title: Comprehensive diagnostic testing for stereocilin: an approach for analyzing medically important genes with high homology.
abstract: Next-generation sequencing (NGS) technologies have revolutionized genetic testing by enabling simultaneous analysis of unprecedented numbers of genes. However, genes with high-sequence homology pose challenges to current NGS technologies. Because diagnostic sequencing is moving toward exome analysis, knowledge of these homologous genes is essential to avoid false positive and negative results. An example is the STRC gene, one of >70 genes known to contribute to the genetic basis of hearing loss. STRC is 99.6% identical to a pseudogene (pSTRC) and therefore inaccessible to standard NGS methodologies. The STRC locus is also known to be a common site for large deletions. Comprehensive diagnostic testing for inherited hearing loss therefore necessitates a combination of several approaches to avoid pseudogene interference. We have developed a clinical test that combines standard NGS and NGS-based copy number assessment supplemented with a long-range PCR-based Sanger or MiSeq assay to eliminate pseudogene contamination. By using this combination of assays we could identify biallelic STRC variants in 14% (95% CI, 8%-24%) of individuals with isolated nonsyndromic hearing loss who had previously tested negative on our 70-gene hearing loss panel, corresponding to a detection rate of 11.2% (95% CI, 6%-19%) for previously untested patients. This approach has broad applicability because medically significant genes for many disease areas include genes with high-sequence homology.
authors.affiliation: Department of Pathology, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts.
authors.forename: Diana
authors.initials: D
authors.lastname: Mandelker
authors.affiliation: Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.
authors.forename: Sami S
authors.initials: SS
authors.lastname: Amr
authors.affiliation: Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.
authors.forename: Trevor
authors.initials: T
authors.lastname: Pugh
authors.affiliation: Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.
authors.forename: Sivakumar
authors.initials: S
authors.lastname: Gowrisankar
authors.affiliation: Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.
authors.forename: Rimma
authors.initials: R
authors.lastname: Shakhbatyan
authors.affiliation: Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Duffy
authors.affiliation: Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.
authors.forename: Mark
authors.initials: M
authors.lastname: Bowser
authors.affiliation: Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.
authors.forename: Bryan
authors.initials: B
authors.lastname: Harrison
authors.affiliation: Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.
authors.forename: Katherine
authors.initials: K
authors.lastname: Lafferty
authors.affiliation: Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.
authors.forename: Lisa
authors.initials: L
authors.lastname: Mahanta
authors.affiliation: Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.
authors.forename: Heidi L
authors.initials: HL
authors.lastname: Rehm
authors.affiliation: Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts; Department of Pathology, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts. Electronic address: bfunke@partners.org.
authors.forename: Birgit H
authors.initials: BH
authors.lastname: Funke
mesh_terms: D001483:Base Sequence; D015331:Cohort Studies; D017931:DNA Primers; D018628:Gene Dosage; D034381:Hearing Loss / Q000235:genetics; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins; D008565:Membrane Proteins / Q000032:analysis* / Q000235:genetics; D017421:Sequence Analysis / Q000379:methods
chemical_list: D017931:DNA Primers; D036341:Intercellular Signaling Peptides and Proteins; D008565:Membrane Proteins; C499079:STRC protein, human