PUBLICATION
Quantifying Hematopoietic Stem Cell Clonal Diversity by Selecting Informative Amplicon Barcodes
- Authors
- Teets, E.M., Gregory, C., Shaffer, J., Blachly, J.S., Blaser, B.W.
- ID
- ZDB-PUB-200209-3
- Date
- 2020
- Source
- Scientific Reports 10: 2153 (Journal)
- Registered Authors
- Keywords
- none
- MeSH Terms
-
- Algorithms
- Animals
- Clonal Evolution*
- Genotyping Techniques/methods*
- Genotyping Techniques/standards
- Hematopoiesis*
- Hematopoietic Stem Cells/cytology
- Hematopoietic Stem Cells/metabolism*
- Mutation*
- Sequence Analysis, DNA/methods
- Sequence Analysis, DNA/standards
- Zebrafish
- PubMed
- 32034234 Full text @ Sci. Rep.
Citation
Teets, E.M., Gregory, C., Shaffer, J., Blachly, J.S., Blaser, B.W. (2020) Quantifying Hematopoietic Stem Cell Clonal Diversity by Selecting Informative Amplicon Barcodes. Scientific Reports. 10:2153.
Abstract
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping