estd216 - Kasak et al 2015 - dbVar Study

estd216 (Kasak et al. 2015)

Organism:: Human
Study Type:: Case-Control
Submitter:: Laura Kasak
Description:: The study aimed to determine the contribution of copy number variants in the genetic etiology of normal and complicated pregnancies. The samples represented (i) maternal blood DNA drawn from healthy pregnant women during 1st or 2nd trimester and (ii) maternal and paternal blood DNA drawn at term pregnancy cases representing normal and complicated gestations (severe preeclampsia, PE; gestational diabetes, GD; small-for-gestational age newborn, SGA; large-for-gestational age newborn, LGA). We performed CNV calling based on genome-wide genotyping dataset (Illumina HumanOmniExpress-24-v1 BeadChip) by applying three algorithms, QuantiSNP, GADA (Genome Alteration Detection Algorithm) and CNstream in parallel. The acquired CNV calls were merged with HD-CNV (Hotspot Detector for Copy Number Variants) program and only the CNVs predicted by at least two programs, were considered in subsequent analysis. See Variant Summary counts for estd216 in dbVar Variant Summary.
Curatorial Comment:: PLEASE NOTE: All clinical variants in dbVar (including the variants in this study) have been re-accessioned in the study Clinical Structural Variants (nstd102). The new accessions are preferred and will be kept up to date with changes made in ClinVar. We recommend using the new nstd102 accessions whenever possible. A file mapping old accessions to new is available at https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/release_notes/nstd102_accession_mapping.txt.
Publication(s):: Kasak et al. 2015

Links

Source: NCBI

Detailed Information: Download 879 Variant Regions, Download 879 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	61	61	Remapped	NC_000001.11
NC_000002.12	Chr2	78	78	Remapped	NC_000002.12
NC_000003.12	Chr3	86	86	Remapped	NC_000003.12
NC_000004.12	Chr4	49	49	Remapped	NC_000004.12
NC_000005.10	Chr5	56	56	Remapped	NC_000005.10
NC_000006.12	Chr6	36	36	Remapped	NC_000006.12
NC_000007.14	Chr7	52	52	Remapped	NC_000007.14
NC_000008.11	Chr8	52	52	Remapped	NC_000008.11
NC_000009.12	Chr9	28	28	Remapped	NC_000009.12
NC_000010.11	Chr10	46	46	Remapped	NC_000010.11
NC_000011.10	Chr11	41	41	Remapped	NC_000011.10
NC_000012.12	Chr12	40	40	Remapped	NC_000012.12
NC_000013.11	Chr13	36	36	Remapped	NC_000013.11
NC_000014.9	Chr14	32	32	Remapped	NC_000014.9
NC_000015.10	Chr15	32	32	Remapped	NC_000015.10
NC_000016.10	Chr16	18	18	Remapped	NC_000016.10
NC_000017.11	Chr17	37	37	Remapped	NC_000017.11
NC_000018.10	Chr18	25	25	Remapped	NC_000018.10
NC_000019.10	Chr19	46	46	Remapped	NC_000019.10
NC_000020.11	Chr20	8	8	Remapped	NC_000020.11
NC_000021.9	Chr21	5	5	Remapped	NC_000021.9
NC_000022.11	Chr22	15	15	Remapped	NC_000022.11
NT_187516.1	Chr1\|NT_187516.1	3	3	Remapped	NT_187516.1
NW_012132914.1	Chr1\|NW_012132914.1	1	1	Remapped	NW_012132914.1
NT_187523.1	Chr2\|NT_187523.1	8	8	Remapped	NT_187523.1
NT_187647.1	Chr2\|NT_187647.1	8	8	Remapped	NT_187647.1
NW_019805488.1	Chr3\|NW_019805488.1	1	1	Remapped	NW_019805488.1
NT_187546.1	Chr5\|NT_187546.1	1	1	Remapped	NT_187546.1
NT_187651.1	Chr5\|NT_187651.1	5	5	Remapped	NT_187651.1
NT_187652.1	Chr5\|NT_187652.1	1	1	Remapped	NT_187652.1
NW_003315917.2	Chr5\|NW_003315917.2	6	6	Remapped	NW_003315917.2
NT_187555.1	Chr6\|NT_187555.1	2	2	Remapped	NT_187555.1
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_187562.1	Chr7\|NT_187562.1	8	8	Remapped	NT_187562.1
NT_187653.1	Chr7\|NT_187653.1	1	1	Remapped	NT_187653.1
NW_019805493.1	Chr7\|NW_019805493.1	1	1	Remapped	NW_019805493.1
NT_187576.1	Chr8\|NT_187576.1	1	1	Remapped	NT_187576.1
NW_018654717.1	Chr8\|NW_018654717.1	2	2	Remapped	NW_018654717.1
NT_187579.1	Chr10\|NT_187579.1	1	1	Remapped	NT_187579.1
NT_187587.1	Chr12\|NT_187587.1	7	7	Remapped	NT_187587.1
NW_018654718.1	Chr12\|NW_018654718.1	8	8	Remapped	NW_018654718.1
NT_187600.1	Chr14\|NT_187600.1	3	3	Remapped	NT_187600.1
NW_018654722.1	Chr14\|NW_018654722.1	4	4	Remapped	NW_018654722.1
NT_187607.1	Chr16\|NT_187607.1	1	1	Remapped	NT_187607.1
NT_187661.1	Chr17\|NT_187661.1	1	1	Remapped	NT_187661.1
NT_187663.1	Chr17\|NT_187663.1	13	13	Remapped	NT_187663.1
NT_187614.1	Chr17\|NT_187614.1	1	1	Remapped	NT_187614.1
NW_019805503.1	Chr18\|NW_019805503.1	2	2	Remapped	NW_019805503.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	61	61	Submitted	NC_000001.10
NC_000002.11	Chr2	78	78	Submitted	NC_000002.11
NC_000003.11	Chr3	86	86	Submitted	NC_000003.11
NC_000004.11	Chr4	49	49	Submitted	NC_000004.11
NC_000005.9	Chr5	56	56	Submitted	NC_000005.9
NC_000006.11	Chr6	36	36	Submitted	NC_000006.11
NC_000007.13	Chr7	52	52	Submitted	NC_000007.13
NC_000008.10	Chr8	52	52	Submitted	NC_000008.10
NC_000009.11	Chr9	28	28	Submitted	NC_000009.11
NC_000010.10	Chr10	46	46	Submitted	NC_000010.10
NC_000011.9	Chr11	41	41	Submitted	NC_000011.9
NC_000012.11	Chr12	40	40	Submitted	NC_000012.11
NC_000013.10	Chr13	36	36	Submitted	NC_000013.10
NC_000014.8	Chr14	32	32	Submitted	NC_000014.8
NC_000015.9	Chr15	32	32	Submitted	NC_000015.9
NC_000016.9	Chr16	18	18	Submitted	NC_000016.9
NC_000017.10	Chr17	37	37	Submitted	NC_000017.10
NC_000018.9	Chr18	25	25	Submitted	NC_000018.9
NC_000019.9	Chr19	46	46	Submitted	NC_000019.9
NC_000020.10	Chr20	8	8	Submitted	NC_000020.10
NC_000021.8	Chr21	5	5	Submitted	NC_000021.8
NC_000022.10	Chr22	15	15	Submitted	NC_000022.10

