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A recombination is required to explain the
results. This is most likely in individual
II4 on the maternal chromosome between the
markers A and B (as illustrated above).
[Theoretically, it is not impossible that
recombinations have occurred in both II2 and
II3 instead of in II4, and that the
haplotypes in I2 are 1,3,1,2 and 3,1,3,3 (A
to D), but because this requires 2 unlikely
events in the same interval, it is much less
likely than the situation illustrated. In
any case, the carrier risk calculation to
II4 will be the same.]
The recombination position is between ‘A’
and ‘B’. But the position within this
interval is unknown. At one extreme, it
could be directly adjacent to ‘A’ – i.e.
directly adjacent to the 5’ end of the gene.
Consequently, there would be zero risk that
II4 is a DMD carrier. At the other extreme,
it could be directly adjacent to ‘B’.
Consequently, II4 would share one third of
the maternal DMD haplotype with her affected
brother. We are concerned with risk here, so
have to consider the most likely position,
or average position. In the original
question, we were advised to assume that
both mutation positions and recombinations
positions are random with respect to the
coding sequence. Therefore, on average, the
recombination position will cause one sixth
of II4’s maternal haplotypes to be shared
with her brother, II3.
But what is the position of the mutation? We
don’t know of course. But what matters is
its position with respect to the
recombination. A common mistake is to assume
that if the mutation lies 5’ to marker ‘B’
then II4 will be a carrier. So the question
we need to ask is: What is the risk that the
mutation lies 5’ to the recombination? This
is straightforward to calculate where there
is random distribution of mutations with
respect to the coding sequence, as advised
in the question. The carrier risk is the
same as the proportion of shared haplotypes
between II3 and II4, i.e. one sixth.
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Recombination distribution:
The dystrophin gene lies in a recombination
hotspot. On average, 1cM (1% chance of
recombination) equates to a physical
distance of around 1Mb. The dystrophin gene
spans around 2.4Mb but the chance of
recombination within this interval is around
10% at each meiosis.
Furthermore, recombination is non-random
over this interval, with recombination
hotspots coinciding very approximately with
the deletion/duplication hotspots. When one
considers the 5’ third of the dystrophin
gene, the recombination distribution is
biased towards the 3’ end of this interval,
so it is more likely that the recombination
is positioned closer to marker ‘B’ than
marker ‘A’. However, this is an inexact
science!
Mutation distribution:
Data on mutation distribution are much more
precisely known.
Gene rearrangements are non-random, with
well established distributions established
for deletions and duplications, (http://www.dmd.nl/).
For small mutations (point mutations) which
concern us in this question, the
distribution is effectively random with
respect to the coding sequence.
But the coding sequence is far from random
with respect to the physical map. Being the
largest know gene in nature, dystrophin
contains several exceptionally large introns.
Particularly large are introns 1, 2, 7 and
44.
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Questions you should ask yourself include:
Which are the closest informative markers to
the recombination that has been identified?
If this is a large physical distance, are
there additional markers that could be
assayed to refine the recombination
position?
Is the recombination distribution even over
this interval, or is the recombination
distribution polarised?
Is the mutation distribution even over this
interval? Remember to consider if you have
excluded certain classes of mutation by
other experiments (e.g. deletions and
duplications excluded by MLPA in this
example). Remember too that you need to
consider the mutation distribution with
respect to the physical distance rather than
with respect to the coding sequence. You may
need to examine exon distribution and exon
sizes. |
