Linkage mapping to chromosome 12 in a kindred with ALL and DLBCL. (A) A 5-generation kindred with 10 individuals with leukemia, DLBCL, aplastic anemia, and/or thrombocytopenia. Black crosses indicate samples subjected to WGS, and red crosses indicate samples subjected to WES. Squares and circles represent male and females, respectively. All family members with ALL or DLBCL sequenced harbored the ETV6 deletion. Individuals III.3 and III.4 (DLBCL) both had thrombocytopenia and the deletion; IV.3 and III.2 had normal platelet counts and no ETV6 deletion. (B) Multipoint linkage results highlighting region with a logarithm of the odds (LOD) score of 1.8. (C) Representative reads showing the exon 7 splice site deletion identified by WGS SV analysis (NM_001987.4:G.11885871_11885946del;NM_001987.4:c.1153-55_1173del). (D) RNA-sequencing coverage analysis showing reduced sequence depth at exon 7. (E) Protein truncation resulting from exon skipping. (F) Schematic representation of the ETV6 protein, including the sterile α motif (SAM)/pointed domain of Tel/Yan protein, the polypeptide -binding domain, and the erythroblast transformation-specific domain (ETS). The top pair of electropherograms is from genomic PCR and Sanger sequencing and compares wild-type (WT) and deleted (75-bp) ETV6. Dotted line in the ETV6 cartoon represents exon junctions. The lower electropherogram is from RT-PCR and Sanger sequencing and shows the skipping of exon 7 and splicing of exon 6 to exon 8 in tumor RNA. (G) Results from fragment size analysis showing amplification of both WT and deleted ETV6 alleles.