Detecting ultralow-frequency mutations by Duplex Sequencing.

paper Cited Public

Authors: Kennedy, Scott R; Schmitt, Michael W; Fox, Edward J; Kohrn, Brendan F; Salk, Jesse J; Ahn, Eun Hyun; Prindle, Marc J; Kuong, Kawai J; Shen, Jiang-Cheng; Risques, Rosa-Ana; Loeb, Lawrence A
Year: 2014
Journal: Nature protocols
PMID: 25299156
DOI: 10.1038/nprot.2014.170
PMCID: PMC4271547

Figure 1

Overview of Duplex Sequencing. (a) Schematic of a Duplex Sequencing adapter, showing the random double-stranded tag and the invariant spacer sequence. (b) Ligation of the adapters to the sample DNA results in a unique 12-nt tag sequence on both ends of the molecule. PCR amplification of each strand of a DNA duplex results in two distinct, but related, PCR products. (c) Reads sharing unique α and β tag sequences are grouped together into tag families of form αβ or βα, and an SSCS is created for each tag family. Mutations are of three different types: sequencing mistakes (blue or purple dots); first-round PCR errors (brown dots); true mutations (green dots). Formation of the SSCS removes the first type of error, but not first-round PCR errors. Comparing SSCSs from the paired families with tags αβ and βα generates a DCS, which eliminates these first-round PCR errors. True mutations are scored if and only if they are present at the same position in both strands of the DNA. Figure is adapted from ref. 33, © 2013 Kennedy et al.

LLM interpretation

This figure is a three-part schematic diagram illustrating the Duplex Sequencing workflow. Panel (a) shows the structure of a duplex sequencing adapter with a randomized tag and invariant spacer, while panel (b) depicts the ligation of these adapters and subsequent PCR amplification into $\alpha\beta$ and $\beta\alpha$ tag families. Panel (c) demonstrates the bioinformatic process of grouping reads into single-strand consensus sequences (SSCSs) and then into duplex consensus sequences (DCSs) to distinguish true mutations (green dots) from sequencing and PCR errors.

Figure 2

Schematic of the basic computational workflow for Duplex Sequencing. The blue numbers correspond to the steps in the PROCEDURE.

LLM interpretation

This figure is a flow diagram illustrating the computational workflow for Duplex Sequencing. The process begins with DNA sequencing and proceeds through a series of sequential steps, including tag extraction, read alignment using BWA, and the generation of single-strand consensus sequences (SSCSs) and duplex consensus sequences (DCSs). The workflow concludes with local realignment via GATK and final mutation detection and analysis, with blue numbers mapping each step to a corresponding procedure.

Figure 3

Quality control of the sequencing adapters at each step of synthesis. (a) Representative 14% (wt/vol) polyacrylamide gel for each step of the adapter synthesis. Lane numbers correspond to the following steps in the synthesis protocol described in Box 1. Lane 1: step 1 (annealed adapters); lane 2: step 3 (extended adapters); lane 3: step 4 (cut adapters); and lane 4: step 10 (final adapters). Band sizes are as follows: a = 58 nt; b = 56 nt; c = 83 nt; d = 75 nt; e = 48 nt; and f = 9 nt. (b) Schematic of the adapters at each step on the synthesis. Lane and gel band designations correspond to the designations in a.

LLM interpretation

This figure consists of a polyacrylamide gel electrophoresis image (a) and a corresponding schematic diagram (b) illustrating the quality control of sequencing adapter synthesis. The gel shows four lanes representing different synthesis steps, with bands labeled a–f corresponding to specific nucleotide lengths (ranging from 9 to 83 nt). The schematic maps these bands to the structural changes of the adapters across the four steps, showing the progression from annealed to final adapters.

Figure 4

Representative tag family size distributions. (a) Optimal family size distribution. (b) Tag family size distribution that is too small because of too much PCR input. (c) Tag family size distribution that is too large because of too little PCR input. We have found that a family size that is centered around approximately six members maximizes the final number of DCS reads. Samples that exhibit a small peak family size can be sequenced again and the raw sequencing data from the two sequencing runs can be combined and analyzed. Importantly, further sequencing of a sample with a large peak family size will not increase the final depth of coverage.

LLM interpretation

This figure consists of three histograms (a, b, and c) showing the distribution of tag family sizes, with the x-axis representing "Tag family size (no. of reads per family)" and the y-axis representing "Fraction of total reads." Panel (a) shows an optimal distribution peaking around six members, while panel (b) shows a distribution skewed toward smaller family sizes (peaking at 2). Panel (c) shows a much broader distribution with a peak shifted toward significantly larger family sizes (approximately 125).

