nstd43 (Kim et al. 2009)
- Organism:
- Human
- Study Type:
- Control Set
- Submitter:
- Database of Genomic Variants
- Description:
- We detected structural variations using three methods: diploid GA sequencing, BAC end sequencing, and microarrays. 1. To confirm reliable large deletions in diploid GA sequencing, three criteria had to be met: (1) relative coverage drops compared to those of the flanking regions; (2) the existence of stretched paired-end sequence; and (3) the loss of heterozygous SNPs under the regions. Relative increase of sequencing coverage was used as a confirmation tool for copy number gains. 2. BACs less than 40 kb were considered as significantly short. The co-localization of two or more short BACs was considered as the candidate region of amplification. 3. Putative structural variations were detected with microarrays (Illumina BeadChip 370K, 610K, and Agilent 24M aCGH; Supplementary Methods). For Illumina BeadChips, normalized bead intensity data and genotype calls were obtained with Illumina BeadStudio 3.1 software. Results from Agilent 24M aCGH were analysed on Nexus software (BioDiscovery Inc.). Each aberration call was manually checked to confirm the accuracy of the calls. See Variant Summary counts for nstd43 in dbVar Variant Summary.
- Project:
- PRJNA38505
- Publication(s):
- Kim et al. 2009