GENETICS OF DEAFNESS

CONGENITAL DEAFNESS ~ 1 in 900 children has congenital hearing impairment >20 dB in one or more frequencies 50 % inherited 50% environmental Ototoxic drugs Acustic trauma Infections 70% Nonsyndromic 30% Syndromic Usher Alport Pendred Norrie Waardenburg Branchio-Oto-Renal Jervell and Lange-Nielsen ~%77 AR ~%77 AR ~%22 AD ~%22 AD ~%1 X-linked <%1 Mitochondrial Known Genes 29 6 18 6

WHY IS IT IMPORTANT TO ELUCIDATE GENETIC DEFECTS UNDERLYING HEREDITARY DISORDERS? Diagnosis To answer the question on heredity of their disease or the disease in the family Adequate mutation based genetic counseling Early diagnoses for family members Insight in genes/proteins essential for development and function of the inner ear Handles for therapy

DAILY PRACTICE

AUDIOGRAMS

ARTA

Myosin VIIa Asn458Ile

THE INNER EAR

LESSONS FROM DEAFNESS GENES Kazmierczak et al 2007

IDENTIFICATION OF DISEASE GENES Familystudies – good clinical characterization Identification of the chromosomal location of the genetic defect - Linkage analysis – homozygosity mapping Identification of the mutated gene - Which genes are in the linkage interval – genome browsers? - Which of those genes are good candidates? - databases * Expression pattern * Function of the gene * Animal models * Selection of genes for mutation analysis - Mutation analysis - Interpretation of sequence variants Alternative: Next Generation sequencing

TURKISH FAMILIES - CONSANGUINITY Homozygous mutations Homozygosity mapping – linkage analysis

mutation x  N M  N M  N M x  N M  N M M  M HOMOZYGOSITY MAPPING

Single Nucleotide Polymorphisms - SNPs Person A: Person B: …cctcctagggttgcaaagcctccttggctatg… …cctcctagggttgcatagcctccttggctatg… …cctcctagggttgcatagcctccttggctatg… ~ 500,000 SNPs G T A C

FAMILY TR57 Linkage interval: 11q13.2–q13.4, ~ 59 known genes , 18 hypothetical gene

DFNB63 LOCUS Fam TR57 26 known or predicted genes ~5.29 Mb DFNB63 15.5 Fam FT1A-G PKDF702 FT2 1.03 Mb 15.4 DFNA32 15.3 15.2 15.1 USH1C 14.3 14.2 D11S2371 D11S1337 D11S4179 D11S1291 D11S916 D11S1314 D11S4139 D11S4136 D11S4113 D11S987 14.1 13 26 known or predicted genes DFNB51 12 11.2 11.12 11.11 11 12.1 ~5.29 Mb 12.2 12.3 DFNB63 13.1 FGF3 13.2 13.3 DFNB63 13.4 13.5 MYO7A 14.1 14.2 14.3 21 22.1 22.2 22.3 23.1 DFNB24 23.2 23.3 TECTA 24.1 24.2 24.3 25 DFNB20

LRTOMT CHARACTERISATION Genome browser build 36.1 LRTOMT1 LRTOMT2

EFFECT OF MUTATIONS Catechol-O-methyltransferase domein 3’ UTR A215A G163VfsX4 (c.358+4G>A) 3’ UTR E110K A29SfsX54 (c.358+4G>A) W105R R81Q Catechol-O-methyltransferase domein

MOLECULAR MODELING

EFFECT OF MISSENSE MUTATIONS

LRTOMT IN THE MOUSE

INNER EAR

SUMMARY Applied bioinformatics is essential for several steps in disease gene identification and analyses The structure and function of the human genome and genes is not completely characterized yet LRTOMT is the causative gene for DFNB63. The precise effect of the mutations on inner ear function needs to be elucidated.