IPC분류정보
국가/구분 |
United States(US) Patent
공개
|
국제특허분류(IPC7판) |
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출원번호 |
US-0993375
(2018-05-30)
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공개번호 |
US-0346994
(2018-12-06)
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발명자
/ 주소 |
- Begovich, Ann
- Cheung, Cindy
- Chi, Javelin
- Hillman, Grantland
- Kuo, Dwight
- Lee, Michael
- Manohar, Chitra
- Ma, Xiaoju Max
- Ordinario, Ellen
- Rajamani, Jaya
- Truong, Huan
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출원인 / 주소 |
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인용정보 |
피인용 횟수 :
0 인용 특허 :
0 |
초록
Provided herein are methods and compositions for multiplex detection of a large number of actionable gene fusions with very high sensitivity and specificity. The present methods and compositions can detect ALK, RET, and ROS1 gene fusions, optionally in combination with other mutations and fusions.
대표청구항
▼
1. A multiplex assay composition comprising: A. at least one primer set and probe that specifically amplify and detect at least one ALK fusion gene;B. at least one primer set and probe that specifically amplify and detect at least one RET fusion gene;C. at least one primer set and probe that specifi
1. A multiplex assay composition comprising: A. at least one primer set and probe that specifically amplify and detect at least one ALK fusion gene;B. at least one primer set and probe that specifically amplify and detect at least one RET fusion gene;C. at least one primer set and probe that specifically amplify and detect at least one ROS1 fusion gene; andD. a primer set and probe that specifically amplify and detect an internal control. 2. The composition of claim 1, wherein the at least one ALK fusion gene is selected from the group consisting of: EML4 exon 13-ALK exon 20, EML4 exon 20-ALK exon 20, EML4 exon 6a/b-ALK exon 20, EML4 exon 2-ALK exon 20, EML4 exon 18-ALK exon 20, KIF5B exon 17-ALK exon 20, and KIF5B exon 24-ALK exon 20. 3. The composition of claim 1 or 2, wherein A includes at least one primer set and probe that amplify and detect more than 2 ALK fusion genes. 4. The composition of any one of the foregoing claims, wherein A includes at least one primer set and probe that amplify and detect EML4 exon 13-ALK exon 20, EML4 exon 20-ALK exon 20, EML4 exon 6a/b-ALK exon 20, EML4 exon 2-ALK exon 20, EML4 exon 18-ALK exon 20, KIF5B on 17-ALK exon 20, and KIF5B exon 24-ALK exon 20. 5. The composition of any one of the foregoing claims, wherein the at least one RET fusion gene is selected from the group consisting of: KIF5B exon 15-RET exon 12, KIF5B exon 16-RET exon 12, KIF5B exon 22-RET exon 12, KIF5B exon 23-RET exon 12, CCDC6 exon 1-RET exon 12, and NCOA4 exon 6-RET exon 12. 6. The composition of any one of the foregoing claims wherein B includes at least one primer set and probe that amplify and detect more than 2 RET fusion genes. 7. The composition of any one of the foregoing claims, wherein B includes at least one primer set and probe that amplify and detect KIF5 exon 15-RET exon 12, KIF5B exon 16-RET exon 12, KIF5B exon 22-RET exon 12, KIF5B exon 23-RET exon 12, CCDC6 exon 1-RET exon 12, and NCOA4 exon 6-RET exon 12. 8. The composition of any one of the foregoing claims, wherein the at least one ROS1 fusion gene is selected from the group consisting of; CD74 exon 6-ROS1 exon 34, CD74 exon 6-ROS1 exon 32, EZR exon 10-ROS1 exon 34, TPM3 exon 8-ROS1 exon 35, SDC4 exon 4-ROS1 exon 34, SDC4 exon 2-ROS1 exon 34, SDC4 exon 2-ROS1 exon 32, SDC4 exon 4-ROS1 exon 32, SLC34A2 exon 13-ROS1 exon 34, SLC34A2 exon 13-ROS1 exon 32v2, SLC34A2 exon 4-ROS1 exon 32, SLC34A2 exon 4-ROS1 exon 35, and LRIG3 exon 16-ROS1 exon 35. 9. The composition of any one of the foregoing claims, wherein C includes at least one primer set and probe that amplify and detect more than 2 ROS1 fusion genes. 