nstd11 - Walter et al 2009 - dbVar Study

nstd11 (Walter et al. 2009)

Organism:: Human
Study Type:: Tumor vs. Matched-Normal
Submitter:: Rhonda Ries
Description:: We performed genome-wide copy number analysis with paired normal and tumor DNA obtained from 86 adult patients with de novo AML using 1.85 million feature SNP arrays. See Variant Summary counts for nstd11 in dbVar Variant Summary.
Publication(s):: Walter et al. 2009
dbGaP:: Subjects in this study are not consented to be included in a public DNA archive. To gain access to subject level data, see dbGaP.
dbGaP Release Date:: 2010-01-12

Links

Source: NCBI

Detailed Information: Download 181 Variant Regions, Download 211 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	3	4	Remapped	NC_000001.11
NC_000002.12	Chr2	3	3	Remapped	NC_000002.12
NC_000003.12	Chr3	9	10	Remapped	NC_000003.12
NC_000004.12	Chr4	2	4	Remapped	NC_000004.12
NC_000005.10	Chr5	11	11	Remapped	NC_000005.10
NC_000006.12	Chr6	5	5	Remapped	NC_000006.12
NC_000007.14	Chr7	11	14	Remapped	NC_000007.14
NC_000008.11	Chr8	6	15	Remapped	NC_000008.11
NC_000009.12	Chr9	13	13	Remapped	NC_000009.12
NC_000010.11	Chr10	6	7	Remapped	NC_000010.11
NC_000011.10	Chr11	11	13	Remapped	NC_000011.10
NC_000012.12	Chr12	9	9	Remapped	NC_000012.12
NC_000013.11	Chr13	3	4	Remapped	NC_000013.11
NC_000014.9	Chr14	2	3	Remapped	NC_000014.9
NC_000015.10	Chr15	2	3	Remapped	NC_000015.10
NC_000016.10	Chr16	19	19	Remapped	NC_000016.10
NC_000017.11	Chr17	13	14	Remapped	NC_000017.11
NC_000018.10	Chr18	12	12	Remapped	NC_000018.10
NC_000019.10	Chr19	6	7	Remapped	NC_000019.10
NC_000020.11	Chr20	8	8	Remapped	NC_000020.11
NC_000021.9	Chr21	18	20	Remapped	NC_000021.9
NC_000022.11	Chr22	3	5	Remapped	NC_000022.11
NC_000023.11	ChrX	5	6	Remapped	NC_000023.11
NC_000024.10	ChrY	1	2	Remapped	NC_000024.10
NT_187607.1	Chr16\|NT_187607.1	1	1	Remapped	NT_187607.1
NW_017852933.1	Chr16\|NW_017852933.1	1	1	Remapped	NW_017852933.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	3	4	Remapped	NC_000001.10
NC_000002.11	Chr2	3	3	Remapped	NC_000002.11
NC_000003.11	Chr3	9	10	Remapped	NC_000003.11
NC_000004.11	Chr4	2	4	Remapped	NC_000004.11
NC_000005.9	Chr5	11	11	Remapped	NC_000005.9
NC_000006.11	Chr6	5	5	Remapped	NC_000006.11
NC_000007.13	Chr7	11	14	Remapped	NC_000007.13
NC_000008.10	Chr8	6	15	Remapped	NC_000008.10
NC_000009.11	Chr9	13	13	Remapped	NC_000009.11
NC_000010.10	Chr10	6	7	Remapped	NC_000010.10
NC_000011.9	Chr11	11	13	Remapped	NC_000011.9
NC_000012.11	Chr12	9	9	Remapped	NC_000012.11
NC_000013.10	Chr13	3	4	Remapped	NC_000013.10
NC_000014.8	Chr14	2	3	Remapped	NC_000014.8
NC_000015.9	Chr15	2	3	Remapped	NC_000015.9
NC_000016.9	Chr16	19	19	Remapped	NC_000016.9
NC_000017.10	Chr17	13	14	Remapped	NC_000017.10
NC_000018.9	Chr18	12	12	Remapped	NC_000018.9
NC_000019.9	Chr19	6	7	Remapped	NC_000019.9
NC_000020.10	Chr20	8	8	Remapped	NC_000020.10
NC_000021.8	Chr21	18	20	Remapped	NC_000021.8
NC_000022.10	Chr22	3	5	Remapped	NC_000022.10
NC_000023.10	ChrX	5	6	Remapped	NC_000023.10
NC_000024.9	ChrY	1	2	Remapped	NC_000024.9
NW_003871072.2	Chr11\|NW_003871072.2	1	1	Remapped	NW_003871072.2

