Quantifying Hematopoietic Stem Cell Clonal Diversity by Selecting Informative Amplicon Barcodes
| Autor: | Emily M Teets, Jami Shaffer, Bradley W. Blaser, James S. Blachly, Charles Thomas Gregory |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
Genotyping Techniques Sequence analysis lcsh:Medicine Computational biology Biology Barcode DNA barcoding Somatic evolution in cancer Article law.invention Clonal Evolution 03 medical and health sciences 0302 clinical medicine law Animals lcsh:Science Zebrafish Phylogeny Selection (genetic algorithm) Multidisciplinary Haematopoietic stem cells lcsh:R Sequence Analysis DNA Amplicon Hematopoietic Stem Cells Hematopoiesis Haematopoiesis 030104 developmental biology 030220 oncology & carcinogenesis Mutation Mutation (genetic algorithm) Bootstrapping (biology) lcsh:Q Algorithms |
| Zdroj: | Scientific Reports, Vol 10, Iss 1, Pp 1-13 (2020) Scientific Reports |
| ISSN: | 2045-2322 |
| Popis: | Hematopoietic stem cells (HSCs) are functionally and genetically diverse and this diversity decreases with age and disease. Numerous systems have been developed to quantify HSC diversity by genetic barcoding, but no framework has been established to empirically validate barcode sequences. Here we have developed an analytical framework, Selection of informative Amplicon Barcodes from Experimental Replicates (SABER), that identifies barcodes that are unique among a large set of experimental replicates. Amplicon barcodes were sequenced from the blood of 56 adult zebrafish divided into training and validation sets. Informative barcodes were identified and samples with a high fraction of informative barcodes were chosen by bootstrapping. There were 4.2 ± 1.8 barcoded HSC clones per sample in the training set and 3.5 ± 2.1 in the validation set (p = 0.3). SABER reproducibly quantifies functional HSCs and can accommodate a wide range of experimental group sizes. Future large-scale studies aiming to understand the mechanisms of HSC clonal evolution will benefit from this new approach to identifying informative amplicon barcodes. |
| Databáze: | OpenAIRE |
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