Table 1.
Overview of the genes covered by the CLL panels.
Fig 1.
Algorithm of variant analysis.
A) Variants with an allelic frequency below 5% were discarded, resulting in 4,396 variants. B) Only the 3,322 non-synonymous variants were used for further analysis. The variant count per gene is represented in the bar chart. C) Variants located in areas of high background noise and/or in homopolymeric regions, and single strand variants were visually identified in the Integrative Genomic Viewer (IGV, Broad Institute) and removed. In doubtful cases, Sanger sequencing was performed to prove or disprove an alteration. Furthermore variants without functional impact on the protein determined by at least two of four applied program algorithms as described in material and method were removed. This resulted in 102 final mutations in 60 CLL specimens.
Table 2.
Patient characteristics.
Fig 2.
Alteration type, number of occurrence and location of detected mutations in TP53, SF3B1, NOTCH1 and ATM are shown.
TP53: AD activation domain (amino acid 1–50); PD proline-rich domain (amino acid 63–97); TD tetramerization domain (amino acid 323–356); ND negative regulation domain (amino acid 363–393); SF3B1: The majority of SF3B1 alterations were clustered in the region encoding the highly conserved HEAT (huntingtin, elongation factor 3, protein phosphatase 2A, target of rapamycin 1) repeats 5–8. Only one alteration occurred in the N-terminal (amino acids 1–450), domain, which is an important docking or binding domain for numerous splicing factor partners like U2AF1/2, and cyclin E. NOTCH1: (EGF)-like epidermal growth factor repeats (amino acid 20–1426), LNR Lin-12 NOTCH repeats (amino acid 1449–1571), HD-N/C heterodimerization domain (N-terminus; C-terminus), RAM RAM domain, ANK ankyrin repeat domain (amino acid 1927–2089); PEST Pro-Glu-Ser-Thr motif for degradation (amino acid 2507–2526); ATM: FAT FRAP-ATM-TRRAP (amino acid 1960–2566), KD protein kinase domain (amino acid 2712–2962), PRD PIKK-regulatory domain (amino acid 2961–3025), FATC FAT-c-term domain (amino acid 3024–3056); aa amino acid
Fig 3.
Genetic profile of 60 CLL samples carrying gene mutations determined by NGS.
Each row represents the variants of one patient, each column summarizes the mutations occurring in one specific gene. Per each gene the number of mutations is given per patient. Dark blue samples indicate patients with aberration on chromosome 11 (del11q) for ATM mutated cases or on chromosome 17 (del17p) for TP53 mutated cases, determined by FISH.
Table 3.
Statistical correlations between gene mutation status and clinical and biological parameters.