Figure 5

Optimal peak family size. Replicates of the same sample at different lane fractions. (a) Plot compares peak family size to the number of final DCSs that are formed for every read originally dedicated to a sample. The maximum efficiency of DCS formations occurs at a peak family size of six and corresponds to ~40 raw reads being required to form one DCS read. (b) The total number of DCSs increases until a peak family size of ~16 is reached. A peak family size >16 does not result in an increase in the final number of DCSs.

LLM interpretation

This figure consists of two line plots (a and b) analyzing the relationship between peak family size (x-axis) and DCS read metrics. Plot (a) shows the ratio of DCS reads to total reads, which peaks at a peak family size of six before declining. Plot (b) shows the total number of DCS reads, which increases steadily as peak family size increases, plateauing around a size of 16.

Figure 6

Example Agilent TapeStation 2200 electropherograms. (a) Electropherogram of an optimal post-PCR sample at Step 47. (b) Electropherogram from Step 47 showing higher molecular species resulting from too many PCR cycles. See Experimental design for details on determining the number of PCR cycles. (c) Electropherogram of the postligation at Step 36; note that the double peaks are normal. The peaks can vary in size and intensity without affecting the final results.

LLM interpretation

This figure consists of three electropherograms (a, b, and c) plotting sample intensity (FU) against size (bp). Panel (a) shows a single primary peak at 333 bp, while panel (b) displays a broader peak at 346 bp with additional higher molecular species appearing before the upper marker. Panel (c) shows multiple peaks, specifically at 182, 504, and 681 bp, representing a postligation sample.

#	Section	Preview
0	INTRODUCTION	Next-generation DNA sequencing (NGS) defines the modern genomic era. This powerful technology has…
1	INTRODUCTION	There is growing need for technologies capable of resolving subclonal mutations. For example,…
2	INTRODUCTION — The concept of DS	To overcome the high error rate of next-generation sequencing and thereby facilitate the study of…
3	INTRODUCTION — The concept of DS	share the same tag sequences derived from each of the two single parental strands (Fig. 1b). After…
4	INTRODUCTION — Alternatives to DS	As the need for accurate sequencing methods has increased, three main strategies besides DS have…
5	INTRODUCTION — Alternatives to DS	would be incorrectly called a genetic variant. A similar process can occur in CirSeq and…
6	INTRODUCTION — Advantages of DS	The primary advantage of DS over other approaches is its superior accuracy. In our original…
7	INTRODUCTION — Advantages of DS	Similarly to our results with mtDNA, we have found that DS can help mitigate artifactual mutations…
8	INTRODUCTION — Limitations of DS	DS is a uniquely sensitive method that is capable of detecting and quantifying mutations that occur…
9	INTRODUCTION — Overview of the procedure	Sequencing library construction for DS is similar to the standard Illumina library preparation…
10	INTRODUCTION — Overview of the procedure	input amount depends on a number of factors, including the number of reads devoted to a sample, the…
11	INTRODUCTION — Overview of the procedure	In addition to the updated protocol, we also include a comprehensive computational pipeline that we…
12	INTRODUCTION — Overview of the procedure	Each read obtained from a DS run consists of a 12-nt tag sequence, followed by an invariant 5-bp…
13	INTRODUCTION — Overview of the procedure	The family members are then compared at each sequence position, and the identity of a position is…
14	INTRODUCTION — Overview of the procedure	Next, the two related SSCS reads corresponding to the two initial DNA strands are grouped together…
15	Experimental design	In the following sections, we will highlight important considerations that should be taken into…
16	Experimental design — Sample requirements	The amount of fragmented DNA actually used in the PCR amplification step is typically in the…
17	Experimental design — DNA fragmentation	We physically shear the DNA by sonication using a Covaris acoustic ultrasonicator. The shearing time…
18	Experimental design — Size selection	Many protocols for next-generation sequencing library preparation use PAGE, with excision and…
19	Experimental design — End repair and dA-tailing	Similar to the standard Illumina library construction protocol, the sheared DNA is subjected to end…

