Genotip İmpütasyonunun Antik Anadolu İnsan Genomlarında Değerlendirilmesi
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Date
2024-06-14Author
Çubukcu, Hande
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Genotype
imputation presents a solution to the high amount of missing information in low
coverage ancient DNA samples. In this thesis, by using the phasing and imputation
tool GLIMPSE, the accuracy of genotype imputation and the amount of missing
variants on autosomal biallelic SNPs are evaluated using different genotype posterior
probability filters at four different coverages using ten high coverage and over a
hundred low coverage genomes from Anatolia and West Eurasia. The effect of using
imputed data in frequently used population genetics analyses is investigated. The
accuracy of imputation measured as genotype concordance with high coverage data
reaches 70% to 90% in common variants at 0.1x genome coverage while losing less
than 5% to 15% of all variants using filters between 80% and 99%. Missing amount
in common variants using the same data reaches %20 and %50 in commonly used
Human Origins dataset positions. Pseudohaploid data have more affinity towards the
reference genome compared to the imputed data, pointing to mitigation of reference
bias by imputation. On the other hand, imputed data show tendency towards the
reference panel populations as the coverage decreases. Allele frequency calculations
using imputation and alignment data show up to 15% difference in low coverage
Anatolian Neolithic samples. Results show that it is possible to get reliable results
using imputed data for common variants for low coverage ancient genome samples
from the region of interest
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