[ensembl-dev] different between eGenetics and GNF/Atlas

Wed Jul 6 15:13:26 BST 2016

Hi:

For work on mitochondrial DNA variants, the "wrong" alleles maybe due to
using different references.

The most widely used is rCRS, inlcuding Ensembl's VEP.

But some sources used YRI (African (Yoruba) Sequence AF347015
<http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AF347015>),
including older version of UCSC (HG19) and some affymetrix SNP array
platforms.

If this is the case, one may convert YRI-based variant notations to
rCRS-based before running VEP.

I have a web tool to do the conversion and even annotation calling VEP:

https://mseqdr.org/mv.php

You can try these 2, and "Convert" or "Convert and Annotate" from
reference "YRI" to "ALL FORMATS".

For example, your 2 variants as input:
m.3971C>T
m.4249T>C

Result:
InputHGVS CommitteeHGVS ClinVar/NCBIHGVS EnsemblHGVS
Mutalyzerm.3971C>Tm.3970C>TNC_012920.1:m.3970C>TMT:g.3970C>TNC_012920.1:g.3970C>T
ENST00000361390.2:c.664C>T
ENST00000361390.2:c.664C>T(p.=)m.4249T>Cm.4248T>CNC_012920.1:m.4248T>CMT:g.4248T>CNC_012920.1:g.4248T>C
ENST00000361390.2:c.942T>C  ENST00000361390.2:c.942T>C(p.=)

Lishuang Shen

Sr. Bioinformatics Scientist
Center for Personalized Medicine
Children's Hospital Los Angeles

http://www.mitomap.org/foswiki/bin/view/MITOMAP/MitoSeqs

>> African (Yoruba) Sequence AF347015
<http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AF347015>,
formerly NC_001807.4. This L3e sequence is 16571 bp in length and has over
40 variant nucleotides from the rCRS. Some sequencing chips (for example,
Affymetrix Genome-Wide Human SNP Array 6.0; Illumina 550 v.1, 550 v.3, 610
v.1) have used nucleotide numbers based on the Yoruban sequence. To convert
Yoruban-based position numbers to ones relative to the revised Cambridge
sequence, follow the rules in the Yoruba Conversion table
<http://www.mitomap.org/Sandbox/YorubanConversion>.

On Wed, Jul 6, 2016 at 2:38 AM, 林琼芬 <qiongfen0 at gmail.com> wrote:

> Hello Will,
> Thanks for you help. I have try the two method you give, but it doesn't
> work. Reference allele has no problem, so as "MT". If there have any other
> solution？
>
> Best regard!
> Lin
>
> 2016-07-04 16:25 GMT+08:00 Will McLaren <wm2 at ebi.ac.uk>:
>
>> Hello Lin,
>>
>> There is a problem with your input - the reference allele that you have
>> specified does not match the reference genome sequence. You can have VEP
>> check your input for this issue by adding --check_ref to your command line.
>>
>> You should also use "MT" to refer to the mitochondrial chromosome in
>> place of "M".
>>
>> Regards
>>
>> Will McLaren
>> Ensembl Variation
>>
>> On 4 July 2016 at 03:53, qiongfen0 at gmail.com <qiongfen0 at gmail.com> wrote:
>>
>>> Dear Thomas,
>>> Thanks for your reply, it has help me so much.
>>> Now, I have another confused, I hope you can help me understand this.
>>> I am using ensembl-tools-release-77 now, when I use VEP to annotate the
>>> variants in mitochondria, some has the result of HGVSp but not have HGVSc
>>> (like the follow printscreen), it may be quiet strange. Then I use the
>>> VEP online  to try again, but it has no result of HGVSc and HGVSp. I
>>> wonder what make this result appear.
>>>
>>>
>>> Hope to hear form you.
>>>
>>> Yours sincerely,
>>> Lin
>>>
>>> *From:* Thomas Maurel <maurel at ebi.ac.uk>
>>> *Date:* 2016-06-28 17:30
>>> *To:* Ensembl developers list <dev at ensembl.org>
>>> *Subject:* Re: [ensembl-dev] different between eGenetics and GNF/Atlas
>>> Dear Lin,
>>>
>>> I am afraid that this data was retired in Ensembl release 76. These
>>> might not match as the data is coming from two different sources:
>>>
>>> GNF/Atlas data came to us via the Gene Expression Atlas project at
>>> EMBL-EBI.
>>>
>>> http://www.ebi.ac.uk/gxa/
>>>
>>> The GNF/Atlas data was published by the Genomics Institute of the
>>> Novartis Research Foundation:
>>>
>>> http://www.gnf.org/technology/organismal/gene-expression-core.htm
>>>
>>> The eGenetics database uses Expressed Sequence Tags (ESTs) annotated
>>> with eVOC ontology terms by SANBI (South African National Bioinformatics
>>> Institute). More information below.
>>>
>>> http://www.ncbi.nlm.nih.gov/pubmed/12799354
>>> http://www.sanbi.ac.za/
>>>
>>> Hope this helps,
>>> Best Regards,
>>> Thomas
>>>
>>> On 28 Jun 2016, at 03:04, qiongfen0 at gmail.com wrote:
>>>
>>> Dear Sirs,
>>> I'm using biomart to filter a series of genes which are specifically
>>> expressed in the brain. In biomart there are two such filters,
>>> 'eGenetics/SANBI EST anatomical system data' and 'GNF/Atlas organism part',
>>> however, the results of these two filters don't match. I searched for it at
>>> biomart help but i couldn't find anything about this. Can anybody help me
>>> to understand the difference of these two filters?
>>> I am looking forward to hearing from you.
>>>
>>> Yours sincerely,
>>> Lin
>>>
>>> Qiongfen Lin
>>> South China Normal University
>>> TEL: +8615118845463| Mail : qiongfen0 at gmail.com
>>>
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>>>
>>> --
>>> Thomas Maurel
>>> Bioinformatician - Ensembl Production Team
>>> European Bioinformatics Institute (EMBL-EBI)
>>> European Molecular Biology Laboratory
>>> Wellcome Trust Genome Campus
>>> Hinxton
>>> Cambridge CB10 1SD
>>> United Kingdom
>>>
>>>
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>>>
>>
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>>
>
>
> --
>
> Arron Lin
>
> BGI Research Institute
>
> Email: qiongfen0 at gmail.com
>
> Beishan Industrial Zone| Yantian  District| Shenzhen 518083
>
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