Name	Type
20-kb locus local	drug
acetic acid	drug
Acrylamide	drug
adapter local	drug
adapter dimer local	drug
adolescents	cohort
Agilent 2100 Bioanalyzer	drug
Agilent SureSelectXT local	drug
Agilent TapeStation 2200 local	drug
Ampure XP beads	drug
beads local	drug
brain tissue	anatomy
cancer	phenotype
Chemical compounds local	drug
Chemotherapy resistance local	phenotype
copy number analysis local	drug
Covaris acoustic ultrasonicator local	drug
dA overhang local	drug
DCS reads local	drug
D-cycloserine	drug
ddH2 local	drug
ddH2O	drug
DNA	drug
DNA adduct local	drug
DNA polymerase local	drug
Drug resistance	phenotype
DS	anatomy
DS local	cohort
dT overhang local	drug
Duplex_Consensus_Sequence local	drug
Duplex consensus sequence (DCS) local	drug
duplex sequencing	drug
Enzymatic digestion local	drug
ethanol consumption	phenotype
false mutation local	phenotype
flies local	cohort
formalin	drug
formalin-fixed samples local	drug
free‑radical theories of aging local	phenotype
frozen brain tissue local	anatomy
Genetic diversity	phenotype
genetic heterogeneity	phenotype
genetic variants	cohort
genomic DNA	drug
glycosylase local	drug
G>T mutations local	variant
HCl	drug
HiSeq2500 local	drug
HpyCH4III local	drug
human mitochondrial DNA local	drug
human nuclear DNA local	drug
humans	cohort
Illumina	drug
Illumina sequencer local	drug
Illumina’s Nextera DNA sample prep kit local	drug
inherited clonal mutations local	variant
in vitro repair kit local	drug
library local	drug
ligation local	drug
M13 bacteriophage local	drug
M13mp2 phagemid local	drug
mice	cohort
Microbial populations local	cohort
molecular barcodes local	drug
mtDNA	drug
mtDNA point mutations local	variant
Mutagenicity local	phenotype
mutational artifacts local	phenotype
mutations	variant
Nebulization local	drug
next-generation sequencing local	drug
NGS methods local	drug
nontarget DNA local	drug
nuclear DNA local	drug
old individuals local	cohort
oligonucleotides	drug
oxidative damage local	drug
oxidative damage to mtDNA local	phenotype
PCR	drug
PCR amplification	drug
PCR-based enrichment methods local	drug
PCR input local	drug
PCR primer local	drug
peak family size local	drug
plasmid local	drug
plasmid DNA local	drug
plasmids	drug
qPCR	drug
raw reads local	drug
Raw_Reads local	drug
reactive oxygen species	drug
ribosomal genes	gene
Sequencing adapters local	drug
single-copy genes local	gene
Single_Strand_Consensus_Sequence local	drug
Single-strand consensus sequences (SSCSs) local	drug
sodium acetate solution local	drug
Sonication local	drug
SSCS local	drug
SSCS:DCS ratio local	drug
subclonal mutation local	phenotype
subclonal mutations	variant
SYBR green	drug
tag families local	drug
Tagmentation local	drug
target DNA local	drug
Target_DNA local	drug
targeted capture local	drug
targeted capture sets local	drug
targeted DNA capture local	drug
Targeted DNA capture local	drug
TBE local	drug
TE local	drug
total DNA local	drug
transposase	drug
urea	drug
viral DNA local	drug
water-bath local	drug

