[ensembl-dev] How realistic are the sequences?

[Emily Perry]

Hi Mahmood

The human genome was produced by the genome reference consortium:
https://www.ncbi.nlm.nih.gov/grc/human

It was produced by cloning genome segments from a number of individuals 
into BACs, sequencing the BACs then arranging the BACs together. The 
BACs are now represented in the genome as contigs, and each contig 
represents sequence from a single individual. Contigs with the same 
two-letter prefix come from the same individual. The GRC may have more 
information on the ethnic make-up of the individuals used, but I know 
that a lot of the genome comes from a man identified as RP11, who was 
African American. The individuals used for the genome were healthy.

Since each sequence is an individual sequence, sometimes a minor, or 
even private, allele can be reference allele. The transcript haplotype 
page shows you the CDS and protein sequences found in actual 1000 
Genomes individuals, listing the frequency of these sequences in 
different ethnic groups, eg:
http://www.ensembl.org/Homo_sapiens/Transcript/Haplotypes?db=core;g=ENSG00000072110;r=14:68874143-68979440;t=ENST00000193403

The 1000 Genomes individuals all self-reported as healthy.

All the best

Emily

On 18/08/2017 11:34, Mahmood Naderan wrote:
> Hi,
> Question is how much realistic is the sequences presented as 
> "reference" in the Ensembl database? In other words, is the reference 
> sequence of a gene relates to a healthy human?! Perhaps no! Are the 
> sequences relates to a group of humans? Then which side of the world 
> or ethnic?
>
> I appreciate any feedback on this question.
>
> Regards,
> Mahmood
>
>
>
>
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-- 
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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