Variant Details

Variant: nssv545969

Internal ID

15206661

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr9:136501021..136727572	hg38	UCSC Ensembl
Inner	chr9:139395473..139622024	hg19	UCSC Ensembl
Inner	chr9:138515294..138741845	hg18	UCSC Ensembl

Cytoband

9q34.3

Allele length

Assembly	Allele length
hg38	226552
hg19	226552
hg18	226552

Variant Type

CNV loss

Copy Number

Allele State

Heterozygous

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

nsv469918

Supporting Variants

Samples

HGDP00328

Known Genes

AGPAT2, EGFL7, FAM69B, MIR126, MIR4673, MIR4674, NOTCH1, SNHG7, SNORA17, SNORA43

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)

nssv545969

Frequency

Sample Size	443
Observed Gain	0
Observed Loss	1
Observed Complex	0
Frequency	n/a