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Human DNA polymerase ε is a source of C>T mutations at CpG dinucleotides.	Tomkova M et al.	—	2024	→
Increased TP53 somatic evolution in peritoneal washes of individuals with BRCA1 germline mutations.	Tee XR et al.	—	2024	→
Liquid biopsy for improving diagnosis and monitoring of CNS lymphomas: A RANO review.	Nayak L et al.	—	2024	→
MADDD-seq, a novel massively parallel sequencing tool for simultaneous detection of DNA damage and mutations.	Vermulst M et al.	—	2024	→
Measurable residual disease (MRD)-testing in haematological cancers: A giant leap forward or sideways?	Shen Q et al.	—	2024	→
Methods and applications of genome-wide profiling of DNA damage and rare mutations.	Pfeifer GP et al.	—	2024	→
Neutral evolution of rare cancer mutations in the computer and the clinic.	Beckman RA	—	2024	→
Next-Generation Molecular Residual Disease Assays: Do We Have the Tools to Evaluate Them Properly?	Stetson D et al.	—	2024	→
Optimizing design of genomics studies for clonal evolution analysis.	Srivatsa A et al.	—	2024	→
Origins of Second Malignancies in Children and Mutational Footprint of Chemotherapy in Normal Tissues.	Sánchez-Guixé M et al.	—	2024	→
Power analyses to inform Duplex Sequencing study designs for MutaMouse liver and bone marrow.	Esina E et al.	—	2024	→
Precise diagnosis and prognosis assessment of malignant lung nodules: a narrative review.	Wen M et al.	—	2024	→
Somatic <i>MED12</i> Mutations in Myometrial Cells.	Li Y et al.	—	2024	→
[Sperm Mosaic Variants and Their Influence on the Offspring].	Yang X	—	2024	→
Surpassing sensitivity limits in liquid biopsy.	Moser T et al.	—	2024	→
The Evolutionary Interplay of Somatic and Germline Mutation Rates.	Beichman AC et al.	—	2024	→
Tissue mosaicism following stem cell aging: blood as an exemplar.	Kapadia CD et al.	—	2024	→
TP53 somatic evolution in cervical liquid-based cytology and blood from individuals with and without ovarian cancer and BRCA1 or BRCA2 germline mutations.	Ghezelayagh TS et al.	—	2024	→
Tumour-informed liquid biopsies to monitor advanced melanoma patients under immune checkpoint inhibition.	Schroeder C et al.	—	2024	→
Ultra-deep mutational landscape in chronic lymphocytic leukemia uncovers dynamics of resistance to targeted therapies.	Woolston DW et al.	—	2024	→
A critical spotlight on the paradigms of FFPE-DNA sequencing.	Steiert TA et al.	—	2023	→
Adopting duplex sequencing technology for genetic toxicity testing: A proof-of-concept mutagenesis experiment with N-ethyl-N-nitrosourea (ENU)-exposed rats.	Smith-Roe SL et al.	—	2023	→
Cell-free circulating RAS mutation concentrations significantly impact the survival of metastatic colorectal cancer patients.	Muendlein A et al.	—	2023	→
Characterization of Leukemic Resistance to CD19-Targeted CAR T-cell Therapy through Deep Genomic Sequencing.	Chen GM et al.	—	2023	→
Clinical applications of circulating tumor DNA in central nervous system lymphoma.	Foerster AK et al.	—	2023	→
Clinical applications of circulating tumor DNA in Hodgkin lymphoma.	Heger JM et al.	—	2023	→
Clonal selection of hematopoietic stem cells after gene therapy for sickle cell disease.	Spencer Chapman M et al.	—	2023	→
Comprehensive benchmarking and guidelines of mosaic variant calling strategies.	Ha YJ et al.	—	2023	→
CRISPR-Cas9 Targeted Enrichment and Next-Generation Sequencing for Mutation Detection.	Malekshoar M et al.	—	2023	→
DELFMUT: duplex sequencing-oriented depth estimation model for stable detection of low-frequency mutations.	Wu G et al.	—	2023	→
Detection of DNA replication errors and 8-oxo-dGTP-mediated mutations in E. coli by Duplex DNA Sequencing.	Bhawsinghka N et al.	—	2023	→
Detection of Nine Oncogenes Amplification in Lung and Colorectal Cancer Formalin-Fixed Paraffin-Embedded Tissue Samples using Combined Next-Generation Sequencing-Based Script and Digital Droplet Polymerase Chain Reaction.	Bontoux C et al.	—	2023	→
Duplex sequencing provides detailed characterization of mutation frequencies and spectra in the bone marrow of MutaMouse males exposed to procarbazine hydrochloride.	Dodge AE et al.	—	2023	→
Early-Stage Breast Cancer Detection in Breast Milk.	Saura C et al.	—	2023	→
Error-corrected duplex sequencing enables direct detection and quantification of mutations in human TK6 cells with strong inter-laboratory consistency.	Cho E et al.	—	2023	→
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing.	You X et al.	—	2023	→
Impact of risk factors on early cancer evolution.	Weeden CE et al.	—	2023	→
Lung adenocarcinoma promotion by air pollutants.	Hill W et al.	—	2023	→
