2012
DOI: 10.1002/gepi.21686
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Maximum Likelihood Pedigree Reconstruction Using Integer Linear Programming

Abstract: Large population biobanks of unrelated individuals have been highly successful in detecting common genetic variants affecting diseases of public health concern. However, they lack the statistical power to detect more modest gene-gene and gene-environment interaction effects or the effects of rare variants for which related individuals are ideally required. In reality, most large population studies will undoubtedly contain sets of undeclared relatives, or pedigrees. Although a crude measure of relatedness might… Show more

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Cited by 64 publications
(34 citation statements)
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“…name/) for a related problem of maximising likelihood ratios for forensic identification cases and is restricted in practice to small numbers (about 12) of individuals [18]. A dynamic programming approach can yield a maximum likelihood solution for pedigrees of up to 30 individuals [13] while recent work exploiting efficient integer linear programming optimisation algorithms to perform a complete search can deliver a guaranteed maximum likelihood pedigree for over a thousand individuals [15,46]. Both the above make simplifying assumptions about the genetic model and, crucially, require complete data, by which we mean that all pedigree members are present in the genotyped sample.…”
Section: Introductionmentioning
confidence: 99%
“…name/) for a related problem of maximising likelihood ratios for forensic identification cases and is restricted in practice to small numbers (about 12) of individuals [18]. A dynamic programming approach can yield a maximum likelihood solution for pedigrees of up to 30 individuals [13] while recent work exploiting efficient integer linear programming optimisation algorithms to perform a complete search can deliver a guaranteed maximum likelihood pedigree for over a thousand individuals [15,46]. Both the above make simplifying assumptions about the genetic model and, crucially, require complete data, by which we mean that all pedigree members are present in the genotyped sample.…”
Section: Introductionmentioning
confidence: 99%
“…For parent sets of size 0 or 1, corresponding values can be derived using the population allele frequencies (Cussens et al, 2013).…”
Section: Methodsmentioning
confidence: 99%
“…As shown previously (Cussens, 2010;Cussens et al, 2013), the first constraint ensuring that each individual can only have one parent set (of size 0, 1 or 2) is given by:…”
Section: Likelihood Optimisation Using Ilpmentioning
confidence: 99%
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