Table 1 Genomic aberrations and their proportions detected by the LYNX NGS panel in various biological materials from a patient with aggressive B-cell lymphoma with CNS involvement during disease. Gene mutation descriptions correspond to MANE (matched annotation from NCBI and EBI) transcripts
Biological material | Â | Â | Â | Bone marrow (DNA) | CSF (cfDNA) | CSF pellet (DNA) | Plasma (cfDNA) |
|---|---|---|---|---|---|---|---|
Gene mutations | Gene | HGVSc | HGVSp | Frequency (%) | Frequency (%) | Frequency (%) | Frequency (%) |
| Â | KMT2D | c.8936_8937del | p.Leu2979ArgfsTer10 | 21.7 | 32.7 | 29.8 | ND |
|  | KMT2D | c.7900 C > T | p.Gln2634Ter | 49.1 | 63.3 | 64.4 | ND |
|  | BTG1 | c.428T > A | p.Val143Glu | 34.5 | 48.5 | 44.7 | ND |
|  | BTG1 | c.425T > G | p.Met142Arg | 34.9 | 47.2 | 45 | ND |
|  | BTG1 | c.362T > C | p.Ile121Thr | 32.9 | 47.2 | 46.3 | ND |
| Â | BTG1 | c.90dup | p.Leu31AlafsTer23 | 34.9 | 38.2 | 43.8 | ND |
|  | BTG1 | c.85 A > C | p.Lys29Gln | 34.6 | 34.3 | 43.4 | ND |
| Â | CREBBP | c.2177_2184del | p.Pro726LeufsTer103 | 23.2 | 45.8 | 39.6 | ND |
|  | BCL2 | c.392 C > T | p.Ala131Val | 27.3 | 36.1 | 44 | ND |
|  | BCL2 | c.338 C > T | p.Ala113Val | 29.5 | 38.3 | 44.8 | ND |
|  | BCL2 | c.323 A > G | p.Tyr108Cys | 29 | 47.6 | 46 | ND |
|  | BCL2 | c.179 C > T | p.Ala60Val | 32.4 | 37.4 | 51.1 | ND |
|  | BCL2 | c.97G > A | p.Gly33Arg | 28.8 | 34 | 42.3 | ND |
|  | BCL2 | c.13G > C | p.Gly5Arg | 19.5 | 39.8 | 40.3 | ND |
|  | ASXL1 | c.1534 C > T | p.Gln512Ter | 6.3 | 3.6 | 2.3 | 32.1 |
|  | EP300 | c.3610T > G | p.Cys1204Gly | 33 | 47.3 | 43.6 | ND |
Translocation | Gene partners | Coordinate | Coordinate partner | Frequency (%) | Frequency (%) | Frequency (%) | Frequency (%) |
| Â | IGH/BCL2 | 14:105,863,241 | 18:63,120,802 | 63 | 100 | 96 | ND |
Copy number alterations | Genome localization (hg38) | Type | Affected genes (included in LYNX) | Frequency (%) | Frequency (%) | Frequency (%) | Frequency (%) |
|  | chr2:58183800–68,149,300 | gain | XPO1 | 70 | 100 | 100 | ND |
| Â | chr8:4617400-145005800 | gain | PAG1, UBR5, MYC | 70 | 80 | 100 | ND |
|  | chr12:38525800–73,670,100 | gain | KMT2D, STAT6 | 80 | 90 | 100 | ND |
| Â | chr1:0-49650114 | CN-LOH | TNFRSF14, ID3 | 70 | 100 | 100 | ND |
|  | chr9:21726012–22,249,845 | biallelic loss | CDKN2A, CDKN2B | 80 | 100 | 100 | ND |
|  | chr13:47033917–48,010,829 | loss | - | 30 | 80 | 70 | ND |
IG rearrangements | Locus | V gene | J gene | Frequency (%) | Frequency (%) | Frequency (%) | Frequency (%) |
inactivating | IGK | IGKV2-26 | - (KDE element) | 97 | 91 | 93 | ND |
productive | IGK | IGKV1-5 | IGKJ4 | ND | 100 | 98 | ND |
unproductive | IGL | IGLV3-22 | IGLJ3 | 72 | 46 | 48 | ND |