Date   
Viral susceptibility panel

Haimel Matthias
 

Dear All,

Please let me send the following messages on behalf of Eleanor:

I hope you are all well. I was sorry to not be able to make your last workshop meeting in March. It sounds like the HPO annotation is moving along well.

I wanted to let you know about a publicly available research gene panel that Genomics England has been creating in PanelApp relating to a Viral susceptibility (https://panelapp.genomicsengland.co.uk/panels/111/), and to ask if any of you would be able to help in providing your expert opinions on the genes that are listed.

As background, Genomics England is sequencing genomes from patients who have tested positive for COVID-19 to contribute to research efforts in uncovering the genetic determinants that may explain why some people are have a more severe response after contracting the virus. As part of this initiative we have created a research gene panel of host genes involved in Viral susceptibility and this will be used to aid interpretation of patient genomes. Some background information of how we have sourced the genes can be found in the panel description box.

In PanelApp, genes are rated based on the level of evidence to support the association with the phenotype or disorder the panel is designed for.

To summarise our rating system for this research panel:

·         Green: Good evidence that variations in this gene could explain at least part of the severity of this infection.

·         Amber: Some evidence that variations in this gene could explain at least part of the severity of this infection.

·         Red: Limited evidence that variations in this gene could explain at least part of the severity of this infection.

Further information about the rating system can be found in the panel description (https://panelapp.genomicsengland.co.uk/panels/111/).

We would greatly appreciate if you could review our gene panel content, particularly to:

i) Add missing genes, particularly from SARS-CoV2 studies and publications, you feel should be part of the panel.

ii) Suggest whether Amber or Red genes should be promoted to Green status.

iii) Suggest whether Green genes are not appropriate for this panel, with evidence.

You can register as a PanelApp reviewer here: https://panelapp.genomicsengland.co.uk/accounts/registration/. Once registered, you can add reviews and evidence to the existing genes/entities on the panel, and add missing genes. Your name as a reviewer will be displayed in PanelApp, acting as a record of your contribution and expertise. If you have a large gene list to be added, you can email it to us at panelapp@....

We intend to finalise the panel by the middle of May, and we would really appreciate to get any input as soon as possible. Please do contact us if you have any questions about the panel or the review process (panelapp@....)

Thank you very much for your time. I look forward to hearing from you.

With best wishes,

Eleanor Williams

 

 

Eleanor Williams PhD | Scientific Curator | Genomics England |  eleanor.williams@...| Address: Genomics England, Queen Mary University of London, Dawson Hall, London, EC1M 6BQ | https://panelapp.genomicsengland.co.uk Work days: Tuesday, Wednesday, Thursday

 

HPO - data analysis has started

Pazmandi Julia
 

Dear HPO enthusiasts,
 
We thank you very much for evaluating the disease annotations and sending us the excel sheets!

In total, we now have the evaluation of 57 diseases, of which 36 have undergone a review by two experts. Matthias and I have started summarising and analysing the data, and filling in the results section of the manuscript.We will send you an updated and more complete version of the manuscript as soon as the results section is complete. 

We would like to wish you all the best:
Julia, Matthias, Marielle and Kaan

HPO Excel submission

Haimel Matthias
 

Dear All,

Thank you for finding time to work yourself through the long list of Excel sheets of HPO terms.

Please keep in mind that the data submission date is approaching this Friday. Excel sheets submitted by the 10th April will be included into the over-arching manuscript.

We would like to wish you all the best and a save Easter,

Julia, Matthias, Marielle and Kaan

 

HPO workshop 12-13th March 2020

Pazmandi Julia
 

Dear HPO enthusiast,
 
If you have not done already, please register to our HPO workshop in Vienna, on the 12-13th March. As detailed in the agenda attached, the meeting will start on the morning of the 12th (Thursday) and end at around 3pm on the 13th (Friday). We can offer 2 nights of accommodation (the night of the 11th and 12th March) and will be able to cover transportation costs up to €300. 

Please let us know if you are able to attend the workshop by sending an email to Maximilian.Rau@... 

Best wishes,
Julia, Marielle and Matthias 

HPO workshop 2020 #workshop2020 #meeting

Pazmandi Julia
 

Dear HPO enthusiast,
 
As advertised at the end of last year, we are going to have a HPO workshop in Vienna, on the 12-13th March. Please find the draft agenda attached to this message. As detailed in the agenda, the meeting will start on the morning of the 12th (Thursday) and end at around 3pm on the 13th (Friday). We can offer 2 nights of accommodation (the night of the 11th and 12th March) and will be able to cover transportation costs up to €300. 
Please let us know if you are able to attend the workshop by sending an email to Maximilian.Rau@..., by the 7th of February.
 
Best wishes,
Julia, Marielle and Matthias  

Happy Holidays, see you next year! #workshop2020 #hpo #holiday

Pazmandi Julia
 

Dear HPO Enthusiasts,

Thank you very much for your hard work this year. We wish you a merry holiday season! 
We are very much looking forward to seeing you again after the holidays, on the 12-13th March in Vienna for our 2020 HPO meeting! 

Best regards,
Julia, Matthias, Marielle and Kaan


2019 HPO workshop - thank you and a summary

Pazmandi Julia
 

Dear Participants of the 2019 HPO workshop,

Thank you very much to all of you for working with us in Vienna the past week!
We had an exceptionally fruitful meeting, with a lot of discussion and actionable points agreed on. With this email, we would like to provide you with a  a summary of the discussion rounds over the two days, as well as direct your attention to the groups.io platform: https://hpo-immune-mediated-disorders.groups.io/g/update/files/2019%20HPO%20workshop, where you will be able to find the presentations from the workshop in a PDF format as well.  

We are looking forward to working with you on completing the HPO annotation of rare, immune mediated diseases in the future!

Best wishes from Vienna,
Marielle, Kaan, Julia and Matthias 

#workshop2019 #agenda #meeting #hpo #workshop2019 #agenda #meeting #hpo

Pazmandi Julia
 

Dear HPO enthusiasts,

We are delighted to share the program of the upcoming HPO terminology workshop on the 17-18th October in Vienna!
If you have not registered yet, please let us know if you are able to join before the 4th of September, by sending a confirmation to maximilian.rau@... and Johannes.pfeifenschneider@.... 
With the budget that ESID and ERN RITA kindly provide, we are able to provide accommodation of up to one night for every attendee, and reimburse travel costs of up to €300.

Looking forward to seeing you in Vienna!

Best,
Julia, Matthias, Marielle and Kaan

HPO workshop invitation

Haimel Matthias
 

Dear Group Members,

We are happy to announce the date of the upcoming HPO terminology workshop for our working group members on the 17th–18th October in Vienna! Kaan Boztug and his team are organizing the meeting on behalf of the ESID Working Party Genetics and the ERN RITA.

The workshop will start on Thursday around 12.00, and will end on Friday afternoon (+/-16.00).

With the budget that ESID and ERN-RITA kindly provide, we are able to pay accommodation of up to one night for every attendee; furthermore, we will be able to reimburse travel costs of up to EUR 300. 

Please let us know if you are able to join before Sept 2nd by sending a confirmation to: maximilian.rau@... and Johannes.pfeifenschneider@...

Best wishes,
Julia, Matthias, Marielle, and Kaan

 

Re-annotation of diseases

Haimel Matthias
 

Dear All,

 

Thanks to your hard work – exiting times are starting now.

We squiezed every drop of HPO out of your collected publications and your expertise will refine these terms to the most comprehensive disease annotations.

The attached document gives you a practical guide of the whole process.

 

Your group champions will be in contact soon to provide you with more details and to organise the distribution of the disease annotations with the group lead.

 

If something is not clear in at any step – please let us know.

 

Best wishes,

Matthias and Julia

 

 

Save the date – HPO meeting Vienna autumn 2019 #workshop #update

Pazmandi Julia
 

Dear All,
 
We are happy to announce the date of the upcoming HPO terminology workshop for our working group members on the 17th–18th  October in Vienna! Kaan Boztug and his team organise the meeting on behalf of the ESID Working Party Genetics and the ERN RITA. This time we will invite guests from Orphanet and try to finalize a manuscript of our work done so far. 
The meeting will start on Thursday around 12.00, and will end on Friday afternoon (+/-16.00).
 
The plan is that accommodation will be provided to attendees, and we will be able to reimburse travel costs up to €300. 
 
Please let us know if you  will be able to join before the 19th of July to: Maximilian.Rau@... . 
 
Julia, Matthias, Marielle and Kaan

HPO June 2019 release #update

Pazmandi Julia
 

Dear All,

 

Some great news!

The new June 2019 version of HPO is now live:  https://groups.io/g/human-phenotype-ontology/message/12, and we are excited to share that our suggested changes are part of the new release! Please find them under this link: https://github.com/obophenotype/human-phenotype-ontology/issues?q=is%3Aissue+author%3Amh11

 

Best,

Julia and Matthias 

#update #summary #update #summary

Pazmandi Julia
 

 

Dear All,

 

We would like to thank you again for your continuous support for our initiative. Please find a general update and summary on the activities of our effort below.

Spreading the word 

In order to increase visibility, two abstract have been submitted to the 2019 ESID meeting: one by the groups of “Serology / Antibody Deficiencies ” lead by Esther de Vries, and one general one on the behalf of the whole consortium. We would like to thank you again for spreading the word among your circles – we have welcomed 7 new members during the past months!

 

The next workshop

We are delighted to share that we are working towards organizing  a further 1,5 day meeting in Vienna in Autumn (September or October) of this year. The date and program will be announced in the next three weeks. We are hoping to see many of you there!

 

Automated HPO annotation for diseases

With the help of your efforts, we now have a(n almost complete) collection of publications detailing phenotypes of rare immune mediated disorders. In the last months, our main focus in Vienna was to start the semi-automated annotation process, which would allow us to extract HPO terms from these publications and annotate diseases. After a long time of trial and error, Matthias and me are currently testing a method which looks promising. We are planning to send out the first results of this annotation in June. Once the annotation process works optimally, we will be able to send the full list of annotations to the functional working groups for inspection and double-checking.

