Reference alignment of SNP microarray signals for copy number analysis of tumors.
Bioinformatics
; 25(3): 315-21, 2009 Feb 01.
Article
en En
| MEDLINE
| ID: mdl-19052058
ABSTRACT
UNLABELLED A new procedure to align single nucleotide polymorphism (SNP) microarray signals for copy number analysis is proposed. For each individual array, this reference alignment procedure (RAP) uses a set of selected markers as internal references to direct the signal alignment. RAP aligns the signals so that each array has a similar signal distribution among its reference markers. An accompanying reference selection algorithm (RSA) uses genotype calls and initial signal intensities to choose two-copy markers as the internal references for each array. After RSA and RAP are applied, each array has a similar distribution of signals of two-copy markers so that across-array signal comparisons are biologically meaningful. An upper bound for a statistical metric of signal misalignment is derived and provides a theoretical basis to choose RSA-RAP over other alignment procedures for copy number analysis of cancers. In our study of acute lymphoblastic leukemia, RSA-RAP gives copy number analysis results that show substantially better concordance with cytogenetics than do two other alignment procedures. AVAILABILITY:
Documented R code is freely available from www.stjuderesearch.org/depts/biostats/refnorm.
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Aberraciones Cromosómicas
/
Biología Computacional
/
Análisis de Secuencia por Matrices de Oligonucleótidos
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Polimorfismo de Nucleótido Simple
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Neoplasias
Límite:
Humans
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2009
Tipo del documento:
Article
País de afiliación:
Estados Unidos