Assessing relatedness between groups of individuals

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Assessing relatedness between groups of
individuals

• David Balding
• Imperial College London
• RSS GAS meeting Manchester 11 Jan 06

The new work reported here was done by PhD
student Lianne Mayor (currently writing up)
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Problem

• Given a group of individuals
• some of known relatedness,
• some with DNA profiles available,
• We wish to
• confirm (or otherwise) specific hypothesized
  relationships
• identify unsuspected relationships

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Example missing fathers of DI offspring (more
later)

• MS EN BM WM
• BS JS DG BE WE
• MA JW EV PM
• MM SF SH MF
• Genotypes available at 9 to 17 STR loci
• Accepted relationships shown identified
  parents are mothers sib-pairs could be wrong?

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Genotype data STR ( microsatellite) loci

• Alleles determined by number of copies of a 2 to
  5 nucleotide motif repeats, e.g.
• ACTGACTGACTGACTGACTG
• 5 copies of ACTG repeat.
• Can be variation within repeats, but only length
  variation is recorded, not sequence.
• Widely used in forensic work, for relatedness and
  identification 10 to 25 loci used (2 alleles per
  locus).
• e.g. paternity case genotypes of mother, child
  and putative father usually available.
• but either or both parent could be missing
• high mutation rate may be functionally important

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Use of LR for relatedness is now well
established - but infeasible for many
individuals/hypotheses - start by considering
pairs

• Hypotheses (not exhaustive)
• HS two individuals are (paternal)
  half-siblings UN unrelated.
• Under HS there are two equally likely cases,
• paternal allele shared ibd
• paternal alleles not ibd.
• LR for a single locus

(1)
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Example pairwise LR

• E.g. Person 1 AB, Person 2 BC share allele B.
• E.g. P1 AB, P2 CD no shared alleles.
• P(genotypesHS,ibd)0.
• From (1) LR ½.
• NB 1 no exclusions
• NB 2 half-sib relationship is effectively the
  same as uncle/nephew and grandparent/grandchild

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How much does it help if mothers genotypes are
available?

• Mothers C A D B
• Offspring A A A B

Maternal alleles
Paternal alleles
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Pairwise LR with mothers genotypes

• Mothers genotypes, where available, help to
  identify the paternal allele in the offspring.
• After some manipulation we can obtain

• Assumes mothers genotypes independent not
  strictly true.
• Surprisingly (?) still only 4 distinct forms for
  LR

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Mayor Balding to appear For Sci Int 06.

• Reliable inferences in the absence of maternal
  genotypes requires many more than the 10 25
  loci routinely used.
• Inclusion of maternal genotypes more than halves
  the number of loci required (22 with mothers,
  50 without).
• More power to discriminate half-sibs than
  profiling the same number of additional loci in
  the offspring alone.

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Simulation study (using Af Amer data)
Missclassification counts out of 10K
HS
UN
HS
without mothers
UN
with mothers
Number of loci
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Population structure ?? query profiles are
Syrian Arab? reference freqs Moroccan Arab
HS UN
Misclassification counts from 10K
HS
UN
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DI Offspring

• Problem
• 13 individuals, 10 are the offspring of donor
  insemination, 3 are putative natural offspring of
  known donors.
• DI offspring conceived at the clinic of a pioneer
  of human artificial insemination. No records
  available.
• Question who, if any of the individuals, is
  related via fathers to whom?

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Data

• MS EN BM WM
• BS JS DG BE WE
• MA JW EV NI PM
• MM SF SH MF
• Genotypes consist of 9 to 17 STR loci.

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• JW, EV and SF were all thought to be the
  offspring of the same, known donor
• we ignored this information
• Canadian company typed JS, BS and DG at 3 RFLP
  loci and 13 STRs confirmed full-sib relationship
  of JS and BS half-sibs of DG
• we reanalysed the STR data additional STRs
• Further testing in California
• JW not related to JS and BS
• Typing in London
• NI and SF have common father

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Pairwise LRs reference alleles from UK
Donorlink/LGC
Includes maternal data where available
BS
JS
SF
DG
LR gt 100 LR gt 50
MM
BE
MF
SH
NI
WE
JW
EV
PM
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Trio LRs

• With pairs can never make an exclusion.
• with trios can exclude a common father for all
  three individuals (no mutation).
• LR for trios compare one father vs three fathers
• very clearly not exhaustive hypotheses.
• Here, ibd gt all the individuals share a paternal
  allele.
• Also need corresponding LR when mothers available.

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Trio LRs
With maternal information where present
MM
SF
JS
LR gt 10 000 LR gt 1000
MF
BS
BE
SH
DG
JW
EV
WE
PM
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Trio LRs
With maternal information where present
MM
SF
JS
LR gt 10 000
MF
BS
BE
SH
DG
JW
EV
WE
PM
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Familias

• Results of pairwise and trio LR allow us to
  reduce the number of possible pedigrees to 26.
• Familias software that determines the most
  probable pedigree given genotype information
  (Egeland et al, 2000).

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Familias Pedigrees
Probability 0.0003, mutation rate 0.001
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Familias Pedigrees
Probability 0.1710, mutation rate 0.001
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Familias Pedigrees
Probability 0.8287, mutation rate 0.001
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Familias Pedigrees

• Are the donors of JS and BS related?
• Looked ONLY using JS, BS and MS genotypes.
• Donors are father/son
• Donors are brothers
• Donors dont share a common father

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Familias Pedigrees

• Are the donors of JS and BS related?
• Looked ONLY using JS, BS and MS genotypes.
• Donors are father/son 0.56
• Donors are brothers 0.12
• Donors dont share a common father 0.08

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Linkage

• Increase in number of loci used means some loci
  are going to be linked tend to be co-inherited.
• We have also investigated the effect of linkage
  on the classification of half-sibs.
• Can locate 60 loci genome-wide with no spacing lt
  50 cM. At this level effect of linkage is modest
  and we have neglected it

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References

• For the reference allele frequencies
• Butler et al, J. For. Sci. 2003
• Levedakou et al, J. For. Sci. 2001
• LR Methods
• Ayres, For. Sci. Int. 2000
• Familias
• Egeland et al, For. Sci. Int. 2000 see also
  website
• www.math.chalmers.se/mostad/familias/

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Acknowledgments

• LGC Teddington (formerly Lab of Gov Chemist, now
  major bioscience company active in DNA profiling)
• P. Debenham
• J. Walker
• the individuals concerned in the DI offspring
  problem
• Lianne Mayor for doing the work!