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

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 s...

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Detalles Bibliográficos
Autores principales: Raz, Ofir, Tao, Liming, Biezuner, Tamir, Marx, Tzipy, Neumeier, Yaara, Tumanyan, Narek, Shapiro, Ehud
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9181316/
https://www.ncbi.nlm.nih.gov/pubmed/35682839
http://dx.doi.org/10.3390/ijms23116161
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author Raz, Ofir
Tao, Liming
Biezuner, Tamir
Marx, Tzipy
Neumeier, Yaara
Tumanyan, Narek
Shapiro, Ehud
author_facet Raz, Ofir
Tao, Liming
Biezuner, Tamir
Marx, Tzipy
Neumeier, Yaara
Tumanyan, Narek
Shapiro, Ehud
author_sort Raz, Ofir
collection PubMed
description 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.
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spelling pubmed-91813162022-06-10 Whole-Genome Amplification—Surveying Yield, Reproducibility, and Heterozygous Balance, Reported by STR-Targeting MIPs Raz, Ofir Tao, Liming Biezuner, Tamir Marx, Tzipy Neumeier, Yaara Tumanyan, Narek Shapiro, Ehud Int J Mol Sci Article 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. MDPI 2022-05-31 /pmc/articles/PMC9181316/ /pubmed/35682839 http://dx.doi.org/10.3390/ijms23116161 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Raz, Ofir
Tao, Liming
Biezuner, Tamir
Marx, Tzipy
Neumeier, Yaara
Tumanyan, Narek
Shapiro, Ehud
Whole-Genome Amplification—Surveying Yield, Reproducibility, and Heterozygous Balance, Reported by STR-Targeting MIPs
title Whole-Genome Amplification—Surveying Yield, Reproducibility, and Heterozygous Balance, Reported by STR-Targeting MIPs
title_full Whole-Genome Amplification—Surveying Yield, Reproducibility, and Heterozygous Balance, Reported by STR-Targeting MIPs
title_fullStr Whole-Genome Amplification—Surveying Yield, Reproducibility, and Heterozygous Balance, Reported by STR-Targeting MIPs
title_full_unstemmed Whole-Genome Amplification—Surveying Yield, Reproducibility, and Heterozygous Balance, Reported by STR-Targeting MIPs
title_short Whole-Genome Amplification—Surveying Yield, Reproducibility, and Heterozygous Balance, Reported by STR-Targeting MIPs
title_sort whole-genome amplification—surveying yield, reproducibility, and heterozygous balance, reported by str-targeting mips
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9181316/
https://www.ncbi.nlm.nih.gov/pubmed/35682839
http://dx.doi.org/10.3390/ijms23116161
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