array analysis platform genotyping command line interface iaap cli (Illumina Inc)
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Illumina Inc
array analysis platform genotyping command line interface iaap cli
Array Analysis Platform Genotyping Command Line Interface Iaap Cli, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/command+line+interface+(cli)+to/gtc2vcf+script/pmc10961362-69-19-18
Average 90 stars, based on 1 article reviews
Array Analysis Platform Genotyping Command Line Interface Iaap Cli, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/command+line+interface+(cli)+to/gtc2vcf+script/pmc10961362-69-19-18
Average 90 stars, based on 1 article reviews
array analysis platform genotyping command line interface iaap cli - by Bioz Stars,
2026-09
90/100 stars
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1) Product Images from "Development and validation of a pharmacogenomics reporting workflow based on the illumina global screening array chip"
Article Title: Development and validation of a pharmacogenomics reporting workflow based on the illumina global screening array chip
Journal: Frontiers in Pharmacology
doi: 10.3389/fphar.2024.1349203
Figure Legend Snippet: Patient journey for PGx testing workflow. During the pre-test consultation, patients provide informed consent, complete a PGx survey, and submit a DNA sample from a buccal swab. This sample undergoes DNA extraction and array genotyping, followed by bioinformatic analysis to characterize variants in selected PGx genes. Genotype calls are subsequently interpreted into metabolizer profiles and annotated with actionable recommendations from published guidelines. Finally, results are compiled into a PDF report, which is discussed with the patient during a post-test consultation.
Techniques Used: DNA Extraction
Figure Legend Snippet: Validation study design. (A) . DNA from a total of 73 unique reference cell lines were genotyped on the GSA chip to assess genotyping accuracy. Samples were selected due to the availability of well-characterized reference genotype calls (1KGP, GIAB) or reference calls for important PGx genes that have been validated experimentally by multiple labs (GeT-RM). (B) . Breakdown of samples by experiment. GIAB samples were ran in triplicate in a 3:1:1 design to enable measurement of inter- and intra-run reproducibility. Selected GeT-RM samples with known copy number variations (CNV) were also run across three runs to assess inter-run reproducibility of CNV calling.
Techniques Used: Biomarker Discovery
Figure Legend Snippet: Genotyping concordance against 65 accuracy controls (per-site analysis). Heatmap showing concordance of 114 variants with true positives. 1KGP and GIAB samples were utilized as accuracy controls. Imputed sites have a lower callability compared to sites that are directly genotyped. TP (hom alt), True positive homozygous alternate; TN (het), true positive heterozygous; TN, True negative; FP, false positive; FN, false negative; NA, not in reference.
Techniques Used:
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