Efficient acquisition of tens of thousands of short tandem repeats in single-cell whole-genome-amplified DNA
| Autor: | Ehud Shapiro, Zipora Marx, Ofir Raz, Liming Tao |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Science (General)
High-throughput screening Cell Single Cell Genomics Computational biology Biology Genome General Biochemistry Genetics and Molecular Biology chemistry.chemical_compound Q1-390 Cell Line Tumor Protocol medicine Humans Sequencing Genotyping Molecular Biology Whole Genome Sequencing General Immunology and Microbiology Genome Human General Neuroscience High-Throughput Nucleotide Sequencing High Throughput Screening humanities medicine.anatomical_structure chemistry Molecular/Chemical Probes Microsatellite Human genome DNA HeLa Cells Microsatellite Repeats |
| Zdroj: | STAR Protocols, Vol 2, Iss 4, Pp 100828-(2021) STAR Protocols |
| ISSN: | 2666-1667 |
| Popis: | Summary Short tandem repeats (STRs) are highly abundant in the human genome, but existing approaches for accurate genotyping of STRs are limited. Here, we describe a protocol for duplex molecular inversion probes for high-throughput and cost-effective STR enrichment. We have successfully tested panels targeting as many as 50K STRs in several thousands of genomic samples (e.g., HeLa cells, Du145 cells, leukemia cells, melanoma cells). However, because the protocol is plate based, the sample size is limited to a few thousand. For complete details on the use and execution of this protocol, please refer to Tao et al. (2021). Graphical abstract Highlights • This protocol enable us to enrich tens of thousands of STR from single-cell WGA • The protocol can easily deployed in any labs with generic equipment • The highly mutable STR panel is generic across human samples • The panels are highly customizable to include SNV targets like cancer hotspots and flexible from dozens of targets to over 50K targets; probes for different panels can be combined in one reaction Short tandem repeats (STRs) are highly abundant in the human genome, but existing approaches for accurate genotyping of STRs are limited. Here, we describe a protocol for duplex molecular inversion probes for high-throughput and cost-effective STR enrichment. We have successfully tested panels targeting as many as 50K STRs in several thousands of genomic samples (e.g., HeLa cells, Du145 cells, leukemia cells, melanoma cells). However, because the protocol is plate based, the sample size is limited to a few thousand. |
| Databáze: | OpenAIRE |
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