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nstd213 (Pham et al. 2021)

Organism:
Human
Study Type:
Somatic
Submitter:
Minh-Tam Pham
Description:
Phased structural variant analysis from Linked-read sequencing allowed identification of complex rearrangement chains consistent with chromothripsis and chromoplexy, with breakpoints occurred across a single allele, providing further evidence that complex SVs occurred in a concerted event, rather than through accumulation of multiple independent rearrangements. Preprint may be found at https://doi.org/10.1101/2021.08.09.455584. See Variant Summary counts for nstd213 in dbVar Variant Summary.
Project:
PRJNA751700

Detailed Information: Download 5864 Variant Regions, Download 5936 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p13 (hg38)
Submitted: GRCh37 (hg19)

Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.11Chr1448456RemappedNC_000001.11
NC_000002.12Chr2359363RemappedNC_000002.12
NC_000003.12Chr3337339RemappedNC_000003.12
NC_000004.12Chr4359359RemappedNC_000004.12
NC_000005.10Chr5428431RemappedNC_000005.10
NC_000006.12Chr6327342RemappedNC_000006.12
NC_000007.14Chr7388388RemappedNC_000007.14
NC_000008.11Chr8485487RemappedNC_000008.11
NC_000009.12Chr9275276RemappedNC_000009.12
NC_000010.11Chr10286296RemappedNC_000010.11
NC_000011.10Chr11265266RemappedNC_000011.10
NC_000012.12Chr12325326RemappedNC_000012.12
NC_000013.11Chr13256258RemappedNC_000013.11
NC_000014.9Chr14138139RemappedNC_000014.9
NC_000015.10Chr15133133RemappedNC_000015.10
NC_000016.10Chr16168172RemappedNC_000016.10
NC_000017.11Chr17168173RemappedNC_000017.11
NC_000018.10Chr18137138RemappedNC_000018.10
NC_000019.10Chr197475RemappedNC_000019.10
NC_000020.11Chr20218218RemappedNC_000020.11
NC_000021.9Chr216969RemappedNC_000021.9
NC_000022.11Chr225656RemappedNC_000022.11
NC_000023.11ChrX238246RemappedNC_000023.11
NC_000024.10ChrY3234RemappedNC_000024.10
NT_187516.1Chr1|NT_187516.111RemappedNT_187516.1
NT_187519.1Chr1|NT_187519.111RemappedNT_187519.1
NW_003315907.2Chr1|NW_003315907.211RemappedNW_003315907.2
NW_017852928.1Chr1|NW_017852928.111RemappedNW_017852928.1
NW_018654707.1Chr1|NW_018654707.1910RemappedNW_018654707.1
NT_187531.1Chr2|NT_187531.111RemappedNT_187531.1
NW_011332690.1Chr2|NW_011332690.122RemappedNW_011332690.1
NT_187536.1Chr3|NT_187536.111RemappedNT_187536.1
NW_011332691.1Chr3|NW_011332691.111RemappedNW_011332691.1
NW_019805489.1Chr3|NW_019805489.11011RemappedNW_019805489.1
NW_019805490.1Chr3|NW_019805490.133RemappedNW_019805490.1
NT_187679.1Chr4|NT_187679.111RemappedNT_187679.1
NW_003315914.1Chr4|NW_003315914.111RemappedNW_003315914.1
NW_003315915.1Chr4|NW_003315915.177RemappedNW_003315915.1
NW_017363814.1Chr4|NW_017363814.111RemappedNW_017363814.1
NT_187651.1Chr5|NT_187651.111RemappedNT_187651.1
NW_003315917.2Chr5|NW_003315917.211RemappedNW_003315917.2
NW_003315918.1Chr5|NW_003315918.111RemappedNW_003315918.1
NW_016107298.1Chr5|NW_016107298.144RemappedNW_016107298.1
NT_187552.1Chr6|NT_187552.122RemappedNT_187552.1
NT_187553.1Chr6|NT_187553.122RemappedNT_187553.1
NT_187556.1Chr6|NT_187556.111RemappedNT_187556.1
NW_004166862.2Chr6|NW_004166862.211RemappedNW_004166862.2
NW_009646200.1Chr6|NW_009646200.111RemappedNW_009646200.1
NT_187558.1Chr7|NT_187558.111RemappedNT_187558.1
NT_187560.1Chr7|NT_187560.111RemappedNT_187560.1
NT_187564.1Chr7|NT_187564.111RemappedNT_187564.1
NW_017852929.1Chr7|NW_017852929.111RemappedNW_017852929.1
NW_017852930.1Chr7|NW_017852930.111RemappedNW_017852930.1
NW_018654714.1Chr7|NW_018654714.133RemappedNW_018654714.1
NW_018654715.1Chr7|NW_018654715.144RemappedNW_018654715.1
