Changes

==Steps in the Curation Process==

==Summary:==

#To become a curator, contact ccga@cancergenomics.org to request access to the CCGA site.  You will also be connected with an Associate Editor.

#Choose or be assigned a few gene pages to curate.

#Read this tutorial and curate the page by reviewing appropriate related literature and authoring content on the gene page (DO NOT PLAGIARIZE!)

# After you have decided to become a curator, contact ???, read this tutorial, watch the tutorial and sign your Honor Agreement.

#Contact the Associate Editor for questions and upon completion of gene page curation.

# Contact your editor and gain permission to the CCGA site

# Chose or be assigned a few GENE pages to curate

# Curate the page by reading suggested reading materials and authoring content on the GENE page (DO NOT PLAGIARIZE!)

# Contact Editor upon completion of GENE page curation.

==Introduction:==

==Introduction:==

Thank you for volunteering to help curate the Compendium of Cancer Genome Aberrations (CCGA)!  Your help will make this resource a valuable tool for users of the CCGA, including researchers, clinicians and others.  This short, written description will help you get started and should serve as a collection of best practices and content style as you curate. Please sign and date and return your “Honor Agreement” before starting your curation, which is available here:  .  (TO DO:  make link to Honor Agreement, downloadable by PDF, if possible).There is also a video that should be very helpful to show you how to curate, and is required before you start to curate.  It can be seen here:

Thank you for volunteering to help curate the Compendium of Cancer Genome Aberrations (CCGA)!  Your help will make this resource a valuable tool for users of the CCGA, including researchers, clinicians and others.  This short, written description will help you get started and should serve as a collection of best practices and content style as you curate.  

''TO DO: create a tutorial video based on this script''

The logic for CCGA pages is that there is basic Gene and Protein (and mutation) molecular biology-type information on the “Gene Pages”, and that there is disease and clinical-type information type on “Disease Pages”.  The CCGA is interested in the curation of genes/mutations that arise in cancer.  However, the dividing line between "Gene/Protein/Mutation" information and "Disease" information is sometimes hard to determine (For example, in the case of describing a fusion gene's value in diagnostic or prognostic tests in a specific disease).  Basically, this type of "crossover" Molecular Disease information can be included IN ABBREVIATED form on the GENE pages and will be addressed more fully on the related DISEASE pages.  These guidelines will help you determine what information goes where. Please note that you should plan to spend between 4-8 hours in curating the information on a single gene page, and more if you are unfamiliar with the gene.

==Associate Editor:==

 

Your curation of the gene and protein information will be aided and reviewed by an assigned Associate Editor. Please note that this written document cannot cover all the questions and decisions your will be faced with as you curate.  Therefore, PLEASE feel free to contact your Associate Editor with any questions and upon completion of a page.

==Editor:==

Your curation of the gene and protein information will be aided and edited and reviewed by an “EDITOR”. Your assigned Editor will be your go-to person to help you curate and review your curated information after you are done curating.   Please note that this written document and the curation tutorial cannot cover all the questions and decisions your will be faced with as you curate.  Therefore, PLEASE feel free to contact your editor with any questions.  You will need to contact your assigned editor to get “write” permissions to the CCGA so that you can create and edit pages in the Wiki. 

 

The CCGA web site is based on wiki pages and can be accessed here : http://www.ccga.io/index.php/Main_Page.  please ask your editor for write premissions.

 

The functionality of the wiki pages are described in brief, at MediaWiki, see here:  https://www.mediawiki.org/wiki/MediaWiki. 

 

There are also short videos available on youtube that describe MediaWiki functionality here: https://www.youtube.com/watch?v=F8irbbwNo2E&list=PLAagofQWV6pf0xFyUw7gJg2yYYB-nCS4l.  Others are available, by searching youtube for "MediaWiki tutorial".

==Gene Pages:==

==Gene Pages:==

'''''QUESTION: do we need to designate Genes as Drivers vs. passengers?'''''

You will be asked to choose the gene pages you wish to curate from this list: http://www.ccga.io/index.php/List_of_Gene_Pages.

A “Gene specific Template” has been added to these pages for you to use to add your curated information.

You will be asked to choose from a number gene pages that you would like to curate. See list here: http://www.ccga.io/index.php/List_of_Gene_Pages

Note: The gene pages template already has the required headers, links and other syntax.  Please do not change the syntax of the template so there is consistency between similar pages.

