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nstd83 (Morak et al. 2013)

Organism:
Human
Study Type:
Case-Set
Submitter:
Maria Morak
Description:
The leukemia-initiating ETV6-RUNX1 (ER) fusion occurs already in utero but supporting genetic lesions are required to cause overt leukemia. To assess the timing of such B cell development- (PAX5, n=8; VpreB1, n=3), proliferation- and apoptosis-associated (BTG1, n=3; BMF, n=1) lesions, we analyzed Guthrie card DNA of 10 ER-positive leukemias for their presence. Despite our approach reaching a single cell detection level and the detection of genomic ER fusion in all Guthrie cards, we did not recover any of the specific secondary changes. These results are consistent with the prevailing notion that secondary aberrations occur in the postnatal period, but do not exclude the possibility that at least some of them emerge already prenatally and the affected clones simply have not yet reached a size that is detectable with the presently available approaches. See Variant Summary counts for nstd83 in dbVar Variant Summary.
Publication(s):
Morak et al. 2013

Detailed Information: Download 25 Variant Regions, Download 35 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Submitted: GRCh37 (hg19)

Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
No Placement100Remapped
NC_000009.12Chr988RemappedNC_000009.12
NC_000012.12Chr12313RemappedNC_000012.12
NC_000015.10Chr1511RemappedNC_000015.10
NC_000021.9Chr21010RemappedNC_000021.9
NC_000022.11Chr2233RemappedNC_000022.11
Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
No Placement100Submitted
NC_000009.11Chr988SubmittedNC_000009.11
NC_000012.11Chr12313SubmittedNC_000012.11
NC_000015.9Chr1511SubmittedNC_000015.9
NC_000021.8Chr21010SubmittedNC_000021.8
NC_000022.10Chr2233SubmittedNC_000022.10

Variant Region remap statusVariant Call remap status
Sequence IDChrVariant Regions on sourcePerfectGoodPassFailMultVariant Calls on sourcePerfectGoodPassFailMult
NC_000009.11Chr9880000880000
NC_000012.11Chr1233000013130000
NC_000015.9Chr15110000110000
NC_000021.8Chr2100000010100000
NC_000022.10Chr22303000303000

Samplesets

Number of Samplesets: 1

Name:
deletion sequences
Size:
10
Organisms:
Homo sapiens
Sampleset Phenotype(s):
Childhood B Acute Lymphoblastic Leukemia
  • Download Samples as CSV file
  • Samples for sampleset 1
    Sample IDCell TypeSubject ID SexSubject Phenotype
    1B-Lymphocyte463MaleChildhood B Acute Lymphoblastic Leukemia
    2B-LymphocyteGMaleChildhood B Acute Lymphoblastic Leukemia
    3B-Lymphocyte733MaleChildhood B Acute Lymphoblastic Leukemia
    4B-Lymphocyte806FemaleChildhood B Acute Lymphoblastic Leukemia
    5B-Lymphocyte809FemaleChildhood B Acute Lymphoblastic Leukemia
    6B-Lymphocyte560MaleChildhood B Acute Lymphoblastic Leukemia
    7B-Lymphocyte382FemaleChildhood B Acute Lymphoblastic Leukemia
    8B-Lymphocyte240MaleChildhood B Acute Lymphoblastic Leukemia
    9B-LymphocyteSMaleChildhood B Acute Lymphoblastic Leukemia
    10B-Lymphocyte469MaleChildhood B Acute Lymphoblastic Leukemia

    Experimental Details

    Experiment IDTypeMethodAnalysisNumber of Variant Calls
    1DiscoverySequencingSequence alignment35

    Validations

    No validation data were submitted for this study.

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