nstd23 - Young et al 2008 - dbVar Study

nstd23 (Young et al. 2008)

Organism:: Human
Study Type:: Control Set
Submitter:: Janet Young
Description:: We have undertaken a detailed study of copy-number variation of ORs to elucidate the selective and mechanistic forces acting on this gene family and the true impact of copy-number variation on human OR repertoires. See Variant Summary counts for nstd23 in dbVar Variant Summary.
Publication(s):: Young et al. 2008

Links

Source: NCBI

Detailed Information: Download 10 Variant Regions, Download 157 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Remapped: GRCh37.p13 (hg19)
Submitted: NCBI36 (hg18)

Variant Summary for:

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.11	Chr1	2	9	Remapped	NC_000001.11
NC_000011.10	Chr11	6	83	Remapped	NC_000011.10
NC_000014.9	Chr14	1	27	Remapped	NC_000014.9

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	2	9	Remapped	NC_000001.10
NC_000011.9	Chr11	7	121	Remapped	NC_000011.9
NC_000014.8	Chr14	1	27	Remapped	NC_000014.8

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.9	Chr1	2	9	Submitted	NC_000001.9
NC_000011.8	Chr11	7	121	Submitted	NC_000011.8
NC_000014.7	Chr14	1	27	Submitted	NC_000014.7

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_000001.9	Chr1	2	2	0	0	0	0	9	9	0	0	0	0
NC_000011.8	Chr11	7	7	0	0	0	0	121	121	0	0	0	0
NC_000014.7	Chr14	1	1	0	0	0	0	27	27	0	0	0	0

			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_000001.9	Chr1	2	2	0	0	0	0	9	9	0	0	0	0
NC_000011.8	Chr11	7	6	0	0	1	0	121	83	0	0	38	0
NC_000014.7	Chr14	1	1	0	0	0	0	27	27	0	0	0	0

Samplesets

Number of Samplesets: 1

Description:: 52 individuals of various geographic origins
Size:: 52
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Phenotype
GM10492	B-lymphocyte	GM10492	Male	MBUTI PYGMY	Not reported
GM01814	B-lymphocyte	GM01814	Female	CAUCASIAN	Not reported
GM00946	B-lymphocyte	GM00946	Female	CAUCASIAN	Not reported
GM01310	B-lymphocyte	GM01310	Male	CAUCASIAN	Not reported
GM17037	B-lymphocyte	GM17037	Female	AFRICAN AMERICAN	Not reported
GM17034	B-lymphocyte	GM17034	Female	AFRICAN AMERICAN	Not reported
GM10539	B-lymphocyte	GM10539	Female	MELANESIAN	Not reported
GM11377	B-lymphocyte	GM11377	Male	CAMBODIAN	Not reported
GM10471	B-lymphocyte	GM10471	Female	BIAKA PYGMY	Not reported
GM01805	B-lymphocyte	GM01805	Female	CAUCASIAN	Not reported
GM01806	B-lymphocyte	GM01806	Male	CAUCASIAN	Not reported
GM14492	B-lymphocyte	GM14492	Male	CAUCASIAN	Not reported
GM17040	B-lymphocyte	GM17040	Female	AFRICAN AMERICAN	Not reported
GM10979	B-lymphocyte	GM10979	Female	MAYAN	Not reported
GM10541	B-lymphocyte	GM10541	Male	MELANESIAN	Not reported
GM10969	B-lymphocyte	GM10969	Male	KARITIANA	Not reported
GM10967	B-lymphocyte	GM10967	Female	KARITIANA	Not reported
GM17039	B-lymphocyte	GM17039	Female	AFRICAN AMERICAN	Not reported
GM17032	B-lymphocyte	GM17032	Female	AFRICAN AMERICAN	Not reported
GM11375	B-lymphocyte	GM11375		CAMBODIAN	Not reported
GM10494	B-lymphocyte	GM10494	Male	MBUTI PYGMY	Not reported
GM10542	B-lymphocyte	GM10542	Female	MELANESIAN	Not reported
GM08428	B-lymphocyte	GM08428	Male	CAUCASIAN	Not reported
GM17031	B-lymphocyte	GM17031	Female	AFRICAN AMERICAN	Not reported
GM11523	B-lymphocyte	GM11523	Female	DRUZE	Not reported
GM09948	B-lymphocyte	GM09948	Male	CAUCASIAN	Not reported
GM10534	B-lymphocyte	GM10534	Female	CAUCASIAN	Not reported
GM11373	B-lymphocyte	GM11373	Female	CAMBODIAN	Not reported
GM10469	B-lymphocyte	GM10469	Male	BIAKA PYGMY	Not reported
GM10965	B-lymphocyte	GM10965	Female	KARITIANA	Not reported
GM11522	B-lymphocyte	GM11522	Male	DRUZE	Not reported
GM10473	B-lymphocyte	GM10473	Female	BIAKA PYGMY	Not reported
GM10968	B-lymphocyte	GM10968	Male	KARITIANA	Not reported
GM10472	B-lymphocyte	GM10472	Female	BIAKA PYGMY	Not reported
GM01953	B-lymphocyte	GM01953	Female	CAUCASIAN	Not reported
GM10543	B-lymphocyte	GM10543	Female	MELANESIAN	Not reported
GM17036	B-lymphocyte	GM17036	Female	AFRICAN AMERICAN	Not reported
GM17035	B-lymphocyte	GM17035	Female	AFRICAN AMERICAN	Not reported
GM11524	B-lymphocyte	GM11524	Female	DRUZE	Not reported
GM10976	B-lymphocyte	GM10976	Male	MAYAN	Not reported
GM10540	B-lymphocyte	GM10540	Male	MELANESIAN	Not reported
GM10470	B-lymphocyte	GM10470	Male	BIAKA PYGMY	Not reported
GM11521	B-lymphocyte	GM11521	Female	DRUZE	Not reported
GM10978	B-lymphocyte	GM10978	Female	MAYAN	Not reported
GM11376	B-lymphocyte	GM11376	Female	CAMBODIAN	Not reported
GM17038	B-lymphocyte	GM17038	Female	AFRICAN AMERICAN	Not reported
GM17033	B-lymphocyte	GM17033	Female	AFRICAN AMERICAN	Not reported
GM10966	B-lymphocyte	GM10966	Female	KARITIANA	Not reported
GM11525	B-lymphocyte	GM11525	Female	DRUZE	Not reported
GM00893	B-lymphocyte	GM00893	Female	CAUCASIAN	Not reported
GM10493	B-lymphocyte	GM10493	Female	MBUTI PYGMY	Not reported
GM10975	B-lymphocyte	GM10975	Male	MAYAN	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Number of Variant Calls
1	Discovery	Sequencing	Sequence alignment	71
2	Discovery	Sequencing	Sequence alignment	50
3	Discovery	MLPA	Probe signal intensity	36
4	Validation	MLPA	Probe signal intensity	75
5	Validation	PCR	Manual observation	102

Validations

Experiment ID	Method	Analysis	Number of Variant Calls Validated
4	MLPA	Probe signal intensity	75
5	PCR	Manual observation	102

dbVar

Database of genomic structural variation

nstd23 (Young et al. 2008)

Links

Detailed Information: Download 10 Variant Regions, Download 157 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38.p12 (hg38)GRCh37.p13 (hg19)NCBI36 (hg18)

Remapping summary: NCBI36->GRCh37.p13NCBI36->GRCh38.p12

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

Variant Summary for:

Remapping summary: