Each year, more than 12,000 babies are born with hearing loss in the US alone, and about half of them are due to genetic causes. Knowing the exact genetic lesions allows early diagnosis even before the onset of noticeable symptoms, informs the choice of optimal management plans, and predicts risks for relatives including future babies. In light of promising advances in gene therapy, it will soon become essential to identify the causative genetic lesion so that personalized therapy can specifically target the culprit lesio to maximize efficacy while minimize side-effects. Therefore, the overall goal of this project is to develop accurate and sensitive clinical molecular diagnostic tests to improve care for patients with hearing loss. Targeted high-throughput sequencing of genomic DNA has become state of the art in clinical molecular genetic diagnostics, resulting in the identification of a large numbe of DNA variants. However, the diagnostic yield remains unsatisfactory due to the lack of functional and statistical evidence to determine their clinical significance. This proposal aims to develop OtoScript, a fundamentally different genetic testing platform based on high-throughput sequencing of messenger RNA instead of genomic DNA. The hypothesis is that OtoScript will not only identify genetic variation that may be missed by conventional genomic sequencing, but will also reveal functional consequences at the transcriptional level, allowing accurate assessment of clinical significance. Furthermore, this project will provide a resource for the auditory research community to study the molecular basis of hearing loss.
In Aim 1, the feasibility and validity of OtoScript to identify genetic variations in hearing loss genes will be evaluated. OtoScript performance metrics will be compared to the current standard of care, specifically the clinically validated OtoGenome test in a CLIA-certified clinical laboratory. In Ai 2, the capability of OtoScript to enhance interpretation of genetic testing results will be assesse in four functional aspects at the transcriptional level: levels of gene expression, the number of affected homologous chromosomes, aberrant transcripts, and RNA-editing. In addition, new findings from this study will be disseminated to the research community via the Shared Harvard Inner Ear Laboratory Database (SHIELD, https://shield.hms.harvard.edu/). This novel approach holds the potential to improve the accuracy and efficiency of clinical molecular genetic diagnosis of hearing loss.

Public Health Relevance

Clinical molecular genetic diagnosis informs medical management for patients and their family members. This study aims to develop a new high-throughput platform to increase the diagnostic yield of genetic testing and to shed light on the molecular mechanism of hearing loss. This will in turn improve patient care, and ultimately lead to novel strategies to treat and prevent hearing loss.

Agency
National Institute of Health (NIH)
Institute
National Institute on Deafness and Other Communication Disorders (NIDCD)
Type
Small Research Grants (R03)
Project #
5R03DC013866-02
Application #
8832724
Study Section
Communication Disorders Review Committee (CDRC)
Program Officer
Watson, Bracie
Project Start
2014-04-10
Project End
2017-03-31
Budget Start
2015-04-01
Budget End
2016-03-31
Support Year
2
Fiscal Year
2015
Total Cost
Indirect Cost
Name
Brigham and Women's Hospital
Department
Type
DUNS #
030811269
City
Boston
State
MA
Country
United States
Zip Code
Evrony, Gilad D; Cordero, Dwight R; Shen, Jun et al. (2017) Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome. Genome Res 27:1323-1335
Schilit, Samantha Lp; Currall, Benjamin B; Yao, Ruen et al. (2016) Estrogen-related receptor gamma implicated in a phenotype including hearing loss and mild developmental delay. Eur J Hum Genet 24:1622-1626
Lin, Shuh-Yow; Vollrath, Melissa A; Mangosing, Sara et al. (2016) The zebrafish pinball wizard gene encodes WRB, a tail-anchored-protein receptor essential for inner-ear hair cells and retinal photoreceptors. J Physiol 594:895-914
Kwan, Kelvin Y; Shen, Jun; Corey, David P (2015) C-MYC transcriptionally amplifies SOX2 target genes to regulate self-renewal in multipotent otic progenitor cells. Stem Cell Reports 4:47-60
Scheffer, Déborah I; Zhang, Duan-Sun; Shen, Jun et al. (2015) XIRP2, an actin-binding protein essential for inner ear hair-cell stereocilia. Cell Rep 10:1811-8
Shen, Jun; Scheffer, Déborah I; Kwan, Kelvin Y et al. (2015) SHIELD: an integrative gene expression database for inner ear research. Database (Oxford) 2015:bav071
Scheffer, Déborah I; Shen, Jun; Corey, David P et al. (2015) Gene Expression by Mouse Inner Ear Hair Cells during Development. J Neurosci 35:6366-80
Robertson, Nahid G; O'Malley, Jennifer T; Ong, Cheng Ai et al. (2014) Cochlin in normal middle ear and abnormal middle ear deposits in DFNA9 and Coch (G88E/G88E) mice. J Assoc Res Otolaryngol 15:961-74