A “Gene specific Template” has been produced which provides you with very nice Media Wiki Template to fill in with information you have curated.  It is shown here. http://www.ccga.io/index.php/Gene-Specific_Template. 

Note that the Template already has the markup language you will need for headers, links, and other syntax to be used in the Gene Paes.  Please do not change the syntax of the template, so users of the CCGA pages will want to see the same format from page to page.

Note: Save edits to your page frequently or produce content in a Word format of the template and add it into the wiki site subsequently.  For a Word document template for authoring a <u>'''gene-specific page'''</u> before transferring content online please see [[File:Gene-Specific Template Word Version (9-28-21).docx|none|thumb|Gene-Specific Template]].  

NOTE:  When you do large edits on a Wiki page, the security makes sure yo are a human with test at the top of the page and a simple mathmatical formula you must complete, as below. YOU MUST answe the mathmatical equation for your edits to be saved.

NOTE:  When you do large edits on a Wiki page, the security makes sure you are a human with test at the top of the page and a simple mathematical formula you must complete, as below. YOU MUST answer the mathematical equation for your edits to be saved.

''Your edit includes new external links. To protect the wiki against automated spam, we kindly ask you to solve the following task below and enter the answer in the box in order to save your edit (more info):  45−1 =''

''Your edit includes new external links. To protect the wiki against automated spam, we kindly ask you to solve the following task below and enter the answer in the box in order to save your edit (more info):  45−1 =''

==Gene curation using the “Gene specific Template” MediaWiki Template in CCGA==

==Gene Curation Using the “Gene-Specific Template” in CCGA==

#Go to the gene specific template (http://www.ccga.io/index.php/Gene-Specific_Template )

The template provides an easy "fill in the blanks" WikiMedia page which already has formatted markups (for headers) and has examples for you to follow.  The Template is described briefly below.

#Copy the entire page (eg on a Mac, “command (cmd) a”, and then “cmd c”

#Open in another browser window the gene page you will curate

The template provides an easy "fill in the blanks" WikiMedia page which already has formatted markups (for headers) and has examples for you to follow. The Template is described briefly, below.

Sections:  

#Primary Authors

# Primary Authors

#Synonyms

# Synonyms

#Genomic Location

# Genomic Location

#Cancer Category/Type

# Cancer Category/Type

#Gene Overview

# Gene Overview

#Common Alteration Types

# Common Alteration Types

#Internal Pages

# Internal Pages

#External Links

# External Links

#References

# References

The sections of the Template are for ease of reading for the USER:  HOWEVER, as a curator, you will want to curate and load information in the WIKI in a non-linear fashion.  This is the suggested workflow:

The sections of the Template are for ease of reading for the USER:  HOWEVER, as a curator, you will want to curate and load information in the WIKI in a non-linear fashion.  This is the suggested workflow:

=== 1. PRIMARY AUTHORS section. ===

===1. PRIMARY AUTHORS section.===

By adding your name to the PRIMARY AUTHORS section you can make sure that no-one else is curating this gene now, and so you will get credit for curating this information by your peers.

By adding your name to the PRIMARY AUTHORS section you can make sure that no-one else is curating this gene now, and so you will get credit for curating this information by your peers.  Please list your name and on the next line, type the phrase "Under Review" and the date you last edited it.  When you are done editing and you think it is complete, please delete the "Under Review" and date.

=== 8. EXTERNAL LINKS Section. ===

===8. EXTERNAL LINKS Section.===

To familiarize yourself with the latest information on the Gene you are curating, “Your Gene of Interest” (designated YGI throughout), please start with one of the last sections of the Template, the EXTERNAL LINKS Section.  The listed resources will provide exhaustive (but not necessarily recent) molecular information about YGI, its mutations and its place in disease and cancer and treatment.  The resources suggested as EXTERNAL LINKS as of Dec 2018 are as follows:

To familiarize yourself with the latest information on the Gene you are curating, “Your Gene of Interest” (designated YGI throughout), please start with one of the last sections of the Template, the EXTERNAL LINKS Section.  The listed resources will provide exhaustive (but not necessarily recent) molecular information about YGI, its mutations and its place in disease and cancer and treatment.  The resources suggested as EXTERNAL LINKS as of Dec 2018 are as follows:

