docs/docs/assays.ctdna.html
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<p>
<a href="index.html">CIDC Documentation</a>
</p>
<h1>
Circulating Tumor DNA Assay
</h1>
<p>
<b>Description:</b> Circulating Tumor DNA Assay.
</p>
</div>
<div class="container">
<div class="accordion" id="assay_accordion">
<div class="card">
<div class="card-header" id="assay_metadata">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#assay_metadata_card" aria-expanded="false" aria-controls="assay_metadata_card">
Assay Metadata
</button>
</h2>
</div>
<div id="assay_metadata_card" class="collapse" aria-labelledby="assay_metadata" data-parent="#assay_accordion">
<div class="card-body">
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="assay_creator">
assay_creator
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Indicates what site is filling out the assay.
</td>
<td>
<
string
>
<ul>
<li>"DFCI"</li>
<li>"Mount Sinai"</li>
<li>"Stanford"</li>
<li>"MD Anderson"</li>
<li>"Adaptive"</li>
<li>"Broad"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="batch_id">
batch_id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
ctDNA batch identification number. Unique to every batch.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="protocol_identifier">
protocol_identifier
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Trial identifier used by lead organization, ie. Center for Experimental Therapeutics Program (CTEP) ID or Industry Sponsored ID. This is usually a short identifier. Example: E4412.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="summary_plots">
summary_plots
</span>
</td>
<td width=55%>
Information about a Portable Document Format file.
</td>
<td>
<a href="files.pdf.html">
pdf
</a>
</td>
</tr>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="assay_data">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#assay_data_card" aria-expanded="false" aria-controls="assay_data_card">
Assay Data
</button>
</h2>
</div>
<div id="assay_data_card" class="collapse" aria-labelledby="assay_data" data-parent="#assay_accordion">
<div class="card-body">
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="records_accordion">
<div class="card">
<div class="card-header" id="records">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#records_card" aria-expanded="false" aria-controls="records_card">
records
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
array
>
</div>
</div>
<div id="records_card" class="collapse" aria-labelledby="records">
<div class="card-body">
A single data record from ctDNA assay.
<br>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="bias_qc_plots">
bias_qc_plots
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a Portable Document Format file.
</td>
<td>
<a href="files.pdf.html">
pdf
</a>
</td>
</tr>
<tr>
<td>
<span id="cimac_id">
cimac_id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as CTTTPPPSS.AA for trial code TTT, participant PPP, sample SS, and aliquot AA.
</td>
<td>
<
string
>
as regex <br> <code>^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$</code>
</td>
</tr>
<tr>
<td>
<span id="demultiplexed_bam">
demultiplexed_bam
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a BAM file.
</td>
<td>
<a href="files.bam.html">
bam
</a>
</td>
</tr>
<tr>
<td>
<span id="demultiplexed_bam_index">
demultiplexed_bam_index
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a Bam index file.
</td>
<td>
<a href="files.bam_bai.html">
bam bai
</a>
</td>
</tr>
<tr>
<td>
<span id="fraction_cna_subclonal">
fraction_cna_subclonal
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Fraction of copy number altered bins that are subclonal. Accepts NaN. (0-1)
</td>
<td>
<
number
,
string
>
</td>
</tr>
<tr>
<td>
<span id="fraction_genome_subclonal">
fraction_genome_subclonal
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Fraction of all (genomic) bins that are subclonal. (0-1)
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="gc_map_correction_mad">
gc_map_correction_mad
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Measure of the noise in the data following GC-content bias correction. Computed as the median absolute deviation of differences between adjacent bins.
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="genome-wide_plots">
genome-wide_plots
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a Portable Document Format file.
</td>
<td>
<a href="files.pdf.html">
pdf
</a>
</td>
</tr>
<tr>
<td>
<span id="optimal_solution">
optimal_solution
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a ZIP file.
</td>
<td>
<a href="files.zip.html">
zip
</a>
</td>
</tr>
<tr>
<td>
<span id="other_solutions">
other_solutions
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a ZIP file.
</td>
<td>
<a href="files.zip.html">
zip
</a>
</td>
</tr>
<tr>
<td>
<span id="subclone_fraction">
subclone_fraction
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Fraction of tumor-derived DNA that is subclonal. Accepts NA. (0-1)
</td>
<td>
<
number
,
string
>
</td>
</tr>
<tr>
<td>
<span id="tumor_fraction">
tumor_fraction
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Estimated fraction of tumor-derived DNA. Equivalent to purity in bulk tumor analysis. (0-1)
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="tumor_ploidy">
tumor_ploidy
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Average number of copies of the tumor-derived genome. Note that the overall sample ploidy is 2 * (1 - tumor.fraction) + tumor.fraction * tumor.ploidy.
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="comments">
comments
</span>
</td>
<td width=55%>
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="assay_uploads">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#assay_uploads_card" aria-expanded="false" aria-controls="assay_uploads_card">
Assay Uploads
</button>
</h2>
</div>
<div id="assay_uploads_card" class="collapse" aria-labelledby="assay_uploads" data-parent="#assay_accordion">
<div class="card-body">
<table class="table table-striped">
<thead>
<tr>
<th>Entity</th>
<th>Description</th>
</tr>
</thead>
<tr>
<td width=25%>
<a href='assays.ctdna.ctdna_template.html'>
Metadata file for ctDNA Assay
</a>
</td>
<td>
Metadata information for Circulating Tumor DNA (ctDNA) Assay data submission.
</td>
</tr>
</table>
</div>
</div>
</div>
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