Cargando…
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...
Autores principales: | , , , , , , |
---|---|
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 |
_version_ | 1784723740349693952 |
---|---|
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. |
format | Online Article Text |
id | pubmed-9181316 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT razofir wholegenomeamplificationsurveyingyieldreproducibilityandheterozygousbalancereportedbystrtargetingmips AT taoliming wholegenomeamplificationsurveyingyieldreproducibilityandheterozygousbalancereportedbystrtargetingmips AT biezunertamir wholegenomeamplificationsurveyingyieldreproducibilityandheterozygousbalancereportedbystrtargetingmips AT marxtzipy wholegenomeamplificationsurveyingyieldreproducibilityandheterozygousbalancereportedbystrtargetingmips AT neumeieryaara wholegenomeamplificationsurveyingyieldreproducibilityandheterozygousbalancereportedbystrtargetingmips AT tumanyannarek wholegenomeamplificationsurveyingyieldreproducibilityandheterozygousbalancereportedbystrtargetingmips AT shapiroehud wholegenomeamplificationsurveyingyieldreproducibilityandheterozygousbalancereportedbystrtargetingmips |