Skip to main content
NCBI home page
NIHPA Author Manuscripts logoLink to NIHPA Author Manuscripts
. Author manuscript; available in PMC: 2009 Sep 21.
Published in final edited form as: Clin Genet. 2008 Mar 3;73(4):395–398. doi: 10.1111/j.1399-0004.2008.00976.x

Mapping of a new autosomal recessive non-syndromic hearing impairment locus (DFNB45) to chromosome 1q43-q44

A Bhatti a, K Lee b, M-L McDonald b, MJ Hassan a, R Gutala b, M Ansar a, W Ahmad a, SM Leal b
PMCID: PMC2747313  NIHMSID: NIHMS145366  PMID: 18325041

To the Editor

Hearing impairment (HI) is a common sensory disorder that exhibits extensive genetic heterogeneity. Approximately 60% of congenital HI cases can be attributed to genetic factors and approximately 75% are classified as non-syndromic (1, 2). In this letter, the mapping of a novel autosomal recessive locus for non-syndromic hearing impairment (NSHI) in a six-generational consanguineous Pakistani family, pedigree 4053 (Fig. 1), is reported. The study was initiated with the prior approval of the Institutional Review Boards of Quaid-i-Azam University and Baylor College of Medicine. Informed consent was obtained from all family members who participated in the study. All affected family members have pre-lingual pro-found HI and use sign language for communication. There was no evidence that the HI is syndromic or that there is gross vestibular involvement. The locus responsible for NSHI in this family was localized to chromosome 1q43-q44.

Fig. 1.

Fig. 1

Open in a new tab

Drawing of pedigree 4053. Black symbols represent individuals with hearing impairment and clear symbols represent unaffected individuals. Haplotypes are shown beneath each genotyped individual. The DFNB45 haplotype is highlighted in a box.

In order to carry out a whole genome scan, a total of 396 fluorescently labeled short tandem repeat (STR) markers spaced approximately every 10 cM were genotyped in 10 family members, of which four are hearing impaired. The marker allele frequencies were estimated using genotype data from founders and reconstructed founders from pedigree 4053 and 44 additional families from Pakistan. The occurrence of Mendelian errors and unlikely genotypes were assessed using PEDCHECK and MERLIN (3, 4) and none were uncovered. Linkage analysis was carried out under a fully penetrant autosomal recessive model with a disease allele frequency of 0.001. Two-point linkage analysis was performed with MLINK (5) and gave a maximum LOD score of 3.7 (θ = 0.04) at marker D1S547 (Table 1). Multipoint parametric linkage analysis was performed using ALLEGRO (6) and a maximum multipoint LOD score of 4.4 was obtained at marker D1S1609. In order to fine map DFNB45, 12 additional markers were genotyped; of these markers, six were uninformative (D1S321, D1S1634, D1S2842, D1S1590, D1S2679 and D1S102). Two-point and multi-point linkage analyses were carried out using equal allele frequencies for fine mapping markers because they were only genotyped in family 4053 and accurate allele frequencies could not be estimated for these marker loci. Additionally, in order to evaluate whether false positive results could have been obtained due to using equal and potentially incorrect allele frequencies, a sensitivity analysis (7) was conducted. For the sensitivity analysis, multipoint linkage analyses were carried out by setting the allele frequency for each fine mapping marker's allele that segregated with the hearing impairment phenotype to p and the other allele to 1–p. Multipoint linkage analyses were then carried out, varying p for each of the fine mapping markers between 0.2 and 0.8 in increments of 0.1. After analyzing the fine mapping markers, the maximum two-point LOD score remained at genome scan marker D1S547 (Table 1). Multipoint linkage analysis was repeated with the genome scan markers within the region, and the six fine mapping markers and a maximum multipoint LOD score of 5.2 was obtained at marker D1S404. For the sensitivity analysis, the highest and lowest maximum multi-point LOD scores of 5.3 and 5.0 were obtained when p = 0.2 and 0.8, respectively. These maximum multipoint LOD scores from the sensitivity analysis also occurred at marker D1S404. Haplotypes were reconstructed using SIMWALK2 (8, 9) (Fig. 1). The region that is only homozygous in HI family members spans a 15.3-cM region from markers D1S547 to D1S2836 and contains 5.1 Mb of the genome.

Table 1.

