Multi-platform segmentation for joint detection of copy number variants.
Bioinformatics
; 27(11): 1555-61, 2011 Jun 01.
Article
en En
| MEDLINE
| ID: mdl-21471018
ABSTRACT
MOTIVATION With the expansion of whole-genome studies, there is rapid evolution of genotyping platforms. This leads to practical issues such as upgrading of genotyping equipment which often results in research groups having data from different platforms for the same samples. While having more data can potentially yield more accurate copy-number estimates, combining such data is not straightforward as different platforms show different degrees of attenuation of the true copy-number or different noise characteristics and marker panels. Currently, there is still a relative lack of procedures for combining information from different platforms. RESULTS:
We develop a method, called MPSS, based on a correlated random-effect model for the unobserved patterns and extend the robust smooth segmentation approach to the multiple-platform scenario. We also propose an objective criterion for discrete segmentation required for downstream analyses. For each identified segment, the software reports a P-value to indicate the likelihood of the segment being a true CNV. From the analyses of real and simulated data, we show that MPSS has better operating characteristics when compared to single-platform methods, and have substantially higher sensitivity compared to an existing multiplatform method.AVAILABILITY:
The methods are implemented in an R package MPSS, and the source is available from http//www.meb.ki.se/~yudpaw.
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Algoritmos
/
Variaciones en el Número de Copia de ADN
Tipo de estudio:
Diagnostic_studies
/
Prognostic_studies
Límite:
Aged
/
Female
/
Humans
/
Middle aged
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2011
Tipo del documento:
Article
País de afiliación:
Singapur