Variant Details

Variant: nsv824940

Internal ID

16087414

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr9:69123210..69128454	hg38	UCSC Ensembl
Inner	chr9:71738126..71743370	hg19	UCSC Ensembl
Inner	chr9:70927946..70933190	hg18	UCSC Ensembl

Cytoband

9q21.11

Allele length

Assembly	Allele length
hg38	5245
hg19	5245
hg18	5245

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv1432226, nssv1434555, nssv1426852, nssv1425924, nssv1421974, nssv1436816, nssv1423577, nssv1440488, nssv1438291, nssv1429224, nssv1427829, nssv1422754, nssv1428175, nssv1421877, nssv1427647, nssv1439817, nssv1429970

Samples

NA18947, AK20, NA18999, AK6, NA18547, AK14, AK8, NA18951, NA18537, NA18570, NA18542, NA18564, AK12, AK4, NA18552, NA18968, NA18997

Known Genes

TJP2

Method

Oligo aCGH

Analysis

To select parameters for calling CNVs (that is, the statistical threshold of the ADM2 algorithm, the minimum +/- log2 ratio and the minimum number of consecutive probes in a CNV interval), we calculated the sensitivity and positive predictive value based on the comparison of aCGH-based CNV calls (using our high-resolution Agilent 24M platform) with read-depth sequence data for two samples from Korean individuals (AK1 and AK2). We attempted to obtain `absolute' copy number status of the sample from NA10851, which was used as the reference sample for aCGH experiments in this study. For this, we used read-depth data for NA10851 obtained from massively parallel sequencing by the Illumina GA II data. The read-depth data represent the copy number status of NA10851 as compared to the human reference genome (hg18) because the short read sequences were aligned to hg18.

Platform

Agilent 24M aCGH

Comments

Reference

Park_et_al_2010

Pubmed ID

20364138

Accession Number(s)

nsv824940

Frequency

Sample Size	31
Observed Gain	0
Observed Loss	17
Observed Complex	0
Frequency	n/a