Safety/White List

From 2014.igem.org

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<div class="reminder">
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<h4>PAGE UNDER CONSTRUCTION -- NOT READY FOR USE</h4>
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<h4><span style="font-size: large; color: #337f53;">!&nbsp;</span> Remember <span style="font-size: large; color: #337f53;">&nbsp;!</span></h4>
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<p>This White List is a draft. It is not the final version!</p>
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<p>You must submit a <a href="https://2014.igem.org/Safety/Check_In">Check-In</a> for <strong>ANY organism or part that is NOT on the White List</strong>. In the table below, the "Check-In Required" column is only <strong>examples</strong> of organisms/parts that require a Check-In. If your part/organism is not explicitly listed in the table below, it requires a Check-In.</p>
<p>Questions? Contact <span class="email">&lt;safety (at) igem (dot) org&gt;</span></p>
<p>Questions? Contact <span class="email">&lt;safety (at) igem (dot) org&gt;</span></p>
</div>
</div>
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<ol class="highlightme">
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<p>This page will help you determine which organisms/parts require a <a href="https://2014.igem.org/Safety/Check_In">Check-In</a>, and which do not. If you are planning to acquire and use an organism/part that is not on the White List, you must send a Check-In and receive our reply before you acquire and use that organism/part.</p>
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<li>Obtain Claudia's feedback on white list</li>
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<li>Consult VFDB / protein taxonomies</li>
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<li>Format nicely and post</li>
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<li>Write FAQ</li>
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<li>Remove this note.</li>
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</ol>
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<br />
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<p><a href="https://2014.igem.org/Safety_Hub#requirements.checkin">Click here to read more about Check-Ins.</a></p>
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<br />
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<p><a href="https://2014.igem.org/Safety/Check_In">Click here to submit a Check-In.</a></p>
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<div class="reminder">
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<h4>Remember!</h4>
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<p>You must Check-In for <strong>ANY organism or part that is NOT on the White List</strong>. The right-hand column of the table below is only <strong>examples</strong> of organisms/parts that require a Check-In. If your part/organism is not in the table below, it still requires a Check-In.</p>
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<p>Questions? Contact <span class="email">&lt;safety (at) igem (dot) org&gt;</span></p>
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</div>
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<br />
<br />
<br />
<br />
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<table id="whitelist">
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<table id="wltable">
<tr>
<tr>
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<th></th>
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<th style="width: 10%;"></th>
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<th>White List (no Check-In required)</th>
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<th style="width: 45%;">White List (no Check-In required)</th>
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<th>Check-In Required</th>
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<th style="width: 45%;"><a href="https://2014.igem.org/Safety/Check_In">Check-In</a> Required (examples only!)</th>
</tr>
</tr>
<tr>
<tr>
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<th rowspan="5">Whole Organisms</th>
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<th rowspan="5">Whole Organisms<br />
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<td>Risk Group 1 microorganisms</td>
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<span style="font-size: smaller;">(including viral genomes)</span></th>
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<td>Risk Group 2 microorganisms</td>
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<td><ul><li>Risk Group 1 microorganisms <br /> (For example: <i>E. coli</i> K-12, <i>S. cerevisiae</i>, <i>B. subtilis</i>, <i>Lactobacillus</i> spp.)</li></ul></td>
 +
<td><ul><li>Risk Group 2 microorganisms <br /> (For example: <i>Pseudomonas</i> spp.)</li></ul></td>
</tr>
</tr>
<tr>
<tr>
-
<td rowspan="2">Human and primate cell lines that have been tested and certified free of known pathogens (consult your vendor)</td>
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<td><ul>
-
<td>Human and primate cell lines that may contain pathogens</td>
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<li>Bacteriophages T2, T4, T7, M13, P1, &Phi;X174 (Phi X 174), and &lambda; (Lambda), unless containing a virulence factor (see below)</li>
 +
<li>Phagemids</li>
 +
</ul></td>
 +
<td><ul><li>Other viruses and bacteriophages</li></ul></td>
</tr>
</tr>
<tr>
<tr>
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<td>All primary isolated cells</td>
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<td><ul><li>Human and primate cell lines that have been tested and certified free of known pathogens (consult your vendor; <a href="https://2014.igem.org/Safety/White_List#celllines">see FAQ</a>)</li><li>Cell lines from plants, fungi, or animals that are not primates (such as <a href="http://en.wikipedia.org/wiki/Chinese_hamster_ovary_cell">CHO cells</a> or plant cells)</li></ul></td>
 +
<td><ul><li>Human and primate cell lines that may contain pathogens</li><li>All primary isolated cells (that is, cells taken directly from the body of a multicellular organism)</li></ul></td>
</tr>
</tr>
<tr>
<tr>
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<td><i>C. elegans</i>, <i>Physcomitrella patens</i>, <i>Drosophila</i> spp.</td>
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<td><ul>
-
<td>Other multicellular organisms</td>
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<li><i>C. elegans</i>, <i>Drosophila</i> spp.</li>
 +
<li><i>Physcomitrella patens</i>, <i>Arabidopsis</i> spp., <i>Nicotiana</i> spp.</li>
 +
<li>Human subjects in non-invasive experiments, such as surveys <a href="https://2014.igem.org/Safety/White_List#humansubj">(see FAQ)</a></li></ul></td>
 +
<td><ul><li>Other multicellular organisms</li></ul></td>
</tr>
</tr>
<tr>
<tr>
<td></td>
<td></td>
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<td>...and anything not explicitly listed</td>
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<td><ul><li>...and anything not explicitly listed</li></ul></td>
</tr>
</tr>
<tr>
<tr>
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<th>Parts</th>
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<th rowspan="6">Parts</th>
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<td><ul>
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<td>All Registry parts, except those with a Red Flag placed by the Safety Committee</td>
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<li>Any part from a Risk Group 1 organism, regardless of its function</li>
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<td>Registry parts that have a Red Flag, which looks like <a href="http://parts.igem.org/Template:SafetyFlag">this</a>. A complete list of parts with Red Flags can be found <a href="http://parts.igem.org/Special:WhatLinksHere/Template:SafetyFlag">here</a>.
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<li>All Registry parts, except those flagged by Archetype or Safety Committee</li>
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</td>
-
<li>Non-protein-coding parts in the following categories:</li>
+
</tr>
 +
 
 +
<tr>
 +
<td></td>
 +
<td>Any part from a Risk Group 3 organism, regardless of its function</td>
 +
</tr>
 +
 
 +
<tr>
 +
<td>Non-protein-coding parts in the following categories:
     <ul>
     <ul>
     <li>Promoters, RBSes, Terminators</li>
     <li>Promoters, RBSes, Terminators</li>
     <li>Binding sites for transcriptional regulators, endonucleases, and other proteins that bind to DNA</li>
     <li>Binding sites for transcriptional regulators, endonucleases, and other proteins that bind to DNA</li>
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     <li>CRISPR guide RNAs, microRNAs / interfering RNAs, aptamers</li>
+
    <li>Aptamers and catalytic RNAs</li>
 +
     <li>CRISPR guide RNAs, microRNAs, small interfering RNAs, and short hairpin RNAs that <strong>do not</strong> target human genes</li>
     </ul>
     </ul>
-
<li class="highlightme">Protein-coding genes from animals, plants, or Risk Group 2 microorganisms, in the following categories:</li>
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</td>
 +
<td>
     <ul>
     <ul>
-
     <li>Category 1</li>
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     <li>CRISPR guide RNAs, microRNAs, small interfering RNAs, and short hairpin RNAs that target human genes</li>
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     <li>Category 2</li>
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     <li>Other non-protein-coding genes</li>
     </ul>
     </ul>
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</ul></td>
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</td>
-
<td><ul>
+
</tr>
-
<li>Any part from a Risk Group 3 or 4 organism, regardless of its function</li>
+
 
-
<li>Registry parts with red flags on</li>
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<tr>
-
<li>Non-protein-coding genes that do not fall in any of the white-listed categories</li>
+
<td>Cas9, except when it is genomically integrated into a sexually reproducing organism</td>
-
<li>Protein-coding genes from animals, plants, or Risk Group 2 microorganisms, that do not fall in any of the white-listed categories</li>  
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<td>Cas9 integrated into the genome of a sexually reproducing organism<br /><i>(including organisms that reproduce both sexually and asexually, such as yeast)</i></td>
-
</ul></td>
+
</tr>
 +
 
