Characteristics of the patients and samples included in the study.

<p>(A) Three patients were included in the analysis: pt1 and pt2 displaying a pattern of direct evolution and pt3 of evolution through a CPC based on HH analysis. Biopsies were collected at different time points: at relapse/transformation (pt1 and pt2) and after a watch wait period (pt3). In pt 1 two additional biopsies (AD1548 and 1787) analyzed only on the SNP array are shown. In pt1 all samples had an identical MC whilst in pt2 the MC sequences from samples R1655 FL1 and R3878 FL2 showed 2 different dominant clones carrying 3 discriminating mutations (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134833#pone.0134833.s007" target="_blank">S7 Fig</a>). Because these 3 bases also differ from the germline sequence a pattern of direct evolution could not be excluded. (B) Twenty-two samples, from 4 flow-sorted sub-populations, included in the deep sequencing study: pre-germinal center (PGC) (IgD+CD38+) white circles, the germinal center centroblasts (CB) (IgD+CD38+CD10+CXCR4+) and centrocytes, (CC) (IgD+CD38+CD10+CXCR4-) light grey circles and memory enriched (ME) (IgD-CD38-) dark grey circles. The 2 CC CD77- sorted sub-population from R0012 t-FL and R1381 FL1 biopsies, which were part of the deep sequencing study but not included in the final analysis are not shown. The FL sequences are depicted as white circles, the t-FL clones as grey circles, the germline sequence as black circles and the putative CPC sequence as a dashed grey circle. The 2 samples not included in the deep sequencing of IgH-VH gene are depicted as dotted circles. Each vertical arrow represents a line of therapy; the left hand vertical bar shows the time of diagnosis and the right hand vertical bar the time of death. FL = Follicular Lymphoma; t-FL = transformed Follicular Lymphoma; WW = watch and wait.