Ultraspecific somatic SNV and indel detection in single neurons using primary template-directed amplification

Lj, Luquette; Mb, Miller; Zhou, Zinan; Cl, Bohrson; Galor, Alon; Ma, Lodato; Gawad, Charles; West, Jay; Ca, Walsh; Park, Pj

doi:10.1101/2021.04.30.442032

Cited by 14 publications

(17 citation statements)

References 39 publications

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“…This is especially important for variant calling in normal cells where the introduction of thousands of false positive calls would significantly decrease the precision of somatic variant calling. To that end, SCAN2 was recently developed to better distinguish between false positive and somatic variant calls in PTA data (42). Finally, PTA could be combined with whole transcriptome amplification and protein abundance in the same cells to deconvolute the contributions of cell state and genotype to a given cellular phenotype (43).…”

Section: Discussionmentioning

confidence: 99%

Accurate genomic variant detection in single cells with primary template-directed amplification

Gonzalez-Pena

Natarajan

Xia

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Improvements in whole genome amplification (WGA) would enable new types of basic and applied biomedical research, including studies of intratissue genetic diversity that require more accurate single-cell genotyping. Here, we present primary template-directed amplification (PTA), an isothermal WGA method that reproducibly captures >95% of the genomes of single cells in a more uniform and accurate manner than existing approaches, resulting in significantly improved variant calling sensitivity and precision. To illustrate the types of studies that are enabled by PTA, we developed direct measurement of environmental mutagenicity (DMEM), a tool for mapping genome-wide interactions of mutagens with single living human cells at base-pair resolution. In addition, we utilized PTA for genome-wide off-target indel and structural variant detection in cells that had undergone CRISPR-mediated genome editing, establishing the feasibility for performing single-cell evaluations of biopsies from edited tissues. The improved precision and accuracy of variant detection with PTA overcomes the current limitations of accurate WGA, which is the major obstacle to studying genetic diversity and evolution at cellular resolution.

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Section: Discussionmentioning

confidence: 99%

Accurate genomic variant detection in single cells with primary template-directed amplification

Gonzalez-Pena

Natarajan

Xia

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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“…recently these methods had a relatively low accuracy in mutation detection, but new studies using novel technical and bioinformatic innovations claim to have significantly reduced their error rates (Abascal et al, 2021;Luquette et al, 2021;Xing et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

The Dynamics of Somatic Mutagenesis During Life in Humans

2021

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From conception to death, human cells accumulate somatic mutations in their genomes. These mutations can contribute to the development of cancer and non-malignant diseases and have also been associated with aging. Rapid technological developments in sequencing approaches in the last few years and their application to normal tissues have greatly advanced our knowledge about the accumulation of these mutations during healthy aging. Whole genome sequencing studies have revealed that there are significant differences in mutation burden and patterns across tissues, but also that the mutation rates within tissues are surprisingly constant during adult life. In contrast, recent lineage-tracing studies based on whole-genome sequencing have shown that the rate of mutation accumulation is strongly increased early in life before birth. These early mutations, which can be shared by many cells in the body, may have a large impact on development and the origin of somatic diseases. For example, cancer driver mutations can arise early in life, decades before the detection of the malignancy. Here, we review the recent insights in mutation accumulation and mutagenic processes in normal tissues. We compare mutagenesis early and later in life and discuss how mutation rates and patterns evolve during aging. Additionally, we outline the potential impact of these mutations on development, aging and disease.

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“…ID signatures can provide unique information on both endogenous and exogenous mutagenic processes, but they have been under-studied until recently, in part due to the relatively low mutational burden of IDs compared to SBSs [14, 16, 18, 58–60]. Our reanalysis results in a substantial revision and expansion of the COSMIC catalog of ID signatures.…”

Section: Resultsmentioning

confidence: 99%

“…6 (Continued on the following page.) [14,16,18,[58][59][60]. Our reanalysis results in a substantial revision and expansion of the COSMIC catalog of ID signatures.…”

Section: Deriving a Reference Of Signatures And Signature Assignments...mentioning

confidence: 87%

Accurate and sensitive mutational signature analysis with MuSiCal

Gulhan

Ben-Isvy

et al. 2022

Preprint

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Mutational signature analysis is a recent computational approach for interpreting somatic mutations in the genome. Its application to cancer data has enhanced our understanding of mutational forces driving tumorigenesis and demonstrated its potential to inform prognosis and treatment decisions. However, methodological challenges remain for discovering new signatures and assigning proper weights to existing signatures, thereby hindering broader clinical applications. We present MuSiCal (Mutational Signature Calculator), a rigorous analytical framework with novel algorithms that solves fundamental problems in the standard workflow. Our simulation studies demonstrate that MuSiCal outperforms state-of-the-art algorithms for both signature discovery and assignment. By reanalyzing over 2,700 cancer genomes, we provide an improved reference catalog of signatures and their assignments, discover nine indel signatures absent in the current catalog, resolve long-standing issues with the ambiguous ‘flat’ signatures, and give insights into signatures with unknown etiologies. We expect MuSiCal and the improved catalog to be a step towards establishing best practices for mutational signature analysis.

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Ultraspecific somatic SNV and indel detection in single neurons using primary template-directed amplification

Cited by 14 publications

References 39 publications

Accurate genomic variant detection in single cells with primary template-directed amplification

Accurate genomic variant detection in single cells with primary template-directed amplification

The Dynamics of Somatic Mutagenesis During Life in Humans

Accurate and sensitive mutational signature analysis with MuSiCal

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