Variant DetailsVariant: nsv435891 | Internal ID | 15033695 | | Landmark | | | Location Information | | | Cytoband | Xp11.21 | | Allele length | | Assembly | Allele length | | hg38 | 2791335 | | hg19 | 2788739 | | hg18 | 2788739 |
| | Variant Type | CNV deletion | | Copy Number | | | Allele State | | | Allele Origin | | | Probe Count | | | Validation Flag | | | Merged Status | M | | Merged Variants | | | Supporting Variants | nssv465805 | | Samples | NA15510 | | Known Genes | ALAS2, APEX2, FAM104B, FAM120C, FAM156A, FAM156B, FGD1, FOXR2, GNL3L, GPR173, HSD17B10, HUWE1, IQSEC2, ITIH6, KDM5C, MAGED2, MAGEH1, MIR4536-1, MIR5684, MIR6857, MIR6894, MIR6895, MIR98, MIRLET7F2, MTRNR2L10, PAGE2, PAGE2B, PAGE3, PAGE5, PFKFB1, PHF8, RIBC1, SMC1A, SNORA11, TRO, TSPYL2, TSR2, USP51, WNK3, XAGE3 | | Method | Sequencing | | Analysis | The 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. | | Platform | 454 | | Comments | | | Reference | Korbel_et_al_2007 | | Pubmed ID | 17901297 | | Accession Number(s) | nsv435891
| | Frequency | | Sample Size | 2 | | Observed Gain | 0 | | Observed Loss | 1 | | Observed Complex | 0 | | Frequency | n/a |
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