Variant Details

Variant: nsv821643

Internal ID

16064018

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr5:69272838..71076658	hg38	UCSC Ensembl
Inner	chr5:68568665..70372485	hg19	UCSC Ensembl
Inner	chr5:68604421..70408241	hg18	UCSC Ensembl
Inner	chr5:68604421..70408241	hg17	UCSC Ensembl

Cytoband

5q13.2

Allele length

Assembly	Allele length
hg38	1803821
hg19	1803821
hg18	1803821
hg17	1803821

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv1421392, nssv1421399, nssv1421391, nssv1421393, nssv1421402, nssv1421395, nssv1421401, nssv1421390, nssv1421398, nssv1421394, nssv1421400, nssv1421397

Samples

Known Genes

AK6, CCDC125, CDK7, GTF2H2, GTF2H2B, GTF2H2C, GTF2H2D, GUSBP3, GUSBP9, LOC100272216, LOC441081, LOC647859, MARVELD2, NAIP, OCLN, RAD17, SERF1A, SERF1B, SMA4, SMA5, SMN1, SMN2, TAF9

Method

ROMA

Analysis

Measured intensities without background subtraction were used to calculate ratios. Data were normalized using an intensity-based lowess curve fitting algorithm similar to that described in Yang et al. Log ratio values obtained from color reversal experiments were averaged and displayed as presented in the figures. Copy number polymorphisms (CNPs) were identified based on probe ratios using a Hidden Markov Model.

Platform

A custom Nimblegen photoprint 85,000 probe ROMA oligo array platform was used.

Comments

Reference

Sebat_et_al_2004

Pubmed ID

15273396

Accession Number(s)

nsv821643

Frequency

Sample Size	31
Observed Gain	0
Observed Loss	12
Observed Complex	0
Frequency	n/a