HRP20201397T1 - Postupak i sustavi za analizu slikovnih podataka - Google Patents
Postupak i sustavi za analizu slikovnih podataka Download PDFInfo
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- HRP20201397T1 HRP20201397T1 HRP20201397TT HRP20201397T HRP20201397T1 HR P20201397 T1 HRP20201397 T1 HR P20201397T1 HR P20201397T T HRP20201397T T HR P20201397TT HR P20201397 T HRP20201397 T HR P20201397T HR P20201397 T1 HRP20201397 T1 HR P20201397T1
- Authority
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- Croatia
- Prior art keywords
- cycle
- phase
- channel
- intensity value
- nucleotide
- Prior art date
Links
- 238000000034 method Methods 0.000 title claims 17
- 239000002773 nucleotide Substances 0.000 claims 15
- 125000003729 nucleotide group Chemical group 0.000 claims 15
- 238000012937 correction Methods 0.000 claims 12
- 239000002157 polynucleotide Substances 0.000 claims 5
- 102000040430 polynucleotide Human genes 0.000 claims 5
- 108091033319 polynucleotide Proteins 0.000 claims 5
- 238000009826 distribution Methods 0.000 claims 4
- 238000010348 incorporation Methods 0.000 claims 2
- 238000012163 sequencing technique Methods 0.000 claims 2
- 238000003786 synthesis reaction Methods 0.000 claims 2
- 238000001914 filtration Methods 0.000 claims 1
Classifications
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6869—Methods for sequencing
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
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- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
- Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
- Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
- Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation
Claims (15)
1. Postupak koji obuhvaća:
a) izvođenje množine ciklusa sekvenciranja putem reakcije sinteze na način da se, u svakom ciklusu, generira signal indikativan za inkorporaciju istog nukleotida u množinu identičnih polinukleotida, pri čemu je dio signala šum povezan s fazom ili pred-fazom;
b) detektiranje signala u svakom ciklusu, pri čemu detektiranje signala u svakom ciklusu uključuje detektiranje vrijednosti intenziteta signala u prvom kanalu i detektiranje vrijednosti intenziteta signala u drugom kanalu; i
c) izvođenje ispravaka faza ciklusa za ciklusom putem primjene novog ispravka faze prvog reda kod svakog ciklusa naspram vrijednosti intenziteta;
naznačeno time da se novi ispravak faze prvog reda računa za svaki ciklus, pri čemu novi ispravak faze prvog reda za svaki ciklus uključuje oduzimanje vrijednosti intenziteta neposredno prethodnog ciklusa od vrijednosti intenziteta trenutačnog ciklusa i također uključuje oduzimanje vrijednosti intenziteta neposredno sljedećeg ciklusa od vrijednosti intenziteta trenutačnog ciklusa; i
naznačeno time da se nukleotid inkorporiran u množinu identičnih polinukleotida može identificirati na temelju kombinacije vrijednosti intenziteta određenih u prvom i drugom kanalu.
2. Postupak prema zahtjevu 1, naznačen time da se prvi tip nukleotida detektira u prvom kanalu, drugi tip nukleotida se detektira u drugom kanalu, treći tip nukleotida se detektira u oba prvom i drugom kanalu, i četvrti tip nukleotida se ne detektira ili se minimalno detektira kod prvog i drugog kanala.
3. Postupak prema zahtjevu 1 ili 2, naznačen time da se dvokanalni „base – calling“ postupak izvodi putem izvlačenja slikovnih podataka iz samo dva kanala.
4. Postupak prema bilo kojem od zahtjeva 1 – 3, naznačen time da novi ispravak faze prvog reda uključuje faznu i pred-faznu težinu i postupak dalje uključuje odabir fazne težine X i pred-fazne težine Y, pri čemu odabrane fazne i pred-fazne težine X i Y optimiziraju prosječnu čistoću.
