If you are also interested in your personal exome, sign up now!
GeneTalk will be present at the conference of the german society for human genetics (GFH), 20.-22. 03. 2013 in Dresden, Germany.
Meet us at booth 37.
GeneTalk now helps you when you have a bunch that have to be filtered with the same filter settings. We added two features for supporting such batch processing:
- You can upload a ZIP-file containing serveral VCF files. GeneTalk will unpack your ZIP-file and add all VCF files to your account
- When selecting an individual for filtering, you can now select several individuals (even from different VCF files) that are all filtered with the same filter settings. Of course, filtering several individuals separately will be performed in background; you will get a notification when a file is filtered. You can specify three placeholders for the output of the filtering process:
- ‘*’ will be replaced by the name of the input file
- ‘%’ will be replaced by the identifier of the individual
- ‘#’ will be replaced by the by a consecutive number (this will be handy if all your individuals are located in the same input file and share the same identifier)
Batch processing is not to be confused with segregation filtering (i.e., filtering several individuals as a “collection”): While the former filters each individual separately allowing, for example, filtering for homozygeous positions, the latter can apply filters that affect every individual in the collection such as the compound heterozygeous filter.
Well, at first glance, it might look like we got baked, but actually we baked something for you: The compound heterozygous filter for analyzing multiple samples. This filtering feature is quite tricky and we will explain in a new tutorial soon how to use it. For the meantime Merry Christmas to everyone and don’t forget to mention GeneTalk to all your loved ones that are still struggling with their NGS analysis!
GeneTalk’s Christmas video: http://www.youtube.com/watch?v=HJfVLgQXcXo
You are absolutely right, Mephistopheles. That’s why we uploaded exomes of a CEU Trio to the Demo account, so that you can play around with the new segregation filter! It is a well described Trio from the 1000 genomes paper: NA12787 is the daughter, NA12892 is the mother and NA12791 is the father. In the exome of the daughter we spiked in one somatic cancer mutation that’s causing melanoma and one rare homozygous mutation that is causing mental retardation and an elevated serum alkaline phosphatase. Now, try out the following:
Create a PED file for these three exomes (Manage Files -> Create Collection). Set parents to status “unaffected” and the daughter to status “affected”. Then go to the filtering menue. Here, VCF files with PED information will be listed separately. For these files the inheritance filter offers now the possibility for recessive and dominant segregation. Did you find the disease causing mutations?
GeneTalk now supports coupled filtering of two or more individuals!
The first step is to create a new VCF file that contains all the individuals or, if you already uploaded a such a file, enter the phenotype information for your file.
You can create a file with multiple individuals by using the new function “Create Collection” in the “Manage Files” menu (sorry for the plain table-based editor, we are working on a graphical editor for this).
To edit phenotype information for an existing file, click the pedigree-tree-shaped icon behind the VCF file in the list of your VCF files (“Manage Files”, “List”).
Once you have a file with phenotype information, the file will be shown in the “Select VCF” tab on the “Filter VCF” page under “Collections”. You will find the choices for segregation filtering in the “inheritance mode” tab, after you selected a file with phenotype information.
The segregation filter allows you to focus on variants that fit to a certain segregation pattern with respect to the phenotype that you are analyzing.
- If you are analyzing a disease where the phenotype seems to follow a recessive pattern of inheritance (typical scenario: in a large pedigree: Around one out of four offsprings are affected by the disease and the parents are healthy) then use the recessive setting. With “recessive homozygous” a homozygous variant an affected individual will be filtered out if and only if it is also present as a homozygous variant in an unaffected individual. With “recessive heterozygous” variants will only pass the filter if and only if they do not occur in an unaffected individual.
- If you are analyzing a disease where the phenotype seems to follow a dominant pattern of inheritance (typical scenario: around half of the offsprings are affected and one of the parents is affected, too), then use the dominant setting. A heterozygous variant in an affected will then pass the filter if and only if the variant has not been detected in the individuals that are assigned a not affected.
A usual scenario for will be a Trio analysis. In such a case you will have the variant data of the an affected child and the two parents. If you suspect a recessive disease, you will probably have to set the parents as unaffected and select “recessive”. In case you are looking for a dominant disease gene, either one of the parents is now affected, too. Or, if both parents are unaffected you will filter with the dominant setting for potential “de novo” mutations.
One year ago GeneTalk went online. It is really amazing to see how the platform has grown in one year. Many new features were realized and improved, we got lots of feedback from customers that helped to improve GeneTalk further on. I’m exited to see how GeneTalk will grow in the second year. We have a great deal of ideas and plans, you can look forward to the next improvements.
An article featuring GeneTalk: Seeking an Edge in Clinical Market, German Startup Preps Community-Based Variant Annotation Platform.