Agilent oligonucleotide array based cgh for genomic dna analysis version 7

To fine map the genomic rearrangements to genome-level resolution, we used a custom-designed, high-density oligonucleotide array from Agilent. The array comprises approximately 44,000 interrogating oligonucleotides spanning chrX: 98,028,855-113,513,744 (NCBI build 37/hg19) with an average genome resolution of 386 bp between probes (chrX: 97,915,511-113,400,000 in NCBI build 36/hg18 was converted to GRCh37/hg19 using UCSC Genome Browser; https://genome.ucsc.edu/cgi-bin/hgLiftOver). The experimental procedures were performed according to the manufacturer’s protocol (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Version 7.2, Agilent Technologies) with some modifications as described [26 (link), 36 (link)]. Gender-matched control DNA from Coriell repository (male individual NA10851) was used for hybridization. Agilent Feature Extraction software and Agilent Genomic Workbench (version 7.0.4.0) were used to process scanned array images (version10) and analyze extracted files, respectively.

Nine hundred nano-grams of genomic DNA from proband (sample to be tested) and an equal amount of DNA sample from a control (NA10851) were used. The experimental procedures, including DNA fragmental and labeling, array hybridization, array washing and scanning and imaging processing, were identical for inter-/intra-species aCGH, following the manufacturer’s protocol (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis version 7.2, Agilent Technologies, Santa Clara, California, USA) with modifications [64 (link)]. Human reference sequence hg19 assembly was used to define the genomic coordinated of detected CNVs.
aCGH experiments were performed on DNA samples from human subjects without NPHP1 (N = 10), DNA samples from human subjects affected with NPHP1 (N = 8), and nonhuman primate DNA samples of baboon (N = 1), rhesus macaque (N = 2), orangutan (N = 1), gorilla (N = 3) and chimpanzee (N = 7). Human DNA sample of NA10851 were used as the universal reference for the aCGH experiment. The DNA samples of MM52, HF087, CHM and HCC1937 were not available for the experiment.