BAC clones (BACPAC Resources) were used to develop break-apart probes for the following genes: BRAF (RP11-837G3, RP11-948O19), NTRK1 (CH17-67O18, RP11-1038N13), PTPRZ1 (CH17-132B19, RP11-99L10), IL6R (CH17-169C19, RP11-627K14), TPM3 (CH17-317C21, CH17-169C19), EML4 (CH17-315G08, RP11-885P15), ARID1B (RP11-230C9, CH17-280H05), and BAIAP2L1 (RP11-958G24, CH17-112O19). Break-apart FISH for ALK was performed by using a commercially available probe set (CytoCell, Cat# LPS 019-A). In addition, BAC clones (CH17-132B19, RP11-99L10 and CH17-57M15, CH17-240N01) were used to develop a fusion probe set for PTPRZ1–NFAM1. Dual-color FISH was performed on 4-µm FFPE sections, as previously described.20 (link)
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Comprehensive FISH Probe Development
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Corresponding Organization :
Other organizations : St. Jude Children's Research Hospital, Délégation Paris 5, Université Paris Cité, Institut Curie
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Variable analysis
independent variables
- BAC clones used to develop break-apart probes for the following genes: BRAF (RP11-837G3, RP11-948O19), NTRK1 (CH17-67O18, RP11-1038N13), PTPRZ1 (CH17-132B19, RP11-99L10), IL6R (CH17-169C19, RP11-627K14), TPM3 (CH17-317C21, CH17-169C19), EML4 (CH17-315G08, RP11-885P15), ARID1B (RP11-230C9, CH17-280H05), and BAIAP2L1 (RP11-958G24, CH17-112O19)
- Commercially available probe set (CytoCell, Cat# LPS 019-A) used for break-apart FISH for ALK
- BAC clones (CH17-132B19, RP11-99L10 and CH17-57M15, CH17-240N01) used to develop a fusion probe set for PTPRZ1–NFAM1
- Outcomes measured using dual-color FISH on 4-µm FFPE sections
- 4-µm FFPE sections used for dual-color FISH, as previously described in reference 20
- No positive or negative controls were explicitly mentioned in the text.
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