# Atlas of Genetics and Cytogenetics in Oncology and Haematology

#Atlas of Genetics and Cytogenetics in Oncology and Haematology

# COSMIC  

#COSMIC

# CIViC

#CIViC

# St. Jude ProteinPaint

#St. Jude ProteinPaint

# Precision Medicine Knowledgebase (Weill Cornell)

#Precision Medicine Knowledgebase (Weill Cornell)

# Cancer Index

#Cancer Index

# OncoKB

#OncoKB

# NCBI Gene

#NCBI Gene

# My Cancer Genome

#My Cancer Genome

# UniProt

#UniProt

# Pfam

#Pfam

# GeneCards

#GeneCards

# OMIM

#OMIM

# LOVD(3)

#LOVD(3)

# TICdb

#TICdb

# In some cases, a specialized source that may be available for some genes, for example '''[http://p53.iarc.fr/ ''TP53'' by IARC]''' - ''TP53'' a database with reference sequences and mutational landscapes

#In some cases, a specialized source that may be available for some genes, for example '''[http://p53.iarc.fr/ ''TP53'' by IARC]''' - ''TP53'' a database with reference sequences and mutational landscapes

Please note that some genes may have special resources devoted to them.  An example is the International Agency for Research on Cancer page devoted to TP53 (see http://p53.iarc.fr/).  This is unusual, but P53 is the most studied gene and protein on earth, so in this case, a specialized resource is justified.  TO find if there are any special resources for YGI, perform a google search on YGI and include words like "database" or "resource".  Ask your Editor.

Please note that some genes may have special resources devoted to them.  An example is the International Agency for Research on Cancer page devoted to TP53 (see http://p53.iarc.fr/).  This is unusual, but P53 is the most studied gene and protein on earth, so in this case, a specialized resource is justified.  TO find if there are any special resources for YGI, perform a google search on YGI and include words like "database" or "resource".  Ask your Editor.

<big>'''''PLEASE NOTE:  DO NOT PLAGIARIZE.  You can borrow phrases here or there without attribution.  Yo can even use a sentence here and there if you attribute the quote directly ( eg: "From NCBI").  However, you CANNOT cut and paste whole paragraphs from other resources into the CCGA pages.'''''</big>

<big>'''''PLEASE NOTE:  DO NOT PLAGIARIZE.  You can borrow phrases here or there without attribution.  Yo can even use a sentence here and there if you attribute the quote directly ( eg: "From NCBI").  However, you CANNOT cut and paste whole paragraphs from other resources into the CCGA pages.'''''</big>

=== 2. SYNONYMS Section ===

===2. SYNONYMS Section===

As you read though the EXTERNAL LINKS resources, you will find many of them have lists of synonyms, esp. NCBI Gene and GeneCards.  Please italicize the alternative gene names (synonyms).

As you read though the EXTERNAL LINKS resources, you will find many of them have lists of synonyms, esp. NCBI Gene and GeneCards.  Please italicize the alternative gene names (synonyms).

=== 3. GENOMIC LOCATION Section. ===

===3. GENOMIC LOCATION Section.===

This information is most easily obtained from GeneCards, in the GeneCards section "Genomics" and subsection "Genomic Locations for YFG" and subsection "Genomic View for YFG"and sub-subsection "Cytogenetic band"

This information is most easily obtained from GeneCards, in the GeneCards section "Genomics" and subsection "Genomic Locations for YFG" and subsection "Genomic View for YFG"and sub-subsection "Cytogenetic band". 

=== 5. GENE OVERVIEW Section ===

===5. GENE OVERVIEW Section===

This is where you will be compelled to find and read journal articles and book text.  You may have found some relevant articles listed at some of the EXTERNAL LINKS sites (esp. Uniprot and NCBI Gene), but you will have to search for new, relevant articles in PubMed and also from the Hematological Cancer resource "WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues (download from http://publications.iarc.fr/_publications/media/download/1511/700ac655d7f248cf1044efd985275086ed4f341f.pdf).  Note that you will be finding information that will fit in other sections of the gene template, like CANCER CATEGORY TYPE and COMMON ALTERATION TYPES and REFERENCES.  This section should describe in 1 paragraph (approx 5-7 sentences):

