docs/docs/assays.ihc.ihc_template.html
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<p>
<a href="index.html">CIDC Documentation</a>
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<h1>
IHC assay template
</h1>
<p>
<b>Description:</b> ImmunoHistoChemistry (IHC) submission.
</p>
</div>
<div class="container">
<div class="accordion" id="IHC_accordion">
<div class="card">
<div class="card-header" id="IHC">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#IHC_card" aria-expanded="false" aria-controls="IHC_card">
Worksheet - IHC
</button>
</h2>
</div>
<div id="IHC_card" class="collapse" aria-labelledby="IHC" data-parent="#IHC_accordion">
<div class="card-body">
<div class="accordion" id="IHC_preamble_accordion">
<div class="card">
<div class="card-header" id="IHC_preamble">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#IHC_preamble_card" aria-expanded="false" aria-controls="IHC_preamble_card">
Preamble Rows
</button>
</h2>
</div>
<div id="IHC_preamble_card" class="collapse" aria-labelledby="IHC_preamble" data-parent="#IHC_preamble_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="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="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="slide scanner model">
slide scanner model
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Model version of the slide scanner instrument.
</td>
<td>
<
string
>
<ul>
<li>"Vectra 2.0"</li>
<li>"Hamamatsu"</li>
<li>"AT2 Turbo"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="staining platform">
staining platform
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Staining platform used for tissue sample labeling.
</td>
<td>
<
string
>
<ul>
<li>"auto"</li>
<li>"manual"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="autostainer model">
autostainer model
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Model version of the autostainer instrument.
</td>
<td>
<
string
>
<ul>
<li>"Bond RX"</li>
<li>"Bond MAX"</li>
<li>"Other"</li>
<li>"N/A"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="antibody name">
antibody name
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Antibody type collected for this study.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="company">
company
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Company from which antibody sample was derived.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="clone">
clone
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Resulting type of antibody clone from primary antibody sample.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="catalogue number">
catalogue number
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Antibody registry catalog number assigned to antibody sample.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="lot number">
lot number
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Identification number assigned to the particular quantity or lot of material from manufacturer.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="dilution">
dilution
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Concentration ratio for antibody dilution.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="incubation time">
incubation time
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Time duration of antibody incubation.
</td>
<td>
<
string
: time
>
</td>
</tr>
<tr>
<td>
<span id="incubation temperature">
incubation temperature
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Temperature used for antibody incubation.
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
<div class="accordion" id="IHC_body_accordion">
<div class="card">
<div class="card-header" id="IHC_body">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#IHC_body_card" aria-expanded="false" aria-controls="IHC_body_card">
Data Columns
</button>
</h2>
</div>
<div id="IHC_body_card" class="collapse" aria-labelledby="IHC_body" data-parent="#IHC_body_accordion">
<div class="card-body">
<h5 class="text-muted">Sample</h4>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<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="IHC image">
IHC image
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about an image file.
</td>
<td>
<a href="files.image.html">
image
</a>
</td>
</tr>
</table>
<h5 class="text-muted">Marker call</h4>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="marker positive">
marker positive
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Indicates whether the marker is considered positive by clinical trial guidelines (if applicable).
</td>
<td>
<
string
>
<ul>
<li>"positive"</li>
<li>"negative"</li>
<li>"no_call"</li>
</ul>
</td>
</tr>
</table>
<h5 class="text-muted">Chromogenic IHC (please specify one score/metric)</h4>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="tumor proportion score">
tumor proportion score
</span>
</td>
<td width=55%>
Tumor Proportion Score (TPS) is the percentage of viable tumor cells showing marker staining relative to all viable tumor cells. (0-1)
</td>
<td>
<
number
,
string
>
</td>
</tr>
<tr>
<td>
<span id="combined positive score">
combined positive score
</span>
</td>
<td width=55%>
Combined Positive Score (CPS) is the percentage of marker staining cells (tumor cells and cells that are non-tumor) relative to all viable tumor cells. (0-1)
</td>
<td>
<
number
,
string
>
</td>
</tr>
<tr>
<td>
<span id="inflammatory cells">
inflammatory cells
</span>
</td>
<td width=55%>
Percentage of inflammatory cells (non-tumor cells) showing marker staining relative to all inflammatory cells. (0-1)
</td>
<td>
<
number
,
string
>
</td>
</tr>
<tr>
<td>
<span id="positive inflammatory cell area">
positive inflammatory cell area
</span>
</td>
<td width=55%>
Area of PD-L1+ Inflammatory Cells over the area of TSI + IT as a percentage. (0-1)
</td>
<td>
<
number
,
string
>
</td>
</tr>
<tr>
<td>
<span id="intensity">
intensity
</span>
</td>
<td width=55%>
A measure of the intensity or brightness of the protein. (0-3)
</td>
<td>
<
number
,
string
>
</td>
</tr>
<tr>
<td>
<span id="% expression">
% expression
</span>
</td>
<td width=55%>
A percentage of the relevant cells considered positive. (0-100)
</td>
<td>
<
number
,
string
>
</td>
</tr>
<tr>
<td>
<span id="h score">
h score
</span>
</td>
<td width=55%>
A summation of the percentage of area stained at each intensity level multiplied by the weighted intensity. (0-300)
</td>
<td>
<
integer
,
string
>
</td>
</tr>
<tr>
<td>
<span id="comment">
comment
</span>
</td>
<td width=55%>
A text comment regarding this slide.
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
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