Whole-Genome Amplification-Surveying Yield, Reproducibility, and Heterozygous Balance, Reported by STR-Targeting MIPs

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2022 Jun 10

PMID 35682839

Authors

Ofir Raz

Liming Tao

Tamir Biezuner

Tzipy Marx

Yaara Neumeier

Narek Tumanyan

Ehud Shapiro

Affiliations

Soon will be listed here.

Abstract

Whole-genome amplification is a crucial first step in nearly all single-cell genomic analyses, with the following steps focused on its products. Bias and variance caused by the whole-genome amplification process add numerous challenges to the world of single-cell genomics. Short tandem repeats are sensitive genomic markers used widely in population genetics, forensics, and retrospective lineage tracing. A previous evaluation of common whole-genome amplification targeting ~1000 non-autosomal short tandem repeat loci is extended here to ~12,000 loci across the entire genome via duplex molecular inversion probes. Other than its improved scale and reduced noise, this system detects an abundance of heterogeneous short tandem repeat loci, allowing the allelic balance to be reported. We show here that while the best overall yield is obtained using RepliG-SC, the maximum uniformity between alleles and reproducibility across cells are maximized by Ampli1, rendering it the best candidate for the comparative heterozygous analysis of single-cell genomes.

Citing Articles

Tracking Somatic Mutations for Lineage Reconstruction.

Neumeier Y, Raz O, Tao L, Marx Z, Shapiro E Methods Mol Biol. 2025; 2886:23-45.

PMID: 39745634 DOI: 10.1007/978-1-0716-4310-5_2.

Protocol for genome-wide analysis of somatic variants at single-cell resolution using primary template-directed DNA amplification.

Derks L, van Leeuwen A, Steemers A, Trabut L, van Roosmalen M, Poort V STAR Protoc. 2024; 6(1):103499.

PMID: 39709610 PMC: 11726792. DOI: 10.1016/j.xpro.2024.103499.

Special Issue on Whole Genome Amplification.

Jager R Int J Mol Sci. 2023; 24(11).

PMID: 37298576 PMC: 10254008. DOI: 10.3390/ijms24119626.

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