mitoSomatic: a tool for accurate identification of mitochondrial DNA somatic mutations without paired controls.	Guo W et al.	—	2023	→
Moving toward a conceptualization of measurable residual disease in myelodysplastic syndromes.	Schulz E et al.	—	2023	→
Next-generation sequencing methodologies to detect low-frequency mutations: "Catch me if you can".	Menon V et al.	—	2023	→
Peritoneal cell-free DNA as a sensitive biomarker for detection of peritoneal metastasis in colorectal cancer: a prospective diagnostic study: A prospective diagnostic study.	Yuan Z et al.	—	2023	→
Rapid and Sensitive Detection of Fungicide-Resistant Crop Fungal Pathogens Using an Isothermal Amplification Refractory Mutation System.	Song S et al.	—	2023	→
svCapture: efficient and specific detection of very low frequency structural variant junctions by error-minimized capture sequencing.	Wilson TE et al.	—	2023	→
Technological and computational approaches to detect somatic mosaicism in epilepsy.	Boßelmann CM et al.	—	2023	→
The changing face of circulating tumor DNA (ctDNA) profiling: Factors that shape the landscape of methodologies, technologies, and commercialization.	Bronkhorst AJ et al.	—	2023	→
The human brain through the lens of somatic mosaicism.	Bizzotto S	—	2023	→
The multi-tissue landscape of somatic mtDNA mutations indicates tissue-specific accumulation and removal in aging.	Sanchez-Contreras M et al.	—	2023	→
Accurate detection of subclonal variants in paired diagnosis-relapse acute myeloid leukemia samples by next generation Duplex Sequencing.	Kamath-Loeb AS et al.	—	2022	→
An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer.	Johnson BE et al.	—	2022	→
Antiprogestins reduce epigenetic field cancerization in breast tissue of young healthy women.	Bartlett TE et al.	—	2022	→
Applications of molecular barcode sequencing for the detection of low-frequency variants in circulating tumour DNA from hepatocellular carcinoma.	Lee HW et al.	—	2022	→
A quantification method of somatic mutations in normal tissues and their accumulation in pediatric patients with chemotherapy.	Ueda S et al.	—	2022	→
Aristolochic acid-associated cancers: a public health risk in need of global action.	Das S et al.	—	2022	→
Cell-Free Tumor DNA (cf-tDNA) Liquid Biopsy: Current Methods and Use in Brain Tumor Immunotherapy.	Wadden J et al.	—	2022	→
Circulating tumor DNA: current challenges for clinical utility.	Dang DK et al.	—	2022	→
Circulating tumor DNA for prognosis assessment and postoperative management after curative-intent resection of colorectal liver metastases.	Reinert T et al.	—	2022	→
Circulating tumor DNA in B-cell lymphoma: technical advances, clinical applications, and perspectives for translational research.	Lauer EM et al.	—	2022	→
Circulating tumor DNA in cancer diagnosis, monitoring, and prognosis.	Saha S et al.	—	2022	→
Circulating tumor DNA in Hodgkin lymphoma.	Maco M et al.	—	2022	→
Circulating tumor DNA to guide rechallenge with panitumumab in metastatic colorectal cancer: the phase 2 CHRONOS trial.	Sartore-Bianchi A et al.	—	2022	→
Colorectal Cancer Is Associated with the Presence of Cancer Driver Mutations in Normal Colon.	Matas J et al.	—	2022	→
Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer.	Stackpole ML et al.	—	2022	→
De novo mutation rates at the single-mutation resolution in a human <i>HBB</i> gene region associated with adaptation and genetic disease.	Melamed D et al.	—	2022	→
Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing.	Salazar R et al.	—	2022	→
Distinguishing excess mutations and increased cell death based on variant allele frequencies.	Tibély G et al.	—	2022	→
Duplex sequencing identifies genomic features that determine susceptibility to benzo(a)pyrene-induced in vivo mutations.	LeBlanc DPM et al.	—	2022	→
Duplex Sequencing Uncovers Recurrent Low-frequency Cancer-associated Mutations in Infant and Childhood <i>KMT2A</i>-rearranged Acute Leukemia.	Pilheden M et al.	—	2022	→
Establishing Linkages Among DNA Damage, Mutagenesis, and Genetic Diseases.	Basu AK et al.	—	2022	→
Estimating somatic mutation rates by bottlenecked duplex sequencing in non-model organisms: <i>Daphnia magna</i> as a case study.	Sobel E et al.	—	2022	→
Human genetic risk of treatment with antiviral nucleoside analog drugs that induce lethal mutagenesis: The special case of molnupiravir.	Waters MD et al.	—	2022	→
Molecular features encoded in the ctDNA reveal heterogeneity and predict outcome in high-risk aggressive B-cell lymphoma.	Meriranta L et al.	—	2022	→
