The important bit:-
Has anybody out there in Netland used or attempted Happy mapping? Any comments
appreciated especially regarding efficacy, speed, accuracy, and problems.
The story bit:- (For those who want to know.)
One day, in a dark and dingy basement lab (OOH SCARY), Igor looked out from
his hole in the corner and thought...Well it was more like he noticed some
addled ramblings floating about in a phenol/chloroform fume steeped blob he
lovingly refered to as his brain: It would have hurt such a simple creature,
but years of slow, pains-taking and mind numbing mapping work had taken it's
toll on the senses (AHH SHAME).
Anyway, he thought "For the past two years, using standard mapping
techniques, I've typed 500 backcross progeny for 6 loci (A-F) in and around a
4.2cM (8.4Mbp) region that contains X, the locus that Master is interested in.
The data resulting so far indicates the gene locus order:-
A - 3.5cM - (B/C/D/X) - 0.7cM - E/F
Since X can only be typed by phenotypic tests, more backcross progeny will
have to be typed until recombinants are found which resolve the order of
B/C/D/X, but how many will this be?
If happy mapping works, loci B,C,D,E and F may be ordered without further
backcross typing, and the data generated should give an indication of the
distances involved between these loci such that estimates can be made as to
how many progeny would be necessary in order to find recombinants which
seperate and order the loci.
If C is an anchor marker, an initial strategy would probably be to
show whether loci B and D are proximal or distal to C by happy mapping the
0.7cM region between C and E/F. According to the authors 7 loci over 1.24Mbp
were mapped using 140 test aliquots, but they had foreknowledge of the real
order. Assuming 0.7cM is equivalent to 1.4Mbp, is such a rapid mapping
repeatable, or if not, what would be a real guesstimate of number of tests be?
Mapping this region may also allow the ordering of E and F relative to C.
If one or both of B and D prove to be proximal to C (in the 3.5cM
region between A and C), could this be happy mapped with sufficient integrity
of order and distance using A and C as boxing markers?
Regards to all who got this far
datherton at uk.ac.ox.path.vax