Hi Ewenn

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I’ll do my best to answer your questions though I am by no means an expert on the technicalities of microarrays.

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A SNP is a single nucleotide polymorphism. It is a simple change to a nucleotide (also known as a base) such as an A changing to a G. It does not designate the position in the genome. It is simply the name given to the mutation that occurs at that specific position. Some positions in the genome have a higher mutation rate so you sometimes get SNPs which occur in different haplogroups. These are known as parallel mutations. The same SNP name would be used but the name would have a .1, .2 etc included after the SNP name to denote the fact that it occurred in a different part of the tree. To classify as a SNP it is supposed to occur in at least 1% of the population. In order to identify a SNP you therefore need to test lots of people in the population so that you are able to ascertain that a minority of people have, for example, a T at a particular position in the genome whereas the rest of the population have a G.

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FGC57405 would only be included on a SNP chip if this SNP was (1) known at the time the chip was launched and (2) if it was included in the collection of SNPs chosen for inclusion on the chip. Companies do have the ability to include a limited number of custom SNPs on the chip in addition to the fixed selection of SNPs provided by the company but they obviously can’t include everything. It’s only since the launch of next generation sequencing tests that we’ve been able to discover tens of thousands of new SNPs.

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The rsID is simply the reference number for the position on the genome where the SNP has occurred. There are rsIDs for each chromosome.

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As far as I can make out Z291 and FGC57423 are on two completely different parts of the R1b tree so they would have different rsIDs. Here are the ancestral SNP paths:

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R-M207>M173>M343>L754>L761>L389>P297>M269>L23>L51>P310>L151>P312>Z46516>ZZ11>U152>L2>Z258>Z367>L20>Z291

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R-M207>M173>M343>L754>L761>L389>P297>M269>L23>L51>P310>L151>U106>Z2265>S19589>FGC57430>FGC57423

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Single SNPs aren’t normally used in isolation to provide a haplogroup assignment. You need to have the full SNP list. Even if there was a no call at one position in the SNP chain, you would still be able to provide the haplogroup assignment because of all the other SNPs in the SNP progression list.

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Some companies allow you to download your raw data so that you can get the full rsID list and your result for each position whereas other companies (eg Living DNA) simply provide you with a SNP list.

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Affymetrix and Illumina are the names of the two main companies that manufacture microarrays. The SNPs which appear on the microarray are selected by the companies to give a good balance of SNPs spread out across the genome. The two companies will, therefore, have a different selection of SNPs on their microarrays. The Y-SNPs are selected for their phylogenetic relevance. Some SNPs don’t perform well on microarrays so this is something that is also taken into consideration. Each microarray will include a fixed number of SNPs and. by definition. these SNPs have to have been discovered in order to be included on the chip.

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There is no problem with calling Ts. Microarrays are perfectly capable of calling all four DNA letters (As, Cs, Ts and Gs) with a high level of accuracy.

For example the call rate is 99.5% for the GSA v3. See:

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If FGC57405 is not included on any of the chips it’s probably not because of any difficulties in calling the SNP but because it occurs at a position in the genome that did not feature in the research that was available at the time and it was therefore still waiting to be discovered. Alternatively, if it was known at the time, it may be that for one reason or another it did not make the shortlist of SNPs that were included on the chip.

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I don’t think there’s an easy way to check when a Y-SNP was discovered. You can, however, do a manual check on the earlier versions of the ISOGG Y-SNP tree:

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That might give you an idea of when FGC57405 was first discovered.

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This page on the Illumina website provides information about the technology of microarrays:

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Best wishes

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Debbie

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