Supplementary Figure.1

RANBP2-ALK fusion was detected in a re-biopsy sample obtained after ceritinib therapy.

ALK fusions were detected by reverse-transcription PCR (RT-PCR) using RNA

extracted from fresh-frozen biopsy samples. Synthesis of cDNA templates was performed

with total RNA (1 μg), Random Primer (hexadeoxyribonucleotide mixture; pd(N)6)

(TAKARA BIO, Shiga, Japan) and Omniscript RT Kit (QIAGEN). Information on the

primers for detecting CARS-ALK, CTLC-ALK, RANBP2-ALK, ATIC-ALK, SEC31L1-

ALK (both long-form and short-form fusion transcripts), TPM3-ALK and TPM4-

ALK fusion genes which have been previously reported in patients with IMT [5], was

kindly provided by Dr. Geoffrey Shapiro (Dana-Farber Cancer Institute, Boston, MA,

USA). RANBP2-ALK fusion was also confirmed by 5’-RACE (rapid amplification of

cDNA ends) assay (data not shown).

Supplementary Figure.2

A: Results of amplicon-based massively parallel sequencing with DNA extracted from re-

biopsy tissue sample. Amplicon-based massively parallel sequencing was performed on a

MiSeq platform (Illumina, San Diego, CA) using TruSeq Amplicon Cancer Panel and an

additional custom panel (Illumina). Detection of somatic mutations in cancer-related genes

from outputted raw data was performed in accordance with Serizawa et al [22]. Data

visualization was performed with Integrated Genome Viewer [23].

B: Results of validation for K478T mutation with Sanger sequencing. DNA

sequencing template was amplified by polymerase chain reaction (PCR) with the

PyroMark PCR Kit (QIAGEN) using 10 ng of genomic DNA and primers 5’-

GCTATTATCCTGAGTCTTATGTCT-3’ and 5’-GCTTTGGATCTGCATGAA-3’),

and purified by AMPure XP beads (Beckman Coulter, Miami, FL, USA). The

sequencing reaction was performed with BigDye® Terminator v3.1Result kit (Life Technologies, Gaithersburg, MD, USA), 10 ng purified PCR product and

sequencing primer (5’-TATCCTGAGTCTTATGTCTG-3’). The nucleotide sequence

was detected with 3130xL Genetic Analyzer (Life Technologies), and analyzed with CLC main workbench (CLC Bio, Aarhus, Denmark).

References

[22] Serizawa M, Yokota T, Hosokawa A, Kusafuka K, Sugiyama T, Tsubosa Y, et al. The

efficacy of uracil DNA glycosylase pretreatment in amplicon-based massively parallel

sequencing with DNA extracted from archived formalin-fixed paraffin-embedded esophageal

cancer tissues. Cancer Genet. 2015;208:415

[23] Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, et al.

Integrative genomics viewer. Nat. Biotechnol 2011;29:24