Fig. 2

TIPseq in primary glioblastoma GBM oncosphere lines and corresponding blood samples. a. TIPseq data. (Leftmost panel) The schematic depicts a minus (-) strand L1 as a leftward facing orange arrow. The LINE-1 sequence ends with a 3′ polyA tail, shown as a homopolymer of thymine (T) on the complementary strand. The gray right triangle illustrates the shape of sequencing reads piling up (vertically, downward) when mapped against in the reference genome (i.e., with genome coordinates depicted on the horizontal axis). (Central panel) TIPseq read alignments corresponding to an insertion detected in blood and not the patient’s oncosphere cell line. The insertion is in an intron of the NPAS3 gene (14q13.1). Read depth is illustrated on the top (gray) and individual reads are represented as blue and red bars denoting orientation. (Rightmost panel) An agarose gel electrophoresis of a validation PCR. The open arrowhead (lower) marks the pre-insertion allele and the solid arrowhead (upper) marks the amplicon spanning the LINE-1 insertion. The insertion is detected in the blood (B) sample for this patient and not the corresponding tumor cells (C). The LINE-1 is 5.4 kb. b. Copy number and loss of heterozygosity (LOH) studies on the oncosphere cell lines. Results for chromosomes 8, 11 and 14 are shown in Circos plots. The seven samples are each depicted as two circular tracks of data. The blue track indicates copy number; medium blue is diploid, darker blue shows amplifications, and lighter blue shows deletions. The orange track highlights regions with LOH. (Leftmost circle) Two insertions on chromosome 8 are marked with arrowheads at 25 and 120 MB; both were identified in a blood sample and not the corresponding patient’s oncosphere cell line, which showed a copy neutral LOH of the entire chromosome (847). (Central circle) Three LINE-1 insertions on chromosome 11 found in blood only are marked; two are the same insertion at 33.6 MB found in two different patient samples (847, 922). Both tumor cell lines had deletions with copy number decreases and LOH at this site. One of these cases (847) also had loss of material near 94.3 MB associated with deletion of a second LINE-1. (Rightmost circle) Two LINE-1 are marked with arrowheads at 30.2 and 33.2 MB on acrocentric chromosome 14. These were found in genomic DNA from blood, but were lost owing to LOH in the corresponding oncosphere lines (897, 772)