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	61	48	9	0	0	4	61	48	9	0	0	4
NC_000002.11	Chr2	78	54	13	3	0	8	78	54	13	3	0	8
NC_000003.11	Chr3	86	81	4	0	0	1	86	81	4	0	0	1
NC_000004.11	Chr4	49	48	0	1	0	0	49	48	0	1	0	0
NC_000005.9	Chr5	56	48	1	0	0	7	56	48	1	0	0	7
NC_000006.11	Chr6	36	34	0	0	0	2	36	34	0	0	0	2
NC_000007.13	Chr7	52	32	9	0	0	11	52	32	9	0	0	11
NC_000008.10	Chr8	52	49	0	0	0	3	52	49	0	0	0	3
NC_000009.11	Chr9	28	28	0	0	0	0	28	28	0	0	0	0
NC_000010.10	Chr10	46	40	0	5	0	1	46	40	0	5	0	1
NC_000011.9	Chr11	41	40	0	1	0	0	41	40	0	1	0	0
NC_000012.11	Chr12	40	25	0	0	0	15	40	25	0	0	0	15
NC_000013.10	Chr13	36	35	0	1	0	0	36	35	0	1	0	0
NC_000014.8	Chr14	32	21	2	2	0	7	32	21	2	2	0	7
NC_000015.9	Chr15	32	29	2	1	0	0	32	29	2	1	0	0
NC_000016.9	Chr16	18	14	0	3	0	1	18	14	0	3	0	1
NC_000017.10	Chr17	37	23	0	0	0	14	37	23	0	0	0	14
NC_000018.9	Chr18	25	23	0	0	0	2	25	23	0	0	0	2
NC_000019.9	Chr19	46	46	0	0	0	0	46	46	0	0	0	0
NC_000020.10	Chr20	8	7	1	0	0	0	8	7	1	0	0	0
NC_000021.8	Chr21	5	3	2	0	0	0	5	3	2	0	0	0
NC_000022.10	Chr22	15	14	1	0	0	0	15	14	1	0	0	0

Samplesets

Number of Samplesets: 7

Sampleset ID:: 1
Name:: I_trimester
Sampleset Type:: Control
Description:: Maternal blood DNA samples obtained from females who underwent elective (surgical) termination of pregnancy during first trimester
Size:: 8
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Normal pregnancy
Sex:: Female