This is where you will be compelled to find and read journal articles and book text.  You may have found some relevant articles listed at some of the EXTERNAL LINKS sites (esp. Uniprot and NCBI Gene), but you will have to search for new, relevant articles in PubMed and also from the Hematological Cancer resource "WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues (download from http://publications.iarc.fr/_publications/media/download/1511/700ac655d7f248cf1044efd985275086ed4f341f.pdf).  Note that you will be finding information that will fit in other sections of the gene template, like CANCER CATEGORY TYPE and COMMON ALTERATION TYPES and REFERENCES.  This section should describe in 1 paragraph (approx 5-7 sentences):

# the molecular function of the gene/protein

 

# its normal cellular role, for example in cellular processes or cellular pathways.

#the molecular function of the gene/protein

# its role in diseases, esp. cancer diseases in the CCGA.

#its normal cellular role, for example in cellular processes or cellular pathways.

# interesting or frequent mutations and their effects on specific cancers.

#its role in diseases, esp. cancer diseases in the CCGA.

# role in drug resistance, if any.

#interesting or frequent mutations and their effects on specific cancers.

# diagnostic or prognostic value, if any.

#role in drug resistance, if any.

#diagnostic or prognostic value, if any.

A few examples are shown below.

A few examples are shown below.

For molecular information and some disease and mutation information, this section is most informed by reading the EXTERNAL LINKS resources of:

For molecular information and some disease and mutation information, this section is most informed by reading the EXTERNAL LINKS resources of:

# UniProt (by far the best)

 

# GeneCards

#UniProt (by far the best)

# NCBI Gene

#GeneCards

# CIViC

#NCBI Gene

# Cancer Index

#CIViC

# My Cancer Genome

#Cancer Index

# Pfam

#My Cancer Genome

#Pfam

For mutational information, this section is most informed by:

For mutational information, this section is most informed by:

# Atlas of Genetics and Cytogenetics in Oncology and Haematology

 

# COSMIC  

#Atlas of Genetics and Cytogenetics in Oncology and Haematology

# LOVD(3)

#COSMIC

# TICdb

#LOVD(3)

# St. Jude ProteinPaint

#TICdb

# Precision Medicine Knowledgebase (Weill Cornell)

#St. Jude ProteinPaint

# OncoKB

#Precision Medicine Knowledgebase (Weill Cornell)

#OncoKB

For Disease information, the best resources are:

For Disease information, the best resources are:

# OMIM

 

# WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues (download from http://publications.iarc.fr/_publications/media/download/1511/700ac655d7f248cf1044efd985275086ed4f341f.pdf)

#OMIM

# Pubmed (search for YFG, esp. in context of "cancer" or specific cancers)

#WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues (download from http://publications.iarc.fr/_publications/media/download/1511/700ac655d7f248cf1044efd985275086ed4f341f.pdf)

#Pubmed (search for YFG, esp. in context of "cancer" or specific cancers)

Note that in this section, you must also go to PubMed (https://www.ncbi.nlm.nih.gov/pubmed/) and search for articles about YGI and cancer or specific cancers.  The best articles to read are usually the most recent and should be are freely available to the public (eg, PubMed Central).  If you are new to YGI and some of these cancers, then a recent review article may be helpful.  Also very helpful is to use the book "WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues" (download from http://publications.iarc.fr/_publications/media/download/1511/700ac655d7f248cf1044efd985275086ed4f341f.pdf) Search through the PDF file for YGI and read those sections where YGI is mentioned.   

Note that in this section, you must also go to PubMed (https://www.ncbi.nlm.nih.gov/pubmed/) and search for articles about YGI and cancer or specific cancers.  The best articles to read are usually the most recent and should be are freely available to the public (eg, PubMed Central).  If you are new to YGI and some of these cancers, then a recent review article may be helpful.  Also very helpful is to use the book "WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues" (download from http://publications.iarc.fr/_publications/media/download/1511/700ac655d7f248cf1044efd985275086ed4f341f.pdf) Search through the PDF file for YGI and read those sections where YGI is mentioned.   

We suggest when writing in the wiki, that you use a reference "placeholder" in the text you are writing.  For example, use the first author's last name and year as a placeholder in the text, at the end of a sentence. Then, write the full reference into the REFERENCE Section (section 9) using the proper syntax suggested for either book, article or internet source.  Then, when you are done with all sections and the reference section, you can replace the "placeholders" with the the numbered reference.