Two-point LOD score result of STR marker locia

Marker
name		 Physical map
position (bp)b 		Genetic map
position (cM)c 		Two-point LOD score at θ =
0.00 0.01 0.02 0.03 0.04 0.05 0.10 0.20 0.30
D1S235 233,960,377 261.73 −12.60 −4.50 −3.35 −2.70 −2.25 −1.90 −0.94 −0.23 −0.05
D1S1594 238,846,611 276.43 −2.11 −0.42 −0.16 −0.03 0.06 0.12 0.24 0.21 0.12
D1S304 239,355,103 278.08 1.57 1.53 1.48 1.44 1.39 1.35 1.13 0.74 0.40
D1S547 239,822,560 278.98 3.46 3.64 3.72 3.74 3.74 3.73 3.51 2.76 1.82
D1S404 241,101,798 283.40 1.83 1.78 1.72 1.67 1.61 1.56 1.30 0.82 0.42
D1S1609 242,132,608 284.63 3.14 3.06 2.97 2.89 2.80 2.72 2.30 1.50 0.81
D1S423 243,612,279 290.89 1.32 1.28 1.24 1.20 1.16 1.12 0.93 0.59 0.31
D1S2836 244,936,700 294.30 −inf −2.06 −1.50 −1.19 −0.98 −0.82 −0.41 −0.12 −0.03
D1S2215 245,668,734 295.09 −2.43 −0.36 −0.11 0.03 0.11 0.16 0.26 0.20 0.10
D1S2682 246,197,009 300.63 −8.86 −3.31 −2.46 −1.98 −1.65 −1.40 −0.71 −0.21 −0.05
Open in a new tab

STR, short tandem repeat.

a

Markers in italic flank the haplotype. Genome scan markers are displayed in bold.

b

NCBI Build 36.1 genome assembly (23).

c

The Rutgers Combined Linkage – Physical Map of The Human Genome (24).

Within the 5.1-Mb (10) region of the DFNB45 locus, there are 15 genes with known function. Three of these genes, CHML, OPN3 and MAP1LC3C, are excellent candidates for DFNB45 because of their function and/or expression and thus, were sequenced as previously described (11). The choroideremia-like gene (CHML: MIM 118825) encodes an extracellular matrix protein involved in cell adhesion and is also expressed as a transcript in zebrafish hair cells (12). CHML lies within intron 1 of the opsonin3 (OPN3: MIM 606695) gene (13) and this gene was also sequenced. The microtubule-associated protein 1 light chain 3 gamma (MAP1LC3C: MIM 609605) is expressed in zebrafish hair cells. These three genes were excluded as causative because sequencing revealed no potentially functional variants. It should be noted that as only the promoter and exonic regions of these genes were sequenced, it is conceivable one of these genes is involved in the etiology of HI and the functional variant lies outside the sequenced region.

Eight additional loci for NSHI map to chromo-some 1 (14-22). The region of homozygosity for DFNB45 overlaps with 2.7 Mb (23) of the physical region for the autosomal dominant NSHI locus DFNA34 (22) that maps between markers D1S102 (first base position 242,232,988) and D1S3739 (last base position 247,115,645). Marker D1S102 lies between markers D1S1609 and D1S423, while marker D1S3739 is telomeric to marker D1S2836 (Table 1). Identification of mutations in the causative gene(s) will determine whether or not DFNA34 and DFNB45 are due to the same gene.

In summary, a whole genome scan was carried out using DNA samples from a consanguineous six-generational Pakistani family with autosomal recessive NSHI. A maximum multipoint LOD score of 5.2 was obtained at marker D1S404. The region of homozygosity maps the novel locus DFNB45 to a 5.1-Mb region on chromosome 1q43-q44 between markers D1S1547 and D1S2836.

Acknowledgements

We wish to thank the family members for their invaluable participation and cooperation. This work was funded by Higher Education Commission (HEC), Government of Pakistan and the National Institutes of Health (NIH) – National Institute on Deafness and other Communication Disorders grant DC03594. Genotyping services were provided by the Center for Inherited Disease Research (CIDR). CIDR is fully funded through a federal contract from the NIH to The Johns Hopkins University, contract number N01-HG-65403.

Footnotes

Electronic database information

The URLs for data presented herein are as follows: University of California Santa Cruz Human Genome Project working draft, March 2006 human reference sequence (National Center for Biotechnology Information Build 36.1), http://genome.cse.ucsc.edu/ (physical positions of marker loci).

Rutgers Combined Linkage – Physical Map of the Human Genome, http://compgen.rutgers.edu/maps/index.shtml (genetic positions of the STR marker loci).

