title: Overview of recurrent chromosomal losses in retinoblastoma detected by low coverage next generation sequencing.
abstract: Genes are frequently lost or gained in malignant tumors and the analysis of these changes can be informative about the underlying tumor biology. Retinoblastoma is a pediatric intraocular malignancy, and since deletions in chromosome 13 have been described in this tumor, we performed genome wide sequencing with the Illumina platform to test whether recurrent losses could be detected in low coverage data from DNA pools of Rb cases. An in silico reference profile for each pool was created from the human genome sequence GRCh37p5; a chromosome integrity score and a graphics 40 Kb window analysis approach, allowed us to identify with high resolution previously reported non random recurrent losses in all chromosomes of these tumors. We also found a pattern of gains and losses associated to clear and dark cytogenetic bands respectively. We further analyze a pool of medulloblastoma and found a more stable genomic profile and previously reported losses in this tumor. This approach facilitates identification of recurrent deletions from many patients that may be biological relevant for tumor development.
authors.affiliation: Unidad de Investigación Médica en Enfermedades Infecciosas, Centro Médico Nacional SXXI, Instituto Mexicano del Seguro Social, México D.F., Mexico.
authors.forename: A J
authors.initials: AJ
authors.lastname: García-Chequer
authors.affiliation: Lab. Bioinformática Genómica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D.F., Mexico.
authors.forename: A
authors.initials: A
authors.lastname: Méndez-Tenorio
authors.affiliation: Lab. Bioinformática Genómica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D.F., Mexico.
authors.forename: G
authors.initials: G
authors.lastname: Olguín-Ruiz
authors.affiliation: Lab. Bioinformática Genómica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D.F., Mexico.
authors.forename: C
authors.initials: C
authors.lastname: Sánchez-Vallejo
authors.affiliation: Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.
authors.forename: P
authors.initials: P
authors.lastname: Isa
authors.affiliation: Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.
authors.forename: C F
authors.initials: CF
authors.lastname: Arias
authors.affiliation: Unidad de Investigación Médica en Enfermedades Infecciosas, Centro Médico Nacional SXXI, Instituto Mexicano del Seguro Social, México D.F., Mexico.
authors.forename: J
authors.initials: J
authors.lastname: Torres
authors.affiliation: Unidad de Investigación Médica en Enfermedades Infecciosas, Centro Médico Nacional SXXI, Instituto Mexicano del Seguro Social, México D.F., Mexico.
authors.forename: A
authors.initials: A
authors.lastname: Hernández-Angeles
authors.affiliation: Hospital Infantil de México Federico Gómez, México D.F., Mexico.
authors.forename: M A
authors.initials: MA
authors.lastname: Ramírez-Ortiz
authors.affiliation: Hospital Infantil de México Federico Gómez, México D.F., Mexico.
authors.forename: C
authors.initials: C
authors.lastname: Lara
authors.affiliation: Hospital Infantil de México Federico Gómez, México D.F., Mexico.
authors.forename: M L
authors.initials: ML
authors.lastname: Cabrera-Muñoz
authors.affiliation: Hospital Infantil de México Federico Gómez, México D.F., Mexico.
authors.forename: S
authors.initials: S
authors.lastname: Sadowinski-Pine
authors.affiliation: Hospital de Pediatría, CMN SXXI, Instituto Mexicano del Seguro Social, México D.F., Mexico.
authors.forename: J C
authors.initials: JC
authors.lastname: Bravo-Ortiz
authors.affiliation: Hospital de Pediatría, CMN SXXI, Instituto Mexicano del Seguro Social, México D.F., Mexico.
authors.forename: G
authors.initials: G
authors.lastname: Ramón-García
authors.affiliation: Hospital de Pediatría, CMN SXXI, Instituto Mexicano del Seguro Social, México D.F., Mexico.
authors.forename: J
authors.initials: J
authors.lastname: Diegopérez-Ramírez
authors.affiliation: Hospital de Pediatría, CMN SXXI, Instituto Mexicano del Seguro Social, México D.F., Mexico.
authors.forename: G
authors.initials: G
authors.lastname: Ramírez-Reyes
authors.affiliation: Hospital de Pediatría, CMN SXXI, Instituto Mexicano del Seguro Social, México D.F., Mexico.
authors.forename: R
authors.initials: R
authors.lastname: Casarrubias-Islas
authors.affiliation: Unidad de Microarreglos, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México D.F., Mexico.
authors.forename: J
authors.initials: J
authors.lastname: Ramírez
authors.affiliation: Columbia University, New York, USA.
authors.forename: M A
authors.initials: MA
authors.lastname: Orjuela
authors.affiliation: Unidad de Investigación Médica en Enfermedades Infecciosas, Centro Médico Nacional SXXI, Instituto Mexicano del Seguro Social, México D.F., Mexico. Electronic address: vponce@ifc.unam.mx.
authors.forename: M V
authors.initials: MV
authors.lastname: Ponce-Castañeda
mesh_terms: D002872:Chromosome Deletion; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D008527:Medulloblastoma / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D012008:Recurrence; D019572:Retinal Neoplasms / Q000235:genetics*; D012175:Retinoblastoma / Q000235:genetics*
keywords: Pediatric tumors; losses; low coverage; medulloblastoma; next-generation sequencing; retinoblastoma