 +
<tr>
 +
<td>
 +
Proteins or protein-coding genes from animals, plants, or Risk Group 1 / Risk Group 2 microorganisms, EXCEPT those in the list of "dangerous categories" on the right
 +
</td>
 +
<td>
 +
Proteins or protein-coding genes in the following dangerous categories:
 +
    <ul>
 +
    <li>Virulence factors <a href="https://2014.igem.org/Safety/White_List#virulencefactor">(see FAQ)</a></li>
 +
    <li>Factors that help pathogens evade or shut down the immune system</li>
 +
    <li>Factors that help pathogens halt the host's DNA/RNA replication, transcription, or translation</li>
 +
    <li>Factors that regulate the immune system, such as cytokines and interferons</li>
 +
    <li>Proteins that are toxic to humans</li>
 +
    <li>Enzymes that produce a molecule that is toxic to humans</li>
 +
    </ul>
 +
</td>
 +
</tr>
 +
 
 +
<tr>
 +
<td></td>
 +
<td>...and anything not explicitly listed</td>
</tr>
</tr>
</table>
</table>
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<h4>Banned Organisms/Parts</h4>
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<h4 style="text-align: center;"><span style="font-size: large; color: #FF1200;">X&nbsp;&nbsp;</span> Banned Organisms/Parts <span style="font-size: large; color: #FF1200;">&nbsp;&nbsp;X</span></h4>
<p>Some of the most dangerous organisms and parts are not allowed in iGEM, even with a Check-In:</p>
<p>Some of the most dangerous organisms and parts are not allowed in iGEM, even with a Check-In:</p>
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</ul>
</ul>
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<p>If you find that you want to use a banned organism/part, you should redesign your project to use a substitute from a safer Risk Group. Consult your advisor or contact us at <span class="email">&lt;safety AT igem DOT org&gt;</span> to get some advice on choosing a substitute.</p>
+
<p>If you find that you want to use a banned organism/part, you should redesign your project to use a safer substitute. Consult your advisor or contact us at <span class="email">&lt;safety AT igem DOT org&gt;</span> to get advice on choosing a substitute.</p>
</div>
</div>
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<h3>Notes</h3>
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<a class="anchor" id="faq"></a>
 +
<h3>Frequently Asked Questions</h3>
-
<p><em>What if I'm not sure whether my organism/part requires a Check-In?</em></p>
+
<ul>
 +
<li>
 +
<p class="faq">What if I'm not sure whether my organism/part requires a Check-In?</p>
<p>Ask us! Contact safety AT igem DOT org. Alternatively, because the Check-In form is short, you could choose to send a Check-In even if you are unsure.</p>
<p>Ask us! Contact safety AT igem DOT org. Alternatively, because the Check-In form is short, you could choose to send a Check-In even if you are unsure.</p>
 +
</li>
-
<p><em>We are going to handle an organism in lab, but we will only extract some DNA from it using PCR -- we won't use it as our chassis. Do we still have to send a Check-In?</em></p>
+
<li>
 +
<p class="faq">Where can I submit a Check-In?</p>
-
<p><em>Our project is to detect a dangerous organism. In order to test our project, of course we need to handle the dangerous organism (or parts of it), but it will not be part of what we build. Do we still have to send a Check-In?</em></p>
+
<p>Use the link in the left sidebar, or <a href="https://2014.igem.org/Safety/Check_In">click here</a>, to submit a Check-In. </p>
 +
</li>
 +
 
 +
<li>
 +
<p class="faq">How do I find out the Risk Group of an organism?</p>
 +
 
 +
<p>The <a href="https://2014.igem.org/Safety/Risk_Group_Guide">Risk Group Guide</a> lists iGEM's recommended sources for Risk Group information. It also has some advice on how to find an alternative source, if none of the recommended sources include your organism.</p>
 +
</li>
 +
 
 +
<li>
 +
<p class="faq">What if the White List changes during the summer?</p>
 +
 
 +
<p>As we learn more, we might <strong>add</strong> things to the White List, but we will not <strong>remove</strong> things from the White List until after the Jamboree each year. So, if something is on the White List now, it will stay on the White List for the whole 2014 season. (We may change the White List for future years.)</p>
 +
</li>
 +
 
 +
<li>
 +
<p class="faq">What exactly counts as a "whole organism"?<a class="anchor" id="wholepart"></a></p>
 +
 
 +
<p>For the purposes of this White List, a "whole organism" is an entire cell or multicellular organism, whether alive or dead. Intact, isolated viral genomes are also considered "whole organism", because many viral genomes can be pathogenic if they enter a host cell, even without the viral capsule.</p>
 +
 
 +
<p>(Isolated non-viral genomes are considered parts. Individual nucleic acids and proteins are also parts.)</p>
 +
</li>
 +
 
 +
<li>
 +
<p class="faq">We are going to handle an organism in lab, but we will only extract some DNA from it using PCR -- we won't use it as our chassis. Do we still have to send a Check-In?</p>
<p>Yes. The Check-In requirement applies to all organisms and all parts that you will handle in the lab, even if they will not be part of your final project.</p>
<p>Yes. The Check-In requirement applies to all organisms and all parts that you will handle in the lab, even if they will not be part of your final project.</p>
 +
</li>
-
<p><em>What about experiments on human subjects, such as surveys or software user-testing?</em></p>
+
<li>
 +
<p class="faq">Our project is to detect a dangerous organism. In order to test our project, we want to handle the dangerous organism (or parts of it), but it will not be part of what we build. Do we still have to send a Check-In?</p>
-
<p>Human experimental subjects are not covered under the iGEM safety program. If you conduct any experiments with human subjects (including non-invasive work such as surveys or software user-testing), you must find out the rules and regulations that cover those experiments in your country / at your university. Some experiments and surveys might require the approval of a review board on human experimental subjects, and some might not require any approval.</p>
+
<p>Yes. The Check-In requirement applies to all organisms and all parts that you will handle in the lab, even if they will not be part of your final project.</p>
 +
</li>
 +
<li>
 +
<p class="faq">What is a virulence factor?<a class="anchor" id="virulencefactor"></a></p>
 +
 +
<p><a href="http://www.mgc.ac.cn/VFs/main.htm">Virulence Factors of Pathogenic Bacteria</a> is a good resource where you can look up virulence factors in some well-studied pathogens. It gives this definition: "Virulence factors refer to the properties (i.e., gene products) that enable a microorganism to establish itself on or within a host of a particular species and enhance its potential to cause disease. Virulence factors include bacterial toxins, cell surface proteins that mediate bacterial attachment, cell surface carbohydrates and proteins that protect a bacterium, and hydrolytic enzymes that may contribute to the pathogenicity of the bacterium."</p>
 +
 +
<li>
 +
<p class="faq">We are going to use a lot of parts. May we combine them on a single Check-In?</p>
 +
 +
<p>If the parts all come from the same parent organism, you may combine them on a single Check-In, but make sure you give complete information about each part. If the parts come from different parent organisms, please send separate Check-Ins, or contact safety (at) igem (dot) org to ask about combining several Check-Ins into a spreadsheet.</p>
 +
</li>
 +
 +
<li>
 +
<p class="faq">How can I find out if my cell line is free of pathogens? What pathogens should I be concerned about?<a class="anchor" id="celllines"></a></p>
 +
 +
<p>If you bought the cells from a vendor or a culture collection, then you can consult their catalog. Many catalogs will list safety and pathogen information -- if you cannot find it, contact the vendor. If you received the cells from another lab, you should find out where they originally came from.</p>
 +
 +
<p>Cell lines can contain harmful viruses. Sometimes, the viral genome is integrated into the cell's genome. Most viruses have a limited "host range", which means that they can only infect closely related species. Therefore, viruses living in a human or monkey cell line are likely to be dangerous to humans, but viruses living in an insect cell line probably cannot infect humans. If you work with a cell line from humans or other <a href="http://en.wikipedia.org/wiki/Primate">primates</a>, you should check whether it contains viruses or viral genomic DNA. Viruses have Risk Group numbers, so if your cell line contains any viruses, you must handle it at the laboratory Safety Level that is appropriate for the highest Risk group virus it contains.</p>
 +
 +
<p>Some dangerous viruses that infect human cell lines: <a href="http://en.wikipedia.org/wiki/Hepatitis_B">HBV (hepatitis B virus)</a>, <a href="http://en.wikipedia.org/wiki/Hepatitis_C">HCV (hepatitis C virus)</a>, <a href="http://en.wikipedia.org/wiki/HIV">HIV (human immunodeficiency virus) 1 & 2</a>, <a href="http://en.wikipedia.org/wiki/Human_T-lymphotropic_virus">HTLV (human T-lymphotropic virus) 1 & 2</a>, <a href="http://en.wikipedia.org/wiki/Cytomegalovirus">CMV (cytomegalovirus)</a>.</p>
 +
</li>
 +
 +
<li>
 +
<p class="faq">What about experiments on human subjects, such as surveys or software user-testing?<a class="anchor" id="humansubj"></a></p>
 +
 +
<p>Human experimental subjects are not covered under the iGEM safety program. If you conduct any experiments with human subjects (including non-invasive work such as surveys or software user-testing), you must find out the rules and regulations that cover those experiments in your country / at your university. Some experiments and surveys might require the approval of a review board on human experimental subjects, and some might not require any approval.</p>
 +
</li>
 +
</ul>
</div>
</div>