We suggest when writing in the wiki, that you use a reference "placeholder" in the text you are writing.  For example, use the first author's last name and year as a placeholder in the text, at the end of a sentence. Then, write the full reference into the REFERENCE Section (section 9) using the proper syntax suggested for either book, article or internet source.  Then, when you are done with all sections and the reference section, you can replace the "placeholders" with the the numbered reference.

=== 4. CANCER CATEGORY/TYPE Section ===

===4. CANCER CATEGORY/TYPE Section===

'''''Question:  how many links to diseases in CCGA should we do?  And how do we find the links.  Eg, look at how many "sub diseae pages there are for AML, but the RUNX1 Gene page does not link to them all.'''''

'''''Question:  how many links to diseases in CCGA should we do?  And how do we find the links.  Eg, look at how many "sub diseae pages there are for AML, but the RUNX1 Gene page does not link to them all.'''''

The extent of the content should be a short paragraph for each cancer type (1-7 sentences).  The content should include:   

The extent of the content should be a short paragraph for each cancer type (1-7 sentences).  The content should include:   

# Frequency of YGI mutations or fusion genes associated to patients with that specific disease,  

 

# Whether the mutation is a common mutation in that specific disease (if it is uncommon, you are likely NOT to reference that fact, because you would end up referencing dozens or hundreds of mutations and diseases),  

#Frequency of YGI mutations or fusion genes associated to patients with that specific disease,

# Whether the gene or mutation is a target of drugs

#Whether the mutation is a common mutation in that specific disease (if it is uncommon, you are likely NOT to reference that fact, because you would end up referencing dozens or hundreds of mutations and diseases),

# Whether there is diagnostic value in this gene or mutation(s)

#Whether the gene or mutation is a target of drugs

# Whether there is prognostic value in this gene or mutation(s)

#Whether there is diagnostic value in this gene or mutation(s)

# Whether there are companion diagnostics (with certain therapies) based on this gene or mutation(s)

#Whether there is prognostic value in this gene or mutation(s)

#Whether there are companion diagnostics (with certain therapies) based on this gene or mutation(s)

In some cases, you will find that some CCGA Diseases/Cancer Types have not yet been created.  Please DO NOT create a disease page.  Instead, within the Gene page, simply  curate that information in a heading and contact your editor. As CCGA grows, we will add new Diseases/Cancer types and link to the Gene pages later (see example of CML, below).

In some cases, you will find that some CCGA Diseases/Cancer Types have not yet been created.  Please DO NOT create a disease page.  Instead, within the Gene page, simply  curate that information in a heading and contact your editor. As CCGA grows, we will add new Diseases/Cancer types and link to the Gene pages later (see example of CML, below).

The example of RUNX1 is shown below.

The example of RUNX1 is shown below.

* '''[http://www.ccga.io/index.php/Acute_Myeloid_Leukemia_(AML)_and_Related_Precursor_Neoplasms Acute Myeloid Leukemia (AML) and Related Precursor Neoplasms]'''

*'''[http://www.ccga.io/index.php/HAEM4:Acute_Myeloid_Leukemia_(AML)_and_Related_Precursor_Neoplasms Acute Myeloid Leukemia (AML) and Related Precursor Neoplasms]'''

--- '''[http://www.ccga.io/index.php/Acute_Myeloid_Leukemia_(AML)_with_t(8;21)(q22;q22.1);_RUNX1-RUNX1T1 Acute Myeloid Leukemia (AML) with t(8;21)(q22;q22.1); RUNX1-RUNX1T1]'''

--- '''[http://www.ccga.io/index.php/Acute_Myeloid_Leukemia_(AML)_with_Mutated_RUNX1 Acute Myeloid Leukemia (AML) with Mutated RUNX1]'''

--- '''[http://www.ccga.io/index.php/HAEM5:Acute_myeloid_leukaemia_with_RUNX1::RUNX1T1_fusion Acute Myeloid Leukemia (AML) with t(8;21)(q22;q22.1); RUNX1-RUNX1T1]'''

 

--- '''[http://www.ccga.io/index.php/HAEM4:Acute_Myeloid_Leukemia_(AML)_with_Mutated_RUNX1 Acute Myeloid Leukemia (AML) with Mutated RUNX1]'''

