Cechova, M*
Dotaz
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Ever since the introduction of high-throughput sequencing following the human genome project, assembling short reads into a reference of sufficient quality posed a significant problem as a large portion of the human genome-estimated 50-69%-is repetitive. As a result, a sizable proportion of sequencing reads is multi-mapping, i.e., without a unique placement in the genome. The two key parameters for whether or not a read is multi-mapping are the read length and genome complexity. Long reads are now able to span difficult, heterochromatic regions, including full centromeres, and characterize chromosomes from "telomere to telomere". Moreover, identical reads or repeat arrays can be differentiated based on their epigenetic marks, such as methylation patterns, aiding in the assembly process. This is despite the fact that long reads still contain a modest percentage of sequencing errors, disorienting the aligners and assemblers both in accuracy and speed. Here, I review the proposed and implemented solutions to the repeat resolution and the multi-mapping read problem, as well as the downstream consequences of reference choice, repeat masking, and proper representation of sex chromosomes. I also consider the forthcoming challenges and solutions with regards to long reads, where we expect the shift from the problem of repeat localization within a single individual to the problem of repeat positioning within pangenomes.
- MeSH
- centromera chemie MeSH
- délka genomu MeSH
- genom lidský * MeSH
- lidé MeSH
- mapování chromozomů metody MeSH
- metylace DNA MeSH
- mikrosatelitní repetice * MeSH
- pohlavní chromozomy chemie MeSH
- telomery chemie MeSH
- výpočetní biologie metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
- MeSH
- biologie výchova organizace a řízení MeSH
- informatika MeSH
- komunikace MeSH
- kooperační chování * MeSH
- lidé MeSH
- výpočetní biologie * výchova metody organizace a řízení MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
- úvodníky MeSH
Satellite DNAs are present on every chromosome in the cell and are typically enriched in repetitive, heterochromatic parts of the human genome. Sex chromosomes represent a unique genomic and epigenetic context. In this review, we first report what is known about satellite DNA biology on human X and Y chromosomes, including repeat content and organization, as well as satellite variation in typical euploid individuals. Then, we review sex chromosome aneuploidies that are among the most common types of aneuploidies in the general population, and are better tolerated than autosomal aneuploidies. This is demonstrated also by the fact that aging is associated with the loss of the X, and especially the Y chromosome. In addition, supernumerary sex chromosomes enable us to study general processes in a cell, such as analyzing heterochromatin dosage (i.e. additional Barr bodies and long heterochromatin arrays on Yq) and their downstream consequences. Finally, genomic and epigenetic organization and regulation of satellite DNA could influence chromosome stability and lead to aneuploidy. In this review, we argue that the complete annotation of satellite DNA on sex chromosomes in human, and especially in centromeric regions, will aid in explaining the prevalence and the consequences of sex chromosome aneuploidies.
- MeSH
- aneuploidie MeSH
- centromera genetika MeSH
- heterochromatin * genetika MeSH
- lidé MeSH
- lidské chromozomy MeSH
- pohlavní chromozomy genetika MeSH
- satelitní DNA * genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
Cell chimerism determination is important for the monitoring of engraftment dynamics and for relapse prediction. Our cohort of 474 patients was divided into two groups according to the determination methods used over time, and by their chimerism status. A significant difference in survival was observed between mixed vs complete chimerism (P < 0.0001 vs P < 0.0002) in both patient groups, and also vs microchimerism (P = 0.0201) in the second group. Detection of mixed chimerism is thus a high-risk factor, and microchimerism is potentially a risk factor in the post-transplantation course. Methods with a high sensitivity for monitoring cell chimerism significantly improve the assessment of patients post-transplant, and they enable the identification of patients with high relapse risk. Supported by MH CZ-DRO (00023736, UHKT).
- MeSH
- analýza přežití MeSH
- dospělí MeSH
- genetické testování metody MeSH
- hematologické nádory genetika imunologie mortalita terapie MeSH
- homologní transplantace MeSH
- imunologická tolerance * MeSH
- kohortové studie MeSH
- kvantitativní polymerázová řetězová reakce MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- myeloablativní agonisté terapeutické užití MeSH
- nemoc štěpu proti hostiteli diagnóza genetika imunologie mortalita MeSH
- přežívání štěpu * MeSH
- příprava pacienta k transplantaci metody MeSH
- recidiva MeSH
- rejekce štěpu diagnóza genetika imunologie mortalita MeSH
- rizikové faktory MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- tandemové repetitivní sekvence MeSH
- testování histokompatibility MeSH
- transplantace hematopoetických kmenových buněk * MeSH
- transplantační chiméra genetika imunologie MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- MeSH
- domovy pro seniory MeSH
- odměny a ceny MeSH
- senioři MeSH
- sociální péče MeSH
- Check Tag
- senioři MeSH
