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Microsatellite instability (MSI) Level 1 data is sent by MDA to be submitted and evaluated by the Biospecimen Core Resource (BCR) at Nationwide Children’s Hospital (TCGA Center 23).

Overview

MSI-Mono-Dinucleotide Assay is performed to test a panel of four mononucleotide repeat loci (polyadenine tracts BAT25, BAT26, BAT40, and transforming growth factor receptor type II) and three dinucleotide repeat loci (CA repeats in D2S123, D5S346, and D17S250). Two additional pentanucleotide loci (Penta D and Penta E) are included in this assay to evaluate sample identity. Multiplex fluorescent-labeled PCR and capillary electrophoresis were used to identify MSI if a variation in the number of microsatellite repeats was detected between tumor and matched non-neoplastic tissue or mononuclear blood cells. Equivocal or failed markers were re-evaluated by singleplex PCR.

Summary of files

  • Level 1 data submitted as standard MAGE-TAB archives
    • *.fsa (fragment analysis) trace files that come off ABI machine
    • *.txt text file summarizing fsa file
  • There are no Level 2 data
  • Level 3 data is included in BCR clinical-based submissions
    • Submitted in aux XML 
    • XML tag: mononucleotide_and_dinucleotide_marker_panel_analysis_status
    • classifications: microsatellite-stable (MSS), low level MSI (MSI-L) if less than 40% of markers were altered and high level MSI (MSI-H) if greater than 40% of markers were altered.

Level 3 data

Tumor DNA was classified as microsatellite-stable (MSS) if zero markers were altered, low level MSI (MSI-L) if less than 40% of markers were altered and high level MSI (MSI-H) if greater than 40% of markers were altered. In the MSI-Mono-Dinucleotide Assay, this equated to MSI-L classification if one or two markers were altered, and MSI-H if three to seven markers were altered. Penta D and E markers were scored in the same manner as the MSI markers indicated below, however they did not contribute to MSI Class calculation.

<auxiliary:tcga_bcr xmlns:auxiliary="http://tcga.nci/bcr/xml/auxdata/2.5" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:admin="http://tcga.nci/bcr/xml/administration/2.5" xmlns:shared="http://tcga.nci/bcr/xml/clinical/shared/2.5" xsi:schemaLocation="http://tcga.nci/bcr/xml/auxdata/2.5 http://tcga-data.nci.nih.gov/docs/xsd/BCR/tcga.nci/bcr/xml/auxdata/2.5/TCGA_BCR.Auxiliary_Data.xsd" schemaVersion="2.5">
<admin:admin>
<admin:bcr xsd_ver="1.17">Nationwide Children's Hospital</admin:bcr>
<admin:batch_number xsd_ver="1.17">73.19.0</admin:batch_number>
<admin:disease_code xsd_ver="2.3">UCEC</admin:disease_code>
<admin:day_of_dcc_upload xsd_ver="1.17">4</admin:day_of_dcc_upload>
<admin:month_of_dcc_upload xsd_ver="1.17">6</admin:month_of_dcc_upload>
<admin:year_of_dcc_upload xsd_ver="1.17">2012</admin:year_of_dcc_upload>
</admin:admin>
<auxiliary:patient>
<shared:bcr_patient_barcode cde="2673794" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B5-A0JN</shared:bcr_patient_barcode>
<shared:tissue_source_site cde="" xsd_ver="2.4" procurement_status="Completed" owner="">B5</shared:tissue_source_site>
<shared:patient_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A0JN</shared:patient_id>
<shared:bcr_patient_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">b60f22ac-a659-4f33-b01d-820e86a9a5c9</shared:bcr_patient_uuid>
<auxiliary:microsatellite_instability_test_results>
<auxiliary:microsatellite_instability_test_result>
<auxiliary:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0477759c-42c2-4bb4-9c2a-268d7c43e906</auxiliary:bcr_aliquot_uuid>
<auxiliary:mononucleotide_and_dinucleotide_marker_panel_analysis_status cde="3226963" xsd_ver="2.4" procurement_status="Completed" owner="">MSI-L</auxiliary:mononucleotide_and_dinucleotide_marker_panel_analysis_status>
<auxiliary:mononucleotide_marker_panel_analysis_status cde="3226962" xsd_ver="2.4" procurement_status="Not Available" owner=""/>
</auxiliary:microsatellite_instability_test_result>
</auxiliary:microsatellite_instability_test_results>
</auxiliary:patient>
</auxiliary:tcga_bcr>

Level 1 Summaries (txt)

Individual markers were assigned a value of 0 through 6 based on the presence or absence of a MSI shift, allele homo/heterozygosity and loss of heterozygosity (LOH) if observed in the tumor. LOH for a marker was assigned if the ratio of allele peak heights between tumor and matched normal control was less than 0.7 or greater than 1.6. Markers were classified as follows:

  • 0= Marker not evaluable.
  • 1= MSI; homozygous in Normal.
  • 2= MSI; heterozygous in Normal with discernable LOH.
  • 3= MSI; heterozygous in Normal where LOH was either not present or could not be calculated due to MSI interference with peak heights.
  • 4= No MSI; homozygous in Normal.
  • 5= No MSI; heterozygous in Normal with discernable LOH.
  • 6= No MSI; heterozygous in Normal where LOH is not present.
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