PMC:4574214 / 3563-5058 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4574214","sourcedb":"PMC","sourceid":"4574214","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4574214","text":"CNV detection and evaluation\nWhole genome microarray (Agilent 244K) was performed to detect structural variants in a clinical cohort. Subjects were eligible if they had a height measurement recorded between the ages of 2 and 20 years and had a chromosomal microarray performed as part of their clinical evaluation. All information was obtained with appropriate consent from Boston Children’s hospital [M09-06-0290]. Subjects with aneuploidy and poor microarray quality were not included, leaving a final sample size of 4,411 individuals including 415 patients with short stature, 196 patients with tall stature and 3800 patients with normal stature. All CNV data were called with NEXUS software (BioDiscovery, El Segundo, California). The recurrent copy-number variations involving ARID1B gene were validated by multiplex ligation-dependent probe amplification (MLPA). MLPA probe and reagents from MRC Holland (SALSA MLPA P433 ARID1A-ARID1B probemix). Data analysis and visualization was done on Coffalyzer software. A CNV is defined as non-benign when it does not overlap with CNV reported in DGV (Database of Genomic variants) or overlaps with CNV with less than 1 % population frequency in DGV. Non-benign recurrent or overlapping CNVs were identified in the subjects with short stature and compared to their occurrence in normal stature population. The UCSC genome browser’s custom track was used to depict the overlapping nature of CNVs and to delineate the minimal region of overlap (MRO).","divisions":[{"label":"Title","span":{"begin":0,"end":28}}],"tracks":[]}