Variant Details

Variant: nsv471322

Internal ID

15211195

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr9:124247835..124357163	hg38	UCSC Ensembl
Inner	chr9:127010114..127119442	hg19	UCSC Ensembl
Inner	chr9:126049935..126159263	hg18	UCSC Ensembl

Cytoband

9q33.3

Allele length

Assembly	Allele length
hg38	109329
hg19	109329
hg18	109329

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv545905, nssv545911, nssv545906, nssv545910, nssv545908, nssv545907

Samples

HGDP00315, HGDP00290, HGDP00323, HGDP00288, HGDP00951, HGDP00789

Known Genes

LOC100129034, NEK6, PSMB7

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)

nsv471322

Frequency

Sample Size	443
Observed Gain	0
Observed Loss	6
Observed Complex	0
Frequency	n/a