Latest revision as of 21:32, 1 November 2014


Questions or feedback?
Email safety AT igem DOT org!

!  Remember  !

You must submit a Check-In for ANY organism or part that is NOT on the White List. In the table below, the "Check-In Required" column is only examples of organisms/parts that require a Check-In. If your part/organism is not explicitly listed in the table below, it requires a Check-In.

Questions? Contact

This page will help you determine which organisms/parts require a Check-In, and which do not. If you are planning to acquire and use an organism/part that is not on the White List, you must send a Check-In and receive our reply before you acquire and use that organism/part.

Click here to read more about Check-Ins.

Click here to submit a Check-In.



White List (no Check-In required) Check-In Required (examples only!)
Whole Organisms
(including viral genomes)
  • Risk Group 1 microorganisms
    (For example: E. coli K-12, S. cerevisiae, B. subtilis, Lactobacillus spp.)
  • Risk Group 2 microorganisms
    (For example: Pseudomonas spp.)
  • Bacteriophages T2, T4, T7, M13, P1, ΦX174 (Phi X 174), and λ (Lambda), unless containing a virulence factor (see below)
  • Phagemids
  • Other viruses and bacteriophages
  • Human and primate cell lines that have been tested and certified free of known pathogens (consult your vendor; see FAQ)
  • Cell lines from plants, fungi, or animals that are not primates (such as CHO cells or plant cells)
  • Human and primate cell lines that may contain pathogens
  • All primary isolated cells (that is, cells taken directly from the body of a multicellular organism)
  • C. elegans, Drosophila spp.
  • Physcomitrella patens, Arabidopsis spp., Nicotiana spp.
  • Human subjects in non-invasive experiments, such as surveys (see FAQ)
  • Other multicellular organisms
  • ...and anything not explicitly listed
Parts All Registry parts, except those with a Red Flag placed by the Safety Committee Registry parts that have a Red Flag, which looks like this. A complete list of parts with Red Flags can be found here.
Any part from a Risk Group 3 organism, regardless of its function
Non-protein-coding parts in the following categories:
  • Promoters, RBSes, Terminators
  • Binding sites for transcriptional regulators, endonucleases, and other proteins that bind to DNA
  • Aptamers and catalytic RNAs
  • CRISPR guide RNAs, microRNAs, small interfering RNAs, and short hairpin RNAs that do not target human genes
  • CRISPR guide RNAs, microRNAs, small interfering RNAs, and short hairpin RNAs that target human genes
  • Other non-protein-coding genes
Cas9, except when it is genomically integrated into a sexually reproducing organism Cas9 integrated into the genome of a sexually reproducing organism
(including organisms that reproduce both sexually and asexually, such as yeast)
Proteins or protein-coding genes from animals, plants, or Risk Group 1 / Risk Group 2 microorganisms, EXCEPT those in the list of "dangerous categories" on the right Proteins or protein-coding genes in the following dangerous categories:
  • Virulence factors (see FAQ)
  • Factors that help pathogens evade or shut down the immune system
  • Factors that help pathogens halt the host's DNA/RNA replication, transcription, or translation
  • Factors that regulate the immune system, such as cytokines and interferons
  • Proteins that are toxic to humans
  • Enzymes that produce a molecule that is toxic to humans
...and anything not explicitly listed


X   Banned Organisms/Parts   X

Some of the most dangerous organisms and parts are not allowed in iGEM, even with a Check-In:

  • Whole organisms from Risk Group 3
  • Whole organisms from Risk Group 4
  • Parts from Risk Group 4 organisms

If you find that you want to use a banned organism/part, you should redesign your project to use a safer substitute. Consult your advisor or contact us at to get advice on choosing a substitute.