 

Thank you very much again for your support. Until the first round of annotations gets sent out, we would like to ask the groups to help us by:

·       Spreading word by talking to collogues, mentioning the initiative or by submitting abstracts and talking at conferences.

·       Finishing collection publications so that the all- disease-wide annotation process can progress

·       Review disease ontology structure regarding all remaining diseases

 

Thank you once more for your participation and support so far. Let’s continue working towards an accurate and comprehensive HPO repertoire for immune mediated disorders!

 

Best,

Julia and Matthias

#abstract #spreadtheword #abstract #spreadtheword

Pazmandi Julia
 

Dear All,

We are happy to announce that on the behalf of our initiative, we have submitted an abstract to the 2019 ESID meeting. Please find the abstract attached below.
With this, we would like to thank you very much for the continuous support, even in times of less activity. An update about current, ongoing activities is coming very soon. 

Best,
Julia 

Minutes from the Immunodeficiencies affecting cellular and humoral immunity working group meeting #minutes

Pazmandi Julia
 

Dear HPO enthusiasts,

Please find the minutes from the latest Immunodeficiencies affecting cellular and humoral immunity working group meeting attached to this email.



our HPO initiative - summary and update

Pazmandi Julia
 

Dear All,

We would like to thank you all for your participation in the HPO initiative so far. This email aims to summarize what has happened and what we have achieved until now – as well as shed light on future directions.

Summary - the kick-off meeting

During our kick-off meeting in Vienna we have successfully re-annotated 18 diseases with HPO terms. Subsequently, we have reviewed and revised four branches of the HPO tree:  neutrophils, lymphocyte count structure, humoral immunity hierarchy, immune system physiology.  All these changes have been officially submitted to the HPO git page. Two of the changes (regarding immune system physiology, humoral immunity hierarchy) have been successfully implemented, the other two are in the final stages of acceptance.

From October until now

After our kick of meeting the focus has shifted to complete two tasks within the first 4 months of operation.

Firstly, to collect publications detailing phenotypes for specific diseases, to use as knowledge base in the semi-automated disease re-annotation lead by Peter Robinson. Two groups have completed the collection of publications so far. Peter, Matthias and I are currently working on starting the annotation process.

Secondly, we aimed to address the precision of the diseases ontologies towards immune mediated disorders. For this, we have asked the different groups to go through diseases one-by-one and report any discrepancies. To date, one group is near completion.

In order to raise awareness and spread the word, we have submitted two abstracts on our initiative: one to the Immunogenomics of Diseases meeting this February on behalf of the whole group, as well as an abstract to ISSAID, focused on the autoinflammatory group headed by Anna Simon.  Meanwhile, Matthias has set up a groups.io page with email lists to facilitate easier communication.

Next steps  

We will begin the annotation process using the collected publications and tools from Peter’s team. As the first round of annotation is completed, we will ask for help from different groups to review the automated annotation from the publications for correctness. Until then, we would like the groups to focus on three main things:

  • ·       Spreading the word by talking to collogues, mentioning the initiative or by submitting abstracts and talking at conferences.
  • ·       Finishing collection publications so that the all- disease-wide annotation process can start
  • ·       Review disease ontology structure regarding all remaining diseases

 Thank you again for your participation and support so far. Let’s continue working towards an accurate and comprehensive HPO repertoire for immune mediated disorders!


Best,
Julia and Matthias

Re: #abstract #spreadtheword #abstract #spreadtheword

Pazmandi Julia
 

A short update to the last message: we were limited with the numbers of allowed people on the abstract but of course everyone shall feel included! 

Best,
Julia 

On 23.01.2019, at 10:38, Pazmandi Julia <Julia.Pazmandi@...> wrote:

Dear All,

In order to spread the word and recruit new members, our initiative will be presented at the Immunogenomics of Disease: Accelerating to Patient Benefit 2019 meeting on the 5-7th February. Please find our abstract, and the slide advertising the poster attached.  

We strongly encourage all groups to identify meetings of interest and submit abstracts to spread the word as well! 

<pazmandi_julia_lightningtalk.pdf><Abstract_HPO_immunogenomics.docx>

#abstract #spreadtheword #abstract #spreadtheword

Pazmandi Julia
 

Dear All,

In order to spread the word and recruit new members, our initiative will be presented at the Immunogenomics of Disease: Accelerating to Patient Benefit 2019 meeting on the 5-7th February. Please find our abstract, and the slide advertising the poster attached.  

We strongly encourage all groups to identify meetings of interest and submit abstracts to spread the word as well! 

#minutes #minutes

Pazmandi Julia
 

Dear All,

To start of the year, the autoinflammatory working group had a Skype meeting on the 14th January, which covered a variety of topics.

Please find the minutes attached!

 

Best wishes,

Julia 

Immunodeficiency working group #minutes

Haimel Matthias
 

Dear all,

 

Please find the minutes from the autoinflammatory working group attached, which used Zoom for a conference call on the 13th November.

Well done for the progress  and nice to see the next call already scheduled.

 

Best wishes,

Matthias