Affymetrix사의 SNP array 플랫폼 가운데 하나. CNV도 확인할 수 있다. GEO platform GPL6801 GWAS study에도 많이 사용됨. 줄여서 SNP6라고도 함.

Chip contents #

Total 1.8 million marker

• 906,600 SNP markers
  • Unbiased selection of 482,000 SNPs (from 5.0)
  • Additional 424,000 SNPs
    • Tag SNPs
    • SNPs from chromosomes X and Y
    • Mitochondrial SNPs
    • New SNPs added to the dbSNP database
    • SNPs in recombination hotspots
• 946,000 CNV probes
  • 202,000 probes targetting 5,677 known CNV region from the Toronto Database of Genomic Variants
  • Regions resolve into 3,182 distinct, non-overlapping segments (on average 61 probes per region)
  • 744,000 probes, evenly spaced along the genome

특징 #

Allele-specific copy number 확인 가능

(Genotype information in addition to the quantitative copy number information from a single assay allows researchers to identify uniparental disomy events and distinguish between different genetic mechanisms of loss of heterozygosity (LOH).)

분석 소프트웨어 #

1. Genotyping Console Software: Affymetrix GUI
2. Affymetrix Power Tools: Command line interface
3. PennCNV

관련자료 #

• Technical Note in Affymetrix homepage
• SNP 6.0 GeneChip arrays: Strengths and limitations for copy number analysis
• Copy-neutral loss of heterozygosity in Cancer in Affymetrix application note

Incoming Links #

Related Articles (Article 0) #

• 암 맞춤의학과 생물정보학

Related Datasets (Dataset 1) #

• METABRIC

Related Medical Scholarly Articles (MedicalScholarlyArticle 2) #

• Comparison of custom capture for targeted next-generation DNA sequencing
• Comprehensive molecular portraits of human breast tumours
• Gene-based comparative analysis of tools for estimating copy number alterations using whole-exome sequencing data
• Landscape of somatic mutations in 560 breast cancer whole-genome sequences
• The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

Related Education Events (EducationEvent 3) #

• 2015 통계유전학워크숍

Related Codes (Code 4) #

• Affymetrix Power Tools
• GISTIC
• PennCNV

Suggested Pages #

• 0.123 TPX2
• 0.083 eQTL
• 0.077 Tumorscape
• 0.070 Cancer genome data analysis and knowledgebase
• 0.051 CPT1A
• 0.039 BCL11A is a triple-negative breast cancer gene with critical functions in stem and progenitor cells
• 0.033 Biochip
• 0.025 June 27
• 0.025 Nucleic Acids Research
• 0.025 Santa Clara
• More suggestions...