nstd220 - Chen et al 2022 - dbVar Study

nstd220 (Chen et al. 2022)

Organism:: Human
Study Type:: Case-Set
Submitter:: Liheng Chen
Description:: This study explored whether adding maternal CNV analysis to NIPT could improve the abnormal detection rate. Using sliding window algorithm counting reads in each continuous bins (100kb size) of each chromosome. We set the thresholds for duplications to be above 2.7 of copy numbers and deletions to be below 1.3 of copy numbers. and were Sequenced with Illumina Nextseq CN550. See Variant Summary counts for nstd220 in dbVar Variant Summary.
Publication(s):: Chen et al. 2022

Links

Source: NCBI

Detailed Information: Download 17 Variant Regions, Download 17 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p13 (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_000002.12	Chr2	2	2	Remapped	NC_000002.12
NC_000004.12	Chr4	1	1	Remapped	NC_000004.12
NC_000015.10	Chr15	1	1	Remapped	NC_000015.10
NC_000016.10	Chr16	5	5	Remapped	NC_000016.10
NC_000017.11	Chr17	3	3	Remapped	NC_000017.11
NC_000022.11	Chr22	1	1	Remapped	NC_000022.11
NC_000023.11	ChrX	4	4	Remapped	NC_000023.11
NT_187607.1	Chr16\|NT_187607.1	3	3	Remapped	NT_187607.1
NT_187614.1	Chr17\|NT_187614.1	1	1	Remapped	NT_187614.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000002.11	Chr2	2	2	Submitted	NC_000002.11
NC_000004.11	Chr4	1	1	Submitted	NC_000004.11
NC_000015.9	Chr15	1	1	Submitted	NC_000015.9
NC_000016.9	Chr16	5	5	Submitted	NC_000016.9
NC_000017.10	Chr17	3	3	Submitted	NC_000017.10
NC_000022.10	Chr22	1	1	Submitted	NC_000022.10
NC_000023.10	ChrX	4	4	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_000002.11	Chr2	2	2	0	0	0	0	2	2	0	0	0	0
NC_000004.11	Chr4	1	1	0	0	0	0	1	1	0	0	0	0
NC_000015.9	Chr15	1	1	0	0	0	0	1	1	0	0	0	0
NC_000016.9	Chr16	5	2	0	0	0	3	5	2	0	0	0	3
NC_000017.10	Chr17	3	2	0	0	0	1	3	2	0	0	0	1
NC_000022.10	Chr22	1	0	1	0	0	0	1	0	1	0	0	0
NC_000023.10	ChrX	4	0	4	0	0	0	4	0	4	0	0	0

Samplesets

Number of Samplesets: 1

Name:: maternal CNVs detected by NIPT
Sampleset Type:: Case
Description:: The samples were derived from cell-free DNA in the peripheral blood of pregnant women. Maternal CNVs were identified by bioinformatics analysis.
Size:: 17
Organisms:: Homo sapiens
Sampleset Phenotype(s):: See phenotypes on samples
Sex:: Female

Samples for sampleset 1
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Age	Subject Phenotype
21J106665	cell-free DNA in the peripheral blood of pregnant women	21J106665	Female	Asian	25 years	Not reported
21J104462	cell-free DNA in the peripheral blood of pregnant women	21J104462	Female	Asian	28 years	Not reported
21J101817	cell-free DNA in the peripheral blood of pregnant women	21J101817	Female	Asian	24 years	short stature
21J104405	cell-free DNA in the peripheral blood of pregnant women	21J104405	Female	Asian	36 years	Not reported
21J108971	cell-free DNA in the peripheral blood of pregnant women	21J108971	Female	Asian	28 years	schizophrenia
21J101249	cell-free DNA in the peripheral blood of pregnant women	21J101249	Female	Asian	25 years	expressive language delay facial asymmetry
21J104606	cell-free DNA in the peripheral blood of pregnant women	21J104606	Female	Asian	26 years	Not reported
21J104345	cell-free DNA in the peripheral blood of pregnant women	21J104345	Female	Asian	34 years	Not reported
21J108961	cell-free DNA in the peripheral blood of pregnant women	21J108961	Female	Asian	28 years	cholelithiasis polysplenia renal cyst
21J101676	cell-free DNA in the peripheral blood of pregnant women	21J101676	Female	Asian	25 years	spontaneous abortion
21J105304	cell-free DNA in the peripheral blood of pregnant women	21J105304	Female	Asian	27 years	Not reported
21J105324	cell-free DNA in the peripheral blood of pregnant women	21J105324	Female	Asian	28 years	Not reported
21J104969	cell-free DNA in the peripheral blood of pregnant women	21J104969	Female	Asian	36 years	spontaneous abortion
21J107686	cell-free DNA in the peripheral blood of pregnant women	21J107686	Female	Asian	26 years	dry skin
21J100568	cell-free DNA in the peripheral blood of pregnant women	21J100568	Female	Asian	37 years	Not reported
21J104580	cell-free DNA in the peripheral blood of pregnant women	21J104580	Female	Asian	32 years	abnormality of the dentition
21J107005	cell-free DNA in the peripheral blood of pregnant women	21J107005	Female	Asian	30 years	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	Sequencing	Read depth	Illumina Nextseq CN550	17

dbVar

Database of genomic structural variation

nstd220 (Chen et al. 2022)

Links

Detailed Information: Download 17 Variant Regions, Download 17 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p13 (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

nstd220 (Chen et al. 2022)

Links

Detailed Information: Download 17 Variant Regions, Download 17 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38.p13 (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: