TY - JOUR
T1 - Overview of recurrent chromosomal losses in retinoblastoma detected by low coverage next generation sequencing
AU - García-Chequer, A. J.
AU - Méndez-Tenorio, A.
AU - Olguín-Ruiz, G.
AU - Sánchez-Vallejo, C.
AU - Isa, P.
AU - Arias, C. F.
AU - Torres, J.
AU - Hernández-Angeles, A.
AU - Ramírez-Ortiz, M. A.
AU - Lara, C.
AU - Cabrera-Muñoz, M. L.
AU - Sadowinski-Pine, S.
AU - Bravo-Ortiz, J. C.
AU - Ramón-García, G.
AU - Diegopérez-Ramírez, J.
AU - Ramírez-Reyes, G.
AU - Casarrubias-Islas, R.
AU - Ramírez, J.
AU - Orjuela, M. A.
AU - Ponce-Castañeda, M. V.
N1 - Publisher Copyright:
© 2015 Elsevier Inc.
PY - 2016/3/1
Y1 - 2016/3/1
N2 - 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.
AB - 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.
KW - Losses
KW - Low coverage
KW - Medulloblastoma
KW - Next-generation sequencing
KW - Pediatric tumors
KW - Retinoblastoma
UR - http://www.scopus.com/inward/record.url?scp=84958872536&partnerID=8YFLogxK
U2 - 10.1016/j.cancergen.2015.12.001
DO - 10.1016/j.cancergen.2015.12.001
M3 - Artículo
C2 - 26883451
SN - 2210-7762
VL - 209
SP - 57
EP - 69
JO - Cancer Genetics
JF - Cancer Genetics
IS - 3
ER -