5. Postupak prema bilo kojem od zahtjeva 1 – 4, naznačen time da dvokanalni „base – calling“ postupak uključuje podešavanje četiri Gaussove distribucije sa skupom podataka od dvokanalnih podataka intenziteta na način da se jedna distribucija primjenjuje za svaki od četiri nukleotida predstavljena u skupu podataka.
6. Postupak prema zahtjevu 5, naznačen time da se Gaussove distribucije podešavaju prema skupu podataka korištenjem algoritma grupiranja, pri čemu, poželjnije, polinukleotidi oblikuju množinu skupina, svaka od skupina imajući par X,Y vrijednosti intenziteta, X i Y se odnoseći na prvi odnosno drugi kanal, pri čemu se za svaki par X,Y vrijenosti intenziteta određuje vjerojatna vrijednost koja predstavlja vjerojatnost da određeni par X,Y vrijednosti intenziteta pripada jednoj od četiri distribucija, i pri čemu, poželjnije, svaki par X, Y vrijednosti intenziteta ima četiri vjerojatne vrijednosti, jednu za svaki od četiri tipa nukleotida, maksimum od četiri vjerojatnih vrijednosti ukazujući na identitet inkorporiranog nukleotida.
7. Postupak prema zahtjevu 5, dalje obuhvaćajući flitriranje podatkovnih točaka niske čistoće putem određivanja čistoće podatkovne točke kao funkciju relativne udaljenosti naspram Gaussovih centroida.
8. Postupak prema bilo kojem od zahtjeva 1 – 7, naznačen time da je vrijednost intenziteta neposredno prethodnog ciklusa (X*I(ciklus)N-1) i da je vrijednost intenziteta neposredno sljedećeg ciklusa (Y*I(ciklus)N+1), pri čemu X i Y predstavljaju fazne odnosno pred-fazne težine.
9. Postupak prema zahtjevu 8, naznačen time da su X i Y odabrani kako bi optimizirali određivanje čistoće.
10. Postupak prema bilo kojem od zahtjeva 1 – 3, naznačen time da novi ispravak faze prvog reda obuhvaća:
I(ciklus)ispravak = I(ciklus) N – A*I(ciklus) N-1 – B*I (ciklus) N+1;
pri čemu se konstante A i B računaju od procijenjenih stopa faze i pred-faze i ponderirane su brojem ciklusa; i, poželjno,
postupak dalje obuhvaća optimiziranje A i B u svakom ciklusu korištenjem
pretraživanja uzorka.
11. Sustav koji obuhvaća:
procesor;
kapacitet skladišta; i
program za generiranje vrijednosti intenziteta ispravljane kroz faze, program uključujući uputstva za:
a) izvođenje množine ciklusa sekvenciranja putem reakcije sinteze na način da se, u svakom ciklusu, generira signal indikativan za inkorporaciju istog nukleotida u množinu identičnih polinukleotida, pri čemu je dio signala šum povezan s fazom ili pred-fazom;
b) detektiranje signala u svakom ciklusu, pri čemu detektiranje signala u svakom ciklusu uključuje detektiranje vrijednosti intenziteta signala u prvom kanalu i detektiranje vrijednosti intenziteta signala u drugom kanalu; i
c) izvođenje ispravaka faza ciklusa za ciklusom putem primjene novog ispravka faze prvog reda kod svakog ciklusa naspram vrijednosti intenziteta;
naznačeno time da se novi ispravak faze prvog reda računa za svaki ciklus, pri čemu novi ispravak faze prvog reda za svaki ciklus uključuje oduzimanje vrijednosti intenziteta neposredno prethodnog ciklusa od vrijednosti intenziteta trenutačnog ciklusa i također uključuje oduzimanje vrijednosti intenziteta neposredno sljedećeg ciklusa od vrijednosti intenziteta trenutačnog ciklusa; i
naznačeno time da se nukleotid inkorporiran u množinu identičnih polinukleotida može identificirati na temelju kombinacije vrijednosti intenziteta određenih u prvom i drugom kanalu.
