Human genome cgh microarray kit

Agilent® oligonucleotide array was performed with Agilent Human Genome CGH Microarray kit 44 K and 60 K for the last two patients according to the manufacturer’s instructions (Feature Extraction 9.1, CGH Analytics 4.5, Santa Clara, California, United States). A consensus cutoff for recording an alteration was a copy number variation involving at least 3 consecutive oligonucleotides presenting an abnormal ratio greater than + 0.58 or lower than − 0.75. An in silico analysis of the unbalanced regions was made using UCSC Genome Browser (https://genome.ucsc.edu/), the Database of Chromosome Imbalance and Phenotype in Humans using Ensemble Resources (DECIPHER: https://decipher.sanger.ac.uk/), the Database of Genomic Variants (DGV: http://dgv.tcag.ca/dgv/app/home) and the Online Mendelian Inheritance in Man database (OMIM: https://omim.org/).

Microarray-based comparative genomic hybridization (Array CGH) analysis was conducted for 343 NB samples using the Human Genome CGH Microarray Kit (44K or 244K, Agilent), following the manufacturer's protocol. In combination with their chromosomal aberration profiles including 1p loss, 11q loss and 17q gain as well as MYCN amplification, each tumor was categorized into genomic subgroups [20 (link), 21 (link)]. Of those, 21 tumors in the Ss subgroup and 17 in the P1a subgroup, along with 18 tumors belonging to the other genomic subgroups including Sa (6), P1s (1), P2a (2), P3s (2), P4s (2), W1s (1) and W4s (4), were employed for WES analysis.

Array-CGH analysis was performed on proband’s DNA from blood using an Agilent Human Genome CGH Microarray Kit 4 × 180 k with an overall median probe space of 40 Kb, using the same protocol previously described (Palazzo 2017 (link)). All nucleotide positions refer to the Human Genome, February 2009 Assembly (hg19). Data analyses were performed using Agilent Cytogenomics V.2.5.8.1.