Related Experiment Video
Updated: Jun 24, 2026
Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing
Published on: February 10, 2023
Haplotyping via minimum recombinant paradigm
Jules Hernández-Sánchez1, Sara Knott
1Institute of Evolutionary Biology, University of Edinburgh, King's Buildings (Ashworth Laboratories), West Main Roads, EH9 3JT, Edinburgh, UK. jules.hernandez@ed.ac.uk
Background:
Haplotypes can increase the power of gene detection over genotypes and are essential to estimate linkage disequilibrium.
Methods:
Haplotyping was based on the minimum recombinant paradigm, whereby a phase is obtained only if it uniquely minimises the number of recombinants within a full sib family. Performance of this method was tested across three different data sets, consisting of genotypes and pedigree.
Results:
The percentage of phased alleles ranged from ~80% to ~95%, and the percentage of correct phases reached ~99% in all cases. A measure of uncertainty was obtained via simulations. A partial haplotyping algorithm consisting of four deterministic rules was almost as effective as a full one consisting of six deterministic rules, and took up to 5 times less time to compute.
Conclusion:
Haplotyping via the minimum recombinant paradigm is consistently reliable and computationally efficient. A single simulation is enough to produce a population-wide uncertainty estimate associated with a set of all reconstructed haplotypes.