The frequency of ''RUNX1'' mutations is between 5-18% of all AML patients tested [3]. The most common chromosomal translocation is t(8;21)(q22;q22)resulting in RUNX1-RUNX1T1 fusion in ''de novo'' AML, at approximately 7% [2,6].  This translocation confers a favorable prognosis in AML and other neoplasms [2,5,6].  Another ''RUNX1'' alteration is the t(3;21)(q26;q22), in which the RUNT domain of ''RUNX1'' is fused to the entire ''EVI1'' gene.  This translocation is rarely found in patients diagnosed with ''de novo'' AML and is more common in those with therapy-related myelodysplastic syndrome (MDS)/AML [9].  Other mutations in ''RUNX1'' include deletions, missense, splicing, frameshift, and nonsense alterations (mostly loss-of-function or decreased function), and occur at a frequency of approximately 10% in AML patients [6]. These mutations are mechanistically distinct from the chromosomal translocations and confer a worse prognosis [2,5,6].

The frequency of ''RUNX1'' mutations is between 5-18% of all AML patients tested [3]. The most common chromosomal translocation is t(8;21)(q22;q22)resulting in RUNX1-RUNX1T1 fusion in ''de novo'' AML, at approximately 7% [2,6].  This translocation confers a favorable prognosis in AML and other neoplasms [2,5,6].  Another ''RUNX1'' alteration is the t(3;21)(q26;q22), in which the RUNT domain of ''RUNX1'' is fused to the entire ''EVI1'' gene.  This translocation is rarely found in patients diagnosed with ''de novo'' AML and is more common in those with therapy-related myelodysplastic syndrome (MDS)/AML [9].  Other mutations in ''RUNX1'' include deletions, missense, splicing, frameshift, and nonsense alterations (mostly loss-of-function or decreased function), and occur at a frequency of approximately 10% in AML patients [6]. These mutations are mechanistically distinct from the chromosomal translocations and confer a worse prognosis [2,5,6].

* '''[http://www.ccga.io/index.php/Acute_lymphoblastic_leukaemia_(ALL) Acute Lymphocytic Leukemia (ALL)]'''

*'''[http://www.ccga.io/index.php/Acute_lymphoblastic_leukaemia_(ALL) Acute Lymphocytic Leukemia (ALL)]'''

iAMP21 is an intrachromosomal amplification of chromosome 21, which includes the genes ''RUNX1'' and ''miR-802'' among others.  This amplification occurs in about 1.5-2% of all Acute Lymphocytic Leukemia cases tested and is associated with poor prognostication [5].  

iAMP21 is an intrachromosomal amplification of chromosome 21, which includes the genes ''RUNX1'' and ''miR-802'' among others.  This amplification occurs in about 1.5-2% of all Acute Lymphocytic Leukemia cases tested and is associated with poor prognostication [5].  

* '''[http://www.ccga.io/index.php/T-ALL T-cell Acute Lymphocytic Leukemia (T-ALL)]'''

*'''[http://www.ccga.io/index.php/T-ALL T-cell Acute Lymphocytic Leukemia (T-ALL)]'''

''RUNX1'' mutations have been described in 20% of patients with early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) [6].

''RUNX1'' mutations have been described in 20% of patients with early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) [6].

* '''[http://www.ccga.io/index.php?title=B_lymphoblastic_leukaemia/lymphoma_with_t(12;21)(p13;q22);_TEL-AML1_(ETV6-RUNX1)_positive&redirect=no B-cell Acute Lymphocytic Leukemia (B-ALL)]'''

*'''[http://www.ccga.io/index.php?title=B_lymphoblastic_leukaemia/lymphoma_with_t(12;21)(p13;q22);_TEL-AML1_(ETV6-RUNX1)_positive&redirect=no B-cell Acute Lymphocytic Leukemia (B-ALL)]'''

The most common chromosomal translocation is t(12;21)(p13;q22) resulting in ETV6-RUNX1 fusion in B-cell acute lymphocytic leukemia (B-ALL) [2].  This translocation occurs in 25% of Pediatric B-ALL but only 2% of Adult B-ALL [5, 6], and confers a favorable prognosis in B-ALL and other neoplasms [2,5,6].  iAMP21 is an intrachromosomal amplification of chromosome 21 which includes the genes ''RUNX1'' and ''miR-802'' among others.  This amplification occurs in about 2% of all B-cell Acute Lymphocytic Leukemia cases tested and is associated with poor prognostication [6].  

The most common chromosomal translocation is t(12;21)(p13;q22) resulting in ETV6-RUNX1 fusion in B-cell acute lymphocytic leukemia (B-ALL) [2].  This translocation occurs in 25% of Pediatric B-ALL but only 2% of Adult B-ALL [5, 6], and confers a favorable prognosis in B-ALL and other neoplasms [2,5,6].  iAMP21 is an intrachromosomal amplification of chromosome 21 which includes the genes ''RUNX1'' and ''miR-802'' among others.  This amplification occurs in about 2% of all B-cell Acute Lymphocytic Leukemia cases tested and is associated with poor prognostication [6].  

* '''Chronic Myeloid Leukemia (CML)'''

*'''Chronic Myeloid Leukemia (CML)'''

A number of simple mutations in ''RUNX1'' have been reported in CML patients, and these mutations may be in part responsible for progression from the chronic phase to blast crisis (BC) [7].

A number of simple mutations in ''RUNX1'' have been reported in CML patients, and these mutations may be in part responsible for progression from the chronic phase to blast crisis (BC) [7].

* '''[http://www.ccga.io/index.php/MDS Myelodysplastic Syndrome (MDS)]'''

*'''[http://www.ccga.io/index.php/MDS Myelodysplastic Syndrome (MDS)]'''

A high frequency (42%) of ''RUNX1'' mutations has been reported among radiation-associated and therapy-related Myelodysplastic Syndrome (MDS) patients [8].  

A high frequency (42%) of ''RUNX1'' mutations has been reported among radiation-associated and therapy-related Myelodysplastic Syndrome (MDS) patients [8].  

* '''CCUS (Clonal cytopenia of undetermined significance) or ICUS (Idiopathic cytopenia of undetermined significance )'''

*'''CCUS (Clonal cytopenia of undetermined significance) or ICUS (Idiopathic cytopenia of undetermined significance )'''

''RUNX1'' mutations are more common in clonal cytopenia of undetermined significance (CCUS) [2].

''RUNX1'' mutations are more common in clonal cytopenia of undetermined significance (CCUS) [2].

* '''Familial platelet disorder with predisposition to acute myeloid leukemia (FPD/AML)'''

*'''Familial platelet disorder with predisposition to acute myeloid leukemia (FPD/AML)'''

Germline mutations of ''RUNX1'' have been reported in the rare autosomal dominant Familial platelet disorder with predisposition to acute myeloid leukemia (FPD/AML) [8].

Germline mutations of ''RUNX1'' have been reported in the rare autosomal dominant Familial platelet disorder with predisposition to acute myeloid leukemia (FPD/AML) [8].

=== 6. COMMON ALTERATION TYPES Section ===

===6. COMMON ALTERATION TYPES Section===

This section should be completed in concert with the GENE OVERVIEW Section and CANCER CATEGORY/TYPE Section.  It is meant to be an "At a Glance" section for the type of alteration that ARE MOST COMMON ACROSS ALL CANCERS.  The types of alterations are:

This section should be completed in concert with the GENE OVERVIEW Section and CANCER CATEGORY/TYPE Section.  It is meant to be an "At a Glance" section for the type of alteration that ARE MOST COMMON ACROSS ALL CANCERS.  The types of alterations are:

* Copy Number Loss

 

* Copy Number Gain

*Copy Number Loss

* LOH (Loss of Heterozygosity)

*Copy Number Gain

* Loss-of-Function Mutation

*LOH (Loss of Heterozygosity)

* Gain-of-Function Mutation

*Loss-of-Function Mutation

* Translocation/Fusion

*Gain-of-Function Mutation

*Translocation/Fusion

In an example for TP53, there are two short paragraphs followed by a table.  This is appropriate, because TP53 is found in a vast number of different cancers.

In an example for TP53, there are two short paragraphs followed by a table.  This is appropriate, because TP53 is found in a vast number of different cancers.

