Variant Details

Variant: nsv471171

Internal ID

15211044

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr7:45653..200682	hg38	UCSC Ensembl
Inner	chr7:45653..200682	hg19	UCSC Ensembl
Inner	chr7:140736..295765	hg18	UCSC Ensembl

Cytoband

7p22.3

Allele length

Assembly	Allele length
hg38	155030
hg19	155030
hg18	155030

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv544754, nssv544765, nssv544798, nssv544787, nssv544810, nssv544776

Samples

HGDP01090, HGDP00457, HGDP00992, HGDP01091, HGDP00064, HGDP01036

Known Genes

FAM20C, LOC100507642

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

Double-copy duplication

Reference

Jakobsson_et_al_2008

Pubmed ID

18288195

Accession Number(s)

nsv471171

Frequency

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