Publications

The following are recent publications from the CLCG team. The abstract for each article is displayed below, follow the Pubmed ID link to view the Pubmed entry and continue on to the full article text.

Taylor KR, Booth KT, Azaiez H, Sloan CM, Kolbe DL, Glanz EN, Shearer AE, DeLuca AP, Anand VN, Hildebrand MS, Simpson AC, Eppsteiner RW, Scheetz TE, Braun TA, Huygen PL, Smith RJ, Casavant TL.
Ann Otol Rhinol Laryngol
Pubmed ID: 26530094

OBJECTIVE: To present audiometric data in 3 dimensions by considering age as an
addition dimension.
METHODS: Audioprofile surfaces (APSs) were fitted to a set of audiograms by
plotting each measurement of an audiogram as an independent point in 3 dimensions
with the x, y, and z axes representing frequency, hearing loss in dB, and age,
respectively.
RESULTS: Using the Java-based APS viewer as a standalone application, APSs were
pre-computed for 34 loci. By selecting APSs for the appropriate genetic locus, a
clinician can compare this APS-generated average surface to a specific patient's
audiogram.
CONCLUSION: Audioprofile surfaces provide an easily interpreted visual
representation of a person's hearing acuity relative to others with the same
genetic cause of hearing loss. Audioprofile surfaces will support the generation
and testing of sophisticated hypotheses to further refine our understanding of
the biology of hearing.

Sherman SK, Maxwell JE, Qian Q, Bellizzi AM, Braun TA, Iannettoni MD, Darbro BW, Howe JR
Cancer Genet.
Pubmed ID: 25554686

Germline mutations in the PTEN tumor-suppressor gene cause autosomal-dominant conditions such as Cowden and Bannayan-Riley-Ruvalcaba syndromes with variable presentations, including hamartomatous gastrointestinal tumors, dermatologic abnormalities, neurologic symptoms, and elevated cancer risk. We describe a father and son with extensive hamartomatous gastrointestinal polyposis who both developed early-onset esophageal cancer. Exome sequencing identified a novel germline PTEN frameshift mutation (c.568_569insC, p.V191Sfs*11). In addition, a missense mutation of SMAD7 (c.115G>A, p.G39R) with an allele frequency of 0.3% in the Exome Variant Server was detected in both affected individuals. Fluorescence in situ hybridization for PTEN in the resected esophageal cancer specimen demonstrated no PTEN copy loss in malignant cells; however, results of an immunohistochemical analysis demonstrated a loss of PTEN protein expression. While the risks of many cancers are elevated in the PTEN hamartoma tumor syndromes, association between esophageal adenocarcinoma and these syndromes has not been previously reported. Esophageal adenocarcinoma and extensive polyposis/ganglioneuromatosis could represent less common features of these syndromes, potentially correlating with this novel PTEN frameshift and early protein termination genotype. Alternatively, because simultaneous disruption of both the PTEN and TGF-β/SMAD4 pathways is associated with development of esophageal cancer in a mouse model and because SMAD4 mutations cause gastrointestinal hamartomas in juvenile polyposis syndrome, the SMAD7 mutation may represent an additional modifier of these individuals' PTEN-mutant phenotype.

See below
AJHG
Pubmed ID:

A. Eliot Shearer1, Robert W. Eppsteiner1, 18, Kevin T. Booth1, 18, Sean S. Ephraim2, 18, José Gurrola II1, Allen Simpson1, E. Ann Black-Ziegelbein1, Swati Joshi3, Harini Ravi3, Angelica C. Giuffre3, Scott Happe3, Michael S. Hildebrand4, Hela Azaiez1, Yildirim A. Bayazit5, Mehmet Emin Erdal6,Jose A. Lopez-Escamez7, Irene Gazquez7, Marta L. Tamayo8,Nancy Y. Gelvez8, Greizy Lopez Leal8, Chaim Jalas9, Josef Ekstein10, Tao Yang11, Shin-ichi Usami12, Kimia Kahrizi13, Niloofar Bazazzadegan13, Hossein Najmabadi13, Todd E. Scheetz2, 14, 15, Terry A. Braun2, 14, 15,