{| class="wikitable sortable"

{| class="wikitable sortable"

|-

|-

! Copy Number Loss   !! Copy Number Gain   !! LOH   !!   Loss-of-Function Mutation   !! Gain-of-Function Mutation !! Translocation/Fusion  

!Copy Number Loss!!Copy Number Gain!!LOH!!Loss-of-Function Mutation!!Gain-of-Function Mutation!!Translocation/Fusion

|-

|-

| X || || X || X || X ||

|X|| ||X||X||X||

|}

|}

{| class="wikitable sortable"

{| class="wikitable sortable"

|-

|-

! Copy Number Loss   !! Copy Number Gain   !! LOH   !!   Loss-of-Function Mutation   !! Gain-of-Function Mutation !! Translocation/Fusion  

!Copy Number Loss!!Copy Number Gain!!LOH!!Loss-of-Function Mutation!!Gain-of-Function Mutation!!Translocation/Fusion

|-

|-

| ||   ||   || X ||   || X

| || || ||X|| ||X

|}

|}

=== 7. INTERNAL PAGES Section ===

===7. INTERNAL PAGES Section===

After you have completed the GENE OVERVIEW, CANCER CATEGORY/TYPE  and COMMON ALTERATION TYPES, you will be more knowledgeable about the other INTERNAL PAGES that are relevant to information on YGI page.  These will include links to diseases, and links to fusion partner genes.  In fact, these links will essentially collect all the related INTERNAL PAGES from the GENE OVERVIEW, CANCER CATEGORY/TYPE  and COMMON ALTERATION TYPES sections, all in one place.

After you have completed the GENE OVERVIEW, CANCER CATEGORY/TYPE  and COMMON ALTERATION TYPES, you will be more knowledgeable about the other INTERNAL PAGES that are relevant to information on YGI page.  These will include links to diseases, and links to fusion partner genes.  In fact, these links will essentially collect all the related INTERNAL PAGES from the GENE OVERVIEW, CANCER CATEGORY/TYPE  and COMMON ALTERATION TYPES sections, all in one place.

A good example is the ABL1 page INTERNAL PAGES Section.

A good example is the ABL1 page INTERNAL PAGES Section.

'''''[http://www.ccga.io/index.php/Chronic_Myeloid_Leukemia_(CML)_with_t(9;22)(q34.1;q11.2);_BCR-ABL1 Chronic Myeloid  Leukemia]'''

'''''[http://www.ccga.io/index.php/Chronic_Myeloid_Leukemia_(CML)_with_t(9;22)(q34.1;q11.2);_BCR-ABL1 Chronic Myeloid  Leukemia]'''''

'''[http://www.ccga.io/index.php/Acute_lymphoblastic_leukaemia_(ALL) Acute Lymphoblastic Leukemia]'''

'''[http://www.ccga.io/index.php/Acute_lymphoblastic_leukaemia_(ALL) Acute Lymphoblastic Leukemia]'''

'''[http://www.ccga.io/index.php/Acute_Myeloid_Leukemia_(AML)_with_BCR-ABL1 Acute Myeloid Leukemia (AML) with BCR-ABL1]'''

'''[http://www.ccga.io/index.php/HAEM5:Acute_myeloid_leukaemia_with_BCR::ABL1_fusion Acute Myeloid Leukemia (AML) with BCR-ABL1]'''

'''[http://www.ccga.io/index.php/Mixed_Phenotype_Acute_Leukemia_(MPAL)_with_t(9;22)(q34.1;q11.2);_BCR-ABL1 Mixed Phenotype Acute Leukemia (MPAL) with t(9;22)(q34.1;q11.2); BCR-ABL1]'''

'''[http://www.ccga.io/index.php/HAEM5:Mixed-phenotype_acute_leukaemia_with_BCR::ABL1_fusion Mixed Phenotype Acute Leukemia (MPAL) with t(9;22)(q34.1;q11.2); BCR-ABL1]'''

See the '''[http://www.ccga.io/index.php/BCR "BCR gene"]''' for additional details of the BCR-ABL1 gene fusion.''

See the '''[http://www.ccga.io/index.php/BCR "BCR gene"]''' for additional details of the BCR-ABL1 gene fusion.

=== 9. REFERENCES section ===

===9. REFERENCES section===

When you are done with all sections and the reference section, you can then replace the "placeholders" authors last name with the the numbered reference in the relevant sections.

When you are done with all sections and the reference section, you can then replace the "placeholders" authors last name with the the numbered reference in the relevant sections.

== <big>Appendix</big> ==

==<big>Appendix</big>==

==Resources:==

==Resources:==

#“WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues.pdf” Download from http://publications.iarc.fr/_publications/media/download/1511/700ac655d7f248cf1044efd985275086ed4f341f.pdf

#“WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues.pdf” Download from http://publications.iarc.fr/_publications/media/download/1511/700ac655d7f248cf1044efd985275086ed4f341f.pdf