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A general model for...
A general model for likelihood computations of genetic marker data accounting for linkage, linkage disequilibrium, and mutations
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- Kling, D. (författare)
- Norges miljø- og biovitenskapelige universitet (NMBU),Norwegian University of Life Sciences (NMBU),Norwegian Institute of Public Health,Norwegian Institute Public Heatlh, Norway; Norwegian University of Life Science, Norway
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- Tillmar, Andreas (författare)
- Linköpings universitet,Avdelningen för mikrobiologi och molekylär medicin,Medicinska fakulteten,National Board Forens Med, Department Forens Genet and Forens Toxicol, Linkoping, Sweden
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- Egeland, T. (författare)
- Norwegian Institute of Public Health,Norges miljø- og biovitenskapelige universitet (NMBU),Norwegian University of Life Sciences (NMBU),Norwegian University of Life Science, Norway; Norwegian Institute Public Heatlh, Norway
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- Mostad, Petter, 1964 (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper, matematisk statistik,Department of Mathematical Sciences, Mathematical Statistics,University of Gothenburg,Chalmers tekniska högskola,Chalmers University of Technology,Norwegian University of Life Science, Norway; University of Gothenburg, Sweden
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(creator_code:org_t)
- 2014-11-26
- 2015
- Engelska.
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Ingår i: International Journal of Legal Medicine. - : Springer Science and Business Media LLC. - 0937-9827 .- 1437-1596. ; 129:5, s. 943-954
- Relaterad länk:
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http://dx.doi.org/10...
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https://gup.ub.gu.se...
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https://doi.org/10.1...
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https://research.cha...
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https://urn.kb.se/re...
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Abstract
Ämnesord
Stäng
- Several applications necessitate an unbiased determination of relatedness, be it in linkage or association studies or in a forensic setting. An appropriate model to compute the joint probability of some genetic data for a set of persons given some hypothesis about the pedigree structure is then required. The increasing number of markers available through high-density SNP microarray typing and NGS technologies intensifies the demand, where using a large number of markers may lead to biased results due to strong dependencies between closely located loci, both within pedigrees (linkage) and in the population (allelic association or linkage disequilibrium (LD)). We present a new general model, based on a Markov chain for inheritance patterns and another Markov chain for founder allele patterns, the latter allowing us to account for LD. We also demonstrate a specific implementation for X chromosomal markers that allows for computation of likelihoods based on hypotheses of alleged relationships and genetic marker data. The algorithm can simultaneously account for linkage, LD, and mutations. We demonstrate its feasibility using simulated examples. The algorithm is implemented in the software FamLinkX, providing a user-friendly GUI for Windows systems (FamLinkX, as well as further usage instructions, is freely available at www.famlink.se). Our software provides the necessary means to solve cases where no previous implementation exists. In addition, the software has the possibility to perform simulations in order to further study the impact of linkage and LD on computed likelihoods for an arbitrary set of markers.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Annan medicin och hälsovetenskap -- Rättsmedicin (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Other Medical and Health Sciences -- Forensic Science (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine (hsv//eng)
Nyckelord
- FamLinkX
- Lander-Green
- Likelihood computations
- X chromosome
- Markov-chain
- Linkage
- Mutation
- Likelihood computations
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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