| 1. |
- Ausmees, Kristiina
(författare)
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Methodology and Infrastructure for Statistical Computing in Genomics : Applications for Ancient DNA
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis concerns the development and evaluation of computational methods for analysis of genetic data. A particular focus is on ancient DNA recovered from archaeological finds, the analysis of which has contributed to novel insights into human evolutionary and demographic history, while also introducing new challenges and the demand for specialized methods.A main topic is that of imputation, or the inference of missing genotypes based on observed sequence data. We present results from a systematic evaluation of a common imputation pipeline on empirical ancient samples, and show that imputed data can constitute a realistic option for population-genetic analyses. We also develop a tool for genotype imputation that is based on the full probabilistic Li and Stephens model for haplotype frequencies and show that it can yield improved accuracy on particularly challenging data. Another central subject in genomics and population genetics is that of data characterization methods that allow for visualization and exploratory analysis of complex information. We discuss challenges associated with performing dimensionality reduction of genetic data, demonstrating how the use of principal component analysis is sensitive to incomplete information and performing an evaluation of methods to handle unobserved genotypes. We also discuss the use of deep learning models as an alternative to traditional methods of data characterization in genomics and propose a framework based on convolutional autoencoders that we exemplify on the applications of dimensionality reduction and genetic clustering.In genomics, as in other fields of research, increasing sizes of data sets are placing larger demands on efficient data management and compute infrastructures. The final part of this thesis addresses the use of cloud resources for facilitating data analysis in scientific applications. We present two different cloud-based solutions, and exemplify them on applications from genomics.
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| 2. |
- van Engelen, Marie Paule E., et al.
(författare)
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The bvFTD phenocopy syndrome : a case study supported by repeated MRI, [18F]FDG-PET and pathological assessment
- 2021
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Ingår i: Neurocase. - : Informa UK Limited. - 1355-4794 .- 1465-3656. ; 27:2, s. 181-189
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Tidskriftsartikel (refereegranskat)abstract
- A clinical syndrome with neuropsychiatric features of bvFTD without neuroimaging abnormalities and a lack of decline is a phenocopy of bvFTD (phFTD). Growing evidence suggests that psychological, psychiatric and environmental factors underlie phFTD. We describe a patient diagnosed with bvFTD prior to the revision of the diagnostic guidelines of FTD. Repeated neuroimaging was normal and there was no FTD pathology at autopsy, rejecting the diagnosis. We hypothesize on etiological factors that on hindsight might have played a role. This case report contributes to the understanding of phFTD and adds to the sparse literature of the postmortem assessment of phFTD.
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| 3. |
- Villa-Islas, Viridiana, et al.
(författare)
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Demographic history and genetic structure in pre-Hispanic Central Mexico
- 2023
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 380:6645
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Tidskriftsartikel (refereegranskat)abstract
- Aridoamerica and Mesoamerica are two distinct cultural areas in northern and central Mexico, respectively, that hosted numerous pre-Hispanic civilizations between 2500 BCE and 1521 CE. The division between these regions shifted southward because of severe droughts ~1100 years ago, which allegedly drove a population replacement in central Mexico by Aridoamerican peoples. In this study, we present shotgun genome-wide data from 12 individuals and 27 mitochondrial genomes from eight pre-Hispanic archaeological sites across Mexico, including two at the shifting border of Aridoamerica and Mesoamerica. We find population continuity that spans the climate change episode and a broad preservation of the genetic structure across present-day Mexico for the past 2300 years. Lastly, we identify a contribution to pre-Hispanic populations of northern and central Mexico from two ancient unsampled “ghost” populations.
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