QuantiSNP

[…] Hapmap Project provided a CNV calling report based on SNP microarray data using QuantiSNP [] and Birdseye []. The 1000 Genome Project also provided a DNA structural variation report as a VCF file based on NSG data. Both reports were published with extra experimental information i […]

[…] is currently the most widely used for Illumina chips (PennCNV: 955 citations; QuantiSNP: 432 citations), particularly for high-density SNP data. Compared to other algorithms such as CNVPartition and QuantiSNP, PennCNV is more reliable for assessing the number of copies when using Illumina high-density arrays because it incorporates the allelic intensity ratio at each SNP marker and the total sign […]

[…] ep process according to Altshuler et al. The first step is to detect copy number variation on each chromosome by analyzing the probe-level intensity data from both the Affymetrix and Illumina arrays. QuantiSNP and Birdseye algorithms are used to identify CNV loci separately. Common CNV loci are further identified, and refined to ensure qualified copy number variant calls. The second step is to det […]

[…] tect submicroscopic CNVs that are not recognized by the routine karyotype analyses.There are several algorithms and tools available for inferring CNVs from SNP data []. The most known are PennCNV [], QuantiSNP [], iPattern [], and some proprietary software (e.g., CNVpartition, implemented in Illumina BeadStudio, and Affymetrix Genotyping Console). PennCNV is an algorithm based on Hidden Markov Mod […]

[…] logy, CNV detection using SNP chip data has been conducted in humans and animals. Several algorithms for inferring CNV based on SNP chip data have been developed, including PennCNV, cnvPartition, and QuantiSNP. No single approach can capture all CNV; thus, one may be complementary to another. However, most studies on CNV using SNP arrays in animals and humans have used only PennCNV software, espec […]

[…] detection, 1534 unrelated individuals with ASD (901 from Pinto et al. and 633 from our cohort) and 8936 controls were analyzed using Illumina SNP arrays (). Two CNV detection algorithms, PennCNV and QuantiSNP, were used and all samples met stringent quality control criteria as described. For SNV detection, 429 individuals (212 independent patients with ASD and 217 controls) were screened for muta […]