Shared haplotype extraction pipeline. The shared haplotype (SH) extraction workflow comprised six stages. Stage 1: the genotype calls were produced using the Illumina SNP bead arrays and transformed into data matrices. Stage 2: the haplotypes were estimated for the cases with Merlin by using the family information, and for the population controls by using the HaploRec software. Stage 3: all SHs were extracted from cases and controls. Stage 4: SHs were filtered to exclude SHs shared by at least four heterozygous or one homozygous control. Stage 5: pre-filtered SHs were then filtered further in six parallel analyses with thresholds that discover SHs present in at least five lymphoma cases. Stage 6: the ten highest scoring hits more than 30 markers long were combined from each filtering in stage 5.