Frequently Asked Questions

  • What if I'm not sure whether my organism/part requires a Check-In?

    Ask us! Contact safety AT igem DOT org. Alternatively, because the Check-In form is short, you could choose to send a Check-In even if you are unsure.

  • Where can I submit a Check-In?

    Use the link in the left sidebar, or click here, to submit a Check-In.

  • How do I find out the Risk Group of an organism?

    The Risk Group Guide lists iGEM's recommended sources for Risk Group information. It also has some advice on how to find an alternative source, if none of the recommended sources include your organism.

  • What if the White List changes during the summer?

    As we learn more, we might add things to the White List, but we will not remove things from the White List until after the Jamboree each year. So, if something is on the White List now, it will stay on the White List for the whole 2014 season. (We may change the White List for future years.)

  • What exactly counts as a "whole organism"?

    For the purposes of this White List, a "whole organism" is an entire cell or multicellular organism, whether alive or dead. Intact, isolated viral genomes are also considered "whole organism", because many viral genomes can be pathogenic if they enter a host cell, even without the viral capsule.

    (Isolated non-viral genomes are considered parts. Individual nucleic acids and proteins are also parts.)

  • We are going to handle an organism in lab, but we will only extract some DNA from it using PCR -- we won't use it as our chassis. Do we still have to send a Check-In?

    Yes. The Check-In requirement applies to all organisms and all parts that you will handle in the lab, even if they will not be part of your final project.

  • Our project is to detect a dangerous organism. In order to test our project, we want to handle the dangerous organism (or parts of it), but it will not be part of what we build. Do we still have to send a Check-In?

    Yes. The Check-In requirement applies to all organisms and all parts that you will handle in the lab, even if they will not be part of your final project.

  • What is a virulence factor?

    Virulence Factors of Pathogenic Bacteria is a good resource where you can look up virulence factors in some well-studied pathogens. It gives this definition: "Virulence factors refer to the properties (i.e., gene products) that enable a microorganism to establish itself on or within a host of a particular species and enhance its potential to cause disease. Virulence factors include bacterial toxins, cell surface proteins that mediate bacterial attachment, cell surface carbohydrates and proteins that protect a bacterium, and hydrolytic enzymes that may contribute to the pathogenicity of the bacterium."

  • We are going to use a lot of parts. May we combine them on a single Check-In?

    If the parts all come from the same parent organism, you may combine them on a single Check-In, but make sure you give complete information about each part. If the parts come from different parent organisms, please send separate Check-Ins, or contact safety (at) igem (dot) org to ask about combining several Check-Ins into a spreadsheet.

  • How can I find out if my cell line is free of pathogens? What pathogens should I be concerned about?

    If you bought the cells from a vendor or a culture collection, then you can consult their catalog. Many catalogs will list safety and pathogen information -- if you cannot find it, contact the vendor. If you received the cells from another lab, you should find out where they originally came from.

    Cell lines can contain harmful viruses. Sometimes, the viral genome is integrated into the cell's genome. Most viruses have a limited "host range", which means that they can only infect closely related species. Therefore, viruses living in a human or monkey cell line are likely to be dangerous to humans, but viruses living in an insect cell line probably cannot infect humans. If you work with a cell line from humans or other primates, you should check whether it contains viruses or viral genomic DNA. Viruses have Risk Group numbers, so if your cell line contains any viruses, you must handle it at the laboratory Safety Level that is appropriate for the highest Risk group virus it contains.

    Some dangerous viruses that infect human cell lines: HBV (hepatitis B virus), HCV (hepatitis C virus), HIV (human immunodeficiency virus) 1 & 2, HTLV (human T-lymphotropic virus) 1 & 2, CMV (cytomegalovirus).

  • What about experiments on human subjects, such as surveys or software user-testing?

    Human experimental subjects are not covered under the iGEM safety program. If you conduct any experiments with human subjects (including non-invasive work such as surveys or software user-testing), you must find out the rules and regulations that cover those experiments in your country / at your university. Some experiments and surveys might require the approval of a review board on human experimental subjects, and some might not require any approval.

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