10. The composition of any one of the foregoing claims, wherein C includes at least one primer set and probe that amplify and detect CD74 exon 6-ROS1 exon 34, CD74 exon 6-ROS1 exon 32, EZR exon 10-ROS1 exon 34, TPM3 exon 8-ROS1 exon 35, SDC4 exon 4-ROS1 exon 34, SDC4 exon 2-ROS1 exon 32v2, SDC4 exon 2-ROS1 exon 32, SLC34A2 exon 13-ROS1 exon 34, SLC34A2 exon 13-ROS1 exon 32v2, SLC34A2 exon 4-ROS1 exon 32, SLC34A2 exon 4-ROS1 exon 35, and LRIG3 exon 16-ROS1 exon 35. 11. The composition of any one of the foregoing claims, further comprising a thermostable DNA polymerase. 12. The composition of any one of the foregoing claims, further comprising reverse transcriptase. 13. The composition of any one of the foregoing claims, further comprising a biological sample from an individual. 14. The composition of claim 13, wherein the biological sample includes RNA from plasma. 15. A multiplex assay composition comprising: A. at least one primer set and probe that specifically amplify and detect at least one ALK fusion gene;B. at least one primer set and probe that specifically amplify and detect at least one RET fusion gene; andC. a primer set and probe that specifically amplify and detect an internal control. 16. The composition of claim 15, wherein the at least one ALK fusion gene is selected from the group consisting of: EML4 exon 13-ALK exon 20, EML4 exon 20-ALK exon 20, EML4 exon 6a/b-ALK exon 20, EML4 exon 2-ALK exon 20, EML4 exon 18-ALK exon 20, KIF5B exon 17-ALK exon 20, and KIF5B exon 24-ALK exon 20. 17. The composition of claim 15 or 16, wherein the at least one RET fusion gene is selected from the group consisting of: KIF5B exon 15-RET exon 12, KIF5B exon 16-RET exon 12, KIF5B exon 22-RET exon 12, KIF5B exon 23-RET exon 12, CCDC6 exon 1-RET exon 12, and NCOA4 exon 6-RET exon 12. 18. The composition of any one of claims 15-17 further comprising a thermostable DNA polymerase. 19. The composition of any one of claims 15-18, further comprising reverse transcriptase. 20. The composition of any one of claims 15-19, further comprising a biological sample from an individual. 21. The composition of claim 20, wherein the biological sample includes RNA from plasma. 22. A method of treating an individual with cancer comprising: A. contacting a biological sample from the individual with the composition of any one of claims 1-12 and 15-19;B. carrying out amplification and detection under conditions that allow formation and detection of an amplification product in the presence of at least one fusion gene in the biological sample;C. determining that at least one fusion gene is present if a fusion gene is detected in step B; andD. treating the individual with a kinase inhibitor therapy if at least one fusion gene is present. 23. The method of claim 22, wherein the biological sample includes DNA or RNA. 24. The method of claim 22, wherein the biological sample is RNA from plasma of the individual. 25. The method of claim 22, wherein the amplification and detection are carried out using quantitative reverse transcription polymerase chain reaction (qRT-PCR). 26. The method of any one of claims 22-25, wherein the kinase inhibitor therapy is selected from the group consisting of alectinib, crizotinib, ceritinib, lorlatinib, brigatinib, cabozantinib, apatinib, vandetanib, ponatinib, lenvatinib, DS6051b, or a variant thereof. 27. A method for determining the presence of at least one fusion gene in a biological sample from an individual with cancer comprising: A. contacting a biological sample from the individual with the composition of any one of claims 1-12 and 15-19;B. carrying out amplification and detection under conditions that allow formation and detection of an amplification product in the presence of at least one fusion gene in the biological sample;C. determining the presence of at least are fusion gene if a fusion gene is detected in step B. 28. The method of claim 27, wherein the biological sample includes DNA or RNA. 29. The method of claim 27, wherein the biological sample is RNA from plasma of the individual. 30. The method of claim 27, wherein the amplification and detection are carried out using quantitative reverse transcription polymerase chain reaction (qRT-PCR).
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