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.9	Chr1	3	4	Submitted	NC_000001.9
NC_000002.10	Chr2	3	3	Submitted	NC_000002.10
NC_000003.10	Chr3	9	10	Submitted	NC_000003.10
NC_000004.10	Chr4	2	4	Submitted	NC_000004.10
NC_000005.8	Chr5	11	11	Submitted	NC_000005.8
NC_000006.10	Chr6	5	5	Submitted	NC_000006.10
NC_000007.12	Chr7	11	14	Submitted	NC_000007.12
NC_000008.9	Chr8	6	15	Submitted	NC_000008.9
NC_000009.10	Chr9	13	13	Submitted	NC_000009.10
NC_000010.9	Chr10	6	7	Submitted	NC_000010.9
NC_000011.8	Chr11	11	13	Submitted	NC_000011.8
NC_000012.10	Chr12	9	9	Submitted	NC_000012.10
NC_000013.9	Chr13	3	4	Submitted	NC_000013.9
NC_000014.7	Chr14	2	3	Submitted	NC_000014.7
NC_000015.8	Chr15	2	3	Submitted	NC_000015.8
NC_000016.8	Chr16	19	19	Submitted	NC_000016.8
NC_000017.9	Chr17	13	14	Submitted	NC_000017.9
NC_000018.8	Chr18	12	12	Submitted	NC_000018.8
NC_000019.8	Chr19	6	7	Submitted	NC_000019.8
NC_000020.9	Chr20	8	8	Submitted	NC_000020.9
NC_000021.7	Chr21	18	20	Submitted	NC_000021.7
NC_000022.9	Chr22	3	5	Submitted	NC_000022.9
NC_000023.9	ChrX	5	6	Submitted	NC_000023.9
NC_000024.8	ChrY	1	2	Submitted	NC_000024.8

