Variant Details

Variant: nsv827709

Internal ID

16090183

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr1:246230271..246237297	hg38	UCSC Ensembl
Inner	chr1:246393573..246400599	hg19	UCSC Ensembl
Inner	chr1:244460196..244467222	hg18	UCSC Ensembl

Cytoband

1q44

Allele length

Assembly	Allele length
hg38	7027
hg19	7027
hg18	7027

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

dgv114n67

Supporting Variants

nssv1434231, nssv1431134

Samples

NA18570, AK18

Known Genes

SMYD3

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)

nsv827709

Frequency

Sample Size	31
Observed Gain	0
Observed Loss	2
Observed Complex	0
Frequency	n/a