Myometrial oxidative stress drives MED12 mutations in leiomyoma.	Li Y et al.	—	2022	→
Novel hybridization- and tag-based error-corrected method for sensitive ctDNA mutation detection using ion semiconductor sequencing.	Tjensvoll K et al.	—	2022	→
Optimized variant calling for estimating kinship.	Woerner AE et al.	—	2022	→
OPUSeq simplifies detection of low-frequency DNA variants and uncovers fragmentase-associated artifacts.	Alekseenko A et al.	—	2022	→
Resistance of mitochondrial DNA to cadmium and Aflatoxin B1 damage-induced germline mutation accumulation in C. elegans.	Leuthner TC et al.	—	2022	→
Simultaneous analysis of mutations and methylations in circulating cell-free DNA for hepatocellular carcinoma detection.	Wang P et al.	—	2022	→
Single-strand specific nuclease enhances accuracy of error-corrected sequencing and improves rare mutation-detection sensitivity.	Otsubo Y et al.	—	2022	→
Sorting of mitochondrial and plastid heteroplasmy in <i>Arabidopsis</i> is extremely rapid and depends on MSH1 activity.	Broz AK et al.	—	2022	→
The present and future of measurable residual disease testing in acute myeloid leukemia.	Blachly JS et al.	—	2022	→
Uterine lavage identifies cancer mutations and increased <i>TP53</i> somatic mutation burden in individuals with ovarian cancer.	Ghezelayagh TS et al.	—	2022	→
A deep molecular response of splenic marginal zone lymphoma to front-line checkpoint blockade.	Miller PG et al.	—	2021	→
Analysis of mutations in tumor and normal adjacent tissue via fluorescence detection.	Kay JE et al.	—	2021	→
A replication-linked mutational gradient drives somatic mutation accumulation and influences germline polymorphisms and genome composition in mitochondrial DNA.	Sanchez-Contreras M et al.	—	2021	→
cfDNA Sequencing: Technological Approaches and Bioinformatic Issues.	Bohers E et al.	—	2021	→
Circulating Tumor DNA Testing for Homology Recombination Repair Genes in Prostate Cancer: From the Lab to the Clinic.	Cimadamore A et al.	—	2021	→
Comprehensive identification of somatic nucleotide variants in human brain tissue.	Wang Y et al.	—	2021	→
ctDNA to Guide Adjuvant Therapy in Localized Colorectal Cancer (CRC).	Masfarré L et al.	—	2021	→
Detecting de novo mitochondrial mutations in angiosperms with highly divergent evolutionary rates.	Broz AK et al.	—	2021	→
Detection of low-frequency DNA variants by targeted sequencing of the Watson and Crick strands.	Cohen JD et al.	—	2021	→
Dissecting single-cell genomes through the clonal organoid technique.	Youk J et al.	—	2021	→
Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA.	Kurtz DM et al.	—	2021	→
Extreme heterogeneity of human mitochondrial DNA from organelles to populations.	Stewart JB et al.	—	2021	→
Genomic Mosaicism Formed by Somatic Variation in the Aging and Diseased Brain.	Costantino I et al.	—	2021	→
Globally defining the effects of mutations in a picornavirus capsid.	Mattenberger F et al.	—	2021	→
Hawk-Seq™ differentiates between various mutations in Salmonella typhimurium TA100 strain caused by exposure to Ames test-positive mutagens.	Otsubo Y et al.	—	2021	→
Increased RNA virus population diversity improves adaptability.	Mattenberger F et al.	—	2021	→
In-depth cell-free DNA sequencing reveals genomic landscape of Hodgkin's lymphoma and facilitates ultrasensitive residual disease detection.	Sobesky S et al.	—	2021	→
Intra-host changes in Kaposi sarcoma-associated herpesvirus genomes in Ugandan adults with Kaposi sarcoma.	Santiago JC et al.	—	2021	→
Liquid biopsy for therapy monitoring in early-stage non-small cell lung cancer.	Nagasaka M et al.	—	2021	→
Mitochondrial DNA variation and cancer.	Kopinski PK et al.	—	2021	→
Mitochondrial mutations in Caenorhabditis elegans show signatures of oxidative damage and an AT-bias.	Waneka G et al.	—	2021	→
Mutagenicity of silver nanoparticles evaluated using whole-genome sequencing in mouse lymphoma cells.	Pan B et al.	—	2021	→
Mutational Pressure Drives Differential Genome Conservation in Two Bacterial Endosymbionts of Sap-Feeding Insects.	Waneka G et al.	—	2021	→
Pathogenic postzygotic mosaicism in the tyrosine receptor kinase pathway: potential unidentified human disease hidden away in a few cells.	Tiemann-Boege I et al.	—	2021	→
Pathways and signatures of mutagenesis at targeted DNA nicks.	Zhang Y et al.	—	2021	→
PolyG-DS: An ultrasensitive polyguanine tract-profiling method to detect clonal expansions and trace cell lineage.	Zhang Y et al.	—	2021	→
Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing.	Ellis P et al.	—	2021	→
Significant impact of circulating tumour DNA mutations on survival in metastatic breast cancer patients.	Muendlein A et al.	—	2021	→
