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Clinical information, synthesized as human phenotype ontology (HPO) terms, impacts on whole exome sequencing (WES) results
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Jacob, Natalie. Clinical information, synthesized as human phenotype ontology (HPO) terms, impacts on whole exome sequencing (WES) results. Retrieved from https://doi.org/doi:10.7282/t3-zess-tn11

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TitleClinical information, synthesized as human phenotype ontology (HPO) terms, impacts on whole exome sequencing (WES) results
NameJacob, Natalie (author); Heiman, Gary (chair); Rutgers University; School of Graduate Studies
Date Created2021
Other Date2021-05 (degree)
SubjectMicrobiology and Molecular Genetics
Extent1 online resource (iv, 20 pages)
DescriptionGenetic testing via whole exome sequencing has emerged as a preferred first-tier test for many physicians so they may provide a comprehensive, cost-effective testing option for their patients. Due to the vast amount of sequencing data produced by a whole exome sequencing test, the data must be filtered through a pipeline using various information such as allele frequency, variant type, and clinical information related to the patient’s specific phenotype. However, obtaining a positive result, where the underlying genetic defect is identified, happens approximately 30% of the time (Farewell et al. 2015). One possible reason for the low positive result rate is not having enough patient-specific clinical information in the bioinformatics program. This case-control study analyzes how the number of Human Phenotype Ontology (HPO) terms impact the results of a whole exome sequencing test. In collaboration with PreventionGenetics, retrospective chart reviews were performed on 300 patients who had received a singleton whole exome sequencing test: 100 patients who had received a positive result (a diagnosis was made), 100 patients who had received a negative result (no variant that may potentially explain the patient’s features was found), and 100 patients who had received an indeterminate result (a variant was found, but there is not enough evidence to identify it as the primary cause of disease). We analyzed the number of HPO terms received from the ordering physician and extracted through medical records by trained personnel at the diagnostic laboratory. Results indicate that increasing the total number of HPO terms does not increase the likelihood of a positive result for the whole exome sequencing test; however, results suggest that there may be a relationship between the number of terms provided by an ordering physician and the outcome of the test. Further studies will need to be conducted to confirm this result.
NoteM.S.
NoteIncludes bibliographical references
Genretheses, External ETD graduate
Persistent URLhttps://doi.org/doi:10.7282/t3-zess-tn11
LanguageEnglish
CollectionSchool of Graduate Studies Electronic Theses and Dissertations
Organization NameRutgers, The State University of New Jersey
RightsThe author owns the copyright to this work.
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