nstd125 - Wills et al 2016 - dbVar Study

nstd125 (Wills et al. 2016)

Organism:: Human
Study Type:: Somatic
Submitter:: Edgar Wills
Description:: Autosomal dominant polycystic liver disease (ADPLD) and autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in PRKCSH, SEC63, and LRP5, PKD1, and PKD2. Liver cyst development in these disorders is explained by somatic loss-of-heterozygosity (LOH) of the wild type allele in the developing cyst. We analyzed 24 liver cyst samples from 23 patients using high resolution microarray (homozygosity of autosomes (>3.0Mb) large CNVs (>1.0Mb)). We found frequent LOH in PRKCSH (22/29), and PKD1/PKD2 (2/3). In the total cohort, 12/23 patients harbored abnormalities outside of familiar areas. In individual ADPLD cases, we identified germline events: a 2q13 complex rearrangement resulting in BUB1 haploinsufficiency, a 47XXX karyotype, and LOH on chromosome 3p. See Variant Summary counts for nstd125 in dbVar Variant Summary.
Publication(s):: Wills et al. 2016

Links

Source: NCBI

Detailed Information: Download 34 Variant Regions, Download 39 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	2	2	Remapped	NC_000001.11
NC_000002.12	Chr2	5	9	Remapped	NC_000002.12
NC_000003.12	Chr3	3	3	Remapped	NC_000003.12
NC_000004.12	Chr4	1	1	Remapped	NC_000004.12
NC_000005.10	Chr5	3	3	Remapped	NC_000005.10
NC_000006.12	Chr6	2	2	Remapped	NC_000006.12
NC_000007.14	Chr7	2	2	Remapped	NC_000007.14
NC_000009.12	Chr9	1	1	Remapped	NC_000009.12
NC_000011.10	Chr11	1	1	Remapped	NC_000011.10
NC_000012.12	Chr12	3	3	Remapped	NC_000012.12
NC_000013.11	Chr13	1	1	Remapped	NC_000013.11
NC_000016.10	Chr16	2	2	Remapped	NC_000016.10
NC_000019.10	Chr19	7	7	Remapped	NC_000019.10
NC_000023.11	ChrX	1	2	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	2	2	Submitted	NC_000001.10
NC_000002.11	Chr2	5	9	Submitted	NC_000002.11
NC_000003.11	Chr3	3	3	Submitted	NC_000003.11
NC_000004.11	Chr4	1	1	Submitted	NC_000004.11
NC_000005.9	Chr5	3	3	Submitted	NC_000005.9
NC_000006.11	Chr6	2	2	Submitted	NC_000006.11
NC_000007.13	Chr7	2	2	Submitted	NC_000007.13
NC_000009.11	Chr9	1	1	Submitted	NC_000009.11
NC_000011.9	Chr11	1	1	Submitted	NC_000011.9
NC_000012.11	Chr12	3	3	Submitted	NC_000012.11
NC_000013.10	Chr13	1	1	Submitted	NC_000013.10
NC_000016.9	Chr16	2	2	Submitted	NC_000016.9
NC_000019.9	Chr19	7	7	Submitted	NC_000019.9
NC_000023.10	ChrX	1	2	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	2	2	0	0	0	0	2	2	0	0	0	0
NC_000002.11	Chr2	5	4	0	1	0	0	9	6	0	3	0	0
NC_000003.11	Chr3	3	0	3	0	0	0	3	0	3	0	0	0
NC_000004.11	Chr4	1	1	0	0	0	0	1	1	0	0	0	0
NC_000005.9	Chr5	3	3	0	0	0	0	3	3	0	0	0	0
NC_000006.11	Chr6	2	0	2	0	0	0	2	0	2	0	0	0
NC_000007.13	Chr7	2	1	1	0	0	0	2	1	1	0	0	0
NC_000009.11	Chr9	1	1	0	0	0	0	1	1	0	0	0	0
NC_000011.9	Chr11	1	1	0	0	0	0	1	1	0	0	0	0
NC_000012.11	Chr12	3	3	0	0	0	0	3	3	0	0	0	0
NC_000013.10	Chr13	1	1	0	0	0	0	1	1	0	0	0	0
NC_000016.9	Chr16	2	1	1	0	0	0	2	1	1	0	0	0
NC_000019.9	Chr19	7	0	7	0	0	0	7	0	7	0	0	0
NC_000023.10	ChrX	1	0	1	0	0	0	2	0	2	0	0	0

Samplesets

Number of Samplesets: 1

Name:: Liver cysts
Description:: high-density SNP array data of liver cyst and peripheral blood DNA
Size:: 27
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Cystic liver disease

Samples for sampleset 1
Sample ID	Cell Type	Subject ID	Subject Phenotype
control		control	Cystic liver disease
1	cyst biliary cells	1	Cystic liver disease
2	cyst biliary cells	2	Cystic liver disease
3	cyst biliary cells	3	Cystic liver disease
4	cyst biliary cells	4	Cystic liver disease
5	cyst biliary cells	5	Cystic liver disease
6	cyst biliary cells	6	Cystic liver disease
7	cyst biliary cells	7	Cystic liver disease
8	cyst biliary cells	8	Cystic liver disease
9	cyst biliary cells	8	Cystic liver disease
10	cyst biliary cells	9	Cystic liver disease
11	cyst biliary cells	10	Cystic liver disease
12	cyst biliary cells	11	Cystic liver disease
13	cyst biliary cells	12	Cystic liver disease
14	cyst biliary cells	13	Cystic liver disease
15	cyst biliary cells	14	Cystic liver disease
16	cyst biliary cells	15	Cystic liver disease
17	cyst biliary cells	16	Cystic liver disease
18	cyst biliary cells	17	Cystic liver disease
19	cyst biliary cells	18	Cystic liver disease
20	cyst biliary cells	19	Cystic liver disease
21	cyst biliary cells	20	Cystic liver disease
22	cyst biliary cells	21	Cystic liver disease
23	cyst biliary cells	22	Cystic liver disease
24	cyst biliary cells	23	Cystic liver disease
25	peripheral leukocytes	1	Cystic liver disease
26	peripheral leukocytes	8	Cystic liver disease
27	peripheral leukocytes	19	Cystic liver disease

Experimental Details

Experiment ID	Type	Method	Analysis	Number of Variant Calls
1	Discovery	SNP array	SNP genotyping analysis	39

dbVar

Database of genomic structural variation

nstd125 (Wills et al. 2016)

Links

Detailed Information: Download 34 Variant Regions, Download 39 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

nstd125 (Wills et al. 2016)

Links

Detailed Information: Download 34 Variant Regions, Download 39 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: