Background
Methods
Sample preparation
Sequencing (WES and WTS)
Detection of somatic SNVs and indels
Copy number analysis
Detection of fusion genes using WES and WTS
Sanger sequencing validation
Results
Clinical and pathological findings
Histological and immunohistochemical (IHC) findings
Somatic mutations
Sequence | Allele frequency | ||||||
---|---|---|---|---|---|---|---|
Gene | Chr | Position | Ref | Var | Coding change | WES | WTS |
APH1A | chr1 | 150,239,812 | A | T | p.L142H | 41/133 (30.83%) | 161/630 (25.56%) |
RNASEL | chr1 | 182,554,694 | G | C | p.H416Q | 21/151 (13.91%) | 2/15 (13.33%) |
GPR124 | chr8 | 37,695,290 | T | A | p.S698T | 26/74 (35.14%) | 0/35 (0%) |
WDR87 | chr19 | 38,384,338 | G | C | p.L669V | 33/177 (18.64%) | 0/0 (0%) |
ZBTB34 | chr9 | 129,642,990 | G | A | p.G434R | 37/160 (23.12%) | 0/0 (0%) |
PEG10 | chr7 | 94,293,260 | G | A | p.R207H | 37/193 (19.17%) | 0/2 (0%) |
TNFSF15 | chr9 | 117,552,937 | A | G | p.V184A | 17/112 (15.18%) | 2/2 (100%) |
NOL6 | chr9 | 33,464,880 | T | A | p.T926S | 16/89 (17.98%) | 20/208 (9.61%) |
ONECUT1 | chr15 | 53,082,000 | G | T | p.L28M | 21/47 (44.68%) | 0/0 (0%) |
CASKIN1 | chr16 | 2,229,210 | A | T | p.S1298T | 4/15 (26.67%) | 0/4 (0%) |
A3GALT2 | chr1 | 33,772,594 | G | A | p.R266C | 7/36 (19.44%) | 0/0 (0%) |
TENM3 | chr4 | 183,721,259 | C | T | p.R2619C | 17/61 (27.87%) | 1/3 (33.33%) |
GZF1 | chr20 | 23,346,065 | C | T | p.R349C | 21/102 (20.59%) | 2/9 (22.22%) |
MAFA | chr8 | 144,512,176 | G | A | p.T134M | 11/44 (25%) | 0/3 (0%) |
TP53 | chr17 | 7,578,403 | C | A | p.C176F | 51/91 (57.14%) | 44/84 (52.38%) |
TGFB2 | chr1 | 218,607,460 | C | T | p.R211C | 10/64 (15.62%) | 0/2 (0%) |
SEL1L2 | chr20 | 13,856,683 | C | T | splice donor variant | 30/120 (25%) | 0/0 (0%) |
SPTA1 | chr1 | 158,627,313 | G | C | p.P920R | 27/99 (27.27%) | 0/0 (0%) |
FAT1 | chr4 | 187,527,274 | T | +GACATC | nonframeshift | 14/51 (27.45%) | 0/0(0%) |
FAT1 | chr4 | 187,527,282 | G | A | p.S3431F | 14/51 (27.45%) | 0/0(0%) |