Suzanne de Bruijn

245 Exploring the missing heritability in subjects with hearing loss and EVA shared haplotype even more (0.57 Mb, CEVA SNP 3-D7S2459). The remaining eight individuals with the complete CEVA haplotype share identical marker alleles in the 0.89 Mb-sized region, although they could not be conclusively assigned to the haplotype as no segregation analysis could be performed. For individual SLC003, a deviating repeat length was identified for marker D7S2420. As we cannot exclude a rare event to be responsible for the change in allele length, this marker was still considered part of the shared CEVA haplotype. Mb SLC003 SLC012 SLC013 SLC031 SLC036 SLC039 SLC040* SLC056 SLC071* SLC078 SLC079 SLC080 (1) 5 (1) (4) (1) 5 1 7 1 4 1 3 (7) (7) (1) (4) (1) 5 3 (7) (1) (4) (1) 5 1 7 1 4 1 5 (5) (7) (1) (4) (1) (5) 7 7 1 4 1 4 (7) 7 (1) (4) (1) 4 7 7 1 4 1 5 7 (7) (1) (4) (1) (5) (7) (7) (1) (4) (1) (3) (7) (7) (1) (4) (1) (5) 106.44 106.89 106.99 107.15 107.24 107.33 Marker D7S501 D7S2420 SNP8 D7S496 SNP11 D7S2459 A B PIK3CG PRKAR2B HBP1 COG5 DUS4L BCAP29 SLC26A4 SNP1 SNP2 SNP3 SNP4 SNP5 SNP6 SNP7 SNP8 SNP9 SNP10 SNP11 SNP12 SHARED CEVA HAPLOTYPE D7S501 D7S2459 GPR22 SLC26A4-AS1 SNP3 SNP8 SNP11 D7S2420 D7S496 Figure 2. Determination of the boundaries of the shared CEVA haplotype. (A) The CEVA haplotype was detected in 10 individuals, in an additional 2 individuals (SLC040 and SLC071, indicated with *), a smaller haplotype was found, termed V1-CEVA. To determine the boundaries of the CEVA haplotype, VNTR marker analysis was performed. The shared haplotype (0.89 Mb, CEVA; 0.57 Mb V1-CEVA is marked in orange. For marker D7S2420 (light-orange) a deviating CA-repeat length was determined in SLC003. Nevertheless, the marker is still considered to be potentially part of the shared haplotype as a change or repeat length cannot be excluded. Genomic positions (Mb) are according to the UCSC Genome Browser (GRCh37/hg19). (B) A schematic overview of the identified shared CEVA haplotype (D7S501-D7S2459). Positions of the CEVA-associated SNPs and the genes located within the haplotype region (CEVA, D7S501-D7S2459; V1-CEVA, SNP3-D7S2459) have been indicated. All SNPs are located within intronic or intergenic regions. Genomic positions of the CEVA-associated SNPs are provided in Table S7 . SLC26A4 (NM_000441.1) is only partially included (exons 10/21) in the shared haplotype. Short-read WGS did not reveal a pathogenic defect on the CEVA haplotype Because of the significant enrichment of the CEVA haplotype in M1 cases, we hypothesized that the subjects with the CEVA haplotype share a yet elusive pathogenic defect. To identify this defect on the CEVA haplotype, short-read WGS was performed in two individuals (SLC012 & SLC036) carrying the CEVA haplotype in trans with a