HML Examples

HML Examples

Example	HML 0.3	HML 0.93	Description
5.1	5.1_0.3	5.1_0.93

Locus	Method	Reporting<br >Format	HML 0.2	HML 0.3	HML 0.3.3	HML 0.9.3
A	DNA	allele code		case.05.1a.v030.xml
A	DNA	genotype list		case.05.1b.v030.xml		case.05.1.v093.xml

| Locus | Method | Reporting<br >Format | HML | | ----- | ------ | --------------------- | ------- | ------- | --------- | ----------| | A | DNA | allele code | case.05.1a.v030.xml | | A | DNA | genotype list | case.05.1b.v030.xml<br >case.05.1.v093.xml | | B | SBT | genotype list | ex_4_1.txt |

Example 5.1

Lab 999 typed a sample for center 123 for the ABDR project. The typing was performed on Jan 23, 2004. The results are:

NMDP ID: 444-333-2   A*0102, A*0103
                     A*0103, A*0106

Example 5.1 in HML 0.3

Using allele codes this result would be reported as A01BC, A01CF, using the following xml:

  <?xml version="1.0" encoding="UTF-8"?>
  <!DOCTYPE hml PUBLIC "-//NMDP//DTD HML 0.3//EN" "http://www.nmdp.org/DTD/hml-0.3.dtd">
  <hml version="0.3">
    <project name="ABDR">
      <reporting-center code="999"/>
      <sample id="444-333-2" center-code="123">
        <typing>
          <interpretation date="20040123">
            <haploid locus="A" method="DNA" type="01BC"/>
            <haploid locus="A" method="DNA" type="01CF"/>
          </interpretation>
        </typing>
      </sample>
    </project>
  </hml>

Starting in HML 0.3, this result can be reported as a genotype list, using the following xml:

  <?xml version="1.0" encoding="UTF-8"?>
  <!DOCTYPE hml PUBLIC "-//NMDP//DTD HML 0.3//EN" "http://www.nmdp.org/DTD/hml-0.3.dtd">
  <hml version="0.3">
    <project name="ABDR">
      <reporting-center code="999"/>
      <sample id="444-333-2" center-code="123">
        <typing>
          <interpretation date="2004-01-23">
            <genotype-list db="HLADB" version="2.4.0">
              <diploid-combination>
                <locus-block>
                  <allele-list>
                    <allele>A*0102</allele>
                  </allele-list>
                </locus-block>
                <locus-block>
                  <allele-list>
                    <allele>A*0103</allele>
                  </allele-list>
                </locus-block>
              </diploid-combination>
              <diploid-combination>
                <locus-block>
                  <allele-list>
                    <allele>A*0103</allele>
                  </allele-list>
                </locus-block>
                <locus-block>
                  <allele-list>
                    <allele>A*0106</allele>
                  </allele-list>
                </locus-block>
              </diploid-combination>
            </genotype-list>
          </interpretation>
        </typing>
      </sample>
    </project>
  </hml>

Example 5.1 in HML 0.93

<?xml version="1.0" ?>
<hml project-name="ABDR" version="0.9.3">
    <reporting-center code="999"/>
    <sample center-code="123" id="444-333-2">
        <typing gene-family="HLA">
            <interpretation allele-db="HLADB" allele-version="2.4.0" date="2004-01-23">
                    <genotype-list>
                      <diploid-combination locus="A">
                        <locus-block>
                          <allele-list>
                            <allele>A*0102</allele>
                          </allele-list>
                        </locus-block>
                        <locus-block>
                          <allele-list>
                            <allele>A*0103</allele>
                          </allele-list>
                        </locus-block>
                      </diploid-combination>
                      <diploid-combination locus="A">
                        <locus-block>
                          <allele-list>
                            <allele>A*0103</allele>
                          </allele-list>
                        </locus-block>
                        <locus-block>
                          <allele-list>
                            <allele>A*0106</allele>
                          </allele-list>
                        </locus-block>
                      </diploid-combination>
                    </genotype-list>
            </interpretation>
        </typing>
    </sample>
</hml>

hml-docs/examples/case.05.1.hml