nstd189 - Perez-Palma et al 2020 - dbVar Study

nstd189 (Perez-Palma et al. 2020)

Organism:: Human
Study Type:: Case-Control
Submitter:: Eduardo Perez-Palma
Submitter URL:: https://www.ebi.ac.uk/ena/browser/view/PRJEB33136
Description:: We examined a sample of 4,778 individuals (1,929 GSD cases and 2,849 controls) including two European cohorts from Germany (n = 3,702) and one admixed Latin American cohort from Chile (n = 1,076). We detected 4,336 large and rare CNVs events (size > 100 kb, frequency < 1%). CNV burden analysis revealed a significant association of CNVs with GSD, with the strongest effect observed in men with CNVs overlapping lipid metabolism genes. See Variant Summary counts for nstd189 in dbVar Variant Summary.
Project:: PRJEB33136
Publication(s):: Pérez-Palma et al. 2020

Links

Source: NCBI

Detailed Information: Download 2181 Variant Regions, Download 2498 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Submitted: GRCh37.p13 (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	84	86	Remapped	NC_000001.11
NC_000002.12	Chr2	101	101	Remapped	NC_000002.12
NC_000003.12	Chr3	94	94	Remapped	NC_000003.12
NC_000004.12	Chr4	87	88	Remapped	NC_000004.12
NC_000005.10	Chr5	43	43	Remapped	NC_000005.10
NC_000006.12	Chr6	149	154	Remapped	NC_000006.12
NC_000007.14	Chr7	153	166	Remapped	NC_000007.14
NC_000008.11	Chr8	78	80	Remapped	NC_000008.11
NC_000009.12	Chr9	88	88	Remapped	NC_000009.12
NC_000010.11	Chr10	188	204	Remapped	NC_000010.11
NC_000011.10	Chr11	85	85	Remapped	NC_000011.10
NC_000012.12	Chr12	71	77	Remapped	NC_000012.12
NC_000013.11	Chr13	49	50	Remapped	NC_000013.11
NC_000014.9	Chr14	86	106	Remapped	NC_000014.9
NC_000015.10	Chr15	281	469	Remapped	NC_000015.10
NC_000016.10	Chr16	116	130	Remapped	NC_000016.10
NC_000017.11	Chr17	52	52	Remapped	NC_000017.11
NC_000018.10	Chr18	25	25	Remapped	NC_000018.10
NC_000019.10	Chr19	45	47	Remapped	NC_000019.10
NC_000020.11	Chr20	36	36	Remapped	NC_000020.11
NC_000021.9	Chr21	30	32	Remapped	NC_000021.9
NC_000022.11	Chr22	151	194	Remapped	NC_000022.11
NC_000023.11	ChrX	81	83	Remapped	NC_000023.11
NT_187515.1	Chr1\|NT_187515.1	1	1	Remapped	NT_187515.1
NT_187529.1	Chr2\|NT_187529.1	1	1	Remapped	NT_187529.1
NW_003315913.1	Chr3\|NW_003315913.1	1	1	Remapped	NW_003315913.1
NT_187540.1	Chr4\|NT_187540.1	1	1	Remapped	NT_187540.1
NT_187558.1	Chr7\|NT_187558.1	1	1	Remapped	NT_187558.1
NT_187561.1	Chr7\|NT_187561.1	1	1	Remapped	NT_187561.1
NT_187653.1	Chr7\|NT_187653.1	1	1	Remapped	NT_187653.1
NW_018654714.1	Chr7\|NW_018654714.1	2	2	Remapped	NW_018654714.1
NW_019805493.1	Chr7\|NW_019805493.1	6	6	Remapped	NW_019805493.1
NT_187576.1	Chr8\|NT_187576.1	16	16	Remapped	NT_187576.1
NW_018654717.1	Chr8\|NW_018654717.1	4	4	Remapped	NW_018654717.1
NT_187581.1	Chr11\|NT_187581.1	1	1	Remapped	NT_187581.1
NW_019805497.1	Chr11\|NW_019805497.1	1	1	Remapped	NW_019805497.1
NT_187587.1	Chr12\|NT_187587.1	2	2	Remapped	NT_187587.1
NW_018654718.1	Chr12\|NW_018654718.1	1	1	Remapped	NW_018654718.1
NW_019805499.1	Chr12\|NW_019805499.1	1	1	Remapped	NW_019805499.1
NT_187600.1	Chr14\|NT_187600.1	7	7	Remapped	NT_187600.1
NT_187660.1	Chr15\|NT_187660.1	23	25	Remapped	NT_187660.1
NT_187603.1	Chr15\|NT_187603.1	8	10	Remapped	NT_187603.1
NW_011332701.1	Chr15\|NW_011332701.1	23	25	Remapped	NW_011332701.1
NT_187607.1	Chr16\|NT_187607.1	10	10	Remapped	NT_187607.1
NT_187663.1	Chr17\|NT_187663.1	1	1	Remapped	NT_187663.1
NT_187614.1	Chr17\|NT_187614.1	4	4	Remapped	NT_187614.1
NW_017363817.1	Chr17\|NW_017363817.1	1	1	Remapped	NW_017363817.1
NT_187693.1	Chr19\|NT_187693.1	4	4	Remapped	NT_187693.1
NW_003571061.2	Chr19\|NW_003571061.2	1	1	Remapped	NW_003571061.2
