Methods of treating cholangiocarcinoma

1. A method of treating a subject having a cholangiocarcinoma, comprising:

acquiring knowledge of the presence of a fusion polypeptide or a fusion nucleic acid molecule encoding the fusion polypeptide in a sample from said subject, wherein the fusion polypeptide comprises an FGFR2-BICC1 fusion polypeptide encoded by a nucleic acid molecule comprising a fusion junction of exon 16 of SEQ ID NO: 1 and exon 18 of SEQ ID NO: 7; and

administering to the subject an effective amount of a kinase inhibitor chosen from: ACTB1003; ARRY-470; ARRY-786; AV369b; AZ-23; AZD-2171 (Cediranib); AZD-4547; BGJ398; BIBF1120; Brivanib; Brivanib Alaninate; Danusertib; Dovitinib; Dovitinib Dilactic Acid; ENMD-2076; JNJ 42756493; K252a; Lenvatinib; Lestaurtinib; Loxo-101; LY2874455; Masitinib; MK-2461; Oxindole-3; Pazopanib; PD173074; PD-173955; PHA-848125; Ponatinib; TSU-68; Tyrphostin AG 1296; R1530; R406; Regorafenib; RXDX-101; RXDX-102; Volasertib, or a combination thereof,

thereby treating the cholangiocarcinoma in the subject.

2. The method of claim 1 , wherein the kinase inhibitor is administered responsive to the determination of the presence of the fusion nucleic acid molecule or the fusion polypeptide in a sample from said subject.

3. The method of claim 2 , wherein the determination of the presence of the fusion nucleic acid molecule or the fusion polypeptide comprises sequencing.

4. The method of claim 1 , wherein the subject is undergoing or has undergone treatment with a different therapeutic agent or therapeutic modality.

5. The method of claim 4 , wherein responsive to the determination of the presence of the fusion nucleic acid molecule or the fusion polypeptide, the method further comprises discontinuing the different therapeutic agent or therapeutic modality.

6. The method of claim 4 , wherein the different therapeutic agent or therapeutic modality is a chemotherapy or a surgical procedure.

7. The method of claim 1 , wherein the FGFR2-BICC1 fusion polypeptide is encoded by a nucleic acid molecule comprising exons 1-16 of SEQ ID NO: 1 and exons 18-21 of SEQ ID NO: 7.

8. The method of claim 1 , wherein the FGFR2-BICC1 fusion polypeptide comprises an FGFR2 receptor tyrosine kinase domain or a functional fragment thereof.

9. The method of claim 1 , wherein the cholangiocarcinoma comprises one or more mutated cells that originate in the bile duct.

10. The method of claim 1 , wherein the cholangiocarcinoma is an intrahepatic carcinoma or an extrahepatic carcinoma.

11. A method of treating a subject having a cholangiocarcinoma, comprising:

detecting the presence of a fusion polypeptide or a fusion nucleic acid molecule encoding the fusion polypeptide in a sample from said subject, wherein the fusion polypeptide comprises an FGFR2-BICC1 fusion polypeptide encoded by a nucleic acid molecule comprising a fusion junction of exon 16 of SEQ ID NO: 1 and exon 18 of SEQ ID NO: 7; and

administering to the subject an effective amount of a kinase inhibitor chosen from: ACTB1003; ARRY-470; ARRY-786; AV369b; AZ-23; AZD-2171 (Cediranib); AZD-4547; BGJ398; BIBF1120; Brivanib; Brivanib Alaninate; Danusertib; Dovitinib; Dovitinib Dilactic Acid; ENMD-2076; JNJ 42756493; K252a; Lenvatinib; Lestaurtinib; Loxo-101; LY2874455; Masitinib; MK-2461; Oxindole-3; Pazopanib; PD173074; PD-173955; PHA-848125; Ponatinib; TSU-68; Tyrphostin AG 1296; R1530; R406; Regorafenib; RXDX-101; RXDX-102; Volasertib, or a combination thereof;

thereby treating the cholangiocarcinoma in the subject.

12. The method of claim 1 , wherein the sample is a nucleic acid sample.

13. The method of claim 1 , wherein the sample is a blood, serum, or plasma sample.

14. The method of claim 1 , wherein the sample comprises a tumor biopsy or a circulating tumor cell or nucleic acid.

15. The method of claim 11 , wherein the sample is a nucleic acid sample.

16. The method of claim 11 , wherein the sample is a blood, serum, or plasma sample.

17. The method of claim 11 , wherein the sample comprises a tumor biopsy or a circulating tumor cell or nucleic acid.