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_000001.9	Chr1	3	0	3	0	0	0	4	0	4	0	0	0
NC_000002.10	Chr2	3	2	1	0	0	0	3	2	1	0	0	0
NC_000003.10	Chr3	9	6	3	0	0	0	10	6	4	0	0	0
NC_000004.10	Chr4	2	0	2	0	0	0	4	0	4	0	0	0
NC_000005.8	Chr5	11	3	8	0	0	0	11	3	8	0	0	0
NC_000006.10	Chr6	5	3	2	0	0	0	5	3	2	0	0	0
NC_000007.12	Chr7	11	4	7	0	0	0	14	4	10	0	0	0
NC_000008.9	Chr8	6	1	5	0	0	0	15	1	14	0	0	0
NC_000009.10	Chr9	13	8	5	0	0	0	13	8	5	0	0	0
NC_000010.9	Chr10	6	5	1	0	0	0	7	5	2	0	0	0
NC_000011.8	Chr11	11	4	6	0	0	1	13	4	8	0	0	1
NC_000012.10	Chr12	9	6	3	0	0	0	9	6	3	0	0	0
NC_000013.9	Chr13	3	0	3	0	0	0	4	0	4	0	0	0
NC_000014.7	Chr14	2	0	2	0	0	0	3	0	3	0	0	0
NC_000015.8	Chr15	2	1	1	0	0	0	3	1	2	0	0	0
NC_000016.8	Chr16	19	15	4	0	0	0	19	15	4	0	0	0
NC_000017.9	Chr17	13	1	12	0	0	0	14	1	13	0	0	0
NC_000018.8	Chr18	12	11	1	0	0	0	12	11	1	0	0	0
NC_000019.8	Chr19	6	5	0	1	0	0	7	5	0	2	0	0
NC_000020.9	Chr20	8	3	5	0	0	0	8	3	5	0	0	0
NC_000021.7	Chr21	18	14	4	0	0	0	20	14	6	0	0	0
NC_000022.9	Chr22	3	0	2	1	0	0	5	0	4	1	0	0
NC_000023.9	ChrX	5	2	3	0	0	0	6	2	4	0	0	0
NC_000024.8	ChrY	1	0	0	1	0	0	2	0	0	2	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	3	0	2	1	0	0	4	0	3	1	0	0
NC_000002.10	Chr2	3	1	2	0	0	0	3	1	2	0	0	0
NC_000003.10	Chr3	9	5	4	0	0	0	10	5	5	0	0	0
NC_000004.10	Chr4	2	0	2	0	0	0	4	0	4	0	0	0
NC_000005.8	Chr5	11	3	8	0	0	0	11	3	8	0	0	0
NC_000006.10	Chr6	5	3	2	0	0	0	5	3	2	0	0	0
NC_000007.12	Chr7	11	4	7	0	0	0	14	4	10	0	0	0
NC_000008.9	Chr8	6	1	5	0	0	0	15	1	14	0	0	0
NC_000009.10	Chr9	13	7	6	0	0	0	13	7	6	0	0	0
NC_000010.9	Chr10	6	3	3	0	0	0	7	3	4	0	0	0
NC_000011.8	Chr11	11	5	6	0	0	0	13	5	8	0	0	0
NC_000012.10	Chr12	9	4	5	0	0	0	9	4	5	0	0	0
NC_000013.9	Chr13	3	0	3	0	0	0	4	0	4	0	0	0
NC_000014.7	Chr14	2	0	2	0	0	0	3	0	3	0	0	0
NC_000015.8	Chr15	2	1	1	0	0	0	3	1	2	0	0	0
NC_000016.8	Chr16	19	12	5	0	0	2	19	12	5	0	0	2
NC_000017.9	Chr17	13	1	9	3	0	0	14	1	9	4	0	0
NC_000018.8	Chr18	12	10	1	1	0	0	12	10	1	1	0	0
NC_000019.8	Chr19	6	4	1	1	0	0	7	4	1	2	0	0
NC_000020.9	Chr20	8	2	5	1	0	0	8	2	5	1	0	0
NC_000021.7	Chr21	18	11	6	1	0	0	20	11	6	3	0	0
NC_000022.9	Chr22	3	0	3	0	0	0	5	0	5	0	0	0
NC_000023.9	ChrX	5	2	3	0	0	0	6	2	4	0	0	0
NC_000024.8	ChrY	1	0	1	0	0	0	2	0	2	0	0	0

Samplesets

Number of Samplesets: 1

Name:: Acute myeloid leukemia (AML) patients
Sampleset Type:: Case
Description:: A total of 86 adult patients (aged >18 years) with de novo AML were chosen for study on the basis of the availability of high-quality, abundant, paiered bone marrow (tumor) and skin (normal) DNA samples
Size:: 86 (sample data available via dbGaP)
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Leukemia, Myeloid, Acute

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Data	Number of Variant Calls
1	Discovery	SNP array	SNP genotyping analysis	GPL6801	dbGaP	211

dbVar

Database of genomic structural variation

nstd11 (Walter et al. 2009)

Links

Detailed Information: Download 181 Variant Regions, Download 211 Variant Calls, Download Both, FTP

Variant Summary

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

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

nstd11 (Walter et al. 2009)

Links

Detailed Information: Download 181 Variant Regions, Download 211 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

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: