[ensembl-dev] Jobs at Ensembl

Paul Flicek flicek at ebi.ac.uk
Mon Oct 9 17:28:39 BST 2017


Hi Andrius,

I'm not sure that I explained the LRG project clearly. The goal is to 
create standard, stable references sequences appropriate for clinical 
reporting. This is necessary because both transcript annotation and the 
underlying genome sequence change over time. Without effective 
standards, variants reported in HGVS nomenclature, but missing 
information such as genome assembly or transcript version, can become 
ambiguous over time.  Interpretation and reinterpretation of variants 
into classifications such as benign or pathogenetic also requires stable 
location information, which is what LRGs provide.

It is also important to note that LRG sequences are just one part of our 
larger toolkit supporting interpretation of genome variation.

Regardless, I think best to take further discussion off this list.  
Please feel free to contact me directly.

Thanks,
Paul	


On 9 Oct 2017, at 17:07, Andrius Baskys, MD, PhD wrote:

> Hello Paul,
> Thank you very much for your comments and information. I noticed from 
> the description you send me that 'Community' who provides you with a 
> feedback does not include practicing physicians, or someone who could 
> use this information to diagnose and treat diseases in real life. I 
> think that is a mistake and it hampers  the implentation of your 
> effort into clinical practice, which is the ultimate goal.
> Hope you will find my comments useful.
> Kind regards,
> Andrius
>
> ⁣Andrius Baskys, MD, PhD
> Newport Beach, CA 92658 USA
> Ph. 877-483-2071
> Intl. +1 626-239-8378
> Fax 877-953-8777​
>
> On Oct 9, 2017, 8:35 AM, at 8:35 AM, Paul Flicek <flicek at ebi.ac.uk> 
> wrote:
>> Hi Andrius,
>>
>> The LRG project works extensively with the community to create
>> transcripts suitable for variant reporting.  The LRG sequences and
>> their
>> component transcripts are standards specifically designed for 
>> clinical
>> use cases, but the LRG project does not interpret variants.
>>
>> Our curators work to ensure that transcripts with clinical relevance
>> are
>> annotated accurately and that they meet the requirements of 
>> diagnostic
>> laboratories, LSDB curators and other users.
>>
>> For more information, we have published a couple of papers describing
>> the project including the most recent one in 2014:
>> http://europepmc.org/articles/PMC3965024. There is also information 
>> at
>> http://www.lrg-sequence.org.
>>
>>
>> Paul
>>
>>
>> On 9 Oct 2017, at 15:56, Andrius Baskys, MD, PhD wrote:
>>
>>> Hi Emily,
>>>
>>> I admire the amazing  work that Ensembl is doing and use it in my
>>> practice as much as possible. However, i noticed your adverts for a
>>> bioinformatician to review "clinically relevant" transcripts and
>>> wonder how would a person who never treated a patient determine what
>>> is clinically relevant? Or is clinical knowledge irrelevant?
>>>
>>> Just curious.
>>>
>>> Kind regards,
>>> Andrius
>>>
>>> ⁣Andrius Baskys, MD, PhD
>>> 1133 Camelback Street #9287
>>> Newport Beach, CA 92658 USA
>>> Ph. 877-483-2071
>>> Intl. +1 626-239-8378
>>> Fax 877-953-8777​
>>>
>>> On Oct 9, 2017, 1:07 AM, at 1:07 AM, Emily Perry <emily at ebi.ac.uk>
>>> wrote:
>>>> Hi All
>>>>
>>>> We have a couple of jobs advertised:
>>>> http://www.ensembl.info/jobs/
>>>>
>>>> *Bioinformatician – GENCODE*
>>>> We’re looking for a bioinformatician to review clinically 
>>>> relevant
>>>> consensus GENCODE and RefSeq transcripts for the CREST project.
>>>> We’re
>>>> looking for degrees in genetics or biological sciences with
>>>> experience
>>>> in Perl and genomics. Closes 21st October.
>>>>
>>>> *Scientific curator – LRG*
>>>> We’re looking for a scientific curator to work on the Locus
>>>> Reference
>>>> Genomic project, curating clinically relevant gene annotation.
>>>> We’re
>>>> looking for degrees in genetics or biological sciences with
>>>> understanding of genetic variation and genomics. Closes 12th
>>>> November.
>>>>
>>>> All the best
>>>>
>>>> Emily
>>>>
>>>> -- 
>>>> Dr Emily Perry (Pritchard)
>>>> Ensembl Outreach Project Leader
>>>>
>>>> European Bioinformatics Institute (EMBL-EBI)
>>>> European Molecular Biology Laboratory
>>>> Wellcome Trust Genome Campus
>>>> Hinxton
>>>> Cambridge
>>>> CB10 1SD
>>>> UK
>>>>
>>>>
>>>>
>>>>
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