12. Sustav prema zahtjevu 11, naznačen time da se prvi tip nukleotida detektira u prvom kanalu, drugi tip nukleotida se detektira u drugom kanalu, treći tip nukleotida se detektira u oba prvom i drugom kanalu, i četvrti tip nukleotida se ne detektira ili se minimalno detektira kod prvog i drugog kanala.
13. Sustav prema zahtjevu 11 ili zahtjevu 12, naznačen time da se, za svaki ciklus, dvokanalni „base – calling“ postupak izvodi putem izvlačenja slikovnih podataka iz samo dva kanala.
14. Sustav prema bilo kojem od zahtjeva 11 – 13, naznačen time da novi ispravak faze prvog reda uključuje faznu i pred-faznu težinu i postupak dalje uključuje odabir fazne težine X i pred-fazne težine Y, pri čemu odabrane fazne i pred-fazne težine X i Y optimiziraju glavnu čistoću.
15. Sustav prema zahtjevu 14, naznačen time da su fazna i pred-fazna težina odabrane korištenjem pretraživanja uzorka kroz moguće fazne i pred-fazne težine.
Applications Claiming Priority (5)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201361911319P | 2013-12-03 | 2013-12-03 | |
| US201361915455P | 2013-12-12 | 2013-12-12 | |
| US201361915426P | 2013-12-12 | 2013-12-12 | |
| EP14867596.0A EP3077943B1 (en) | 2013-12-03 | 2014-12-03 | Methods and systems for analyzing image data |
| PCT/US2014/068409 WO2015084985A2 (en) | 2013-12-03 | 2014-12-03 | Methods and systems for analyzing image data |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| HRP20201397T1 true HRP20201397T1 (hr) | 2020-11-27 |
Family
ID=53274278
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| HRP20201397TT HRP20201397T1 (hr) | 2013-12-03 | 2020-09-01 | Postupak i sustavi za analizu slikovnih podataka |
Country Status (15)
| Country | Link |
|---|---|
| US (3) | US10689696B2 (hr) |
| EP (3) | EP3715467A1 (hr) |
| AU (3) | AU2014360530B2 (hr) |
| CA (2) | CA3181696A1 (hr) |
| CY (1) | CY1123264T1 (hr) |
| DK (1) | DK3077943T3 (hr) |
| ES (1) | ES2808824T3 (hr) |
| HR (1) | HRP20201397T1 (hr) |
| HU (1) | HUE050641T2 (hr) |
| LT (1) | LT3077943T (hr) |
| PL (1) | PL3077943T3 (hr) |
| PT (1) | PT3077943T (hr) |
| RS (1) | RS60736B1 (hr) |
| SI (1) | SI3077943T1 (hr) |
| WO (1) | WO2015084985A2 (hr) |
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| EP3621739B1 (en) | 2018-01-05 | 2023-07-05 | Illumina Inc. | Predicting reagent chiller instability and flow cell heater failure in sequencing systems |
| US11288576B2 (en) | 2018-01-05 | 2022-03-29 | Illumina, Inc. | Predicting quality of sequencing results using deep neural networks |
| WO2019136388A1 (en) | 2018-01-08 | 2019-07-11 | Illumina, Inc. | Systems and devices for high-throughput sequencing with semiconductor-based detection |
| SG11201911764VA (en) | 2018-01-08 | 2020-01-30 | Illumina Inc | High-throughput sequencing with semiconductor-based detection |
| CN108629765B (zh) * | 2018-04-20 | 2020-09-08 | 山东第一医科大学(山东省医学科学院) | 基于序列阈值差的精子显微视频序列滤波质量客观评价方法 |
| NL2023314B1 (en) | 2019-03-21 | 2020-09-28 | Illumina Inc | Artificial intelligence-based quality scoring |
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| US11210554B2 (en) | 2019-03-21 | 2021-12-28 | Illumina, Inc. | Artificial intelligence-based generation of sequencing metadata |
