nstd76 - Watson et al 2013 - dbVar Study

nstd76 (Watson et al. 2013)

Organism:: Human
Study Type:: Control Set
Submitter:: Corey Watson
Description:: The immunoglobulin heavy chain locus (IGH) encodes variable (IGHV), diversity (IGHD), joining (IGHJ), and constant (IGHC) genes, and is responsible for antibody heavy chain biosynthesis. Using a hydatidiform mole BAC clone resource, and fosmid clone libraries from nine diploid genomes of diverse ethnic origin, we have characterized 9 large structural variants (4 insertions; 1 tandem duplication; 2 deletions; 2 complex events) in this region at nucleotide resolution, accounting for over 220 Kbp of novel sequence. See Variant Summary counts for nstd76 in dbVar Variant Summary.
Publication(s):: Watson et al. 2013

Links

Source: NCBI

Detailed Information: Download 9 Variant Regions, Download 12 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_000014.9	Chr14	9	12	Remapped	NC_000014.9
NT_187600.1	Chr14\|NT_187600.1	6	9	Remapped	NT_187600.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000014.8	Chr14	9	12	Submitted	NC_000014.8

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_000014.8	Chr14	9	1	2	0	0	6	12	1	2	0	0	9

Samplesets

Number of Samplesets: 2

Sampleset ID:: 1
Size:: 1
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1
Sample ID	Cell Type	Subject ID	Ethnicity	Subject Phenotype
CHORI-17	Hydatidiform Mole	CHORI-17	unknown	Not reported

Sampleset ID:: 2
Size:: 8
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 2
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Age	Subject Phenotype
NA12156	B-Lymphocyte	NA12156	Female	CEPH, UTAH/MORMON	81 Years	Not reported
NA18507	B-Lymphocyte	NA18507	Male	Yoruban		Not reported
NA12878	B-Lymphocyte	NA12878	Female	CEPH, UTAH/MORMON		Not reported
NA18502	B-Lymphocyte	NA18502	Female	Yoruban		Not reported
NA18956	B-Lymphocyte	NA18956	Female	Japanese		Not reported
NA15510	B-Lymphocyte	NA15510		unknown		Not reported
NA19240	B-Lymphocyte	NA19240	Female	Yoruban		Not reported
NA18555	B-Lymphocyte	NA18555	Female	Han Chinese		Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	Sequencing	Sequence alignment	capillary-based Sanger sequencing	12

dbVar

Database of genomic structural variation

nstd76 (Watson et al. 2013)

Links

Detailed Information: Download 9 Variant Regions, Download 12 Variant Calls, Download Both, FTP

Variant Summary

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

Variant Summary for:

Remapping summary:

Samplesets

Number of Samplesets: 2

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

nstd76 (Watson et al. 2013)

Links

Detailed Information: Download 9 Variant Regions, Download 12 Variant Calls, Download Both, FTP

Variant Summary

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

Remapping summary: GRCh37->GRCh38.p12

Samplesets

Number of Samplesets: 2

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: