Variant Details

Variant: nsv470002

Internal ID

15209875

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr4:2699371..2834901	hg38	UCSC Ensembl
Inner	chr4:2701098..2836628	hg19	UCSC Ensembl
Inner	chr4:2670896..2806426	hg18	UCSC Ensembl

Cytoband

4p16.3

Allele length

Assembly	Allele length
hg38	135531
hg19	135531
hg18	135531

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv546248, nssv546247

Samples

HGDP00298, HGDP00302

Known Genes

FAM193A, SH3BP2, TNIP2

Method

SNP array

Analysis

We used the previously validated default quality control criteria, excluding samples with a log R ratio standard deviation of >0.28, a median B allele frequency of >0.55 or <0.45, or a B allele frequency drift of >0.002 (for more details see Wang et al. 2007). As the PennCNV algorithm is more sensitive and specific to CNVs covering greater numbers of SNPs in the HumanHap550 array, use of a minimum number of SNPs in CNV detection increases the reliability of CNV calls (with a consequent reduction in calls per individual). We set 10 SNPs as the minimum detection threshold in the algorithm.

Platform

Illumina HumanHap550 Genotyping BeadChip v3

Comments

Reference

Jakobsson_et_al_2008

Pubmed ID

18288195

Accession Number(s)

nsv470002

Frequency

Sample Size	443
Observed Gain	0
Observed Loss	2
Observed Complex	0
Frequency	n/a