docs/docs/manifests.h_and_e_template.html
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<a href="index.html">CIDC Documentation</a>
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<h1>
Biospecimen manifest for H&E
</h1>
<p>
<b>Description:</b> Biospecimen manifest for transferring Hematoxylin and Eosin stained slides.
</p>
</div>
<div class="container">
<div class="accordion" id="Shipment_accordion">
<div class="card">
<div class="card-header" id="Shipment">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Shipment_card" aria-expanded="false" aria-controls="Shipment_card">
Worksheet - Shipment
</button>
</h2>
</div>
<div id="Shipment_card" class="collapse" aria-labelledby="Shipment" data-parent="#Shipment_accordion">
<div class="card-body">
<div class="accordion" id="Shipment_preamble_accordion">
<div class="card">
<div class="card-header" id="Shipment_preamble">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Shipment_preamble_card" aria-expanded="false" aria-controls="Shipment_preamble_card">
Preamble Rows
</button>
</h2>
</div>
<div id="Shipment_preamble_card" class="collapse" aria-labelledby="Shipment_preamble" data-parent="#Shipment_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="manifest id">
manifest id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Filename of the manifest used to ship this sample. Example: E4412_PBMC.
</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="assay type">
assay type
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Assay and sample type used.
</td>
<td>
<
string
>
<ul>
<li>"Olink"</li>
<li>"WES"</li>
<li>"RNAseq"</li>
<li>"IHC"</li>
<li>"CyTOF"</li>
<li>"H\u0026E"</li>
<li>"ELISA"</li>
<li>"mIF"</li>
<li>"mIHC"</li>
<li>"TCRseq"</li>
<li>"ATACseq"</li>
<li>"ctDNA"</li>
<li>"Microbiome"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="assay priority">
assay priority
</span>
</td>
<td width=55%>
Priority of the assay as it appears on the intake form.
</td>
<td>
<
string
>
<ul>
<li>"1"</li>
<li>"2"</li>
<li>"3"</li>
<li>"4"</li>
<li>"5"</li>
<li>"6"</li>
<li>"7"</li>
<li>"8"</li>
<li>"9"</li>
<li>"10"</li>
<li>"11"</li>
<li>"12"</li>
<li>"13"</li>
<li>"14"</li>
<li>"15"</li>
<li>"Not Reported"</li>
<li>"Other"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="receiving party">
receiving party
</span>
</td>
<td width=55%>
Site where sample was shipped to be assayed.
</td>
<td>
<
string
>
<ul>
<li>"MDA_Wistuba"</li>
<li>"MDA_Bernatchez"</li>
<li>"MDA_Al-Atrash"</li>
<li>"MSSM_Gnjatic"</li>
<li>"MSSM_Rahman"</li>
<li>"MSSM_Kim-Schulze"</li>
<li>"MSSM_Bongers"</li>
<li>"MSSM_MTC"</li>
<li>"DFCI_Wu"</li>
<li>"DFCI_Hodi"</li>
<li>"DFCI_Severgnini"</li>
<li>"DFCI_Livak"</li>
<li>"Broad_Cibulskis"</li>
<li>"Stanf_Maecker"</li>
<li>"Stanf_Bendall"</li>
<li>"NCH"</li>
<li>"Adaptive"</li>
<li>"FNLCR_MoCha"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="courier">
courier
</span>
</td>
<td width=55%>
Courier utilized for shipment.
</td>
<td>
<
string
>
<ul>
<li>"FEDEX"</li>
<li>"USPS"</li>
<li>"UPS"</li>
<li>"Inter-Site Delivery"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="tracking number">
tracking number
</span>
</td>
<td width=55%>
Air bill number assigned to shipment. Example: 4567788343.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="account number">
account number
</span>
</td>
<td width=55%>
Courier account number to pay for shipping if available. Example: 45465732.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="shipping condition">
shipping condition
</span>
</td>
<td width=55%>
Type of shipment made.
</td>
<td>
<
string
>
<ul>
<li>"Frozen_Dry_Ice"</li>
<li>"Frozen_Shipper"</li>
<li>"Ice_Pack"</li>
<li>"Ambient"</li>
<li>"Not Reported"</li>
<li>"Other"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="date shipped">
date shipped
</span>
</td>
<td width=55%>
Date of shipment.
</td>
<td>
<
string
: date
>
</td>
</tr>
<tr>
<td>
<span id="date received">
date received
</span>
</td>
<td width=55%>
Date of receipt.
</td>
<td>
<
string
: date
>
</td>
</tr>
<tr>
<td>
<span id="quality of shipment">
quality of shipment
</span>
</td>
<td width=55%>
Indication that specimens were received in good condition.
</td>
<td>
<
string
>
<ul>
<li>"Specimen shipment received in good condition"</li>
<li>"Specimen shipment received in poor condition"</li>
<li>"Not Reported"</li>
<li>"Other"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="ship from">
ship from
</span>
</td>
<td width=55%>
Contact information for shipment.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="ship to">
ship to
</span>
</td>
<td width=55%>
Physical shipping address of the destination.
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="Samples_accordion">
<div class="card">
<div class="card-header" id="Samples">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Samples_card" aria-expanded="false" aria-controls="Samples_card">
Worksheet - Samples
</button>
</h2>
</div>
<div id="Samples_card" class="collapse" aria-labelledby="Samples" data-parent="#Samples_accordion">
<div class="card-body">
<div class="accordion" id="Samples_body_accordion">
<div class="card">
<div class="card-header" id="Samples_body">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Samples_body_card" aria-expanded="false" aria-controls="Samples_body_card">
Data Columns
</button>
</h2>
</div>
<div id="Samples_body_card" class="collapse" aria-labelledby="Samples_body" data-parent="#Samples_body_accordion">
<div class="card-body">
<h5 class="text-muted">IDs</h4>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="entry (#)">
entry (#)
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Provides a numbered identifier for patient (sample) entry in a shipment manifest.
</td>
<td>
<
integer
>
</td>
</tr>
<tr>
<td>
<span id="collection event name">
collection event name
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Categorical description of timepoint at which the sample was taken.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="cohort name">
cohort name
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Categorical description of cohorts, arms, and treatment groups.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="participant ID">
participant ID
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Trial Participant Identifier. Crypto-hashed after upload.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="parent sample ID">
parent sample ID
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Sample identifier assigned by the biorepository site. Crypto-hashed after upload.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="processed sample ID">
processed sample ID
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Aliquot identifier assigned by the biorepository site. Crypto-hashed after upload.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="CIMAC_ID_accordion">
<div class="card">
<div class="card-header" id="CIMAC_ID">
<div class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#CIMAC_ID_card" aria-expanded="false" aria-controls="CIMAC_ID_card">
CIMAC ID
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
string
>
</div>
</div>
</div>
<div id="CIMAC_ID_card" class="collapse" aria-labelledby="CIMAC_ID">
<div class="card-body">
Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as CTTTPPPSS.AA for trial code TTT, participant PPP, sample SS, and aliquot AA.
<br>
All files are
<sup><mark>required</mark></sup>
<br>
<table class="table table-striped">
<thead>
<tr>
<th>File name</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
cimac_participant_id
</td>
<td width=55%>
Participant identifier assigned by the CIMAC-CIDC Network. Formated as: CTTTPPP for trial code TTT and participant PPP (first 7 characters of CIMAC ID).
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
</table>
<h5 class="text-muted">Specimen Info Filled by Biorepository</h4>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="type of sample">
type of sample
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Type of sample sent.
</td>
<td>
<
string
>
<ul>
<li>"Tumor Tissue"</li>
<li>"Normal Tissue"</li>
<li>"Skin Tissue"</li>
<li>"Blood"</li>
<li>"Bone Marrow"</li>
<li>"Cerebrospinal Fluid"</li>
<li>"Lymph Node"</li>
<li>"Stool"</li>
<li>"Cell Product"</li>
<li>"White Blood Cell Apheresis"</li>
<li>"Urine"</li>
<li>"Not Reported"</li>
<li>"Other"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="type of tumor sample">
type of tumor sample
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
The type of tumor sample obtained (primary or metastatic).
</td>
<td>
<
string
>
<ul>
<li>"Metastatic Tumor"</li>
<li>"Primary Tumor"</li>
<li>"Not Reported"</li>
<li>"Other"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="sample collection procedure">
sample collection procedure
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Indicates the specimen source of the sample shipped. Example: Na Heparin blood draw aliquots (2 of three), FFPE block #52
</td>
<td>
<
string
>
<ul>
<li>"Blood Draw"</li>
<li>"Excision"</li>
<li>"Core Biopsy"</li>
<li>"Punch Biopsy"</li>
<li>"Endoscopic Biopsy"</li>
<li>"Bone Marrow Core Biopsy"</li>
<li>"Bone Marrow Aspirate"</li>
<li>"Lumbar Puncture"</li>
<li>"Aspirate"</li>
<li>"Fine-Needle Aspiration"</li>
<li>"Not Reported"</li>
<li>"Other"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="fixation/stabilization type">
fixation/stabilization type
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Type of specimen fixation or stabilization that was employed by the site directly after collection.
</td>
<td>
<
string
>
<ul>
<li>"Archival FFPE"</li>
<li>"Fresh Specimen"</li>
<li>"Frozen Specimen"</li>
<li>"Formalin-Fixed Paraffin-Embedded"</li>
<li>"Optimum cutting temperature medium"</li>
<li>"Thaw-Lyse"</li>
<li>"Not Reported"</li>
<li>"Other"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="processed sample type">
processed sample type
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
The type of processing that was performed on the collected specimen by the Biobank for storage.