Samples for sampleset 1
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
Sample 4	Sample 4	Female	Estonia	Normal pregnancy
Sample 5	Sample 5	Female	Estonia	Normal pregnancy
Sample 6	Sample 6	Female	Estonia	Normal pregnancy
Sample 3	Sample 3	Female	Estonia	Normal pregnancy
Sample 2	Sample 2	Female	Estonia	Normal pregnancy
Sample 7	Sample 7	Female	Estonia	Normal pregnancy
Sample 8	Sample 8	Female	Estonia	Normal pregnancy
Sample 1	Sample 1	Female	Estonia	Normal pregnancy

Sampleset ID:: 2
Name:: II_trimester
Sampleset Type:: Control
Description:: Maternal blood DNA samples obtained from females who underwent therapeutic medically induced abortion during second trimester due to maternal medical risks of pregnancy
Size:: 8
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Normal pregnancy
Sex:: Female

Samples for sampleset 2
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
Sample 15	Sample 15	Female	Estonia	Normal pregnancy
Sample 13	Sample 13	Female	Estonia	Normal pregnancy
Sample 12	Sample 12	Female	Estonia	Normal pregnancy
Sample 16	Sample 16	Female	Estonia	Normal pregnancy
Sample 9	Sample 9	Female	Estonia	Normal pregnancy
Sample 11	Sample 11	Female	Estonia	Normal pregnancy
Sample 14	Sample 14	Female	Estonia	Normal pregnancy
Sample 10	Sample 10	Female	Estonia	Normal pregnancy

Sampleset ID:: 3
Name:: normal term
Sampleset Type:: Control
Description:: Maternal and paternal blood DNA samples drawn postpartum from the normal term pregnancy families
Size:: 16
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Normal pregnancy

Samples for sampleset 3
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
Sample 30	Sample 30	Female	Estonia	Normal pregnancy
Sample 18	Sample 18	Male	Estonia	Normal pregnancy
Sample 29	Sample 29	Female	Estonia	Normal pregnancy
Sample 26	Sample 26	Female	Estonia	Normal pregnancy
Sample 24	Sample 24	Male	Estonia	Normal pregnancy
Sample 21	Sample 21	Male	Estonia	Normal pregnancy
Sample 27	Sample 27	Female	Estonia	Normal pregnancy
Sample 19	Sample 19	Male	Estonia	Normal pregnancy
Sample 22	Sample 22	Male	Estonia	Normal pregnancy
Sample 28	Sample 28	Female	Estonia	Normal pregnancy
Sample 23	Sample 23	Male	Estonia	Normal pregnancy
Sample 17	Sample 17	Male	Estonia	Normal pregnancy
Sample 20	Sample 20	Male	Estonia	Normal pregnancy
Sample 25	Sample 25	Female	Estonia	Normal pregnancy
Sample 31	Sample 31	Female	Estonia	Normal pregnancy
Sample 32	Sample 32	Female	Estonia	Normal pregnancy

Sampleset ID:: 4
Name:: SGA
Sampleset Type:: Case
Description:: Maternal and paternal blood DNA samples drawn postpartum from the term pregnancy cases with small-for-gestational age (SGA) newborns
Size:: 15
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Low birth weight

Samples for sampleset 4
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
Sample 33	Sample 33	Male	Estonia	Low birth weight
Sample 38	Sample 38	Male	Estonia	Low birth weight
Sample 44	Sample 44	Female	Estonia	Low birth weight
Sample 41	Sample 41	Female	Estonia	Low birth weight
Sample 47	Sample 47	Female	Estonia	Low birth weight
Sample 36	Sample 36	Male	Estonia	Low birth weight
Sample 39	Sample 39	Male	Estonia	Low birth weight
Sample 46	Sample 46	Female	Estonia	Low birth weight
Sample 42	Sample 42	Female	Estonia	Low birth weight
Sample 43	Sample 43	Female	Estonia	Low birth weight
Sample 35	Sample 35	Male	Estonia	Low birth weight
Sample 40	Sample 40	Female	Estonia	Low birth weight
Sample 34	Sample 34	Male	Estonia	Low birth weight
Sample 45	Sample 45	Female	Estonia	Low birth weight
Sample 37	Sample 37	Male	Estonia	Low birth weight

Sampleset ID:: 5
Name:: LGA
Sampleset Type:: Case
Description:: Maternal and paternal blood DNA samples drawn postpartum from the term pregnancy cases with large-for-gestational age (LGA) newborns
Size:: 15
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Exceptionally large at birth

