Table 2.
Clinical and molecular findings and large-scale genomic copy number changes detected by Affymetrix Genome-Wide Human SNP Array 6.0.
| Case | Sex | Site | Disease status | Genotypec | Copy number losses | Copy number gains |
|---|---|---|---|---|---|---|
| 18a, f | M | stomach | primary | KIT exon 11: p.P551_Q556delinsT | 1p36.12-34.3; 4pter-p16.1; 9; 14q; 15q; 22q12.1-qter | |
| 19a, f | F | other | recurrent | KIT exon 11: p.W567_V559delinsF | 1p; 4q12-q25; 9; 10, 12pter-p11.22; 15q; 19q12-qter; 21q22.2-qter; 22q | |
| 20a, f | F | stomach | primary | KIT exon 11: p.V560_I571del | 2q32.1-qter; 6q13-q21, 6q21-q25.3; 9; 14q; 15q; 21q11.2-q22.3; 22q | 2q24.3-q31.2; 5; 6pter-q13, 6q25.3-qter; 7; 8; 13q; 16p; 18; 19; 20 |
| 21a | M | stomach | primary | KIT exon 11: p.E554_K558del | 1pter-p34.3; 3pter-p14.1; 6p21.31-p21.1, 6p12.3-p12.1, 6q; 9; 10q; 14q; 21q; 22q | 1q; 3p14.1-qter; 5; 6p22.2-p21.31; 8; 10pter-p11.21; 12; 13q; 16p; 17; 19 |
| 22a, f | F | other | recurrent | KIT exon 11: p.K550_W557del | 2q12.1-q21.1; 5pter-p13.3; 9; 14q; 15q; 22q | |
| 23a, f | M | sm. int | primary | KIT exon 11: p.M552_Y553del | 1p; 6; 13q31.1-qter; 15q; 19pter-p13.12 | 8qe; 21q |
| 24a, f | M | other | recurrent | KIT exon 11:p.V560E | 1p; 2p; 11; 13q; 14q; 15q; 22q | |
| 25 | M | sm. int | recurrent | BRAF exon 15: p.V600E | 1p; 6q; 9p; 11q; 13q13.2-qter; 14q; 15q13.2-qter; 17q12-q21.32; 18; 19q13.12-qter; 22q11.21-q12.3, 22q13.1-qter | 1q; 4; 5; 6p; 7; 11p; 13q12.2-q13.3; 15q11.2-q13.1; 16; 17pe, 17q21.33-q24.3e, 17q25.1-qtere; 19pter-q13.12e; 21q |
| 26 | F | sm. int | recurrent | none identified | 1pter-p36.21, 1p36.13-p22.2, 1p21.3-pter; 4q; 6q; 9pter-p21.3, 9p21.3-p21.1d, 9p21.1-pcen; 10; 11q12.1-qter; 13q; 14q; 15q; 17pter-q12; 18; 19q12-q13.42; 22q | 1q; 2; 3; 4p; 5pter-p13.2e, 5p13.1-qter; 6p; 7pe, 7q; 8; 9qe; 11pter-p14.2e, 11p14.2-q12.1; 12; 16; 17q21.33-qter; 19pter-q12, 19q13.42-qter; 20p13e, 20p13-qter; 21q |
| 27b | F | stomach | recurrent | none identified | ||
| 28a | M | other | recurrent | none identified | ||
| 29a | F | stomach | recurrent | none identified | ||
| 30a, f | M | other | recurrent | none identified | ||
| 31a, f | F | stomach | primary | none identified | 16q |
a
Case from RTOG S0132/ACRIN 6665 clinical trial.
b
Pediatric case.
c
Nomenclature conforms to guidelines from the Human Genetic Variation Society (http://www.hgvs.org/mutnomen).
d
Homozygous deletion.
e
Portions with CN gain > 3.
f
Tumor specimens were obtained following 8–12 weeks neo-adjuvant IM therapy.