Somatic mutation landscapes at single-molecule resolution.	Abascal F et al.	—	2021	→
The Feasibility of Patient-Specific Circulating Tumor DNA Monitoring throughout Multi-Modality Therapy for Locally Advanced Esophageal and Rectal Cancer: A Potential Biomarker for Early Detection of Subclinical Disease.	Boniface C et al.	—	2021	→
Type III-A CRISPR immunity promotes mutagenesis of staphylococci.	Mo CY et al.	—	2021	→
Ultrasensitive detection of tumor-specific mutations in saliva of patients with oral cavity squamous cell carcinoma.	Shanmugam A et al.	—	2021	→
Utility of Serial cfDNA NGS for Prospective Genomic Analysis of Patients on a Phase I Basket Study.	Smyth LM et al.	—	2021	→
When Tissue is an Issue the Liquid Biopsy is Nonissue: A Review.	Rodríguez J et al.	—	2021	→
Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues.	Arbeithuber B et al.	—	2020	→
Applying next-generation sequencing to unravel the mutational landscape in viral quasispecies.	Lu IN et al.	—	2020	→
Challenges and opportunities of cfDNA analysis implementation in clinical practice: Perspective of the International Society of Liquid Biopsy (ISLB).	Rolfo C et al.	—	2020	→
Characterization of TP53 mutations in Pap test DNA of women with and without serous ovarian carcinoma.	Krimmel-Morrison JD et al.	—	2020	→
Detection of genome-wide low-frequency mutations with Paired-End and Complementary Consensus Sequencing (PECC-Seq) revealed end-repair-derived artifacts as residual errors.	You X et al.	—	2020	→
Direct quantification of in vivo mutagenesis and carcinogenesis using duplex sequencing.	Valentine CC et al.	—	2020	→
Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring.	Zviran A et al.	—	2020	→
<i>MSH1</i> is required for maintenance of the low mutation rates in plant mitochondrial and plastid genomes.	Wu Z et al.	—	2020	→
Integration of intra-sample contextual error modeling for improved detection of somatic mutations from deep sequencing.	Abelson S et al.	—	2020	→
Liquid Biopsy in Colorectal Carcinoma: Clinical Applications and Challenges.	Kolenčík D et al.	—	2020	→
Next-Generation Genotoxicology: Using Modern Sequencing Technologies to Assess Somatic Mutagenesis and Cancer Risk.	Salk JJ et al.	—	2020	→
POLQ suppresses interhomolog recombination and loss of heterozygosity at targeted DNA breaks.	Davis L et al.	—	2020	→
Quantification of cancer driver mutations in human breast and lung DNA using targeted, error-corrected CarcSeq.	Harris KL et al.	—	2020	→
Real-Time Molecular Monitoring in Acute Myeloid Leukemia With Circulating Tumor DNA.	Thakral D et al.	—	2020	→
SinoDuplex: An Improved Duplex Sequencing Approach to Detect Low-frequency Variants in Plasma cfDNA Samples.	Ren Y et al.	—	2020	→
Targeted Sequencing of Circulating Cell Free DNA Can Be Used to Monitor Therapeutic Efficacy of Tyrosine Kinase Inhibitors in Non-small Cell Lung Cancer Patients.	Chiou CC et al.	—	2020	→
Technologies and Computational Analysis Strategies for CRISPR Applications.	Clement K et al.	—	2020	→
The promise of toxicogenomics for genetic toxicology: past, present and future.	David R	—	2020	→
The stochastic nature of errors in next-generation sequencing of circulating cell-free DNA.	Nix DA et al.	—	2020	→
Tumor DNA as a Cancer Biomarker through the Lens of Colorectal Neoplasia.	Cohen JD et al.	—	2020	→
Ultra-accurate Duplex Sequencing for the assessment of pretreatment ABL1 kinase domain mutations in Ph+ ALL.	Short NJ et al.	—	2020	→
Visualizing, quantifying, and manipulating mitochondrial DNA in vivo.	Prole DL et al.	—	2020	→
Abnormal oxidative metabolism in a quiet genomic background underlies clear cell papillary renal cell carcinoma.	Xu J et al.	—	2019	→
Adaptive mutability of colorectal cancers in response to targeted therapies.	Russo M et al.	—	2019	→
A high-resolution landscape of mutations in the <i>BCL6</i> super-enhancer in normal human B cells.	Shen JC et al.	—	2019	→
Application of amplicon-based targeted sequencing with the molecular barcoding system to detect uncommon minor EGFR mutations in patients with treatment-naïve lung adenocarcinoma.	Namba K et al.	—	2019	→
Bioinformatics Analysis for Circulating Cell-Free DNA in Cancer.	Huang CC et al.	—	2019	→
Cancer-Associated Mutations but No Cancer: Insights into the Early Steps of Carcinogenesis and Implications for Early Cancer Detection.	Kennedy SR et al.	—	2019	→
Clinically-relevant postzygotic mosaicism in parents and children with developmental disorders in trio exome sequencing data.	Wright CF et al.	—	2019	→
