Variant Details

Variant: nsv469998

Internal ID

15209871

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr4:815805..1093743	hg38	UCSC Ensembl
Inner	chr4:809593..1087531	hg19	UCSC Ensembl
Inner	chr4:799593..1077531	hg18	UCSC Ensembl

Cytoband

4p16.3

Allele length

Assembly	Allele length
hg38	277939
hg19	277939
hg18	277939

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv546239, nssv546237, nssv546233, nssv546236, nssv546234, nssv546235, nssv546238, nssv546232

Samples

HGDP00543, HGDP00290, HGDP00288, HGDP00661, HGDP00298, HGDP00978, HGDP00550, HGDP00825

Known Genes

CPLX1, DGKQ, FGFRL1, GAK, IDUA, RNF212, SLC26A1, TMEM175

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)

nsv469998

Frequency

Sample Size	443
Observed Gain	0
Observed Loss	8
Observed Complex	0
Frequency	n/a