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Detection of de novo copy number deletions from targeted sequencing of trios.
Fu, Jack M; Leslie, Elizabeth J; Scott, Alan F; Murray, Jeffrey C; Marazita, Mary L; Beaty, Terri H; Scharpf, Robert B; Ruczinski, Ingo.
Afiliación
  • Fu JM; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
  • Leslie EJ; Department of Human Genetics, Emory University, Atlanta, GA, USA.
  • Scott AF; Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.
  • Murray JC; Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
  • Marazita ML; Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA.
  • Beaty TH; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
  • Scharpf RB; Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
  • Ruczinski I; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
Bioinformatics ; 35(4): 571-578, 2019 02 15.
Article en En | MEDLINE | ID: mdl-30084993
MOTIVATION: De novo copy number deletions have been implicated in many diseases, but there is no formal method to date that identifies de novo deletions in parent-offspring trios from capture-based sequencing platforms. RESULTS: We developed Minimum Distance for Targeted Sequencing (MDTS) to fill this void. MDTS has similar sensitivity (recall), but a much lower false positive rate compared to less specific CNV callers, resulting in a much higher positive predictive value (precision). MDTS also exhibited much better scalability. AVAILABILITY AND IMPLEMENTATION: MDTS is freely available as open source software from the Bioconductor repository. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Asunto(s)

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Algoritmos / Programas Informáticos / Eliminación de Secuencia / Variaciones en el Número de Copia de ADN Tipo de estudio: Diagnostic_studies Idioma: En Revista: Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Algoritmos / Programas Informáticos / Eliminación de Secuencia / Variaciones en el Número de Copia de ADN Tipo de estudio: Diagnostic_studies Idioma: En Revista: Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos