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MacLean et al., Human Mutation
HUMAN MUTATION Supplementary Material Online
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Supplementary Material for the article:
MacLean et al., Human Mutation
Double Strand DNA Break Repair with Replication Slippage
on Two Strands: A Novel Mechanism of Deletion Formation
Helen E. MacLean, Jenny M. Favaloro, Garry L. Warne, and Jeffrey D. Zajac
Supplementary Appendix S1
Calculating Relative Chance of Parentage
To confirm the genetic relationship between the affected XY aunt (II-3) and her parents, the relative
chance of parentage was calculated. This calculation is usually applied to determine the relative
chance of paternity (Lee, 1980), but was adapted for the reverse situation in this case. Genetic loci
on the X chromosome were examined, so in these cases only the affected XY aunt (II-3) and her
putative mother (I-1) were examined. Blood typing was also performed, on the affected XY aunt
and both her putative parents.
We examined four polymorphic loci on the X chromosome in the affected aunt (II-3) and the
grandmother (I-1): the AR CAG repeat (Beilin, et al., 2001), ALAS2 (Cox, et al., 1992), DXS453
(Weber, et al., 1990) and DXS441 (Ram, et al., 1992). At each locus the grandmother was
homozygous for one allele (Table S1), and the hemizygous XY aunt shared a common allele with
her putative mother. Blood group analysis was also performed on the affected aunt and her putative
parents, with the ABO, Rh, Kell, Duffy, Kidd, Lewis, P and MNSs systems examined (Table S2).
For each genetic locus, the probability of individual I-1 having a child with individual II-3’s allele
was compared to the probability of a random mother having a child with individual II-3’s allele, the
latter being equivalent to the allele frequency in the Caucasian population. The combined
probability of parentage was obtained by multiplying the probability at each locus. The relative
chance of parentage was calculated by dividing the combined probability of individual I-1 being the
mother by the sum of the combined probabilities that individual I-1 or a random female is the
mother, expressed as a percentage.
For each blood type system, the parents’ phenotypes were used to determine all possible offspring’s
phenotypes according to the Hardy-Weinberg equilibrium, and the probability of individual II-3’s
phenotype occurring was calculated. The probability that individual II-3 inherited each blood type
from random parents is the same as the frequency of that phenotype in the general population. For
the Rh, Kell, Duffy and Kidd systems, the observed phenotype arises from only one genotype, and
the gene frequencies of the alleles in the general population are known. For the Lewis system, the
MacLean et al., Human Mutation
HUMAN MUTATION Supplementary Material Online
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observed phenotype and the phenotype frequency in the general population are known. For the
ABO, P and MNSs systems, different genotypes were possible based on the observed phenotypes.
In these cases, the probability that the parents were each genotype was calculated, based on the
frequency of the gene alleles in the general population. The possible offspring’s phenotypes were
then calculated as the sum of the probabilities from each potential genotype. Calculations were
carried out for each of the blood groups based on the gene frequencies for the ABO, MNSs, Rh,
Kell, Duffy and Kidd antigens in the Tasmanian population (Mitchell, 1983), and the phenotype
frequencies for the Lewis and P antigens in the Australian Caucasian population (CSL-Biosciences,
1994).
Based on the combined genetic and blood type analysis, the probability that I-1 is the mother of II-3
is 99.995% (Table S3).
MacLean et al., Human Mutation
HUMAN MUTATION Supplementary Material Online
Page S 3
Supplementary Table S1. Polymorphic X chromosome alleles in the affected aunt (II-3) and
her putative mother
Locus
Allele in XY aunt (II-3) Allele in putative mother (I-1)
AR CAG repeat
23
20, 23
DXS441
183 bp
183 bp (homozygous)
DXS453
170 bp
170 bp (homozygous)
ALAS2
161 bp
161 bp (homozygous)
MacLean et al., Human Mutation
HUMAN MUTATION Supplementary Material Online
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Supplementary Table S2. Blood typing in the affected aunt (II-3) and her putative parents
System
Phenotype
XY aunt (II-3)
Putative mother (I-1) Putative father
ABO/Rh
A Rh(D) Pos
A Rh(D) Pos
O Rh(D) Pos
Rh
CDe/cde
CDe/cde
CDe/cde
Kell
K-
K-
K-
Duffy
Fy (a+b-)
Fy (a+b+)
Fy (a+b-)
Kidd
Jk (a+b+)
Jk (a-b+)
Jk (a+b+)
Lewis
Le (a-b-)
Le (a-b-)
Le (a-b-)
P
P1 negative
P1 positive
P1 positive
MNSs
MMSs
MMSs
MNSs
MacLean et al., Human Mutation
HUMAN MUTATION Supplementary Material Online
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Supplementary Table S3. Probability that the grandmother (I-1) is the mother of the affected
aunt (II-3)
Marker
Probability of I-1 having child Probability of random mother having
with II-3’s allele
child with II-3’s allelea
AR CAG repeat
0.5
0.114
DXS441
1.0
0.40
DXS453
1.0
0.21
ALAS2
1.0
0.18
ABO
0.5763
0.3742
Rh
0.5
0.3518
Kell
1.0
0.9114
Duffy
0.5
0.1863
Kidd
0.5
0.4987
Lewis
1.0
0.0630
P
0.1117
0.2520
MNSs
0.25
0.1647
Combined
1.00610-3 (X)
5.0210-8 (Y)
Probability
Relative chance of
= X/(X+Y)  100
Parentage
= 99.995%
a
calculated from allele frequencies of different loci, as described
MacLean et al., Human Mutation
HUMAN MUTATION Supplementary Material Online
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Supplementary References
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polymorphic marker within intron 7 of the ALAS2 gene and suggestion of at least two loci
for X-linked sideroblastic anemia. Hum Mol Genet 1(8):639-41.
CSL-Biosciences. 1994. Blood Group Reference Guide. Parkville, Victoria, Australia: CSL
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Lee CL. 1980. Numerical expression of paternity test results using predetermined indexes. Am J
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Mitchell RJ. 1983. Red cell antigen, plasma protein and red cell enzyme polymorphisms in the
island of Tasmania. Hum Hered 33(2):119-24.
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polymorphisms at the DXS453, DXS454 and DXS458 loci. Nucleic Acids Res 18(13):4037.