1993 |
Avraham, Karen B |
F32Activity Code Description: To provide postdoctoral research training to individuals to broaden their scientific background and extend their potential for research in specified health-related areas. |
Cloning and Characterization of the Snell's Waltzer Gene @ National Cancer Institute-Frederick |
0.91 |
1994 |
Avraham, Karen B |
F32Activity Code Description: To provide postdoctoral research training to individuals to broaden their scientific background and extend their potential for research in specified health-related areas. |
Cloning and Characterization of the Snells Waltzer Gene @ National Cancer Institute-Frederick |
0.91 |
2011 — 2015 |
Avraham, Karen B. Kanaan, Moien |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Gene Discovery For Hearing Loss in Middle East by Massively Parallel Sequencing
DESCRIPTION (provided by applicant): The goal of this project is to discover new genes for hearing loss by identifying inherited mutations in multiplex families. Targeted DNA capture and massively parallel sequencing technologies will be used to identify mutations in the deaf population of the Middle East, including 270 Israeli Jews and 212 Palestinian Arabs. We will explore the physiological processes underlying deafness using mouse mutants. This project will be led and directed by Karen Avraham (Tel Aviv) and Moien Kanaan (Bethlehem), who have worked together for 15 years with 11 joint publications on genetic deafness and 2 reviews on peace building through scientific collaboration. Discovery and characterization of new genes for hearing impairment involves five aims. In AIM 1, we will fully sequence 192 affected individuals for 246 genes for syndromic and non-syndromic hearing loss, in humans and mice, with a custom 1.6 MB design of cRNA oligonucleotides. We will use a multiplex barcoding strategy and sequence on an Illumina GAIIx Genome Analyzer. Mutations will be validated by Sanger sequencing. In AIM 2, homozygosity mapping using the Affymetrix 6.0 array will be conducted for families not resolved in Aim 1. In addition to identifying homozygous regions, SNP data will be analyzed to detect homozygous CNVs. In AIM 3, exome sequencing will be carried out and variants that map within homozygous regions, obtained from Aim 2, will be evaluated first. For families with no extended homozygous regions, variants exome-wide will be evaluated for compound heterozygosity. One flow cell lane will be run for each proband. In AIM 4, the targeted pools of Aim 1 will be revised to include new genes for screening of all unresolved probands, familial or sporadic. Clinical features of hearing loss will be compared across mutations and genes. In AIM 5, newly identified proteins will be characterized by expression analysis in lymphoblastoid cell lines, protein-specific functional assays, silencing or overexpression by viral transfection in cochlear cultures;, protein localization throughout development of wildtype mice;hearing and vestibular testing, and inner ear morphology, including high-resolution scanning electron microscopy, in mouse models for human deafness Discovery of new deafness genes will allow for early clinical diagnosis, enabling prediction of phenotypes and enhanced rehabilitation, in particular for children. Characterization of critical proteins will enable a comprehensive understanding of the biological mechanisms involved in pathophysiology of hearing loss. PUBLIC HEALTH RELEVANCE: NARRATIVE The goal of this project is to identify new mutations and genes responsible for inherited hearing loss using state-of-the-art genomic tools such as DNA capture and massively parallel sequencing technologies. Middle Eastern family structure facilitates identification of these genes, which may be present in other populations in the world and thus have far reaching consequences, including in the United States. The research will lead toward enhanced clinical diagnostics, a biological understanding of a comprehensive list of proteins involved in auditory function, and a potential for development of therapeutics for deafness.
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2018 — 2021 |
Avraham, Karen B. Kanaan, Moien King, Mary-Claire (co-PI) [⬀] |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Genomic Approaches to Discovery and Characterization of Genes For Inherited Hearing Loss
The goal of this project is to discover and characterize new genes for inherited hearing loss by studying highly informative families from the Middle East. Families from regions with traditions of consanguinity or endogamy have been particularly informative for gene discovery for hearing loss, with other mutations responsible for both recessive and dominant hearing losses subsequently identified in other families. Over the past 19 years, our partnership has discovered seven new genes for hearing loss, contributed to the genotype-phenotype profiles of many others, evaluated the roles of microRNAs in hearing development, and characterized the functions of our mutant genes in patient cells and mouse models. During the current grant period, we published SYNE4 as a new gene for hearing loss and are in the midst of functional studies of five other candidate genes: ATOH1, CDKL3, CTBS, GOSR2, and OTOP2. We have also been at the forefront of application of genomic technologies to hearing research. We were among the first groups to apply exome sequencing to gene discovery for any phenotype and to develop targeted hybridization pools for thorough and efficient screening of candidate deafness genes. Our partnership has complementary strengths at Tel Aviv University, Bethlehem University, and the University of Washington in Seattle. Our greatest asset is our relationship with hundreds of highly informative Palestinian and Israeli families, each with multiple relatives with hearing loss who have been evaluated by audiology and for syndromic features. Complete families participate, are willing to be re-contacted, and remain in touch with us indefinitely. In Aim 1, we will enroll each year all informative members of 80-100 multiplex Palestinian and Israeli families (400-500 individuals) with hearing loss, and use our targeted gene panel to sequence for mutations in known genes for hearing loss. In Aim 2, families not resolved by Aim 1 will be evaluated by whole genome sequencing. Variants prioritized for functional studies will be rare coding sequence variants of predicted damaging effect in new candidate genes that co-segregate with hearing loss; and rare non-coding variants that lie in potential regulatory regions, as defined by several parameters, and that co-segregate with hearing loss. In Aim 3, we will undertake functional studies of these new candidate genes and mutations. Our approaches will include functional analysis of wild type and mutant proteins in transfected cells and cochlear explants, and generation of mouse models of mutations from human families by CRISPR/Cas9 genome editing, followed by characterization of their hearing and inner ear phenotypes. In summary, we propose to use modern tools of genetics and genomics to reveal and characterize genes essential for development and maintenance of hearing. Our discoveries will aid in the development of biological strategies for treatment or cures for deafness.
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