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

AbstractPrimary template-directed amplification (PTA) is an improved amplification technique for single-cell DNA sequencing. We generated whole-genome analysis of 76 single neurons and developed SCAN2, a computational method to accurately identify both clonal and non-clonal somatic (i.e., limited to a single neuron) single nucleotide variants (SNVs) and small insertions and deletions (indels) using PTA data. Our analysis confirms an increase in non-clonal somatic mutation in single neurons with age, but revises estimates for the rate of this accumulation to be 15 SNVs per year. We also identify artifacts in other amplification methods. Most importantly, we show that somatic indels also increase by at least 2 indels per year per neuron and that indels may have a larger impact on gene function than somatic SNVs in human neurons.

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Accurate SNV detection in single cells by transposon-based whole-genome amplification of complementary strands

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2013106118 ◽

2021 ◽

Vol 118 (8) ◽

pp. e2013106118

Author(s):

Dong Xing ◽

Longzhi Tan ◽

Chi-Han Chang ◽

Heng Li ◽

X. Sunney Xie

Keyword(s):

Single Cell ◽

Whole Genome Amplification ◽

Single Cells ◽

Human Sperm ◽

Whole Genome ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Genome Amplification ◽

Human Blood Cells ◽

Human Neurons

Single-nucleotide variants (SNVs), pertinent to aging and disease, occur sporadically in the human genome, hence necessitating single-cell measurements. However, detection of single-cell SNVs suffers from false positives (FPs) due to intracellular single-stranded DNA damage and the process of whole-genome amplification (WGA). Here, we report a single-cell WGA method termed multiplexed end-tagging amplification of complementary strands (META-CS), which eliminates nearly all FPs by virtue of DNA complementarity, and achieved the highest accuracy thus far. We validated META-CS by sequencing kindred cells and human sperm, and applied it to other human tissues. Investigation of mature single human neurons revealed increasing SNVs with age and potentially unrepaired strand-specific oxidative guanine damage. We determined SNV frequencies along the genome in differentiated single human blood cells, and identified cell type-dependent mutational patterns for major types of lymphocytes.

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Whole genome analysis of four Bangladeshi individuals

10.1101/2020.05.21.109058 ◽

2020 ◽

Author(s):

Salim Khan ◽

Shahina Akter ◽

Barna Goswami ◽

Ahashan Habib ◽

Tanjina Akhtar Banu ◽

...

Keyword(s):

Pilot Study ◽

Cardiovascular Diseases ◽

Genome Sequencing ◽

Biological Pathways ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Single Nucleotide Variants ◽

Whole Genome Analysis ◽

Single Nucleotide ◽

Comprehensive Method

AbstractWhole-genome sequencing (WGS) is a comprehensive method for analysing entire genomes and this has been instrumental in characterizing the single nucleotide polymorphisms associated with different diseases including cancer, diabetes, cardiovascular diseases and many others. In this paper we undertake a pilot study for sequencing four Bangladeshi individuals and profiling their single nucleotide variants. Our findings shed possible light on specific biological pathways effected by such variants in this population.

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Defining the Yeast Resistome through in vitro Evolution and Whole Genome Sequencing

10.1101/2021.02.17.430112 ◽

2021 ◽

Author(s):

Sabine Ottilie ◽

Madeline R. Luth ◽

Erich Hellemann ◽

Gregory M. Goldgof ◽

Eddy Vigil ◽

...

Keyword(s):

Drug Resistance ◽

Transcription Factors ◽

Enrichment Analysis ◽

Neutral Evolution ◽

Whole Genome ◽

Genetic Determinants ◽

Single Nucleotide Variants ◽

Whole Genome Analysis ◽

Single Nucleotide

SummaryIn vitro evolution and whole genome analysis were used to comprehensively identify the genetic determinants of chemical resistance in the model microbe, Saccharomyces cerevisiae. Analysis of 355 curated, laboratory-evolved clones, resistant to 80 different compounds, demonstrates differences in the types of mutations that are identified in selected versus neutral evolution and reveals numerous new, compound-target interactions. Through enrichment analysis we further identify a set of 137 genes strongly associated with or conferring drug resistance as indicated by CRISPR-Cas9 engineering. The set of 25 most frequently mutated genes was enriched for transcription factors and for almost 25 percent of the compounds, resistance was mediated by one of 100 independently derived, gain-of-function, single nucleotide variants found in 170-amino-acid domains in two Zn2C6 transcription factors, YRR1 and YRM1 (p < 1x 10 −100). This remarkable enrichment for transcription factors as drug resistance genes may explain why it is challenging to develop effective antifungal killing agents and highlights their important role in evolution.

