Congenital non-syndromal autosomal recessive deafness in Bengkala, an isolated Balinese village

The historical demography of the Martha's Vineyard signing community

The deaf population of Martha's Vineyard has fascinated scholars for more than a century since Alexander Graham Bell's research on the frequent occurrence of deafness there and since Groce's book on the island's signing community (Groce, N. E. (1985). Everyone here spoke sign language: Hereditary deafness on Martha's Vineyard. Cambridge, MA: Harvard University Press.). In Groce's work, and in that of subsequent scholars, the Vineyard signing community has often been portrayed as remote and outlying, having developed independently of mainland signing communities for roughly 133 years until 1825. We re-examine that interpretation in light of historical, demographic, and genealogical evidence covering the period 1692-2008. We argue that the Vineyard signing community began in Chilmark in 1785, 93 years later than previously thought, and that it had had a brief period of independent development, roughly 40 years, before becoming well connected, through deaf education, to the nascent New England signing community. We consider the implications of the Vineyard community's history for our understanding of how village signing communities develop.

Development of sign phonology in Kata Kolok

Much like early speech, early signing is characterised by modifications. Sign language phonology has been analysed on the feature level since the 1980s, yet acquisition studies predominately examine handshape, location, and movement. This study is the first to analyse the acquisition of phonology in the sign language of a Balinese village with a vibrant signing community and applies the same feature analysis to adult and child data. We analyse longitudinal data of four deaf children from the Kata Kolok Child Signing Corpus. The form comparison of child productions and adult targets yields three main findings: i) handshape modifications are most frequent, echoing cross-linguistic patterns; ii) modification rates of other features differ from previous studies, possibly due to differences in methodology or KK's phonology; iii) co-occurrence of modifications within a sign suggest feature interdependencies. We argue that nuanced approaches to child signing are necessary to understand the complexity of early signing.

Emergence or Grammaticalization? The Case of Negation in Kata Kolok

Typological comparisons have revealed that signers can use manual elements and/or a non-manual marker to express standard negation, but little is known about how such systematic marking emerges from its gestural counterparts as a new sign language arises. We analyzed 1.73 h of spontaneous language data, featuring six deaf native signers from generations III-V of the sign language isolate Kata Kolok (Bali). These data show that Kata Kolok cannot be classified as a manual dominant or non-manual dominant sign language since both the manual negative sign and a side-to-side headshake are used extensively. Moreover, the intergenerational comparisons indicate a considerable increase in the use of headshake spreading for generation V which is unlikely to have resulted from contact with Indonesian Sign Language varieties. We also attest a specialized negative existential marker, namely, tongue protrusion, which does not appear in co-speech gesture in the surrounding community. We conclude that Kata Kolok is uniquely placed in the typological landscape of sign language negation, and that grammaticalization theory is essential to a deeper understanding of the emergence of grammatical structure from gesture.

Identification of Novel Candidate Genes and Variants for Hearing Loss and Temporal Bone Anomalies

Background: Hearing loss remains an important global health problem that is potentially addressed through early identification of a genetic etiology, which helps to predict outcomes of hearing rehabilitation such as cochlear implantation and also to mitigate the long-term effects of comorbidities. The identification of variants for hearing loss and detailed descriptions of clinical phenotypes in patients from various populations are needed to improve the utility of clinical genetic screening for hearing loss. Methods: Clinical and exome data from 15 children with hearing loss were reviewed. Standard tools for annotating variants were used and rare, putatively deleterious variants were selected from the exome data. Results: In 15 children, 21 rare damaging variants in 17 genes were identified, including: 14 known hearing loss or neurodevelopmental genes, 11 of which had novel variants; and three candidate genes IST1, CBLN3 and GDPD5, two of which were identified in children with both hearing loss and enlarged vestibular aqueducts. Patients with variants within IST1 and MYO18B had poorer outcomes after cochlear implantation. Conclusion: Our findings highlight the importance of identifying novel variants and genes in ethnic groups that are understudied for hearing loss.

A novel nonsense mutation in MYO15A is associated with non-syndromic hearing loss: a case report

Background

Hearing loss is genetically heterogeneous and is one of the most common human defects. Here we screened the underlying mutations that caused autosomal recessive non-syndromic hearing loss in a Chinese family.

Case presentation

The proband with profound hearing loss had received audiometric assessments. We performed target region capture and next generation sequencing of 127 known deafness-related genes because the individual tested negative for hotspot variants in the GJB2, GJB3, SLC26A4, and MTRNR1 genes. We identified a novel c.6892C > T (p.R2298*) nonsense mutation and a c.10251_10253delCTT (p.F3420del) deletion in MYO15A. Sanger sequencing confirmed that both mutations were co-segregated with hearing loss in this family and were absent in 200 ethnically matched controls. Bioinformatics analysis and protein modeling indicated the deleterious effects of both mutations. The p.R2298* mutation leads to a truncated protein and a loss of the functional domains.

Conclusions

Our results demonstrated that the hearing loss in this case was caused by novel, compound heterozygous mutations in MYO15A. The p.R2298* mutation in MYO15A was reported for the first time, which has implications for genetic counseling and provides insight into the functional roles of MYO15A mutations.

Electronic supplementary material

The online version of this article (10.1186/s12881-018-0657-y) contains supplementary material, which is available to authorized users.

Mutational Spectrum of MYO15A and the Molecular Mechanisms of DFNB3 Human Deafness

Deafness in humans is a common neurosensory disorder and is genetically heterogeneous. Across diverse ethnic groups, mutations of MYO15A at the DFNB3 locus appear to be the third or fourth most common cause of autosomal-recessive, nonsyndromic deafness. In 49 of the 67 exons of MYO15A, there are currently 192 recessive mutations identified, including 14 novel mutations reported here. These mutations are distributed uniformly across MYO15A with one enigmatic exception; the alternatively spliced giant exon 2, encoding 1,233 residues, has 17 truncating mutations but no convincing deafness-causing missense mutations. MYO15A encodes three distinct isoform classes, one of which is 395 kDa (3,530 residues), the largest member of the myosin superfamily of molecular motors. Studies of Myo15 mouse models that recapitulate DFNB3 revealed two different pathogenic mechanisms of hearing loss. In the inner ear, myosin 15 is necessary both for the development and the long-term maintenance of stereocilia, mechanosensory sound-transducing organelles that extend from the apical surface of hair cells. The goal of this Mutation Update is to provide a comprehensive review of mutations and functions of MYO15A.

Small Traditional Human Communities Sustain Genomic Diversity over Microgeographic Scales despite Linguistic Isolation

At least since the Neolithic, humans have largely lived in networks of small, traditional communities. Often socially isolated, these groups evolved distinct languages and cultures over microgeographic scales of just tens of kilometers. Population genetic theory tells us that genetic drift should act quickly in such isolated groups, thus raising the question: do networks of small human communities maintain levels of genetic diversity over microgeographic scales? This question can no longer be asked in most parts of the world, which have been heavily impacted by historical events that make traditional society structures the exception. However, such studies remain possible in parts of Island Southeast Asia and Oceania, where traditional ways of life are still practiced. We captured genome-wide genetic data, together with linguistic records, for a case–study system—eight villages distributed across Sumba, a small, remote island in eastern Indonesia. More than 4,000 years after these communities were established during the Neolithic period, most speak different languages and can be distinguished genetically. Yet their nuclear diversity is not reduced, instead being comparable to other, even much larger, regional groups. Modeling reveals a separation of time scales: while languages and culture can evolve quickly, creating social barriers, sporadic migration averaged over many generations is sufficient to keep villages linked genetically. This loosely-connected network structure, once the global norm and still extant on Sumba today, provides a living proxy to explore fine-scale genome dynamics in the sort of small traditional communities within which the most recent episodes of human evolution occurred.

Relaxed Observance of Traditional Marriage Rules Allows Social Connectivity without Loss of Genetic Diversity

Marriage rules, the community prescriptions that dictate who an individual can or cannot marry, are extremely diverse and universally present in traditional societies. A major focus of research in the early decades of modern anthropology, marriage rules impose social and economic forces that help structure societies and forge connections between them. However, in those early anthropological studies, the biological benefits or disadvantages of marriage rules could not be determined. We revisit this question by applying a novel simulation framework and genome-wide data to explore the effects of Asymmetric Prescriptive Alliance, an elaborate set of marriage rules that has been a focus of research for many anthropologists. Simulations show that strict adherence to these marriage rules reduces genetic diversity on the autosomes, X chromosome and mitochondrial DNA, but relaxed compliance produces genetic diversity similar to random mating. Genome-wide data from the Indonesian community of Rindi, one of the early study populations for Asymmetric Prescriptive Alliance, are more consistent with relaxed compliance than strict adherence. We therefore suggest that, in practice, marriage rules are treated with sufficient flexibility to allow social connectivity without significant degradation of biological diversity.

Screening for MYO15A gene mutations in autosomal recessive nonsyndromic, GJB2 negative Iranian deaf population

MYO15A is located at the DFNB3 locus on chromosome 17p11.2, and encodes myosin-XV, an unconventional myosin critical for the formation of stereocilia in hair cells of cochlea. Recessive mutations in this gene lead to profound autosomal recessive nonsyndromic hearing loss (ARNSHL) in humans and the shaker2 (sh2) phenotype in mice. Here, we performed a study on 140 Iranian families in order to determine mutations causing ARNSHL. The families, who were negative for mutations in GJB2, were subjected to linkage analysis. Eight of these families showed linkage to the DFNB3 locus, suggesting a MYO15A mutation frequency of 5.71% in our cohort of Iranian population. Subsequent sequencing of the MYO15A gene led to identification of 7 previously unreported mutations, including 4 missense mutations, 1 nonsense mutation, and 2 deletions in different regions of the myosin-XV protein.

Non-syndromic, autosomal-recessive deafness

Non-syndromic deafness is a paradigm of genetic heterogeneity with 85 loci and 39 nuclear disease genes reported so far. Autosomal-recessive genes are responsible for about 80% of the cases of hereditary non-syndromic deafness of pre-lingual onset with 23 different genes identified to date. In the present article, we review these 23 genes, their function, and their contribution to genetic deafness in different populations. The wide range of functions of these DFNB genes reflects the heterogeneity of the genes involved in hearing and hearing loss. Several of these genes are involved in both recessive and dominant deafness, or in both non-syndromic and syndromic deafness. Mutations in the GJB2 gene encoding connexin 26 are responsible for as much as 50% of pre-lingual, recessive deafness. By contrast, mutations in most of the other DFNB genes have so far been detected in only a small number of families, and their contribution to deafness on a population scale might therefore be limited. Identification of all genes involved in hereditary hearing loss will help in our understanding of the basic mechanisms underlying normal hearing, in early diagnosis and therapy.

Genetic mapping refines DFNB3 to 17p11.2, suggests multiple alleles of DFNB3, and supports homology to the mouse model shaker-2

The nonsyndromic congenital recessive deafness gene, DFNB3, first identified in Bengkala, Bali, was mapped to a approximately 12-cM interval on chromosome 17. New short tandem repeats (STRs) and additional DNA samples were used to identify recombinants that constrain the DFNB3 interval to less, similar6 cM on 17p11.2. Affected individuals from Bengkala and affected members of a family with hereditary deafness who were from Bila, a village neighboring Bengkala, were homozygous for the same alleles for six adjacent STRs in the DFNB3 region and were heterozygous for other distal markers, thus limiting DFNB3 to an approximately 3-cM interval. Nonsyndromic deafness segregating in two unrelated consanguineous Indian families, M21 and I-1924, were also linked to the DFNB3 region. Haplotype analysis indicates that the DFNB3 mutations in the three pedigrees most likely arose independently and suggests that DFNB3 makes a significant contribution to hereditary deafness worldwide. On the basis of conserved synteny, mouse deafness mutations shaker-2 (sh2) and sh2J are proposed as models of DFNB3. Genetic mapping has refined sh2 to a 0.6-cM interval of chromosome 11. Three homologous genes map within the sh2 and DFNB3 intervals, suggesting that sh2 is the homologue of DFNB3.

Human inner ear OCP2 cDNA maps to 5q22-5q35.2 with related sequences on chromosomes 4p16.2-4p14, 5p13-5q22, 7pter-q22, 10 and 12p13-12qter

Mouse Ocp2-rs2 maps to chromosome 11 and encodes an 18.6 kDa peptide abundantly expressed in the organ of Corti. We show that sequences similar to murine Ocp2-rs2 are found on human chromosomes 4p16.2-4p14, 5p13-5q35.2, 7pter-q22, 10 and 12p13-12qter as revealed by Southern blot analyses of human/rodent somatic cell hybrids. A fetal human inner ear cDNA library was screened with a cloned 254 bp PCR product of murine Ocp2-rs2. One of two human cDNA clones (CM1) was sequenced from the 5' end that begins with murine Ocp2-rs2 codon 14 through the stop codon and 258 nucleotides of 3-UTR and was found to have the identical deduced amino acid sequence to Ocp2-rs2. Based on the sequence in the 3'-UTR of CM1, a PCR primer pain was synthesized and used to confirm that a human homologue of Ocp2-rs2, designated OCP2 and expressed in the developing human inner ear, is localized to 5q22-5q35.2. Other OCP2-like sequences located on chromosomes 4p16.2-4p14, 7pter-q22 and 12p13-12qter (but not the chromosome 10 OCP2-like sequence) will PCR amplify the expected size product at a lower annealing temperature using the OCP2 3'-UTR PCR primers indicating that there may be a human OCP2 gene family.