NT_187567.1Chr8|NT_187567.155RemappedNT_187567.1
NT_187571.1Chr8|NT_187571.122RemappedNT_187571.1
NT_187577.1Chr8|NT_187577.155RemappedNT_187577.1
NT_187654.1Chr8|NT_187654.111RemappedNT_187654.1
NW_018654716.1Chr8|NW_018654716.111RemappedNW_018654716.1
NW_018654717.1Chr8|NW_018654717.11515RemappedNW_018654717.1
NT_187578.1Chr9|NT_187578.111RemappedNT_187578.1
NT_187580.1Chr10|NT_187580.111RemappedNT_187580.1
NW_013171806.1Chr10|NW_013171806.111RemappedNW_013171806.1
NW_013171807.1Chr10|NW_013171807.111RemappedNW_013171807.1
NT_187658.1Chr12|NT_187658.111RemappedNT_187658.1
NW_003315938.1Chr12|NW_003315938.111RemappedNW_003315938.1
NW_003571050.1Chr12|NW_003571050.111RemappedNW_003571050.1
NW_009646204.1Chr12|NW_009646204.11717RemappedNW_009646204.1
NW_011332696.1Chr12|NW_011332696.111RemappedNW_011332696.1
NW_015148967.1Chr12|NW_015148967.111RemappedNW_015148967.1
NW_018654718.1Chr12|NW_018654718.111RemappedNW_018654718.1
NT_187595.1Chr13|NT_187595.111RemappedNT_187595.1
NW_011332700.1Chr13|NW_011332700.111RemappedNW_011332700.1
NT_187601.1Chr14|NT_187601.122RemappedNT_187601.1
NT_187660.1Chr15|NT_187660.155RemappedNT_187660.1
NT_187607.1Chr16|NT_187607.145RemappedNT_187607.1
NW_017852933.1Chr16|NW_017852933.156RemappedNW_017852933.1
NT_187663.1Chr17|NT_187663.111RemappedNT_187663.1
NT_187615.1Chr17|NT_187615.111RemappedNT_187615.1
NW_003315952.3Chr17|NW_003315952.311RemappedNW_003315952.3
NW_003315954.1Chr17|NW_003315954.111RemappedNW_003315954.1
NW_016107299.1Chr17|NW_016107299.123RemappedNW_016107299.1
NW_019805503.1Chr18|NW_019805503.177RemappedNW_019805503.1
NW_003315964.2Chr19|NW_003315964.211RemappedNW_003315964.2
NW_003315965.1Chr19|NW_003315965.111RemappedNW_003315965.1
NT_187623.1Chr20|NT_187623.111RemappedNT_187623.1
NT_187626.1Chr21|NT_187626.111RemappedNT_187626.1
NT_187635.1ChrX|NT_187635.111RemappedNT_187635.1
NW_009646195.1Chr1|NW_009646195.133RemappedNW_009646195.1
NT_187562.1Chr7|NT_187562.178RemappedNT_187562.1
NT_187653.1Chr7|NT_187653.111RemappedNT_187653.1
NT_187576.1Chr8|NT_187576.111RemappedNT_187576.1
NT_187593.1Chr13|NT_187593.122RemappedNT_187593.1
NW_011332698.1Chr13|NW_011332698.122RemappedNW_011332698.1
NT_187603.1Chr15|NT_187603.111RemappedNT_187603.1
NW_011332701.1Chr15|NW_011332701.144RemappedNW_011332701.1
NT_187661.1Chr17|NT_187661.111RemappedNT_187661.1
NT_187614.1Chr17|NT_187614.11415RemappedNT_187614.1
NW_009646206.1Chr19|NW_009646206.111RemappedNW_009646206.1
NT_187633.1Chr22|NT_187633.155RemappedNT_187633.1
Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.10Chr1448456SubmittedNC_000001.10
NC_000002.11Chr2359363SubmittedNC_000002.11
NC_000003.11Chr3337339SubmittedNC_000003.11
NC_000004.11Chr4359359SubmittedNC_000004.11
NC_000005.9Chr5428431SubmittedNC_000005.9
NC_000006.11Chr6330345SubmittedNC_000006.11
NC_000007.13Chr7389390SubmittedNC_000007.13
NC_000008.10Chr8485487SubmittedNC_000008.10
NC_000009.11Chr9275276SubmittedNC_000009.11
NC_000010.10Chr10286296SubmittedNC_000010.10
NC_000011.9Chr11265266SubmittedNC_000011.9
NC_000012.11Chr12325326SubmittedNC_000012.11
NC_000013.10Chr13256258SubmittedNC_000013.10
NC_000014.8Chr14138139SubmittedNC_000014.8
NC_000015.9Chr15133133SubmittedNC_000015.9
NC_000016.9Chr16168172SubmittedNC_000016.9
NC_000017.10Chr17168173SubmittedNC_000017.10
NC_000018.9Chr18137138SubmittedNC_000018.9
NC_000019.9Chr197475SubmittedNC_000019.9
NC_000020.10Chr20218218SubmittedNC_000020.10
NC_000021.8Chr216969SubmittedNC_000021.8
NC_000022.10Chr225959SubmittedNC_000022.10
NC_000023.10ChrX238246SubmittedNC_000023.10
NC_000024.9ChrY3234SubmittedNC_000024.9

Variant Region remap statusVariant Call remap status
Sequence IDChrVariant Regions on sourcePerfectGoodPassFailMultVariant Calls on sourcePerfectGoodPassFailMult
NC_000001.10Chr144835531501404563593270141
NC_000002.11Chr2359306203095363310203095
NC_000003.11Chr3337276230079339277230080
NC_000004.11Chr4359306132086359306132086
NC_000005.9Chr542831917403304313221740330
NC_000006.11Chr6330277125371345287175371
NC_000007.13Chr7389317407032390317408032
NC_000008.10Chr848537740501664873784060166
NC_000009.11Chr9275249111037276250111037
NC_000010.10Chr1028622315301142962272130114
NC_000011.9Chr112652338306026623483060
NC_000012.11Chr12325262153090326263153090
NC_000013.10Chr132562209506325822295063
NC_000014.8Chr141381176103513911861035
NC_000015.9Chr15133104141026133104141026
NC_000016.9Chr16168136150031172137160033
NC_000017.10Chr17168112185050173115185052
NC_000018.9Chr18137105112061138106112061
NC_000019.9Chr1974411560297541157029
NC_000020.10Chr20218181273019218181273019
NC_000021.8Chr2169442000116944200011
NC_000022.10Chr2259192441235919244123
NC_000023.10ChrX2381547930524615487305
NC_000024.9ChrY322010006342111006

Samplesets

Number of Samplesets: 1

Name:
Prostate Cancer Cell Line Large Structural Variants Calls
Description:
Large structural variant calls (>30kb) and Copy number vatiants from common Prostate Cancer cell lines
Size:
12
Organisms:
Homo sapiens
Sampleset Phenotype(s):
Prostate neoplasm
Sex:
Male
  • Download Samples as CSV file
    • Samples for sampleset 1
    Sample IDCell TypeSubject ID SexSubject Phenotype
    SAMN20524660Castrate resistant sub-clone of LnCAP dedrived from xenografts in castrate miceLNCaP_C42bMaleNot reported
    SAMN20524663Prostatic epithelial cell lines immortalized by human papillomavirus 18RWPE-1MaleNot reported
    SAMN20524656Androgen responsive metastatic prostate carinoma to the lymph nodeLAPC4MaleNot reported
    SAMN20524655Metastatic prostate carinoma to the brainDU145MaleNot reported
    SAMN20524664Androgen responsive metastatic prostate carcinoma to the vertebral boneVCaPMaleNot reported
    SAMN20524665Castrate resistant sub-clone of VCAP dedrived from xenografts in castrate miceVCaP-CRMaleNot reported
    SAMN20524654Primary prostate carcinomaCWR22Rv1MaleNot reported
    SAMN20524657Castrate resistant sub-clone of LAPC4 dedrived from xenografts in castrate miceLAPC4-CRMaleNot reported
    SAMN20524658Androgen responsive metastatic prostate carinoma to the lymph nodeLNCaPMaleNot reported
    SAMN20524662Metastatic prostate adenocarcinoma to the bonePC3MaleNot reported
    SAMN20524659Castrate resistant sub-clone of LnCAP dedrived from androgen depleted cell cultureLNCaP_AblMaleNot reported
    SAMN20524661Androgen-responsive metastatic prostate carcinoma to the boneMDA-Pca-2bMaleNot reported

    Experimental Details

    Experiment IDTypeMethodAnalysisPlatformsNumber of Variant Calls
    1DiscoverySequencingPaired-end mappingIllumina Hi Seq X Ten5,936

    Validations

    No validation data were submitted for this study.

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