Patent AU-2019272065-B2 (AU)
Title: Deep learning-based framework for identifying sequence patterns that cause sequence-specific errors (SSEs)
Inventor: KASHEFHAGHIGHI DORNA
IPC: G06N3/08
Filed: 2019-07-09
Granted: 2021-03-04
Abstract: INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) 
(19) World Intellectual Property 
(1) Organization11111111111111111111111I1111111111111i1111liiiii 
International Bureau (10) International Publication Number 
(43) International Publication Date W O 2020/014280 Al 
16 January 2020 (16.01.2020) W IPO I PCT 
(51) International Patent Classification: (74) Agent: DURDIK, Paul A. et al.; 637 Main St., Half Moon 
G16B 40/20 (2019.01) G06N3/04 (2006.01) Bay, California 94019 (US).  
GJ6B20/20(2019.01) (81) Designated States (unless otherwise indicated, for every 
(21) International Application Number: kind ofnational protection available): AE, AG, AL, AM, 
PCT/US2019/041078 AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, 
CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, 
(22) International Filing Date: DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, 
09July2019(09.07.2019) HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, 
(25) Filing Language: English KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, 
(26)PublicationLanguage: English MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, 
(30) Priority Data: SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 
62/696,699 11 July 2018 (11.07.2018) US TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.  
2021473 16 August 2018 (16.08.2018) NL (84) Designated States (unless otherwise indicated, for every 
16/505,100 08 July 2019 (08.07.2019) US kind of regional protection available): ARIPO (BW, GH, 
(71) Applicant: ILLUMINA, INC. [US/US]; 5200 Illumina GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, 
Way, San Diego, California 92122 (US). UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, 
TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, 
(72) Inventors: KASHEFHAGHIGHI, Dorna; 5200 Illumi- EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, 
na Way, San Diego, California 92122 (US). KIA, Ami- MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, rali;520 Illumina Way, SanDiego, California 92122 (US). OAPI(FBJ,CC G).ICM,GA,GN,GQ,GW, 
FARH, Kai-How; 5200 IllumnaWay, San Diego, Califor- KCM, ML, MR, N, SN, TD, TG).  
nia 92122 (US).  
(54) Title: DEEP LEARNING-BASED FRAMEWORK FOR IDENTIFYING SEQUENCE PATTERNS THAT CAUSE SE
QUENCE-SPECIFIC ERRORS (SSEs) 
(57) Abstract: The technology disclosed presents a deep learning-based framework, which 
identifies sequence patterns that cause sequence-specific errors (SSEs). Systems and methods 
train a variant filter on large-scale variant data to learn causal dependencies between sequence 
patterns and false variant calls. The variant filter has a hierarchical structure built on deep neural 
networks such as convolutional neural networks and fully-connected neural networks. Systems 
and methods implement a simulation that uses the variant filter to test known sequence patterns 
lP-TnWrjaiFill for their effect on variant filtering. The premise of the simulation is as follows: when a pair of 
a repeat pattern under test and a called variant is fed to the variant filter as part of a simulated 
input sequence and the variant filter classifies the called variant as a false variant call, then the 
-Ms repeat pattern is considered to have caused the false variant call and identified as SSE-causing.  
Re 12ai~Opr¶b'i~2l 
0 ~ SSE-CR 
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Declarations under Rule 4.17: 
- as to applicant's entitlement to apply for and be granted a 
patent (Rule 4.17(ii)) 
- as to the applicant's entitlement to claim the priority of the 
earlier application (Rule 4.17(iii)) 
Published: 
- with international search report (Art. 21(3))