Variant Details

Variant: nsv470043

Internal ID

15556602

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr4:67931662..68011858	hg38	UCSC Ensembl
Inner	chr4:68797380..68877576	hg19	UCSC Ensembl
Inner	chr4:68479975..68560171	hg18	UCSC Ensembl

Cytoband

4q13.2

Allele length

Assembly	Allele length
hg38	80197
hg19	80197
hg18	80197

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv546324, nssv546325, nssv546323, nssv546322

Samples

HGDP00315, HGDP00281, HGDP00333, HGDP00313

Known Genes

TMPRSS11A, TMPRSS11GP

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)

nsv470043

Frequency

Sample Size	443
Observed Gain	0
Observed Loss	4
Observed Complex	0
Frequency	n/a