Ethnic-specific differences in minor allele frequency impact variant categorization for genetic screening of nonsyndromic hearing loss (NSHL) and other genetic disorders. We sought to evaluate all previously reported pathogenic NSHL variants in the context of a large number of controls from ethnically distinct populations sequenced with orthogonal massively parallel sequencing methods. We used HGMD, ClinVar, and dbSNP to generate a comprehensive list of reported pathogenic NSHL variants and re-evaluated these variants in the context of 8,595 individuals from 12 populations and 6 ethnically distinct major human evolutionary phylogenetic groups from three sources (Exome Variant Server, 1000 Genomes project, and a control set of individuals created for this study, the OtoDB). Of the 2,197 reported pathogenic deafness variants, 325 (14.8%) were present in at least one of the 8,595 controls, indicating a minor allele frequency (MAF) >0.00006. MAFs ranged as high as 0.72, a level incompatible with pathogenicity for a fully penetrant disease like NSHL. Based on these data, we established MAF thresholds of 0.005 for autosomal-recessive variants (excluding specific variants in GJB2) and 0.0005 for autosomal-dominant variants. Using these thresholds, we recategorized 93 (4.2%) of reported pathogenic variants as benign. Our data show that evaluation of reported pathogenic deafness variants using variant MAFs from multiple distinct ethnicities and sequenced by orthogonal methods provides a powerful filter for determining pathogenicity. The proposed MAF thresholds will facilitate clinical interpretation of variants identified in genetic testing for NSHL. All data are publicly available to facilitate interpretation of genetic variants causing deafness.

Smith Michael F, Davis Steve G
J Bioinform Comput Biol.
Pubmed ID: 18172923

When searching for disease-causing mutations with polymerase chain reaction (PCR)-based methods, candidate genes are usually screened in their entirety, exon by exon. Genomic resources (i.e. www.ncbi.nih.gov, www.ensembl.org, and genome.ucsc.edu) largely support this paradigm for mutation screening by making it easy to view and access sequence data associated with genes in their genomic context. However, the administrative burden of conducting mutation screening in potentially hundreds of genes and thousands of exons in thousands of patients is significant, even with the use of public genome resources. For example, the manual design of oligonucleotide primers for all exons of the 10 Leber's congenital amaurosis (LCA) genes (149 exons) represents a significant information management challenge. The Transcript Annotation Prioritization and Screening System (TrAPSS) is designed to accelerate mutation screening by (1) providing a gene-based local cache of candidate disease genes in a genomic context, (2) automating tasks associated with optimizing candidate disease gene screening and information management, and (3) providing the implementation of an algorithmic technique to utilize large amounts of heterogeneous genome annotation (e.g. conserved protein functional domains) so as to prioritize candidate genes.

Mahajan VB, Skeie JM, Bassuk AG, Fingert JH, Braun TA, Daggett H
PLoS Genetics
Pubmed ID: 23055945

Autosomal dominant neovascular inflammatory vitreoretinopathy (ADNIV) is an autoimmune condition of the eye that sequentially mimics uveitis, retinitis pigmentosa, and proliferative diabetic retinopathy as it progresses to complete blindness. We identified two different missense mutations in the CAPN5 gene in three ADNIV kindreds. CAPN5 encodes calpain-5, a calcium-activated cysteine protease that is expressed in retinal photoreceptor cells. Both mutations cause mislocalization from the cell membrane to the cytosol, and structural modeling reveals that both mutations lie within a calcium-sensitive domain near the active site. CAPN5 is only the second member of the large calpain gene family to cause a human Mendelian disorder, and this is the first report of a specific molecular cause for autoimmune eye disease. Further investigation of these mutations is likely to provide insight into the pathophysiologic mechanisms of common diseases ranging from autoimmune disorders to diabetic retinopathy.