estd236 - Kurtas et al 2018 - dbVar Study

estd236 (Kurtas et al. 2018)

Organism:: Human
Study Type:: Collection
Submitter:: Nehir Edibe Kurtas
Description:: By-whole genome sequencing (WGS) in three unrelated families, we demonstrated that in one parent of each family a balanced chromothripsis was present causing a genomic imbalance in the index case consisting in a deletion and a non-contiguous duplication within 3q22.1-q26.31 in case 1, a simple two-way reciprocal translocation t(6;14) in case 2, and a complex rearrangement involving chromosomes 6, 7 and 15 in case 3. See Variant Summary counts for estd236 in dbVar Variant Summary.
Publication(s):: Kurtas et al. 2018

Links

Source: NCBI

Detailed Information: Download 7 Variant Regions, Download 36 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_000003.12	Chr3	1	6	Remapped	NC_000003.12
NC_000006.12	Chr6	2	11	Remapped	NC_000006.12
NC_000007.14	Chr7	1	3	Remapped	NC_000007.14
NC_000008.11	Chr8	1	1	Remapped	NC_000008.11
NC_000014.9	Chr14	1	3	Remapped	NC_000014.9
NC_000015.10	Chr15	1	2	Remapped	NC_000015.10

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000003.11	Chr3	1	12	Submitted	NC_000003.11
NC_000006.11	Chr6	2	19	Submitted	NC_000006.11
NC_000007.13	Chr7	1	6	Submitted	NC_000007.13
NC_000008.10	Chr8	1	3	Submitted	NC_000008.10
NC_000014.8	Chr14	1	7	Submitted	NC_000014.8
NC_000015.9	Chr15	1	4	Submitted	NC_000015.9

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_000003.11	Chr3	1	0	1	0	0	0	12	0	0	0	0	24
NC_000006.11	Chr6	2	0	2	0	0	0	19	0	0	0	0	30
NC_000007.13	Chr7	1	1	0	0	0	0	6	0	0	0	0	6
NC_000008.10	Chr8	1	1	0	0	0	0	3	1	0	0	0	0
NC_000014.8	Chr14	1	1	0	0	0	0	7	0	0	0	0	8
NC_000015.9	Chr15	1	1	0	0	0	0	4	0	0	0	0	4

Samplesets

Number of Samplesets: 3

Sampleset ID:: 1
Sampleset Type:: Case
Description:: Sampleset Case1 involves two samples from a family case; healthy mother and her affected son.
Size:: 2
Organisms:: Homo sapiens
Sampleset Phenotype(s):: See phenotypes on samples

Samples for sampleset 1
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
1001	1001	Male	Italian	coarctation of aorta delayed speech and language development global developmental delay megalocornea
1002	1002	Female	Italian	Not reported

Sampleset ID:: 2
Sampleset Type:: Case
Description:: Sampleset Case2 involves two samples from a family case; healthy father and his healthy daughter.
Size:: 2
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 2
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
256	256	Female	Italian	Not reported
286	286	Male	Italian	Not reported

Sampleset ID:: 3
Sampleset Type:: Case
Description:: Sampleset Case3 involves two samples from a family case; healthy mother and her affected son.
Size:: 2
Organisms:: Homo sapiens
Sampleset Phenotype(s):: See phenotypes on samples

Samples for sampleset 3
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
1959	1959	Male	Italian	delayed speech and language development global developmental delay hypospadias patent ductus arteriosus after premature birth
1960	1960	Female	Italian	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	Sequencing	Read depth and paired-end mapping	Illumina's TruSeq DNA PCR-Free	0
2	Discovery	PCR	Manual observation	Other	0
3	Discovery	Sequencing	Manual observation	Sanger Sequencing	0
4	Discovery	Oligo aCGH	Merging of experiments	Agilent SurePrint G3 Human CGH	0
5	Discovery	Merging of experiments 1,2,3,4	Merging of experiments 1,2,3,4	See merged experiments	32
6	Discovery	Merging of experiments 2,3,4	Merging of experiments 2,3,4	See merged experiments	4

dbVar

Database of genomic structural variation

estd236 (Kurtas et al. 2018)

Links

Detailed Information: Download 7 Variant Regions, Download 36 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: 3

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

estd236 (Kurtas et al. 2018)

Links

Detailed Information: Download 7 Variant Regions, Download 36 Variant Calls, Download Both, FTP

Variant Summary

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

Remapping summary: GRCh37->GRCh38.p12

Samplesets

Number of Samplesets: 3

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: