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Archiver > GENEALOGY-DNA > 2010-02 > 1266492927


From: Wayne Kauffman <>
Subject: Re: [DNA] FTDNA will introduce Family Finder [CNV]
Date: Thu, 18 Feb 2010 03:35:27 -0800 (PST)
References: <c28.3cb730c1.38ae78a1@aol.com>
In-Reply-To: <c28.3cb730c1.38ae78a1@aol.com>


Ann you are correct that CNV would not be included. With a little work one can follow the protocol for extracting CNV information from the Affy SNP chips. An example of this is found under
http://www.openbioinformatics.org/penncnv/penncnv_tutorial_affy_gw6.html

To look at the Affy raw data one will need to create a free account at Affymetrix.com then download the Genotyping Console. Visit http://www.affymetrix.com/support/technical/sample_data/genomewide_snp5_data.affx and download the example dataset and load it into GTC. With that present you will be able to access the list of SNPs present in the 500K HapMap array. Note that the raw data download is quite large. If FTDNA really provides the .CEL and.CHP files for download anyone running a project will need to consider how they will manage the significant amount of data which is provided.

I haven't worked in the Affymetrix realm for 8 years but there are additional tools within the Affymetrix developer community based on the Affy Power Tools download that may be of use in looking at FF data.

- Wayne Kauffman




________________________________
From: "" <>
To:
Sent: Thu, February 18, 2010 6:04:01 AM
Subject: Re: [DNA] FTDNA will introduce Family Finder [CNV]

Assuming FTDNA is using the 500K Affy chip, CNV would not be included. But
even identical twins can have CNV, so it wouldn't be a very stable way of
determining relationships.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2427204/pdf/main.pdf

Ann Turner

In a message dated 2/17/2010 2:31:26 PM Pacific Standard Time,
writes:

> To the geneticist the FF raw data may the window into evaluating copy
> number variants but I am not sure on this topic.
>

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