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Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment

BMC Genomics ◽

10.1186/1471-2164-14-856 ◽

2013 ◽

Vol 14 (1) ◽

pp. 856 ◽

Cited By ~ 15

Author(s):

Eva C Berglund ◽

Carl Lindqvist ◽

Shahina Hayat ◽

Elin Övernäs ◽

Niklas Henriksson ◽

...

Keyword(s):

Whole Genome ◽

Target Enrichment ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Accurate Detection

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Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants

10.1101/316976 ◽

2018 ◽

Cited By ~ 4

Author(s):

Maxime Garcia ◽

Szilveszter Juhos ◽

Malin Larsson ◽

Pall I. Olason ◽

Marcel Martin ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Open Source ◽

Genome Sequencing ◽

Development Project ◽

Whole Genome ◽

Sequencing Analysis ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Insertion And Deletion ◽

Sample Heterogeneity

AbstractSummaryWhole-genome sequencing (WGS) is a cornerstone of precision medicine, but portable and reproducible open-source workflows for WGS analyses of germline and somatic variants are lacking. We present Sarek, a modular, comprehensive, and easy-to-install workflow, combining a range of software for the identification and annotation of single-nucleotide variants (SNVs), insertion and deletion variants (indels), structural variants, tumor sample heterogeneity, and karyotyping from germline or paired tumor/normal samples. Sarek is implemented in a bioinformatics workflow language (Nextflow) with Docker and Singularity compatible containers, ensuring easy deployment and full reproducibility at any Linux based compute cluster or cloud computing environment. Sarek supports the human reference genomes GRCh37 and GRCh38, and can readily be used both as a core production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups.AvailabilitySource code and instructions for local installation are available at GitHub (https://github.com/SciLifeLab/Sarek) under the MIT open-source license, and we invite the research community to contribute additional functionality as a collaborative open-source development project.

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Integration of single nucleotide variants and whole-genome DNA methylation profiles for classification of rheumatoid arthritis cases from controls

Heredity ◽

10.1038/s41437-020-0301-4 ◽

2020 ◽

Vol 124 (5) ◽

pp. 658-674 ◽

Cited By ~ 1

Author(s):

Mahmoud Amiri Roudbar ◽

Mohammad Reza Mohammadabadi ◽

Ahmad Ayatollahi Mehrgardi ◽

Rostam Abdollahi-Arpanahi ◽

Mehdi Momen ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Dna Methylation ◽

Whole Genome ◽

Single Nucleotide Variants ◽

Single Nucleotide

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Genome aging: somatic mutation in the brain links age-related decline with disease and nominates pathogenic mechanisms

Human Molecular Genetics ◽

10.1093/hmg/ddz191 ◽

2019 ◽

Vol 28 (R2) ◽

pp. R197-R206 ◽

Cited By ~ 10

Author(s):

Michael A Lodato ◽

Christopher A Walsh

Keyword(s):

Human Brain ◽

Somatic Mutation ◽

Somatic Mutations ◽

Late Onset ◽

Whole Genome ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Age Related ◽

The Brain ◽

Over Time

AbstractAging is a mysterious process, not only controlled genetically but also subject to random damage that can accumulate over time. While DNA damage and subsequent mutation in somatic cells were first proposed as drivers of aging more than 60 years ago, whether and to what degree these processes shape the neuronal genome in the human brain could not be tested until recent technological breakthroughs related to single-cell whole-genome sequencing. Indeed, somatic single-nucleotide variants (SNVs) increase with age in the human brain, in a somewhat stochastic process that may nonetheless be controlled by underlying genetic programs. Evidence from the literature suggests that in addition to demonstrated increases in somatic SNVs during aging in normal brains, somatic mutation may also play a role in late-onset, sporadic neurodegenerative diseases, such as Alzheimer’s disease and Parkinson’s disease. In this review, we will discuss somatic mutation in the human brain, mechanisms by which somatic mutations occur and can be controlled, and how this process can impact human health.

