Additional file 1: of KBG syndrome

Reported intragenic variants in the ANKRD11 gene. (XLSX 13 kb

Pedigree with haplotypes, audiograms and two identified variants.

<p>(A) The pedigree and the third longest autozygous region on chromosome 19 that co-segregates with the phenotype. (B) Audiograms of affected members in the family. (C) Electropherograms showing the wild type, homozygous and heterozygous forms of the variant p.T443M in <i>ZNF57</i>. (D) Electropherograms showing the wild type, homozygous and heterozygous form of the variant p.H170N in <i>GIPC3</i>.</p

Novel missense, nonsense, splice site, and frameshift variants in top five autozygous regions.

a<p>These variants were detected when filter for read depth was ≥8×.</p

Five autozygous regions detected with Affymetrix 6.0 arrays in the family.

<p>To define autozygous regions from the exome sequences (*) the following filters were applied to reduce the incident of false positives (phred-like consensus score ≥100 and a minimum read depth of 20).</p

The two-dimensional structure of <i>GIPC3</i> and the localization of identified mutations.

<p>The two-dimensional structure of <i>GIPC3</i> and the localization of identified mutations.</p

Coverage of autozygous regions with whole exome sequencing.

<p>(A) The exome coverage of the five longest autozygous regions. The plot shows the fraction of on-target coverage (Y-axis) and the read depth (X-axis) for the following specified regions. (B) Average coverage at minimum 8× and GC content of five autozygous regions. (C) Coverage of exon 3 in <i>GIPC3</i>. Red arrow indicates mutation point.</p

Molecular modeling of p.T443M in ZNF57.

<p>The zinc finger domain comprises two β-strands (blue) and one α-helix (red); the turns (green) and the loops (light gray) are shown. Amino-acid residue 443 is pink in the wild type (A) and yellow in the mutant (B).</p

Diagrams of structural models for GIPC3.

<p>The ribbon diagrams for the 3D models of the PDZ domain in GIPC3. The wild type (A) and the mutated p.H170N (B) forms are shown. The key for structural features follow; the α-helices (red); the β-strands (blue); the β-turns (green); the loops (light gray); the side-chain for H170 in the wild type (pink) and the side-chain for N170 highlights the mutation (yellow). The surface diagrams show the surface topology and the interpolated charge distribution of the PDZ domain of GIPC3. Both the wild type (C) and the mutated p.H170N protein (D) are provided. The p.H170N mutated form shows one of the substrate molecular recognition pockets as being deeper with a larger volume compared to the wild type. The p.H170N mutated form shows the interpolated charge distribution as being reduced compared with the wild type. Structural and local environment for position 170 with the H-bond patterns are shown. The GIPC3 wild type (E) shows an absence of side-chain to main-chain H-bonds with the H170 side-chain; whilst the asparagine side-chain (yellow) in the mutated protein (F) forms side-chain to main-chain H-bonds.</p

Comprehensive Analysis of Deafness Genes in Families with Autosomal Recessive Nonsyndromic Hearing Loss

<div><p>Comprehensive genetic testing has the potential to become the standard of care for individuals with hearing loss. In this study, we investigated the genetic etiology of autosomal recessive nonsyndromic hearing loss (ARNSHL) in a Turkish cohort including individuals with cochlear implant, who had a pedigree suggestive of an autosomal recessive inheritance. A workflow including prescreening of <i>GJB2</i> and a targeted next generation sequencing panel (Illumına TruSight^TM Exome) covering 2761 genes that we briefly called as mendelian exome sequencing was used. This panel includes 102 deafness genes and a number of genes causing Mendelian disorders. Using this approach, we identified causative variants in 21 of 29 families. Three different <i>GJB2</i> variants were present in seven families. Remaining 14 families had 15 different variants in other known NSHL genes (<i>MYO7A</i>, <i>MYO15A</i>, <i>MARVELD2</i>, <i>TMIE</i>, <i>DFNB31</i>, <i>LOXHD1</i>, <i>GPSM2</i>, <i>TMC1</i>, <i>USH1G</i>, <i>CDH23)</i>. Of these variants, eight are novel. Mutation detection rate of our workflow is 72.4%, confirming the usefulness of targeted sequencing approach in NSHL.</p></div

Pedigrees and Sanger sequencing electropherograms demonstrating mutations found in TNGS in the probands.

<p>Pedigrees and Sanger sequencing electropherograms demonstrating mutations found in TNGS in the probands.</p