Dokument: Characterizing genetic variation across sequencing platforms: Applications to intracellular pathogens and immune receptor genotyping
| Titel: | Characterizing genetic variation across sequencing platforms: Applications to intracellular pathogens and immune receptor genotyping | |||||||
| Weiterer Titel: | Plattformübergreifende Charakterisierung genetischer Variation: Anwendungen auf intrazelluläre Pathogene und die Genotypisierung von Immunrezeptoren | |||||||
| URL für Lesezeichen: | https://docserv.uni-duesseldorf.de/servlets/DocumentServlet?id=74628 | |||||||
| URN (NBN): | urn:nbn:de:hbz:061-20261111-174222-3 | |||||||
| Kollektion: | Dissertationen | |||||||
| Sprache: | Englisch | |||||||
| Dokumententyp: | Wissenschaftliche Abschlussarbeiten » Dissertation | |||||||
| Medientyp: | Text | |||||||
| Autor: | Gohar, Yomna Saber Mohamed Ahmed [Autor] | |||||||
| Dateien: |
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| Beitragende: | Prof. Dr. Alexander Dilthey [Gutachter] Prof. Dr. Marschall, Tobias [Gutachter] | |||||||
| Stichwörter: | Bioinformatics, Computational biology, Genetics | |||||||
| Dokumententyp (erweitert): | Dissertation | |||||||
| Dewey Dezimal-Klassifikation: | 500 Naturwissenschaften und Mathematik » 570 Biowissenschaften; Biologie | |||||||
| Beschreibung: | Genetic variation is enriched in structurally complex regions of the genome—tandem repeats, segmental duplications and highly polymorphic gene families—which evolve rapidly through mutation, recombination and copy-number change. Reliable detection of this variation is constrained by sequencing technology, reference representation, and the model used to infer genotypes. This dissertation addresses these constraints in two systems where conventional short-read analysis fails: genomic divergence among long-term laboratory isolates of the parasite Toxoplasma gondii, and natural diversity at the human killer-cell immunoglobulin-like receptor (KIR) locus. First, we compared three independently maintained T. gondii ME49 isolates using Oxford Nanopore long-read sequencing. Long reads enabled an accurate de novo assembly with substantially improved contiguity (NG50 6.68 Mb versus 1.2 Mb for the current RefSeq) and near-complete chromosome resolution. Pangenome graph-based genotyping against this reference revealed clear intra-strain heterogeneity, including SNVs, indels and structural variants. The most striking was a 13 kb tandem expansion at the virulence-associated ROP8-ROP2A locus that doubled copy number from three to six in two isolates. These results show that laboratory-maintained strains diverge measurably over time and argue for routine genomic monitoring to protect experimental reproducibility. Second, we developed KIR*BLOOM, a copy-number-aware genotyping method for the KIR locus from short-read data, where current tools struggle with near-identical paralogs, extensive copy-number variation and incomplete reference representation.
KIR*BLOOM infers gene copy number from read depth, selects alleles from a curated database under that constraint while treating ambiguous mappings as informative, then refines coding sequences by variant calling. Developed on 52 samples from the 1000 Genomes Project with matched haplotype-resolved assemblies and evaluated on a further 45, it achieved 99.85% precision and 99.92% recall for copy-number inference, and 92.73% precision and 92.69% recall at five-digit allele resolution, outperforming T1K, GraphKIR and Geny. Together, both studies show that detecting complex variation depends critically on the choice of reference and algorithm. Long reads matched to an appropriate reference revealed structural differences between laboratory parasite strains, while a copy-number-aware model improved KIR typing from existing short reads—in both cases, the right combination of reference and method, rather than the sequencing data alone, enabled more reliable detection than standard pipelines. | |||||||
| Lizenz: |  Dieses Werk ist lizenziert unter einer Creative Commons Namensnennung 4.0 International Lizenz | |||||||
| Fachbereich / Einrichtung: | Mathematisch- Naturwissenschaftliche Fakultät » WE Informatik » Bioinformatik | |||||||
| Dokument erstellt am: | 11.11.2026 | |||||||
| Dateien geändert am: | 11.11.2026 | |||||||
| Promotionsantrag am: | 28.05.2026 | |||||||
| Datum der Promotion: | 07.09.2026 |
