Global genetic insight contributed by consanguineous Pakistani families segregating hearing loss

Abstract

Consanguineous Pakistani pedigrees segregating deafness have contributed decisively to the discovery of 31 of the 68 genes associated with nonsyndromic autosomal recessive hearing loss (HL) worldwide. In this study, we utilized genome-wide genotyping, Sanger and exome sequencing to identify 163 DNA variants in 41 previously reported HL genes segregating in 321 Pakistani families. Of these, 70 (42.9%) variants identified in 29 genes are novel. As expected from genetic studies of disorders segregating in consanguineous families, the majority of affected individuals (94.4%) are homozygous for HL-associated variants, with the other variants being compound heterozygotes. The five most common HL genes in the Pakistani population are SLC26A4, MYO7A, GJB2, CIB2 and HGF, respectively. Our study provides a profile of the genetic etiology of HL in Pakistani families, which will allow for the development of more efficient genetic diagnostic tools, aid in accurate genetic counseling, and guide application of future gene-based therapies. These findings are also valuable in interpreting pathogenicity of variants that are potentially associated with HL in individuals of all ancestries. The Pakistani population, and its infrastructure for studying human genetics, will continue to be valuable to gene discovery for HL and other inherited disorders.

Keywords: DFNB; Pakistan; allelic heterogeneity; autosomal recessive hearing loss; deafness; genetic spectrum; pathogenic variant.

Figure 1.. Overview of genetic studies of 321 Pakistani families segregating recessive hearing loss.

Each box has the number of families over the number of variants found in our study. Of 163 variants, 11 of these variants were identified in multiple families as either homozygous or compound heterozygous. In the bottom two rows, only the number of variants is indicated. MS: missense, NS: nonsense, FS: frameshift, SS: splice site.

Figure 2.. Pakistani families co-segregating autosomal recessive HL due to multiple homozygous variants.

Families HL007 and DEM4372 are examples in which there is intra-familial locus heterogeneity of variants in genes known to cause HL. Circles indicate females, squares indicate males. Black-filled symbols represent affected individuals. Double lines indicate consanguineous marriages. In family HL007, homozygous variants in two different genes TPRN and CDH23 co-segregate with HL. Affected individuals are homozygous for either the TPRN (V:6, VI:1, VI:2, VI:13) or the CDH23 variant (V:11, V:12), except for affected individual VII:3 who is double homozygous. In family DEM4372, variants in two different genes TMPRSS3 and OTOG co-segregate with HL in different branches of this family. Novel mutations from this study are in bold font.

Figure 3.. Consanguineous Pakistani families with compound heterozygous variants of reported HL genes.

Eight pedigrees segregating HL due to compound heterozygous variants in MYO7A (PKDF173, DEM4561, DEM4652, PKDF019), TMC1 (HL006, PKDF13B), MYO15A (PKDF1693) and TECTA (PKDF1452) genes. In family DEM4652, the normal hearing father III:2 is heterozygous for two different variants of MYO7A suggesting that the newly identified c.4505A>G variant might be non-pathogenic. Novel mutations from this study are in bold font.

Figure 4.. Distribution of variants in the five most prevalent genes associated with nonsyndromic recessively inherited HL in Pakistani families.

(A) Percentage of identified alleles by gene. (B) Percentage of variants by type and occurrence of identified variants. The percentages are based on the total number of variants identified in this study.

Figure 5.. A new variant of ADGRV1 associated with non-syndromic hearing loss in Pakistani family PKDF1551.

(A) Pedigree of family PKDF1551 segregating HL due to a missense mutation (c.1055C>T, p.(Pro352Leu)) in ADGRV1 (also referred to VLGR1, MIM# 602851, at the USH2C locus). The filled symbols represent affected individuals, and a double horizontal line connecting parents represents a consanguineous marriage. Half-filled symbol represents an individual with potential middle ear infection and/or carrying another variant responsible for his hearing impairment. Exome sequencing was performed on a DNA sample from individual VI:5. (B) Full-field electroretinograms of affected (VI:5, 17 years old) and non-affected individuals (VI:1, 22 years old) revealed no significant difference in a- and b-waves amplitudes among the two subjects, suggesting normal visual function. To show reproducibility, two responses (annotated 1 and 2, green and orange respectively) are superimposed per test and individual. The first crosshair indicates the a-wave while the second crosshair shows the b-wave. No differences in amplitude nor latency for waves a and b were detected in any of the performed tests.

Figure 6.. Distribution of variants in the Pakistani population from 62 studies on hearing loss.

(A) Percentage of identified variants by gene. (B) Distribution of the 10 most prevalent genes in our collaborative studies. The percentages are based on the total number of alleles identified in our collaborative studies.