</td>
<td>
<
string
>
<ul>
<li>"Whole Blood"</li>
<li>"Plasma"</li>
<li>"Serum"</li>
<li>"PBMC"</li>
<li>"Buffy Coat"</li>
<li>"Bone Marrow Mononuclear Cell"</li>
<li>"Supernatant"</li>
<li>"Cell Pellet"</li>
<li>"H\u0026E-Stained Fixed Tissue Slide Specimen"</li>
<li>"Fixed Slide"</li>
<li>"Tissue Scroll"</li>
<li>"FFPE Punch"</li>
<li>"Not Reported"</li>
<li>"Other"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="tumor tissue (% total area)">
tumor tissue (% total area)
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Score the percentage of tumor (including tumor bed) tissue area of the slide (e.g. vs non-malignant or normal tissue) (0-100)
</td>
<td>
<
number
,
string
>
</td>
</tr>
<tr>
<td>
<span id="box number">
box number
</span>
</td>
<td width=55%>
Identifier if sample shipment container includes multiple boxes for each assay.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="sample location">
sample location
</span>
</td>
<td width=55%>
Sample location within the shipping container. Example: A1.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="core number">
core number
</span>
</td>
<td width=55%>
The biopsy core number from which the sample was used.
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="processed sample quantity">
processed sample quantity
</span>
</td>
<td width=55%>
Quantity of the processed sample (e.g. number of slides cut for DNA extraction).
</td>
<td>
<
number
>
</td>
</tr>
</table>
<h5 class="text-muted">Filled by CIMAC Lab</h4>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="viable tumor (% area)">
viable tumor (% area)
</span>
</td>
<td width=55%>
Score the percentage of viable tumor cells comprising the tumor bed area
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="viable stroma (% area)">
viable stroma (% area)
</span>
</td>
<td width=55%>
Score the evaluation of stromal elements (this indicates the % area of tumor bed occupied by non-tumor cells, including inflammatory cells [lymphocytes, histiocytes, etc], endothelial cells, fibroblasts, etc)
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="necrosis (% area)">
necrosis (% area)
</span>
</td>
<td width=55%>
Score the percentage area of necrosis
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="fibrosis (% area)">
fibrosis (% area)
</span>
</td>
<td width=55%>
Score the percentage area of Fibrosis
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="material used">
material used
</span>
</td>
<td width=55%>
Receiving site indicates how much material was used for assay purposes.
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="material used units">
material used units
</span>
</td>
<td width=55%>
Units for the amount of material used; should be the same value as Specimen Analyte units.
</td>
<td>
<
string
>
<ul>
<li>"Microliters"</li>
<li>"Milligrams"</li>
<li>"Milliliters"</li>
<li>"Nanogram per Microliter"</li>
<li>"Milligram per Milliliter"</li>
<li>"Micrograms per Microliter"</li>
<li>"Cells per Vial"</li>
<li>"Slides"</li>
<li>"Not Reported"</li>
<li>"Other"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="material remaining">
material remaining
</span>
</td>
<td width=55%>
Receiving site indicates how much material remains after assay use.
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="material remaining units">
material remaining units
</span>
</td>
<td width=55%>
Units for the amount of material remaining.
</td>
<td>
<
string
>
<ul>
<li>"Microliters"</li>
<li>"Milligrams"</li>
<li>"Milliliters"</li>
<li>"Nanogram per Microliter"</li>
<li>"Milligram per Milliliter"</li>
<li>"Micrograms per Microliter"</li>
<li>"Cells per Vial"</li>
<li>"Slides"</li>
<li>"Not Reported"</li>
<li>"Other"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="material storage condition">
material storage condition
</span>
</td>
<td width=55%>
Storage condition of the material once it was received.
</td>
<td>
<
string
>
<ul>
<li>"RT"</li>
<li>"4oC"</li>
<li>"(-20)oC"</li>
<li>"(-80)oC"</li>
<li>"LN"</li>
<li>"Not Reported"</li>
<li>"Other"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="quality of sample">
quality of sample
</span>
</td>
<td width=55%>
Final status of sample after QC and pathology review.
</td>
<td>
<
string
>
<ul>
<li>"Pass"</li>
<li>"Pass at Risk"</li>
<li>"Fail"</li>
<li>"Not Reported"</li>
<li>"Other"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="sample replacement">
sample replacement
</span>
</td>
<td width=55%>
Indication if sample replacement is/was requested.
</td>
<td>
<
string
>
<ul>
<li>"Replacement Not Requested"</li>
<li>"Replacement Requested"</li>
<li>"Replacement Tested"</li>
<li>"Not Reported"</li>
<li>"Other"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="residual sample use">
residual sample use
</span>
</td>
<td width=55%>
Indication if sample was sent to another location or returned back to biorepository.
</td>
<td>
<
string
>
<ul>
<li>"Sample Returned"</li>
<li>"Sample Sent to Another Lab"</li>
<li>"Sample received from CIMAC"</li>
<li>"Not Reported"</li>
<li>"Other"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="comments">
comments
</span>
</td>
<td width=55%>
Comments on sample testing.
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
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