Table 1.
Variants detected in circulating tumor DNA.
| Gene | Amino Acid Variant | Variant Allele Frequency (%) | Total Depth | Chromosome & Position | [Variant] & Sequence Context | Molecular Tumor Board Discussion |
|---|---|---|---|---|---|---|
| ABL1 | M318T | 0.22 | 3,594 | chr9:133748292 | GTTCA[T>C]GACCT | Putative melanoma |
| KIT | W557G | 0.23 | 3,069 | chr4:55593603 | TACAG[T>G]GGAAG | Pathogenic / Melanoma |
| CCND1 | P220T | 0.24 | 3,321 | chr11:69462845 | GGAGC[C>A]CCAAC | Putative melanoma |
| SMO | T336A | 0.26 | 4,632 | chr7:128846076 | TCCTC[A>G]CCTAT | Putative melanoma |
| BRCA2 | H910R | 0.27 | 3,640 | chr13:32911221 | ACTTC[A>G]TGAAA | Putative melanoma |
| RAF1 | L546R | 0.27 | 3,673 | chr3:12626652 | AAGGA[A>C]GCTCC | Putative melanoma |
| MTOR | N2219fs*60 | 0.29 | 3,400 | chr1:11184560 | CTGAG[T>–]TTTTC | Pathogenic / Indel in homopolymer region / Confirmed melanoma |
| ATM | S214P | 0.32 | 2,820 | chr11:108114823 | TTTTT[T>C]CCAAG | Putative melanoma / Substitution in homopolymer region |
| ALK | N1095fs*14 | 0.36 | 4,448 | chr2:29446284 | TAGTT[G>–]GGGTT | Indel in homopolymer region |
| MDM2 | Y287H | 0.38 | 3,169 | chr12:69230470 | CTGTG[T>C]ATCAG | Pathogenic / Putative melanoma |
| NF1 | A1224V | 0.41 | 3,163 | chr17:29560194 | TATAG[C>T]GATGG | Pathogenic / Putative melanoma |
| CDK12 | R298* | 0.48 | 3,513 | chr17:37619216 | GTAGG[C>T]GACAG | Pathogenic / Putative melanoma |
| STK11 | F25L | 0.48 | 3,127 | chr19:1206985 | ACACG[T>C]TCATC | Putative melanoma |
| ERRFI1 | F115fs*6 | 0.50 | 2,999 | chr1:8074313 | TTCTT[A>–]AAACC | Pathogenic / Indel in homopolymer region / Putative melanoma |
| TP53 | G244C | 0.54 | 2,795 | chr17:7577551 | GCCGC[G>T]CATGC | Putative CHIP |
| MTOR | L1460P | 0.58 | 3,097 | chr1:11217299 | CCACA[A>C]GGGCA | Pathogenic / Putative melanoma |
| PTPN11 | V243A | 0.70 | 3,122 | chr12:112893839 | TAAAG[T>C]CAAAC | |
| BRCA1 | S1387P | 0.70 | 3,131 | chr17:41242987 | CTGAG[A>G]GGATA | |
| PDCD1LG2 | P186fs*14 | 1.71 | 4,155 | chr9:5549529 | CACCC[C>–]CTGGC | Indel in homopolymer region |
| EGFR | S1104A | 1.90 | 3,527 | chr7:55272987 | CTGGC[T>G]CTGTG | |
| BRCA2 | L929fs*31 | 13.43 | 3,261 | chr13:32911277 | TGGTT[T>–]TATAT | Pathogenic / Indel in homopolymer region |
| KRAS | Q61H | 17.41 | 2,837 | chr12:25380275 | TCCTC[T>A]TGACC | Pathogenic / Confirmed colon |
| APC | R302* | 17.46 | 3,952 | chr5:112151261 | CACCT[C>T]GAAGG | Pathogenic / Putative colon |
| APC | S393* | 18.21 | 4,294 | chr5:112154907 | TCACT[C>A]ACAGC | Pathogenic / Putative colon |
| ATM | K2465E | 18.49 | 3,662 | chr11:108201026 | TATGT[A>G]AAGCA | Putative colon |
| GNAS | R199H | 20.22 | 3,036 | chr20:57484415 | GCTTC[G>A]CTGCC | Putative colon |
| APC | T1556fs*3 | 22.00 | 4,169 | chr5:112175957 | AAAAA[–>A]CTATT | Pathogenic / Indel in homopolymer region / Putative colon |
| PTEN | K267fs*9 | 35.90 | 3,309 | chr10:89717774 | TAAAA[A>–]AGGTT | Pathogenic / Indel in homopolymer region / Putative colon |
Note: Variants described as pathogenic were reported on the front page of the Foundation One Liquid assay, Foundation Medicine (Cambridge, MA) report in genomic findings. Other listed variants were reported by Foundation Medicine as variants of unknown significance.
Abbreviations: CHIP, clonal hematopoiesis of indeterminate potential; MTB, molecular tumor board; Total Depth, total depth of sequencing reads.