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Homologous Recombination within Large Chromosomal Regions Facilitates Acquisition of β-Lactam and Vancomycin Resistance in Enterococcus faecium

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00488-16 ◽

2016 ◽

Vol 60 (10) ◽

pp. 5777-5786 ◽

Cited By ~ 20

Author(s):

Mónica García-Solache ◽

Francois Lebreton ◽

Robert E. McLaughlin ◽

James D. Whiteaker ◽

Michael S. Gilmore ◽

...

Keyword(s):

Enterococcus Faecium ◽

Genomic Dna ◽

Large Scale ◽

Vancomycin Resistance ◽

Whole Genome ◽

Whole Genome Analysis ◽

Single Nucleotide ◽

Content Type ◽

Donor Chromosome ◽

Vancomycin Resistant

ABSTRACTThe transfer of DNA betweenEnterococcus faeciumstrains has been characterized both by the movement of well-defined genetic elements and by the large-scale transfer of genomic DNA fragments. In this work, we report on the whole-genome analysis of transconjugants resulting from mating events between the vancomycin-resistantE. faeciumC68 strain and the vancomycin-susceptible D344RRF strain to discern the mechanism by which the transferred regions enter the recipient chromosome. Vancomycin-resistant transconjugants from five independent matings were analyzed by whole-genome sequencing. In all cases but one, the penicillin binding protein 5 (pbp5) gene and the Tn5382vancomycin resistance transposon were transferred together and replaced the correspondingpbp5region of D344RRF. In one instance, Tn5382inserted independently downstream of the D344RRFpbp5gene. Single nucleotide variant (SNV) analysis suggested that entry of donor DNA into the recipient chromosome occurred by recombination across regions of homology between donor and recipient chromosomes, rather than through insertion sequence-mediated transposition. The transfer of genomic DNA was also associated with the transfer of C68 plasmid pLRM23 and another putative plasmid. Our data are consistent with the initiation of transfer by cointegration of a transferable plasmid with the donor chromosome, with subsequent circularization of the plasmid-chromosome cointegrant in the donor prior to transfer. Entry into the recipient chromosome most commonly occurred across regions of homology between donor and recipient chromosomes.

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Association of SLC15A2 genomic variation with the response to sorafenib treatment: Whole-genome analysis in patients with hepatocellular carcinoma.

Journal of Clinical Oncology ◽

10.1200/jco.2015.33.3_suppl.308 ◽

2015 ◽

Vol 33 (3_suppl) ◽

pp. 308-308

Author(s):

Bo Hyun Kim ◽

Yeon-Su Lee ◽

Byung Chul Kim ◽

Aesun Shin ◽

Jin Sook Kim ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Functional Analysis ◽

Genome Analysis ◽

Whole Genome ◽

Whole Genome Analysis ◽

Single Nucleotide ◽

Sorafenib Treatment ◽

Genomic Variations ◽

Validation Tests

308 Background: Reliable biomarkers are required to predict patient response to sorafenib. We attempted to investigate genomic variations associated with responsiveness to sorafenib treatment in patients with unresectable hepatocellular carcinoma (HCC) and their functional relevance. Methods: We obtained blood samples from 4 strong and 3 poor responders to sorafenib treatment and subjected these samples to whole-genome analysis. Next, we performed validation tests for candidate single-nucleotide polymorphisms (SNPs) in the samples of 174 HCC patients who were treated with sorafenib, followed by in vitro functional analysis and in silico analyses of candidate SNPs. Results: On average, 90 gigabases/sample was generated at ~34X sequencing depth. In total, 1813 genomic variations were perfectly matched to sorafenib responses in the clinical data; 708 were located within regions for sorafenib-target genes or drug absorption, distribution, metabolism, and excretion (ADME)-related genes—36 within the coding regions and 6 identified as non-synonymous single-nucleotide variants from 4 ADME-related genes (ABCB1, FMO3, MUSK, and SLC15A2), which potentially cause functional alterations. Validation tests of 174 patients confirmed sequencing results and revealed that patients with the C/C genotype for rs2257212 in SCL15A2 displayed higher risk for cancer progression than did patients with C/T or T/T genotypes (HR: 2.18; 95% CI, 1.15–4.15; P = 0.018). In vitro functional analysis revealed that cells harboring C/C genotype for this SNP displayed lower response to sorafenib treatment than did cells harboring the T/T genotype. Structural prediction analysis revealed change in protein phosphorylation levels, potentially affecting sorafenib-associated enzymatic activity. Conclusions: SLC15A2 could be a robust biomarker of response to sorafenib treatment in HCC patients.

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