A curated catalogue of human genomic structural variation




Variant Details

Variant: dgv16n16



Internal ID11600399
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chr1:148976467..148989036hg38UCSC Ensembl
chr1:144895438..144908007hg19UCSC Ensembl
chr1:143606795..143619364hg18UCSC Ensembl
Cytoband1q21.1
Allele length
AssemblyAllele length
hg3812570
hg1912570
hg1812570
Variant TypeCNV deletion
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnsv435844, nsv436181
SamplesNA15510, NA18505
Known GenesLOC100288142, NBPF12, NBPF9, PDE4DIP
MethodSequencing
AnalysisThe best placements of paired-ends were used for identifying several different categories of SV: (i) deletions (size sd=3 kb) were identified from two or more overlapping discordant paired-ends with paired-end span >cutoff (with the condition that both putative breakpoints are spanned); (ii) simple insertions (3 kb > ssi > 2 kb) were identified from two or more overlapping discordant paired-ends with paired-end span < cutoff; (iii) mated insertions were identified from two unpaired SVs that lie in nearby (i.e. 6 kb) genomic regions and had =2 paired-ends linking to a common, distant genomic region <100 kb; mated insertions may involve tandem duplications or events related to transpositions. (iv) Inversions were called when =2 paired-ends matched different strands. (v) Unmated insertions were predicted from =2 paired ends that support a rearrangement of a genomic region in which loci change relative order without changing the relative orientation (i.e., the strand). (These events are similar to mated insertions; however, unmated insertions have only one assigned breakpoint.) In each case we required at least two paired-ends to support a predicted SV. Furthermore, at least one paired-end had to match the human reference genome at sequence identity =97%. In addition, ends were required to yield best-scoring sequence alignments genome-wide to their respective region as assessed by Blat.
Platform454
Comments
ReferenceKorbel_et_al_2007
Pubmed ID17901297
Accession Number(s)dgv16n16
Frequency
Sample Size2
Observed Gain0
Observed Loss2
Observed Complex0
Frequencyn/a


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