The Genomics and Computational Biology Core (GCBC) provides genomic analysis support for NIDCD intramural investigators. We maintain and operate massively parallel sequencers (Illumina HiSeq and MiSeq), a 96-capillary sequencer (AB3730xl), a microarray scanner (Illumina iScan), a LifeTech Vii7a realtime PCR machine and a Fluidigm BioMarkHD. We provide library preparation for massively parallel (nexgen) sequencing, perform sequencing reactions, and analyze the resulting data. The majority of the samples analyzed by the GCBC are whole-exome sequencing of DNA samples from subjects who stutter or who are deaf. We build custom relational databases of whole-exome sequence variants that aid in the identification of those that are likely to be pathological. A second area of focus is the analysis of gene expression (transcriptomics) and gene regulation (epigenetics) in particular tissues using RNA-seq and ChIP-seq. Whole Exome Sequencing In collaboration with Principal Investigator Dennis Drayna, PhD (project DC000046 Genetic Studies of Human Communications Disorders), the GCBC sequenced and analyzed 168 whole-exome samples of subjects who stutter. Most of the samples were from single individuals and comprise a portion of a large case-control study. A few samples were from families in which stuttering is segregating as a Mendelian trait. In addition, 48 whole-exome libraries were analyzed from subjects who have an unusual auditory perception characteristic. For both of these studies, the data has been added to a relational database that will aid in the identification of shared genes with predicted pathological sequence variants. In collaboration with Principal Investigator Thomas B. Friedman, PhD (project DC000039 Identification of Genes Causing Syndromic and Nonsyndromic Hearing Impairment), the GCBC sequenced and analyzed 96 whole-exome samples of subjects who are deaf. Most of the samples were from subjects in families segregating nonsyndromic deafness. There are over 100 different genes known to cause nonsyndromic deafness, so the families are usually prescreened to remove those that are segregating a gene that has already been identified. In this way, new deafness genes are identified by the sharing of predicted pathological variants among affected siblings. In this way, mutant alleles of the gene MET were found to cause nonsyndromic hearing loss (DFNB97). However, despite the prescreening process, the outcome of whole-exome analysis is the identification of genes already known to cause hearing loss, usually more than one in a given pedigree. This kind of analytical pitfall is described in the paper by Rehman et al. (2015). In collaboration with Principal Investigator Andrew J. Griffith, MD, PhD (project DC000060 Molecular Analysis Of Human Hereditary Deafness), the GCBC sequenced and analyzed 48 whole-exome samples of subjects who are deaf. Most of the samples were from subjects who have a genetic syndrome comprising either deafness and goiter (Pendred syndrome) or deafness and enlarged vestibular aqueduct. Transcriptomics The GCBC is participating in multiple tissue-level RNA-seq projects comparing heat shock treated versus untreated mouse utricles (collaboration with Lisa Cunningham, NIDCD); and mutant versus wild-type transcriptomes in mouse inner ear (collaboration with Thomas Friedman, NIDCD), wounded bone (collaboration with Marian Young, NIDCR) and salivary glands (collaborations with Matt Hoffman, NIDCR and James Melvin, NIDCR). We have also characterized the transcriptomes of nearly 1,000 single cells isolated from inner ear (collaborations with Matt Kelley, NIDCD and Michael Hoa, NIDCD) and salivary glands (collaboration with Matt Hoffman, NIDCR).
| Imtiaz, Ayesha; Belyantseva, Inna A; Beirl, Alisha J et al. (2018) CDC14A phosphatase is essential for hearing and male fertility in mouse and human. Hum Mol Genet 27:780-798 |
| Nakano, Yoko; Kelly, Michael C; Rehman, Atteeq U et al. (2018) Defects in the Alternative Splicing-Dependent Regulation of REST Cause Deafness. Cell 174:536-548.e21 |
| Fan, Jianguo; Jia, Li; Li, Yan et al. (2017) Maturation arrest in early postnatal sensory receptors by deletion of the miR-183/96/182 cluster in mouse. Proc Natl Acad Sci U S A 114:E4271-E4280 |
| Faridi, R; Rehman, A U; Morell, R J et al. (2017) Mutations of SGO2 and CLDN14 collectively cause coincidental Perrault syndrome. Clin Genet 91:328-332 |
| Chattaraj, Parna; Munjal, Tina; Honda, Keiji et al. (2017) A common SLC26A4-linked haplotype underlying non-syndromic hearing loss with enlargement of the vestibular aqueduct. J Med Genet 54:665-673 |
| Honda, Keiji; Kim, Sung Huhn; Kelly, Michael C et al. (2017) Molecular architecture underlying fluid absorption by the developing inner ear. Elife 6: |
| Naz, Sadaf; Imtiaz, Ayesha; Mujtaba, Ghulam et al. (2017) Genetic causes of moderate to severe hearing loss point to modifiers. Clin Genet 91:589-598 |
| Brewer, Carmen C; Zalewski, Christopher K; King, Kelly A et al. (2016) Heritability of non-speech auditory processing skills. Eur J Hum Genet 24:1137-44 |
| Imtiaz, Ayesha; Maqsood, Azra; Rehman, Atteeq U et al. (2016) Recessive mutations of TMC1 associated with moderate to severe hearing loss. Neurogenetics 17:115-123 |
| Santos-Cortez, Regie Lyn P; Faridi, Rabia; Rehman, Atteeq U et al. (2016) Autosomal-Recessive Hearing Impairment Due to Rare Missense Variants within S1PR2. Am J Hum Genet 98:331-8 |
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