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From: "Ken Nordtvedt" <>
Subject: [DNA] Marker State Names
Date: Tue, 10 Oct 2006 08:28:41 -0600
References: <BAY105-F35EE8406606FFACE059400CC160@phx.gbl><002701c6eba1$8c764120$6400a8c0@Ken1><003f01c6eba2$914c3dc0$640fa8c0@Villandra2><004c01c6eba7$f98a8b30$6400a8c0@Ken1><004a01c6ebaf$5a0c7d90$640fa8c0@Villandra2><001301c6ebb0$9b1f5090$6400a8c0@Ken1><4e73350d9cjohn@cartmell.demon.co.uk><REME20061009212441@alum.mit.edu><005d01c6ec21$a9a84150$640fa8c0@Villandra2><307678ED-288B-4AB4-97F9-AE86E4B30FAB@vizachero.com>


The states in which STRs can be in are discrete. So at the cost of loss of
useful information at our finger tips (actually neuron tips) those states
could be given names --- apple, orange, plum, banana, etc., instead of
numbers.

That was actually done with the four discrete states a nucleotide site can
find itself in --- A,G,T,C --- I believe taken from the previous names of
the molecules present in each case. To me that choice A,G,T,C is a bit
unfortunate, although no doubt here to stay, because I always forget which
of the four complements the other on duplication and which states are more
easily mutated to if you begin at a specific state. A,a,B,b would have
conveyed more useful information and been helpful to me, at least.

One lab tells me my DYS452 is in a state 30. Another lab tells me my state
at DYS452 is 11. Different names for the same thing (but containing some
trivial historical information probably about labs' choices of primers or
what not). But what's in common and useful about those two labs' naming
systems? The liklihood that a state of 29 or 31 is "close" to 30 in one
case; and the liklihood that a state of 10 or 12 is "close" to 11 in the
other (close not only meaning structurally close but also close in the sense
of mutational connection which is more important for genetic genealogy) .

The use of the ordered numbers as names for the discrete states encapsulates
and keeps in our mind corresponding relationships between the physical
states of the STRs and their tendency to mostly mutate to two neighboring
states.

What kind of numbers this makes these names for the STR states I will leave
to the priests to debate. Ken





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