References

  • 1.Morton NE. Genetic epidemiology of hearing impairment. Ann N Y Acad Sci. 1991;630:16–31. doi: 10.1111/j.1749-6632.1991.tb19572.x. [DOI] [PubMed] [Google Scholar]
  • 2.Gorlin RJ, Toriello HV, Cohen MM. Hereditary hearing loss and its syndromes. Oxford University Press; New York, NY: 1994. p. xxiii, 457. (Oxford monographs on medical genetics, no. 28). [Google Scholar]
  • 3.O'Connell JR, Weeks DE. PedCheck: a program for identification of genotype incompatibilities in linkage analysis. Am J Hum Genet. 1998;63:259–266. doi: 10.1086/301904. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 4.Abecasis GR, Cherny SS, Cookson WO, Cardon LR. Merlin – rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet. 2002;30:97–101. doi: 10.1038/ng786. [DOI] [PubMed] [Google Scholar]
  • 5.Cottingham RW, Jr, Idury RM, Schaffer AA. Faster sequential genetic linkage computations. Am J Hum Genet. 1993;53:252–263. [PMC free article] [PubMed] [Google Scholar]
  • 6.Gudbjartsson DF, Jonasson K, Frigge ML, Kong A. Allegro, a new computer program for multipoint linkage analysis. Nat Genet. 2000;25:12–13. doi: 10.1038/75514. [DOI] [PubMed] [Google Scholar]
  • 7.Freimer NB, Sandkuijl LA, Blower SM. Incorrect specification of marker allele frequencies: effects on linkage analysis. Am J Hum Genet. 1993;52:1102–1110. [PMC free article] [PubMed] [Google Scholar]
  • 8.Weeks DE, Sobel E, O'Connell JR, Lange K. Computer programs for multilocus haplotyping of general pedigrees. Am J Hum Genet. 1995;56:1506–1507. [PMC free article] [PubMed] [Google Scholar]
  • 9.Sobel E, Lange K. Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker-sharing statistics. Am J Hum Genet. 1996;58:1323–1337. [PMC free article] [PubMed] [Google Scholar]
  • 10.Lander ES, Linton LM, Birren B, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409:860–921. doi: 10.1038/35057062. [DOI] [PubMed] [Google Scholar]
  • 11.Santos RL, Hassan MJ, Sikandar S, et al. DFNB68, a novel autosomal recessive non-syndromic hearing impairment locus at chromosomal region 19p13.2. Hum Genet. 2006;120:85–92. doi: 10.1007/s00439-006-0188-z. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 12.McDermott BM, Jr, Baucom JM, Hudspeth AJ. Analysis and functional evaluation of the hair-cell transcriptome. Proc Natl Acad Sci U S A. 2007;104:11820–11825. doi: 10.1073/pnas.0704476104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Halford S, Freedman MS, Bellingham J, et al. Characterization of a novel human opsin gene with wide tissue expression and identification of embedded and flanking genes on chromosome 1q43. Genomics. 2001;72:203–208. doi: 10.1006/geno.2001.6469. [DOI] [PubMed] [Google Scholar]
  • 14.Talebizadeh Z, Kenyon JB, Askew JW, Smith SD. A new locus for dominant progressive hearing loss DFNA37 mapped to chromosome 1p21. American Society of Human Genetics; Philadelphia, PA: 2000. [Google Scholar]
  • 15.Xia JH, Liu CY, Tang BS, et al. Mutations in the gene encoding gap junction protein beta-3 associated with autosomal dominant hearing impairment. Nat Genet. 1998;20:370–373. doi: 10.1038/3845. [DOI] [PubMed] [Google Scholar]
  • 16.Coucke PJ, Van Hauwe P, Kelley PM, et al. Mutations in the KCNQ4 gene are responsible for autosomal dominant deafness in four DFNA2 families. Hum Mol Genet. 1999;8:1321–1328. doi: 10.1093/hmg/8.7.1321. [DOI] [PubMed] [Google Scholar]
  • 17.Kubisch C, Schroeder BC, Friedrich T, et al. KCNQ4, a novel potassium channel expressed in sensory outer hair cells, is mutated in dominant deafness. Cell. 1999;96:437–446. doi: 10.1016/s0092-8674(00)80556-5. [DOI] [PubMed] [Google Scholar]
  • 18.Coucke P, Van Camp G, Djoyodiharjo B, et al. Linkage of autosomal dominant hearing loss to the short arm of chromosome 1 in two families. N Engl J Med. 1994;331:425–431. doi: 10.1056/NEJM199408183310702. [DOI] [PubMed] [Google Scholar]
  • 19.Masmoudi S, Tlili A, Majava M, et al. Mapping of a new autosomal recessive nonsyndromic hearing loss locus (DFNB32) to chromosome 1p13.3-22.1. Eur J Hum Genet. 2003;11:185–188. doi: 10.1038/sj.ejhg.5200934. [DOI] [PubMed] [Google Scholar]
  • 20.Fagerheim T, Nilssen O, Raeymaekers P, et al. Identification of a new locus for autosomal dominant non-syndromic hearing impairment (DFNA7) in a large Norwegian family. Hum Mol Genet. 1996;5:1187–1191. doi: 10.1093/hmg/5.8.1187. [DOI] [PubMed] [Google Scholar]
  • 21.Kurima K, Peters LM, Yang Y, et al. Dominant and recessive deafness caused by mutations of a novel gene, TMC1, required for cochlear hair-cell function. Nat Genet. 2002;30:277–284. doi: 10.1038/ng842. [DOI] [PubMed] [Google Scholar]
  • 22.Kurima K, Szymko Y, Rudy S, et al. Genetic map localization of DFNA34 and DFNA36, two autosomal dominant nonsyndromic deafness loci. American Society of Human Genetics; Philadelphia, PA: 2000. [Google Scholar]
  • 23.Kent WJ, Sugnet CW, Furey TS, et al. The human genome browser at UCSC. Genome Res. 2002;12:996–1006. doi: 10.1101/gr.229102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 24.Kong X, Murphy K, Raj T, et al. A combined linkage-physical map of the human genome. Am J Hum Genet. 2004;75:1143–1148. doi: 10.1086/426405. [DOI] [PMC free article] [PubMed] [Google Scholar]

RESOURCES