This type of lymphoma is pretty rare and also not much is known about it.
Approach: 10 paired genomes plus 20 unpaired
For normal they used CD19 depleted PBMCs and also took buccal cells as a backup.
They actually did do exome sequencing as well.
They found a large number of strong candidates (>7?)... one was present in 100% of the 10 paired and 87% (26/30) in all 30 patiants. Strangely, it was the same exact SNP in all individuals, but it's a very good functional candidate.
Interestingly, with Sanger sequencing they saw a very small peak of the same variant in the trace from an individual with a very weak case (one of the four that didn't have it). Perhaps all patients with it have this variant?
Detailed circos plots. Mapped out zygosity, CN, allele balance, CGI coverage levels and then testing results. At this detailed level, there were many notable CN/zygosity regions and UPD regions. (Everyone LOVES Circos.)
They made their own wrapper for Annovar because the input/output for Annovar is something the "don't like". (Hey, guess what? You're not alone! I made just such a wrapper myself!)
Nice talk. I loved the Circos. Again, I have to ask whether a lot of these findings couldn't have been done solely through exome-seq, though...