Samples for sampleset 5
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
Sample 58	Sample 58	Female	Estonia	Exceptionally large at birth
Sample 55	Sample 55	Female	Estonia	Exceptionally large at birth
Sample 50	Sample 50	Male	Estonia	Exceptionally large at birth
Sample 61	Sample 61	Female	Estonia	Exceptionally large at birth
Sample 60	Sample 60	Female	Estonia	Exceptionally large at birth
Sample 57	Sample 57	Female	Estonia	Exceptionally large at birth
Sample 49	Sample 49	Male	Estonia	Exceptionally large at birth
Sample 62	Sample 62	Female	Estonia	Exceptionally large at birth
Sample 52	Sample 52	Male	Estonia	Exceptionally large at birth
Sample 53	Sample 53	Male	Estonia	Exceptionally large at birth
Sample 54	Sample 54	Male	Estonia	Exceptionally large at birth
Sample 59	Sample 59	Female	Estonia	Exceptionally large at birth
Sample 51	Sample 51	Male	Estonia	Exceptionally large at birth
Sample 56	Sample 56	Female	Estonia	Exceptionally large at birth
Sample 48	Sample 48	Male	Estonia	Exceptionally large at birth

Sampleset ID:: 6
Name:: Preeclampsia
Sampleset Type:: Case
Description:: Maternal and paternal blood DNA samples drawn postpartum from term pregnancies complicated with maternal severe late preeclampsia
Size:: 16
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Preeclampsia

Samples for sampleset 6
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
Sample 72	Sample 72	Female	Estonia	Preeclampsia
Sample 67	Sample 67	Male	Estonia	Preeclampsia
Sample 76	Sample 76	Female	Estonia	Preeclampsia
Sample 69	Sample 69	Male	Estonia	Preeclampsia
Sample 74	Sample 74	Female	Estonia	Preeclampsia
Sample 68	Sample 68	Male	Estonia	Preeclampsia
Sample 66	Sample 66	Male	Estonia	Preeclampsia
Sample 63	Sample 63	Male	Estonia	Preeclampsia
Sample 71	Sample 71	Female	Estonia	Preeclampsia
Sample 75	Sample 75	Female	Estonia	Preeclampsia
Sample 64	Sample 64	Male	Estonia	Preeclampsia
Sample 70	Sample 70	Male	Estonia	Preeclampsia
Sample 65	Sample 65	Male	Estonia	Preeclampsia
Sample 77	Sample 77	Female	Estonia	Preeclampsia
Sample 78	Sample 78	Female	Estonia	Preeclampsia
Sample 73	Sample 73	Female	Estonia	Preeclampsia

Sampleset ID:: 7
Name:: Gestational diabetes
Sampleset Type:: Case
Description:: Maternal and paternal blood DNA samples drawn postpartum from term pregnancies complicated with maternal gestational diabetes
Size:: 16
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Gestational diabetes mellitus uncontrolled

Samples for sampleset 7
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
Sample 85	Sample 85	Male	Estonia	Gestational diabetes mellitus uncontrolled
Sample 82	Sample 82	Male	Estonia	Gestational diabetes mellitus uncontrolled
Sample 89	Sample 89	Female	Estonia	Gestational diabetes mellitus uncontrolled
Sample 94	Sample 94	Female	Estonia	Gestational diabetes mellitus uncontrolled
Sample 92	Sample 92	Female	Estonia	Gestational diabetes mellitus uncontrolled
Sample 84	Sample 84	Male	Estonia	Gestational diabetes mellitus uncontrolled
Sample 79	Sample 79	Male	Estonia	Gestational diabetes mellitus uncontrolled
Sample 83	Sample 83	Male	Estonia	Gestational diabetes mellitus uncontrolled
Sample 91	Sample 91	Female	Estonia	Gestational diabetes mellitus uncontrolled
Sample 81	Sample 81	Male	Estonia	Gestational diabetes mellitus uncontrolled
Sample 90	Sample 90	Female	Estonia	Gestational diabetes mellitus uncontrolled
Sample 86	Sample 86	Male	Estonia	Gestational diabetes mellitus uncontrolled
Sample 87	Sample 87	Female	Estonia	Gestational diabetes mellitus uncontrolled
Sample 80	Sample 80	Male	Estonia	Gestational diabetes mellitus uncontrolled
Sample 93	Sample 93	Female	Estonia	Gestational diabetes mellitus uncontrolled
Sample 88	Sample 88	Female	Estonia	Gestational diabetes mellitus uncontrolled

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	SNP array	Probe signal intensity	Illumina HumanOmniExpress Beadchip	879

dbVar

Database of genomic structural variation

estd216 (Kasak et al. 2015)

Links

Detailed Information: Download 879 Variant Regions, Download 879 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: 7

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

estd216 (Kasak et al. 2015)

Links

Detailed Information: Download 879 Variant Regions, Download 879 Variant Calls, Download Both, FTP

Variant Summary

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

Remapping summary: GRCh37->GRCh38.p12

Samplesets

Number of Samplesets: 7

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: