| Popis: |
Tumor somatic alterations defined by targeted capture sequencing. (A)Using this capture probe panel, we obtained an average of 8,121,723 sequencing reads per tumor (range: 3,068,132 - 13,084,648), which corresponded to a minimum coverage of >1000x per base targeted in all samples as detailed in Supplemental Table 1. Somatic alteration analysis identified an average of 4.1 mutations and INDELs per tumor (range 0 - 28, of 226 genes tested)). As shown in the oncoplot, while several commonly altered HNSCC genes were identified, we also observed several interesting mutations in DNA damage repair proteins, including three mutations in ATM (R2419G, G1023E and a splice region alteration), ATRX (L532F), BRCA1 (stopgain) and BRCA2 (frameshift alteration). Four of 5 patients harboring these mutations experienced tumor progression. (B) The level of microhomology (in bp) at the breakpoint is numerically depicted. Number of overlapping nucleotides between HPV and host (indicating microhomology) are indicated as positive numbers, 0 indicates a clean break between HPV and host with no overlapping or inserted sequence, and negative numbers indicate the number of inserted base pairs between the HPV and host genome. |
