615152, cg06626599, cg06632207, cg06637517, cg06644373, cg06666008, cg06667574, cg06702880, cg06704518, cg06705930, cg06708634, cg06710082, cg06723863, cg06724305, cg06732395, cg06754197, cg06765217, cg06779449, cg06804210, cg06813578, cg06818052, cg06818777, cg06825142, cg06842954, cg06845853, cg06854084, cg06866686, cg06872257, cg06911121, cg06916239, cg06942183, cg06942701, cg06943420, cg06962944, cg06966811, cg06975048, cg06991300, cg06992285, cg07010088, cg07010228, cg07017875, cg07020001, cg07021644, cg07029873, cg07033624, cg07046818, cg07050616, cg07060233, cg07095230, cg07104660, cg07116997, cg07121856, cg07124117, cg07135614, cg07147475, cg07155223, cg07160932, cg07178825, cg07195011, cg07201017, cg07211140, cg07247419, cg07274716, cg07281879, cg07300846, cg07302910, cg07311313, cg07322064, cg07323141, cg07329360, cg07330230, cg07333715, cg07359633, cg07367232, cg07371589, cg07380026, cg07382347, cg07382943, cg07383092, cg07407736, cg07411620, cg07416664, cg07434271, cg07440414, cg07440775, cg07447773, cg07483304, cg07502389, cg07515422, cg07516252, cg07522913, cg07529210, cg07536910, cg07539798, cg07541200, cg07545037, cg07552803, cg07578695, cg07592963, cg07595776, cg07606384, cg07615087, cg07653946, cg07660671, cg07696699, cg07702750, cg07703462, cg07778029, cg07785447, cg07788369, cg07791578, cg07793808, cg07802350, cg07838106, cg07855083, cg07860213, cg07871947, cg07877559, cg07879739, cg07881405, cg07938743, cg07939836, cg07974511, cg07991112, cg07996594, cg08022244, cg08034867, cg08066129, cg08079908, cg08085357, cg08089301, cg08116462, cg08118159, cg08126211, cg08138435, cg08163199, cg08182446, cg08196968, cg08203284, cg08206318, cg08227526, cg08231710, cg08247587, cg08274589, cg08278487, cg08279075, cg08305551, cg08307030, cg08309809, cg08318726, cg08325845, cg08370178, cg08373003, cg08381274, cg08431536, cg08457898, cg08465346, cg08473330, cg08479590, cg08480826, cg08481464, cg08481491, cg08492173, cg08499046, cg08509840, cg08511651, cg08547691, cg08555653, cg08575330, cg08587845, cg08598654, cg08599448, cg08613144, cg08622757, cg08657492, cg08680048, cg08694699, cg08702941, cg08703872, cg08704562, cg08712054, cg08726248, cg08745288, cg08746900, cg08748969, cg08781140, cg08784129, cg08787968, cg08793877, cg08813062, cg08825084, cg08828819, cg08829841, cg08858649, cg08865099, cg08874512, cg08879910, cg08898155, cg08902977, cg08927006, cg08938793, cg08964780, cg08965276, cg08971771, cg08979319, cg08979895, cg08985979, cg09010671, cg09016822, cg09041678, cg09042277, cg09046055, cg09048251, cg09050331, cg09064304, cg09071155, cg09093485, cg09098195, cg09105193, cg09127400, cg09133032, cg09135656, cg09143801, cg09156097, cg09164580, cg09180848, cg09188099, cg09194159, cg09224689, cg09229918, cg09233651, cg09234518, cg09234616, cg09236434, cg09238180, cg09252999, cg09257796, cg09257824, cg09279736, cg09299055, cg09313705, cg09359114, cg09382096, cg09411999, cg09491991, cg09498572, cg09500443, cg09502866, cg09509183, cg09515953, cg09537620, cg09554509, cg09554951, cg09586183, cg09591524, cg09595479, cg09614415, cg09622982, cg09639151, cg09656389, cg09661370, cg09671258, cg09672187, cg09672383, cg09686443, cg09695430, cg09696159, cg09704116, cg09706122, cg09709472, cg09731996, cg09767822, cg09792881, cg09797337, cg09803262, cg09826050, cg09854626, cg09857513, cg09866983, cg09868598, cg09888562, cg09935388, cg09936824, cg09938227, cg09983051, cg10004780, cg10035294, cg10060574, cg10068417, cg10074409, cg10084644, cg10094489, cg10114327, cg10122865, cg10131194, cg10137231, cg10146929, cg10147797, cg10169241, cg10172669, cg10195901, cg10242160, cg10242602, cg10245273, cg10245988, cg10288510, cg10300188, cg10303487, cg10331779, cg10334767, cg10344832, cg10347335, cg10356613, cg10357657, cg10366797, cg10421979, cg10439765, cg10456990, cg10475970, cg10479082, cg10500362, cg10508993, cg10511988, cg10526374, cg10532489, cg10536898, cg10537450, cg10588696, cg10588962, 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cg26277730, cg26277754, cg26295921, cg26296488, cg26299169, cg26309194, cg26322248, cg26327071, cg26330518, cg26331172, cg26365545, cg26370729, cg26371731, cg26376168, cg26380443, cg26388730, cg26410483, cg26413174, cg26421310, cg26422458, cg26429925, cg26437825, cg26446499, cg26457809, cg26476852, cg26506288, cg26517171, cg26517714, cg26521404, cg26551975, cg26559315, cg26560222, cg26585452, cg26589785, cg26601317, cg26618965, cg26659805, cg26660800, cg26673012, cg26674479, cg26674943, cg26687072, cg26690075, cg26698460, cg26701242, cg26702958, cg26708319, cg26751356, cg26755097, cg26783057, cg26796135, cg26811372, cg26814075, cg26816907, cg26844246, cg26848718, cg26870725, cg26879945, cg26890354, cg26951440, cg26990102, cg26998537, cg27009703, cg27011060, cg27029821, cg27032146, cg27035251, cg27076669, cg27090216, cg27100227, cg27110277, cg27111250, cg27111463, cg27125849, cg27151303, cg27157482, cg27162435, cg27183188, cg27190967, cg27234067, cg27252696, cg27267227, cg27304406, cg27309110, cg27312652, cg27363141, cg27364741, cg27398720, cg27448110, cg27449131, cg27493649, cg27513574, cg27520776, cg27521476, cg27526665, cg27532187, cg27539480, cg27542552, cg27583307, cg27616661, cg27622506, cg27639457, cg27639662, cg27650870, cg27656658, cg27661315, cg12627726, cg06749480, cg07152605, cg12689806, cg22029015, cg10186395, cg02406098, cg20789595, cg19008133, cg07366462, cg01246398, cg08598988, cg25661931, cg22989209, cg04830757, cg26863842, cg26177760, cg24124954, cg24332685, cg21179831, cg21079591, cg25711558, cg03787603, cg11911769, cg09244071, cg15755348, cg26651148, cg14759472, cg26170014, cg10473311, cg21584493, cg26793019, cg02563011, cg02616558, cg22663467, cg26837853, cg12269374, cg08236285, cg12042060, cg14207539, cg23264016, cg26193427, cg12507869, cg05714496, cg22900057, cg09746086, cg00221747, cg05384664, cg06029905, cg02808220, cg24183187, cg22932993, cg21728792, cg14890224, cg01668279, cg16794682, cg12266049, cg15974867, cg04717045, cg12263469, cg06868955, cg26013733, cg13876604, cg08458121, cg02060732, cg05604487, cg04115702, and cg07490808.

