MutationDistiller: Tutorial
MutationDistiller makes the analysis of Next-Generation Sequencing data simple. This tutorial is a use-case scenario taking you through a basic analysis step by step. For detailed information on MutationDistiller's options, settings and background, please refer to the manual.
HPO-based analysis
In the most common use case, you have a vcf file from a patient who suffers from a rare disease, together with a list of HPO terms describing the patient's symptoms. In this tutorial, we will show you how to find the most likely disease-relevant alteration for your specific case. We will start our tutorial at the start page.
Test case
The starting point for a MutationDistiller analysis is a vcf file. If you wish to play around with uploading
a file, you can obtain a test file here. It is a real case from Charité Universitätsmedizin spiked into HG00377 from the 1000G project.
Please save the file on your computer and click on 'First step: Upload vcf', which will direct you to our upload page.
Here, you can enter a name for your project, an email address to get sent your unique project ID to access your project later on,
and of course it is where you can upload your file.
You can also adjust some filter and analysis settings, but for now, we will stick with the default settings. Hit 'submit' and you
will be redirected to the main entry page once file upload has been finished (it should only take a couple of minutes).
Quick access: If you just wish to have a look at the data without having to mess around with up- and downloads, just click on the 'Clinical: HPO'
link on the user mode page, which will redirect you to the main analysis page with optimised settings for an HPO-based search.
Here, just enter the Project ID 3931_857831 to start the analysis.
MutationDistiller main page
On the main analysis page, you can enter all the information you wish to share with MutationDistiller. The vcf file containing
your patient's variants creates the basis
for examining your patient's data. For subseqent queries, you do not have to re-submit the vcf file, instead, you can easily access your project
through the unique ID number provided to you after upload.
In General, your projects will be kept on our servers for two months unless you request earlier deletion. If you do not
want your data to be kept on our servers, just send us an email (see email addresses in the footer of the page). For more information on data protection,
please refer to our data protection guidelines.
Our case
The vcf file we just uploaded comes from a WES run of a 4 year old rare disease patient with unrelated parents. From birth, he was affected
by apnea and generalized muscle weakness. Shortly after, he developed respiratory insuficiency and dysphagia. His symptoms were considered
to stem from a myopathy.
As we cannot be sure whether the patient suffers from a recessive or a dominant disease, we just leave the 'Mode of Inheritance' option blank.
From the symptoms described above, we have collected a list of HPO terms which characterize this patient:
- HP:0003198 - Myopathy
- HP:0002104 - Apnea
- HP:0003324 - Generalized muscle weakness
- HP:0002093 - Respiratory insufficiency
- HP:0002015 - Dysphagia
To do this, you can simply copy the list above into the 'phenotype' text field. Alternatively, you can also find these HPO entries using our auto-completion field. Just start typing and see what the website suggests.
After entering your information, simply hit the gigantic 'Submit' button at the bottom of the page to access your results.
Results
After a couple of seconds, MutationDistiller should redirect you to its output page. Here, you will find a list of the most fitting alterations
found in your vcf file. As a reminder, at the top of the page, you find a list showing the parameters you submitted. Below, a ranked summary list
displays the most crucial points of the alterations and the genes they are located in.
In our case, the top variants catch your eye: MutationDistiller found two alterations in the NEB gene and suggests
that we are looking at a case of compound heterozygosity. (Note: Be aware that without phase information, the program cannot
determine for sure whether the patient is compound heterozygous, hence the question mark!)
These alterations located in the NEB gene are interesting as this gene is known by OMIM and OrphaNet to be relevant for Nemaline Myopathy,
which can be seenin the 'reported diseases & mutations' column.
Moreover, it reaches a high MutationDistiller score and hence matches your search well. Thus, to find out more
about the gene, you click on the gene symbol, which will send you to a lower section of the page where you can find a lot of information on the
gene and alterations in question.
Gene information
For each gene, you can find a wealth of information below the summary list, together with links to other pages. In our case, we find an explanation
why MutationDistiller ranked the NEB gene so highly: Three of the HPO terms you entered were direct hits. In addition, a more specific term was found for 'Myopathy'.
In total, this adds up to a high MutationDistiller score. At this stage, you can make your search more specific by adding or removing HPO terms
in an iterative way. Feel free to play around with this feature.
In addition, we find a number of OMIM and OrphaNet entries which underline the importance of these alterations. Clicking on the OMIM-identifier, for instance,
leads you to the relevant OMIM page listing descriptions of Nemaline myopathy 2 caused by alterations in the NEB gene. As these descriptions fit well with
our case, the NEB variants found in the patient's data seem to be highly relevant.
We hope this tutorial helped you get acquainted with the MutationDistiller software. For further information, please refer to the
manual. If you run into trouble, or find bugs, missing links or other errors,
please do not hesitate to contact us.