Table 1.
Results of RNA Sequencing and Exon Resequencing of the Discovery Cohort of 19 Specimens of Ovarian Clear-Cell Carcinoma (Including a Cell Line).*
| Sample No. | ARID1A Mutation | Exon Resequencing | RNA Sequencing | Immunohistochemical Test for BAF250a Expression | Predicted ARID1A Status | Other Somatic Mutations in Oncogenes or Tumor Suppressors | |
|---|---|---|---|---|---|---|---|
| no. of reads containing mutation/total no. of reads at mutation position (%) | |||||||
| CCC01 | 6018-6020delGCT | 223/1529 (15) | 10/40 (25) | Positive | Heterozygous† | ||
| CCC02 | 404delC‡ | Not applicable§ | No coverage | Negative | Mutation with loss of heterozygosity¶ | CTNNB1 C110G (S37C) | |
| CCC03 | 5518delG‡ | 395/1725 (23) | 1/2 (50) | Positive | Heterozygous† | ||
| CCC04 | Deletion and rearrangement | Not applicable | 6/6 (100) | Negative | Deletion and rearrangement (homozygous) | ||
| CCC06 | C4201T (Q1401*) | 100/914 (11) | 8/26 (31) | Positive | Heterozygous† | ||
| CCC09 | C5164T (R1722*) | 1132/1513 (75) | 30/30 (100) | Negative | Mutation with loss of heterozygosity | ||
| CCC10 | 3948delG‡ | 166/758 (22) | No coverage | Negative | Heterozygous† | ||
| CCC13 |  |
5541insG | 395/1518 (26) | 23/97 (24) | Negative | Heterozygous|| | CTNNB1 C110G (S37C) |
| CCC13 | T5953C (S1985P) | 339/1093 (31) | 25/60 (42) | Negative | Heterozygous|| | CTNNB1 C110G (S37C) | |
| CCC14 | C1680A (Y560*) | 1411/2651 (53) | 3/6 (50) | Negative | Heterozygous | ||
| CCC05 | None | Positive | KRAS G38A (G13D) | ||||
| CCC67 | None | Positive | |||||
| CCC68 | None | Positive | |||||
| CCC66 | None | Positive | |||||
| CCC69 | None | Positive | |||||
| CCC70 | None | Negative | |||||
| CCC71 | None | Positive | |||||
| CCC72 | None | Positive | |||||
| CCC73 | None | Positive | |||||
| TOV21G cell line | 1645insC‡ | 484/1821 (27) | 5/34 (15) | Negative | Heterozygous† | PIK3CA C3139T (H1047Y), KRAS G37T (G13C) | |
The mutations listed are nucleotide mutations, followed by amino acid mutations (if known) in parentheses, with a star indicating a stop codon. CTNNB1 denotes the catenin beta-1 gene, KRAS the v-Ki-ras2 Kirsten rat sarcoma viral oncogene homologue gene, and PIK3CA the phosphoinositide-3-kinase, catalytic, alpha polypeptide gene (Entrez Gene record numbers NM_001904.3, NM_004985.3, and NM_006218.2, respectively).
The percentage of reads containing a mutation in samples CCC01, CCC03, CCC06, and CCC10 and the TOV21G cell line suggests some form of allelic imbalance, with extra copies of the wild-type allele.
The ARID1A mutations in samples CCC02, CCC03, CCC10, and the TOV21G cell line were not initially identified or discovered through RNA sequencing.
For sample CCC02, no reads were available from the exon resequencing of exon 1, but Sanger sequencing showed a dominant peak from the mutation.
For sample CCC02, the predicted ARID1A status is based on microarray data (Affymetrix SNP 6.0).
For sample CCC13, the two somatic mutations in ARID1A can be found both in the trans configuration (on independent alleles) and in the cis configuration (on the same alleles). For details, see Figure 4 in the Supplementary Appendix.