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| US20220067489A1 (en) * | 2020-08-28 | 2022-03-03 | Illumina, Inc. | Detecting and Filtering Clusters Based on Artificial Intelligence-Predicted Base Calls |
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| AU2022305321A1 (en) | 2021-06-29 | 2024-01-18 | Illumina, Inc. | Signal-to-noise-ratio metric for determining nucleotide-base calls and base-call quality |
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2014
- 2014-12-03 EP EP20174757.3A patent/EP3715467A1/en active Pending
- 2014-12-03 PT PT148675960T patent/PT3077943T/pt unknown
- 2014-12-03 ES ES14867596T patent/ES2808824T3/es active Active
- 2014-12-03 WO PCT/US2014/068409 patent/WO2015084985A2/en active Application Filing
- 2014-12-03 EP EP14867596.0A patent/EP3077943B1/en active Active
- 2014-12-03 CA CA3181696A patent/CA3181696A1/en active Pending
- 2014-12-03 PL PL14867596T patent/PL3077943T3/pl unknown
- 2014-12-03 SI SI201431641T patent/SI3077943T1/sl unknown
- 2014-12-03 US US15/153,953 patent/US10689696B2/en active Active
- 2014-12-03 DK DK14867596.0T patent/DK3077943T3/da active
- 2014-12-03 CA CA2928209A patent/CA2928209C/en active Active
- 2014-12-03 LT LTEP14867596.0T patent/LT3077943T/lt unknown
- 2014-12-03 AU AU2014360530A patent/AU2014360530B2/en active Active
- 2014-12-03 EP EP21188289.9A patent/EP3940082A1/en active Pending
- 2014-12-03 HU HUE14867596A patent/HUE050641T2/hu unknown
- 2014-12-03 RS RS20201044A patent/RS60736B1/sr unknown
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2020
- 2020-06-12 US US16/899,716 patent/US20200377938A1/en active Pending
- 2020-08-17 CY CY20201100765T patent/CY1123264T1/el unknown
- 2020-09-01 HR HRP20201397TT patent/HRP20201397T1/hr unknown
- 2020-11-27 AU AU2020277261A patent/AU2020277261B2/en active Active
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2021
- 2021-06-15 US US17/348,212 patent/US20210310065A1/en active Pending
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2023
- 2023-02-10 AU AU2023200758A patent/AU2023200758A1/en active Pending
Also Published As
| Publication number | Publication date |
|---|---|
| US10689696B2 (en) | 2020-06-23 |
| EP3940082A1 (en) | 2022-01-19 |
| EP3077943A4 (en) | 2017-06-28 |
| CA2928209C (en) | 2023-09-26 |
| EP3077943B1 (en) | 2020-06-03 |
| PT3077943T (pt) | 2020-08-21 |
| AU2020277261B2 (en) | 2022-11-10 |
| SI3077943T1 (sl) | 2020-10-30 |
| WO2015084985A2 (en) | 2015-06-11 |
| LT3077943T (lt) | 2020-10-12 |
| AU2014360530B2 (en) | 2020-09-03 |
| US20200377938A1 (en) | 2020-12-03 |
| AU2023200758A1 (en) | 2023-03-09 |
| HUE050641T2 (hu) | 2020-12-28 |
| CA2928209A1 (en) | 2015-06-11 |
| RS60736B1 (sr) | 2020-09-30 |
| AU2014360530A1 (en) | 2016-04-28 |
| CY1123264T1 (el) | 2021-12-31 |
| WO2015084985A3 (en) | 2015-07-30 |
| DK3077943T3 (da) | 2020-09-07 |
| CA3181696A1 (en) | 2015-06-11 |
| ES2808824T3 (es) | 2021-03-02 |
| EP3077943A2 (en) | 2016-10-12 |
| US20210310065A1 (en) | 2021-10-07 |
| AU2020277261A1 (en) | 2021-01-07 |
| PL3077943T3 (pl) | 2020-11-30 |
| US20180274023A1 (en) | 2018-09-27 |
| EP3715467A1 (en) | 2020-09-30 |
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