Question: How can i know my ancestry information with a whole exome sequencing? (Excel File)
1
gravatar for estebantr44
5 weeks ago by
estebantr4410
estebantr4410 wrote:

Originally i did this genetic test to confirm a bening neuromuscular disease, the company gave me an excel file that I have been investigating ever since. ( i guess it used to be a VCF file but im not quite sure.)

1.so how can i calculate my estimated ethnicity and haplogroups? any database with SNPs or specific AIMs?

  1. what other useful information can i find with this file? (i found polymorphisms in my alcohol related enzymes and cytochromes ... the thing is that i dont know what else to look).

I'm a medical student in love of genetics, thanks for any answer.

I attach what my file looks like.

enter image description here

sequencing snp gene genome • 186 views
ADD COMMENTlink modified 5 weeks ago by Kevin Blighe61k • written 5 weeks ago by estebantr4410
0
gravatar for Kevin Blighe
5 weeks ago by
Kevin Blighe61k
University College London
Kevin Blighe61k wrote:

You've got a lot of work to do in order to infer your ethnicity from this data. For example, take a look at my threads here:

The problems are multiple, including:

  • the data format is Excel
  • we have no idea how variants were filtered
  • we have no idea of the original screening panel
  • we have no idea if any of these variants are even informative of ethnicity

Yes, it looks like a former VCF, though.

You may ask the company for the original unfiltered VCF or, even better, the raw FASTQ data.

You may aslo have some luck with Peddy: https://github.com/brentp/peddy

Kevin

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Kevin Blighe61k

Thanks for the reply, you are right im gonna ask for the raw data.

I found an old email and they specify this :

  1. They used Ilumina Hiseq 4000 and the GRCh38 genome for reference.
  2. For sequencing analysis they used: BWA-bactrack, BWA-SW, BWA-MEM.
  3. For variant filtering they used: Bioinfo2Bio, Variant Caller v2.1, GET-evidence, BWA alligner.

I forgot to mention but i already found 18 SNPs related to european ancestry like the rs1426654 P.Thr111 Ala

(i found those according to various databases and studies of skin/eye/hair pigmentation but im not quite sure if those SNPs would help me in my research, can they be consider AIMs? )

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by estebantr4410
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