Variant Details

Variant: dgv3e212

Internal ID

20148459

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
	chr1:1685551..1756235	hg38	UCSC Ensembl
	chr1:1616990..1687674	hg19	UCSC Ensembl

Cytoband

1p36.33

Allele length

Assembly	Allele length
hg38	70685
hg19	70685

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

esv3577681, esv3577680, esv3577683, esv3577690, esv3577685, esv3577687, esv3577692, esv3577679, esv3577684, esv3577688, esv3577689, esv3577691

Samples

401459HF, 401636WR, 400920MK, 401465TB, 400439IM, 401005BL, 400739SS, 401640WJ, 400821FE, 401734PG, 400094RS, 401956DQ, 401592NR, 400294HD, 401036WS, 400083TG, 401841OB, 401491BB, 401096SL, 400199SA, 400191MP, 400155CW, 401860TJ, 400227MM, 401113MJ, 400203NA, 400231LP, 401664SD, 401855RE, 401773AM, 400502GS, 401353BC, 400041LJ, 401979TB, 401386WA, 400383HL, 401274PA, 400070PC, 401540NA, 401589HP, 400758KP, 400076LC, 401444LD, 401414CR, 400249BC, 401067BD, 400248JO, 400319HT, 400177CG, 401595BL, 400458LS, 402009WP, 400712GC, 400156WT, 401268PS, 400376SJ, 401847RK, 401958MF, 401894PD, 400501SJ, 401438HT, 401858TP, 400930MK, 402008MC, 401250WD, 400108BJ, 401735LE, 400833BB, 402042BJ, 400178RH, 401612HB, 401395OP, 400494ML, 401111LH, 401102RD

Known Genes

CDK11A, CDK11B, MMP23A, NADK, SLC35E2, SLC35E2B

Method

SNP array

Analysis

We used four separate algorithms to detect CNVs; Affymetrix Chromosome Analysis Suite (ChAS), iPattern, Nexus and Partek. Our primary analysis was performed based on ChAS CNV calls, which were then supported using the remaining three algorithms to construct a confidence set of CNVs. For all algorithms, we have used 8 probes and >1kb as a base line cutoff for CNV detection.

Platform

Affymetrix CytoScan HD 2.7M array

Comments

Reference

Uddin_et_al_2014

Pubmed ID

25503493

Accession Number(s)

dgv3e212

Frequency

Sample Size	873
Observed Gain	0
Observed Loss	75
Observed Complex	0
Frequency	n/a