SUPPLEMENTAL FIGURES

Chromosomes 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

Supplemental Figure 1. Spatial view across all chromosomes (1-22) of all differentially methylated sites satisfying the criteria p=0.05 and a beta difference of ≥0.4

Supplemental Figure 2

A

B

C

Supplemental Figure 2. The genomic distribution/regional locationof CpG sites. 2A: pie chart of all CpG sites with a known/unknown position in relation to the CpG islands. 2B: All CpG sites with a known position in relation to a CpG island. 2C: the genomic distribution of all CpG sites in rekation to the gene structure. Of note sites may occupy different gene regions within the different transcripts covered.
SUPPLEMENTAL TABLES

SupplementalTable 1A.Clinical and molecular data for IGHV-mutated and IGHV-unmutated CLL patients included in the over time study.

Case / Age/
Sex / Rai/
Binet
Stage / Percent identity
% / IGHV gene
usage / Genomic alterations
at diagnosis / Treated
at
second sampling
(Follow-up)
First /second line / TTT
(months) / Survival
(months)
Mutated 1 / 52/F / 0/A / 94.17 / 4-59 / del(13q) / NO / 79 / 102
Mutated 2 / 68/F / 0/A / 94.98 / 4-34 / del(13q) / NO / 74, / 94
Mutated 3 / 60/F / 0/A / 88.14 / 1-3 / del(13q) / NO / 75 / 91
Mutated 4 / 60/M / 0/A / 93.86 / 4-34 / None / NO / 67 / 85
Mutated 5 / 67/M / I/A / 93.17 / 3-7 / None / NO / 68 / 84
Mutated 6 / 68 F / I/A / 93.96 / 3-72 / None / NO / 70 / 91
Mutated 7 / 66/F / 0/A / 96.25 / 4-34 / None / NO / 76 / 92
Mutated 8 / 64/M / 0/A / 92.51 / 3-33 / del(13q) / NO / 67 / 80
Mutated 9 / 58/M / I/A / 94.28 / 2-5 / del(13q) / NO / 89 / 104
Unmutated 1 / 47/ F / I/B / 100 / 3-74 / del(11q) del(13q) / Alk/Alk / 5 / 98
Unmutated 2 / 62/ F / 0/A / 99.55 / 1-2 / del(11q) / Alk/none / 10 / 91
Unmutated 3 / 67/F / 0/A / 100 / 1-24 / None / Alk+Ster/AB / 27 / 92
Unmutated 4 / 63/ F / 0/A / 100 / 1-69 / del(11q) / Alk/Alk / 51 / 91
Unmutated 5 / 58/ F / 0/A / 100 / 4-39 / T12 / CHOP/none / 11 / 93
Unmutated 6 / 57/M / III/A / 100 / 1-2 / del(11q) / Alk/Alk / 2 / 87
Unmutated 7 / 73/M / I/A / 100 / 1-69 / +12 / Alk/Alk / 45 / 90
Unmutated 8 / 65/F / I/B / 100 / 3-11 / +12 / Alk/none / 14 / 91
Unmutated 9 / 55/M / I/A / 100 / 1-69 / None / Alk/Alk+Ster+Anthr / 34 / 102

IGHV gene analysis:cases with ≥98% identity to germline were characterised as IGHV unmutated, cases with98% identity were considered IGHV mutated.

Known recurrent aberrations, del(13q), del(11q), del(17p) and Trisomy 12, were determined using SNP-array analysis or RQ-PCR (primers available on request).

TTT =time to treatment, Alk=alkylating agents, AB =antibody, Anthr=Anthracyclin, Ster=steroids and CHOP; =Cyclophosphamide+ Vincristine+doxorubicin+prednisolone.

Supplemental Table 1B.Clinical and molecular data for

patient-matched PB and LN compartment cases.

SampleID / Origin / Gender / Mutational status / Genomic
Alterations at diagnosis / Treated
at time of
sampling
Pair 1 / LN/PB / M / UM / None / No
Pair 2 / LN/PB / M / UM / del(11q) del(13q) / Yes
Pair 3 / LN/PB / M / ND / +12 / No
Pair 4 / LN/PB / M / MU / del(13q) / Yes
Pair 5 / LN/PB / M / MU / del(13q), del(17p) / No
Pair 6 / LN/PB / F / UM / None / No
Pair 7 / LN/PB / M / UM / del(11q) / No
Pair 8 / LN/PB / F / MU / del(13q)
del(17p) / No
Pair 9 / LN/PB / M / UM / del(11q) del(13q) / No
Pair 10 / LN/PB / M / UM / del(11q) / No

LN, lymph node, PB, peripheral blood, ND, not defined.

MU indicates IGHV mutated, UM indicates IGHV unmutated

Known recurrent aberrations, del(13q), del(11q), del(17p) and

trisomy 12, were determined using RQ-PCR.

Supplemental Table 2.Characterization of the selected differentially methylated genes listed in Table 2.


Supplemental Table 3. Characterization of the differentially methylated genes within the TGF-Β and TNF pathways

as listed in Table 3.