nstd149 - Gambin et al 2017 - dbVar Study

nstd149 (Gambin et al. 2017)

Organism:: Human
Study Type:: Case-Set
Submitter:: Pawel Stankiewicz
Description:: We retrospectively analyzed data from 63,127 patients referred for clinical chromosomal microarray analysis (CMA) at Baylor Genetics laboratories, including 46,755 individuals tested using exon-targeted arrays, from 2007 to 2017. Small CNVs harboring a single gene or two to five non-disease associated genes were identified, and the genes involved were evaluated for a potential disease association. See Variant Summary counts for nstd149 in dbVar Variant Summary.
Publication(s):: Gambin et al. 2017

Links

Source: NCBI

Detailed Information: Download 36 Variant Regions, Download 41 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	12	17	Remapped	NC_000001.11
NC_000008.11	Chr8	13	13	Remapped	NC_000008.11
NC_000013.11	Chr13	2	2	Remapped	NC_000013.11
NC_000015.10	Chr15	6	6	Remapped	NC_000015.10
NC_000023.11	ChrX	3	3	Remapped	NC_000023.11

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	12	17	Submitted	NC_000001.10
NC_000008.10	Chr8	13	13	Submitted	NC_000008.10
NC_000013.10	Chr13	2	2	Submitted	NC_000013.10
NC_000015.9	Chr15	6	6	Submitted	NC_000015.9
NC_000023.10	ChrX	3	3	Submitted	NC_000023.10

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	12	12	0	0	0	0	17	17	0	0	0	0
NC_000008.10	Chr8	13	12	1	0	0	0	13	12	1	0	0	0
NC_000013.10	Chr13	2	2	0	0	0	0	2	2	0	0	0	0
NC_000015.9	Chr15	6	6	0	0	0	0	6	6	0	0	0	0
NC_000023.10	ChrX	3	3	0	0	0	0	3	3	0	0	0	0

Samplesets

Number of Samplesets: 1

Size:: 41
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1
Sample ID	Subject ID	Subject Phenotype
AGBL4_Pt3	AGBL4_Pt3	Not reported
AGBL4_Pt15	AGBL4_Pt15	Not reported
MEIS2_Pt2	MEIS2_Pt2	Not reported
AGBL4_Pt4	AGBL4_Pt4	Not reported
AGBL4_Pt11	AGBL4_Pt11	Not reported
AGBL4_Pt7	AGBL4_Pt7	Not reported
AGBL4_Pt17	AGBL4_Pt17	Not reported
PTCHD1_Pt3	PTCHD1_Pt3	Not reported
MEIS2_Pt5	MEIS2_Pt5	Not reported
CSMD1_Pt2	CSMD1_Pt2	Not reported
AGBL4_Pt12	AGBL4_Pt12	Not reported
CSMD1_Pt7	CSMD1_Pt7	Not reported
MEIS2_Pt3	MEIS2_Pt3	Not reported
STK3_Pt1	STK3_Pt1	Not reported
PTCHD1_Pt2	PTCHD1_Pt2	Not reported
AGBL4_Pt2	AGBL4_Pt2	Not reported
AGBL4_Pt13	AGBL4_Pt13	Not reported
AGBL4_Pt10	AGBL4_Pt10	Not reported
MEIS2_Pt1	MEIS2_Pt1	Not reported
AGBL4_Pt16	AGBL4_Pt16	Not reported
STK3_Pt3	STK3_Pt3	Not reported
CSMD1_Pt9	CSMD1_Pt9	Not reported
AGBL4_Pt9	AGBL4_Pt9	Not reported
CSMD1_Pt6	CSMD1_Pt6	Not reported
AGBL4_Pt6	AGBL4_Pt6	Not reported
CSMD1_Pt5	CSMD1_Pt5	Not reported
MEIS2_Pt4	MEIS2_Pt4	Not reported
ARGLU1_Pt2	ARGLU1_Pt2	Not reported
AGBL4_Pt14	AGBL4_Pt14	Not reported
AGBL4_Pt5	AGBL4_Pt5	Not reported
PTCHD1_Pt1	PTCHD1_Pt1	Not reported
CSMD1_Pt3	CSMD1_Pt3	Not reported
CSMD1_Pt4	CSMD1_Pt4	Not reported
STK3_Pt2	STK3_Pt2	Not reported
MEIS2_Pt6	MEIS2_Pt6	Not reported
CSMD1_Pt1	CSMD1_Pt1	Not reported
STK3_Pt4	STK3_Pt4	Not reported
AGBL4_Pt1	AGBL4_Pt1	Not reported
AGBL4_Pt8	AGBL4_Pt8	Not reported
ARGLU1_Pt1	ARGLU1_Pt1	Not reported
CSMD1_Pt8	CSMD1_Pt8	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Number of Variant Calls
1	Discovery	Oligo aCGH	Curated	41

dbVar

Database of genomic structural variation

nstd149 (Gambin et al. 2017)

Links

Detailed Information: Download 36 Variant Regions, Download 41 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: 1

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

nstd149 (Gambin et al. 2017)

Links

Detailed Information: Download 36 Variant Regions, Download 41 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

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: