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Operational Example 1 (NGS Class II)

mpresteg edited this page Sep 26, 2014 · 2 revisions
<?xml version="1.0" encoding="UTF-8"?>
<!--

    Histoimmunogenetics Markup Language (HML)
    Copyright (c) 2014 National Marrow Donor Program (NMDP)

    This specification is free software; you can redistribute it and/or modify it
    under the terms of the GNU Lesser General Public License as published
    by the Free Software Foundation; either version 3 of the License, or (at
    your option) any later version.

    This specification is distributed in the hope that it will be useful, but WITHOUT
    ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
    License for more details.

    You should have received a copy of the GNU Lesser General Public License
    along with this specification;  if not, write to the Free Software Foundation,
    Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA.

    > http://www.gnu.org/licenses/lgpl.html

-->

<!-- NOTE: This is a brief example of a DRAFT version of HML in action. It is not intended to be an accurate genotyping result. -->

<hml xmlns="http://schemas.nmdp.org/spec/hml/0.9.5" 
     xmlns:hml="http://schemas.nmdp.org/spec/hml/0.9.5" 
     xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
     xsi:schemaLocation="http://schemas.nmdp.org/spec/hml/0.9.5  http://schemas.nmdp.org/spec/hml/0.9.5/hml-0.9.5.xsd"
     reporting-center="789"
     project-name="LAB"
     version="0.9.5">
  <sample id="120000089" center-code="123">
    <typing gene-family="HLA"><!-- nomenclature="IMGT/HLA Database 3.14.0" -->
      <sbt-ngs locus="HLA-DRB1" test-id="GTR000000000.0" test-id-source="NCBI-GTR">
        <consensus-sequence>
          <targeted-region
              assembly="GRCh38"
              contig="6"
              start="32584377"
              end="32584109"
              strand="-1"
              id="ENSE00001731226"
              description="HLA-DRB1 exon 2"/>
          <sequence alphabet="DNA">
            TTTCTTGGAGCAGGTTAAACATGAGTGTCATTTCTTCAACGGGACGGAGCGGGTGCGGTTCCTGGACA
            GATACTTCTATCACCAAGAGGAGTACGTGCGCTTCGACAGCGACGTGGGGGAGTACCGGGCGGTGACG
            GAGCTGGGGCGGCCTAGCGCCGAGTACTGGAACAGCCAGAAGGACCTCCTGGAGCAGAGGCGGGCCGA
            GGTGGACACCTACTGCAGACACAACTACGGGGTTGTGGAGAGCTTCACA
          </sequence>
          <sequence alphabet="DNA">
            TTTCTTGGAGCAGGTTAAACATGAGTGTCATTTCTTCAACGGGACGGAGCGGGTGCGGTTCCTGGACA
            GATACTTCTATCACCAAGAGGAGTACGTGCGCTTCGACAGCGACGTGGGGGAGTACCGGGCGGTGACG
            GAGCTGGGGCGGCCTGATGCCGAGTACTGGAACAGCCAGAAGGACCTCCTGGAGCAGAGGCGGGCCGA
            GGTGGACACCTACTGCAGACACAACTACGGGGTTGGTGAGAGCTTCACA
          </sequence>
        </consensus-sequence>
      </sbt-ngs>
      <interpretation date="2014-01-01" allele-db="IMGT/HLA" allele-version="3.14.0">
        <!-- 
          EITHER a single glstring element with a URI -OR- a single glstring 
          element containing inline data are expected here.
        -->

        <!-- glstring using inline data: -->
        <glstring>
          HLA-DRB1*04:11:01+HLA-DRB1*04:07:01/HLA-DRB1*04:92
        </glstring>

        <!-- glstring using a URI reference: -->
        <glstring uri="http://gl.immunogenomics.org/imgt-hla/3.14.0/genotype-list/e" />
      </interpretation>
    </typing>
  </sample>
</hml>

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