Variant Details

Variant: esv2758773

Internal ID

9634232

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr19:55724171..55814940	hg38	UCSC Ensembl
Inner	chr19:56235537..56326306	hg19	UCSC Ensembl
Inner	chr19:60927349..61018118	hg18	UCSC Ensembl
Inner	chr19:60927349..61018118	hg17	UCSC Ensembl

Cytoband

19q13.42

Allele length

Assembly	Allele length
hg38	90770
hg19	90770
hg18	90770
hg17	90770

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

esv2757705

Samples

NA18947, NA18561, NA18999, NA18967, NA19171, NA18992, NA18987, NA18994, NA18968, NA18562, NA18965, NA18577

Known Genes

NLRP11, NLRP9, RFPL4A, RFPL4AL1

Method

SNP array

Analysis

The algorithm used to call CNVs using the 500K EA platform was developed to accurately define CNV regions using a large set of reference samples and is described in detail in a separate publication (Komura 2006). The algorithm contains three major parts: 1) Intensity pre-processing using an improved version of Genomic Imbalance Map (GIM) (Ishikawa et al. 2005), including probe selection, noise reduction, normalization, and intensity ratio adjustment based on affinity differences between alleles of a SNP, 2) CNV extraction, which identifies CNVs from all pair-wise comparisons using a modified SW-ARRAY, and 3) A copy number inference step which utilizes signal ratios and SNP information to more precisely define CNV boundaries and the copy number within each region.

Platform

Affymetrix GeneChip Early Access Mapping 500K Set Array (250K_Nsp_SNP)

Comments

Reference

Redon_et_al_2006

Pubmed ID

17122850

Accession Number(s)

esv2758773

Frequency

Sample Size	270
Observed Gain	12
Observed Loss	0
Observed Complex	0
Frequency	n/a