NW_003571055.2	Chr19\|NW_003571055.2	1	1	Remapped	NW_003571055.2
NW_003571054.1	Chr19\|NW_003571054.1	1	1	Remapped	NW_003571054.1
NT_187626.1	Chr21\|NT_187626.1	1	1	Remapped	NT_187626.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	90	92	Submitted	NC_000001.10
NC_000002.11	Chr2	101	101	Submitted	NC_000002.11
NC_000003.11	Chr3	94	94	Submitted	NC_000003.11
NC_000004.11	Chr4	87	88	Submitted	NC_000004.11
NC_000005.9	Chr5	43	43	Submitted	NC_000005.9
NC_000006.11	Chr6	149	154	Submitted	NC_000006.11
NC_000007.13	Chr7	150	163	Submitted	NC_000007.13
NC_000008.10	Chr8	78	80	Submitted	NC_000008.10
NC_000009.11	Chr9	91	91	Submitted	NC_000009.11
NC_000010.10	Chr10	189	205	Submitted	NC_000010.10
NC_000011.9	Chr11	87	87	Submitted	NC_000011.9
NC_000012.11	Chr12	71	77	Submitted	NC_000012.11
NC_000013.10	Chr13	49	50	Submitted	NC_000013.10
NC_000014.8	Chr14	86	106	Submitted	NC_000014.8
NC_000015.9	Chr15	281	469	Submitted	NC_000015.9
NC_000016.9	Chr16	111	125	Submitted	NC_000016.9
NC_000017.10	Chr17	52	52	Submitted	NC_000017.10
NC_000018.9	Chr18	25	25	Submitted	NC_000018.9
NC_000019.9	Chr19	48	50	Submitted	NC_000019.9
NC_000020.10	Chr20	34	34	Submitted	NC_000020.10
NC_000021.8	Chr21	30	32	Submitted	NC_000021.8
NC_000022.10	Chr22	154	197	Submitted	NC_000022.10
NC_000023.10	ChrX	81	83	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	90	76	4	5	1	4	92	76	4	7	1	4
NC_000002.11	Chr2	101	77	6	17	0	1	101	77	6	17	0	1
NC_000003.11	Chr3	94	86	6	1	0	1	94	86	6	1	0	1
NC_000004.11	Chr4	87	80	2	4	0	1	88	81	2	4	0	1
NC_000005.9	Chr5	43	42	1	0	0	0	43	42	1	0	0	0
NC_000006.11	Chr6	149	145	4	0	0	0	154	150	4	0	0	0
NC_000007.13	Chr7	150	123	15	2	0	10	163	133	18	2	0	10
NC_000008.10	Chr8	78	55	2	1	0	20	80	57	2	1	0	20
NC_000009.11	Chr9	91	69	15	4	1	2	91	69	15	4	1	2
NC_000010.10	Chr10	189	73	2	113	1	0	205	73	2	129	1	0
NC_000011.9	Chr11	87	77	1	5	2	2	87	77	1	5	2	2
NC_000012.11	Chr12	71	65	0	2	0	4	77	71	0	2	0	4
NC_000013.10	Chr13	49	47	1	1	0	0	50	48	1	1	0	0
NC_000014.8	Chr14	86	49	4	26	0	7	106	52	4	43	0	7
NC_000015.9	Chr15	281	42	133	74	0	32	469	42	247	144	0	36
NC_000016.9	Chr16	111	37	1	63	0	10	125	37	1	77	0	10
NC_000017.10	Chr17	52	36	5	5	0	6	52	36	5	5	0	6
NC_000018.9	Chr18	25	24	1	0	0	0	25	24	1	0	0	0
NC_000019.9	Chr19	48	44	2	1	0	1	50	46	2	1	0	1
NC_000020.10	Chr20	34	31	2	1	0	0	34	31	2	1	0	0
NC_000021.8	Chr21	30	26	3	0	0	1	32	28	3	0	0	1
NC_000022.10	Chr22	154	95	45	9	5	0	197	132	50	10	5	0
NC_000023.10	ChrX	81	39	34	8	0	0	83	39	36	8	0	0

Samplesets

Number of Samplesets: 2

Sampleset ID:: 1
Name:: GSD Case
Sampleset Type:: Case
Description:: Includes samples from two European cohorts from Germany and one admixed Latin American cohort from Chile
Size:: 1,929 (sample data not available)
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Gallstone disease

Sampleset ID:: 2
Name:: GSD Control
Sampleset Type:: Control
Description:: Includes samples from two European cohorts from Germany and one admixed Latin American cohort from Chile
Size:: 2,849 (sample data not available)
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	SNP array	SNP genotyping analysis	Affymetrix	2,498

dbVar

Database of genomic structural variation

nstd189 (Perez-Palma et al. 2020)

Links

Detailed Information: Download 2181 Variant Regions, Download 2498 Variant Calls, Download Both, FTP

Variant Summary

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

nstd189 (Perez-Palma et al. 2020)

Links

Detailed Information: Download 2181 Variant Regions, Download 2498 Variant Calls, Download Both, FTP

Variant Summary

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