nstd105 - Onozawa et al 2015 - dbVar Study

nstd105 (Onozawa et al. 2015)

Organism:: Human
Study Type:: Collection
Submitter:: Masahiro Onozawa
Description:: We reported a previously unrecognized form of polymorphic insertions, termed Templated Sequence Insertion Polymorphism (TSIP), in which the inserted sequence was templated from a distant genomic region. TSIPs can be grouped into two classes based on nucleotide sequence features at the insertion junctions; Class 1 TSIPs show target site duplication (TSD), polyadenylation, and preference for insertion at a 5’-TTTT/A-3’ sequence, suggesting a LINE-1 based insertion mechanism, whereas class 2 TSIPs show features consistent with repair of a DNA double strand break by non-homologous end joining. We evaluated whole genome sequence from 52 individuals, and identified 171 TSIPs. Mitochondrial sequences were a frequent template for class 2 insertions, used more commonly than any nuclear chromosome. See Variant Summary counts for nstd105 in dbVar Variant Summary.
Publication(s):: Onozawa et al. 2015

Links

Source: NCBI

Detailed Information: Download 171 Variant Regions, Download 171 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Submitted: GRCh37 (hg19)

Variant Summary for:

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.11	Chr1	15	15	Remapped	NC_000001.11
NC_000002.12	Chr2	18	18	Remapped	NC_000002.12
NC_000003.12	Chr3	8	8	Remapped	NC_000003.12
NC_000004.12	Chr4	13	13	Remapped	NC_000004.12
NC_000005.10	Chr5	9	9	Remapped	NC_000005.10
NC_000006.12	Chr6	12	12	Remapped	NC_000006.12
NC_000007.14	Chr7	9	9	Remapped	NC_000007.14
NC_000008.11	Chr8	4	4	Remapped	NC_000008.11
NC_000009.12	Chr9	4	4	Remapped	NC_000009.12
NC_000010.11	Chr10	4	4	Remapped	NC_000010.11
NC_000011.10	Chr11	9	9	Remapped	NC_000011.10
NC_000012.12	Chr12	13	13	Remapped	NC_000012.12
NC_000013.11	Chr13	4	4	Remapped	NC_000013.11
NC_000014.9	Chr14	6	6	Remapped	NC_000014.9
NC_000015.10	Chr15	5	5	Remapped	NC_000015.10
NC_000016.10	Chr16	3	3	Remapped	NC_000016.10
NC_000017.11	Chr17	10	10	Remapped	NC_000017.11
NC_000018.10	Chr18	1	1	Remapped	NC_000018.10
NC_000019.10	Chr19	4	4	Remapped	NC_000019.10
NC_000020.11	Chr20	4	4	Remapped	NC_000020.11
NC_000021.9	Chr21	2	2	Remapped	NC_000021.9
NC_000022.11	Chr22	5	5	Remapped	NC_000022.11
NC_000023.11	ChrX	8	8	Remapped	NC_000023.11
NC_000024.10	ChrY	1	1	Remapped	NC_000024.10
NT_187514.1	Chr1\|NT_187514.1	1	1	Remapped	NT_187514.1
NW_013171804.1	Chr9\|NW_013171804.1	1	1	Remapped	NW_013171804.1
NT_187632.1	Chr22\|NT_187632.1	1	1	Remapped	NT_187632.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	15	15	Submitted	NC_000001.10
NC_000002.11	Chr2	18	18	Submitted	NC_000002.11
NC_000003.11	Chr3	8	8	Submitted	NC_000003.11
NC_000004.11	Chr4	13	13	Submitted	NC_000004.11
NC_000005.9	Chr5	9	9	Submitted	NC_000005.9
NC_000006.11	Chr6	12	12	Submitted	NC_000006.11
NC_000007.13	Chr7	9	9	Submitted	NC_000007.13
NC_000008.10	Chr8	4	4	Submitted	NC_000008.10
NC_000009.11	Chr9	4	4	Submitted	NC_000009.11
NC_000010.10	Chr10	4	4	Submitted	NC_000010.10
NC_000011.9	Chr11	9	9	Submitted	NC_000011.9
NC_000012.11	Chr12	13	13	Submitted	NC_000012.11
NC_000013.10	Chr13	4	4	Submitted	NC_000013.10
NC_000014.8	Chr14	6	6	Submitted	NC_000014.8
NC_000015.9	Chr15	5	5	Submitted	NC_000015.9
NC_000016.9	Chr16	3	3	Submitted	NC_000016.9
NC_000017.10	Chr17	10	10	Submitted	NC_000017.10
NC_000018.9	Chr18	1	1	Submitted	NC_000018.9
NC_000019.9	Chr19	4	4	Submitted	NC_000019.9
NC_000020.10	Chr20	4	4	Submitted	NC_000020.10
NC_000021.8	Chr21	2	2	Submitted	NC_000021.8
NC_000022.10	Chr22	5	5	Submitted	NC_000022.10
NC_000023.10	ChrX	8	8	Submitted	NC_000023.10
NC_000024.9	ChrY	1	1	Submitted	NC_000024.9

Remapping summary:

			Variant Region remap status						Variant Call remap status
Sequence ID	Chr	Variant Regions on source	Perfect	Good	Pass	Fail	Mult	Variant Calls on source	Perfect	Good	Pass	Fail	Mult
NC_000001.10	Chr1	15	14	0	0	0	1	15	14	0	0	0	1
NC_000002.11	Chr2	18	18	0	0	0	0	18	18	0	0	0	0
NC_000003.11	Chr3	8	8	0	0	0	0	8	8	0	0	0	0
NC_000004.11	Chr4	13	13	0	0	0	0	13	13	0	0	0	0
NC_000005.9	Chr5	9	9	0	0	0	0	9	9	0	0	0	0
NC_000006.11	Chr6	12	12	0	0	0	0	12	12	0	0	0	0
NC_000007.13	Chr7	9	9	0	0	0	0	9	9	0	0	0	0
NC_000008.10	Chr8	4	4	0	0	0	0	4	4	0	0	0	0
NC_000009.11	Chr9	4	3	0	0	0	1	4	3	0	0	0	1
NC_000010.10	Chr10	4	4	0	0	0	0	4	4	0	0	0	0
NC_000011.9	Chr11	9	9	0	0	0	0	9	9	0	0	0	0
NC_000012.11	Chr12	13	13	0	0	0	0	13	13	0	0	0	0
NC_000013.10	Chr13	4	4	0	0	0	0	4	4	0	0	0	0
NC_000014.8	Chr14	6	6	0	0	0	0	6	6	0	0	0	0
NC_000015.9	Chr15	5	5	0	0	0	0	5	5	0	0	0	0
NC_000016.9	Chr16	3	3	0	0	0	0	3	3	0	0	0	0
NC_000017.10	Chr17	10	10	0	0	0	0	10	10	0	0	0	0
NC_000018.9	Chr18	1	1	0	0	0	0	1	1	0	0	0	0
NC_000019.9	Chr19	4	4	0	0	0	0	4	4	0	0	0	0
NC_000020.10	Chr20	4	4	0	0	0	0	4	4	0	0	0	0
NC_000021.8	Chr21	2	2	0	0	0	0	2	2	0	0	0	0
NC_000022.10	Chr22	5	4	0	0	0	1	5	4	0	0	0	1
NC_000023.10	ChrX	8	8	0	0	0	0	8	8	0	0	0	0
NC_000024.9	ChrY	1	1	0	0	0	0	1	1	0	0	0	0

Samplesets

Number of Samplesets: 1

Size:: 52
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
NA19704	NA19704	Female	ASW	Not reported
NA06985	NA06985	Female	CEU	Not reported
NA18508	NA18508	Female	YRI	Not reported
NA18505	NA18505	Female	YRI	Not reported
NA20511	NA20511	Male	TSI	Not reported
NA10851	NA10851	Male	CEU	Not reported
NA19700	NA19700	Male	ASW	Not reported
NA18502	NA18502	Female	YRI	Not reported
NA12004	NA12004	Female	CEU	Not reported
NA20847	NA20847	Female	GIH	Not reported
NA07357	NA07357	Male	CEU	Not reported
NA19669	NA19669	Female	MXL	Not reported
NA20846	NA20846	Male	GIH	Not reported
NA19735	NA19735	Male	MXL	Not reported
NA18558	NA18558	Male	CHB	Not reported
NA20845	NA20845	Male	GIH	Not reported
NA06994	NA06994	Male	CEU	Not reported
NA18942	NA18942	Female	JPT	Not reported
NA21737	NA21737	Male	MKK	Not reported
NA20850	NA20850	Male	GIH	Not reported
NA20509	NA20509	Male	TSI	Not reported
HG00731	HG00731	Male	PUR	Not reported
NA12889	NA12889	Male	CEU	Not reported
NA19020	NA19020	Male	LWK	Not reported
NA19703	NA19703	Male	ASW	Not reported
NA19649	NA19649	Male	MXL	Not reported
NA19025	NA19025	Male	LWK	Not reported
NA18537	NA18537	Female	CHB	Not reported
NA21732	NA21732	Male	MKK	Not reported
NA12891	NA12891	Male	CEU	Not reported
NA18940	NA18940	Male	JPT	Not reported
NA12892	NA12892	Female	CEU	Not reported
NA19648	NA19648	Female	MXL	Not reported
NA19701	NA19701	Female	ASW	Not reported
NA21767	NA21767	Female		Not reported
NA18555	NA18555	Female	CHB	Not reported
NA18947	NA18947	Female	JPT	Not reported
NA20510	NA20510	Male	TSI	Not reported
NA19834	NA19834	Male	ASW	Not reported
NA19026	NA19026	Male	LWK	Not reported
NA12890	NA12890	Female	CEU	Not reported
NA18526	NA18526	Female	CHB	Not reported
NA19670	NA19670	Male	MXL	Not reported
NA19129	NA19129	Female	YRI	Not reported
NA18956	NA18956	Female	JPT	Not reported
NA18517	NA18517	Female	YRI	Not reported
NA19017	NA19017	Female	LWK	Not reported
NA21733	NA21733	Female	MKK	Not reported
NA20502	NA20502	Female	TSI	Not reported
NA18504	NA18504	Male	YRI	Not reported
NA18501	NA18501	Male	YRI	Not reported
HG00732	HG00732	Female	PUR	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	Sequencing	Sequence alignment	Complete Genomics Analysis Platform	171
2	Validation	Sequencing	Sequence alignment	Sanger Sequencing Validation	69

Validations

Experiment ID	Method	Analysis	Platform	Number of Variant Calls Validated
2	Sequencing	Sequence alignment	Sanger Sequencing Validation	69

dbVar

Database of genomic structural variation

nstd105 (Onozawa et al. 2015)

Links

Detailed Information: Download 171 Variant Regions, Download 171 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38.p12 (hg38)GRCh37 (hg19)

Remapping summary: GRCh37->GRCh38.p12

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

Variant Summary for:

Remapping summary: