Variant Details

Variant: esv2756866

Internal ID

9632325

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr1:161374465..161711762	hg38	UCSC Ensembl
Inner	chr1:161344255..161681552	hg19	UCSC Ensembl
Inner	chr1:159610879..159948176	hg18	UCSC Ensembl
Inner	chr1:158157328..158413210	hg17	UCSC Ensembl

Cytoband

1q23.3

Allele length

Assembly	Allele length
hg38	337298
hg19	337298
hg18	337298
hg17	255883

Variant Type

CNV gain+loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2758972

Supporting Variants

essv24352, essv13501, essv3903, essv19866, essv8562, essv19311, essv23720, essv5007, essv2565, essv5862, essv15942, essv19737, essv18558, essv24324, essv6057, essv10615, essv3508, essv24647, essv3577, essv623, essv5641, essv19379, essv7633, essv15161, essv9543, essv20874, essv12956, essv6096, essv25032, essv2363, essv20462, essv6439, essv22791, essv13817, essv7922, essv14942, essv17988, essv13240, essv929, essv3254, essv23302, essv25099, essv8043, essv4108, essv3445, essv5783, essv4308, essv8693, essv20987, essv6858, essv22275

Samples

NA18998, NA18861, NA18592, NA12814, NA10851, NA18999, NA18603, NA12801, NA12813, NA18967, NA10846, NA18995, NA18558, NA18547, NA19131, NA18960, NA18571, NA12762, NA18949, NA12005, NA07019, NA19209, NA10839, NA19210, NA07022, NA12753, NA10863, NA18956, NA18515, NA18529, NA18579, NA19103, NA18503, NA12234, NA18573, NA18912, NA18853, NA12264, NA12145, NA18555, NA19132, NA18974, NA18914, NA11882, NA18540, NA18564, NA10859, NA06994, NA18987, NA19211, NA19102

Known Genes

FCGR2A, FCGR2B, FCGR2C, FCGR3A, FCGR3B, FCRLA, HSPA6, HSPA7, RPL31P11

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)

esv2756866

Frequency

Sample Size	270
Observed Gain	28
Observed Loss	23
Observed Complex	0
Frequency	n/a