LINKAGE and inbreeding loops

Martin Farrall mfarrall at scandium.rpms.ac.uk
Wed Mar 2 04:29:21 EST 1994


I have recently encountered some problems when attempting
to analyze families with more than one inbreeding loop.

For example, consider a rare recessive allele segregating
in an extended family.  In the "top" generation, two sisters
(5 and 6) marry two brothers (7 and 8).  Their respective
grand-son (15) and grand-daughter (14) (who are "double"
second cousins?) marry and have affected offspring (16 and 17).
I find that depending on where you break the loops, you get
different lod scores.  Calculation of genetic risks also appear
to be incorrect for certain individuals in the "top" generation.

Here is the pedigree in standard linkage format.

1  1  0  0  1   1  1
1  2  0  0  2   1  1
1  3  0  0  1   1  1
1  4  0  0  2   1  1
1  5  1  2  2   1  1
1  6  1  2  2   1  1
1  7  3  4  1   1  1
1  8  3  4  1   1  1
1  9  7  6  2   1  1
1 10  7  6  1   1  1
1 11  0  0  2   1  1
1 12  0  0  1   1  1
1 13  8  5  2   1  1
1 14 10 11  2   1  1
1 15 12 13  1   1  1
1 16 15 14  2   2  2
1 17 15 14  2   2  2


Similar problems have arisen with the following extended family
with two loops, each loop leading to a first cousin marriage.
The loops are connected by marriage through individuals 7 and 8.

1  1  0  0  1  1  1
1  2  0  0  2  1  1
1  3  0  0  1  1  1
1  4  0  0  2  1  1
1  5  1  2  1  1  1
1  6  0  0  2  1  1
1  7  3  4  1  1  1
1  8  1  2  2  1  1
1  9  3  4  1  1  1
1 10  0  0  2  1  1
1 11  7  8  1  1  1
1 12  5  6  2  1  1
1 13  7  8  1  1  1
1 14  9 10  2  1  1
1 15 11 12  1  2  2
1 16 11 12  1  1  1
1 17 13 14  1  2  2
1 18 13 14  1  1  1


I must admit that I haven't seen a recent LINKAGE manual to know
if there is specific advice with these sort of problems - I'd
appreciate any comments or insight.




Martin Farrall

e-mail: mfarrall at rpms.ac.uk
FAX   : +44 (0)81 749 8341



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