Efficient acquisition of tens of thousands of short tandem repeats in single-cell whole-genome-amplified DNA

STAR Protoc. 2021 Sep 16;2(4):100828. doi: 10.1016/j.xpro.2021.100828. eCollection 2021 Dec 17.

Abstract

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).

Keywords: Genomics; High Throughput Screening; Molecular Biology; Molecular/Chemical Probes; Sequencing; Single Cell.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line, Tumor
  • Genome, Human / genetics*
  • HeLa Cells
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Microsatellite Repeats / genetics*
  • Whole Genome Sequencing / methods*