### Claim 2 (depends on 1)

The array of claim 1 consisting of the 2332 probes.

### Claim 3 (depends on 1)

A method of predicting recurrence free survival in a patient with meningioma comprising:
(a) determining a tumor DNA methylation profile of a meningioma sample from the patient using the array of claim 1, wherein the tumor DNA methylation profile consists of the methylation status of the 2332 loci detected by the array of claim 1; and
(b) calculating a risk of meningioma recurrence by comparing the tumor DNA methylation profile with a reference methylation profile comprising the extent to which the methylation status of the 2332 loci is associated with the risk of recurrence.

### Claim 4 (depends on 3)

The method of claim 3, wherein the calculating the risk is based further on at least one of the WHO grading and Simpson grading of the tumor.

### Claim 5 (depends on 3)

The method of claim 3, further comprising calculating a predicted number of years of recurrence free survival (RFS Score).

### Claim 6 (depends on 5)

The method of claim 5, further comprising stratifying the patient into a high, a medium or a low risk category based on said RFS Score compared to known reference patients.

### Claim 7 (depends on 6)

The method of claim 6, further comprising treating the patient with adjuvant therapy if the patient is in the high or medium risk category.

### Claim 8 (depends on 7)

The method of claim 7, wherein the adjuvant therapy comprises chemotherapy or radiotherapy.