Variant DetailsVariant: nssv466592 | Internal ID | 15379513 | | Landmark | | | Location Information | | | Cytoband | 10q11.22 | | Allele length | | Assembly | Allele length | | hg19 | 2698225 | | hg18 | 2948225 |
| | Variant Type | CNV deletion | | Copy Number | | | Allele State | | | Allele Origin | | | Probe Count | | | Validation Flag | | | Merged Status | S | | Merged Variants | nsv436102 | | Supporting Variants | | | Samples | NA18505 | | Known Genes | AGAP9, ANTXRL, ANTXRLP1, ANXA8, ANXA8L1, ANXA8L2, BMS1P1, BMS1P2, BMS1P5, BMS1P6, CTGLF12P, CTSLP2, FAM21B, FAM25B, FAM25C, FAM25G, FAM35BP, FAM35DP, FRMPD2, FRMPD2P1, GDF10, GDF2, GLUD1P7, GPRIN2, HNRNPA1P33, LINC00842, LOC100996758, NPY4R, PTPN20A, PTPN20B, RBP3, SYT15, ZNF488 | | 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) | nssv466592
| | Frequency | | Sample Size | 2 | | Observed Gain | 0 | | Observed Loss | 1 | | Observed Complex | 0 | | Frequency | n/a |
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