CNV Detection from Circulating Tumor DNA in Late Stage Non-Small Cell Lung Cancer Patients.	Peng H et al.	—	2019	→
Detection of Low-Frequency Mutations and Identification of Heat-Induced Artifactual Mutations Using Duplex Sequencing.	Ahn EH et al.	—	2019	→
Development and Application of Duplex Sequencing Strategy for Cell-Free DNA-Based Longitudinal Monitoring of Stage IV Colorectal Cancer.	Mallampati S et al.	—	2019	→
Extensive subclonal mutational diversity in human colorectal cancer and its significance.	Loeb LA et al.	—	2019	→
FERMI: A Novel Method for Sensitive Detection of Rare Mutations in Somatic Tissue.	Liggett LA et al.	—	2019	→
Gencore: an efficient tool to generate consensus reads for error suppressing and duplicate removing of NGS data.	Chen S et al.	—	2019	→
High efficiency error suppression for accurate detection of low-frequency variants.	Wang TT et al.	—	2019	→
High Fidelity Deep Sequencing Reveals No Effect of ATM, ATR, and DNA-PK Cellular DNA Damage Response Pathways on Adenovirus Mutation Rate.	Risso-Ballester J et al.	—	2019	→
Immortalization of Different Breast Epithelial Cell Types Results in Distinct Mitochondrial Mutagenesis.	Kwon S et al.	—	2019	→
Impact of Polymerase Fidelity on Background Error Rates in Next-Generation Sequencing with Unique Molecular Identifiers/Barcodes.	Filges S et al.	—	2019	→
Impact of preleukemic mutations and their persistence on hematologic recovery after induction chemotherapy for AML.	Murphy T et al.	—	2019	→
In silico error correction improves cfDNA mutation calling.	Kim CS et al.	—	2019	→
Location analysis of 8-oxo-7,8-dihydroguanine in DNA by polymerase-mediated differential coding.	Tang F et al.	—	2019	→
Low-level parental mosaicism affects the recurrence risk of holoprosencephaly.	Hu P et al.	—	2019	→
Minimal Residual Disease Monitoring with Next-Generation Sequencing Methodologies in Hematological Malignancies.	Sánchez R et al.	—	2019	→
Mitochondrial DNA Mutations are Associated with Ulcerative Colitis Preneoplasia but Tend to be Negatively Selected in Cancer.	Baker KT et al.	—	2019	→
Mitochondrially-targeted APOBEC1 is a potent mtDNA mutator affecting mitochondrial function and organismal fitness in Drosophila.	Andreazza S et al.	—	2019	→
New approaches to molecular monitoring in CML (and other diseases).	Radich J et al.	—	2019	→
PCR-free whole exome sequencing: Cost-effective and efficient in detecting rare mutations.	Yamaguchi I et al.	—	2019	→
Precision oncology: lessons learned and challenges for the future.	Yang HT et al.	—	2019	→
RACE-SEQ and Population-Wide Polymorphism Susceptibility Testing for Endonucleolytically Active, RNA-Targeting Therapeutics.	Usher L et al.	—	2019	→
smCounter2: an accurate low-frequency variant caller for targeted sequencing data with unique molecular identifiers.	Xu C et al.	—	2019	→
Targeted Next Generation Sequencing to study insert stability in genetically modified plants.	Boutigny AL et al.	—	2019	→
The potential of cerebrospinal fluid-based liquid biopsy approaches in CNS tumors.	Mattox AK et al.	—	2019	→
Ultrasensitive Detection of Circulating Tumor DNA in Lymphoma via Targeted Hybridization Capture and Deep Sequencing of Barcoded Libraries.	Alcaide M et al.	—	2019	→
Ultra-Sensitive TP53 Sequencing for Cancer Detection Reveals Progressive Clonal Selection in Normal Tissue over a Century of Human Lifespan.	Salk JJ et al.	—	2019	→
Accurate detection of low-level mosaic mutations in pediatric acute lymphoblastic leukemia using single molecule tagging and deep-sequencing.	Yu J et al.	—	2018	→
Aging and the rise of somatic cancer-associated mutations in normal tissues.	Risques RA et al.	—	2018	→
An optimized targeted Next-Generation Sequencing approach for sensitive detection of single nucleotide variants.	Stasik S et al.	—	2018	→
A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data.	Xu C	—	2018	→
A Universal Analysis Pipeline of Hybrid Capture-Based Targeted Sequencing Data with Unique Molecular Indexes (UMIs).	Kim MJ et al.	—	2018	→
Automated size selection for short cell-free DNA fragments enriches for circulating tumor DNA and improves error correction during next generation sequencing.	Hellwig S et al.	—	2018	→
Biotinylated amplicon sequencing: A method for preserving DNA samples of limited quantity.	Cravero K et al.	—	2018	→
Circulating tumour cells and DNA as liquid biopsies in gastrointestinal cancer.	Nordgård O et al.	—	2018	→
Clonal evolution mechanisms in NT5C2 mutant-relapsed acute lymphoblastic leukaemia.	Tzoneva G et al.	—	2018	→
Deleterious mitochondrial DNA point mutations are overrepresented in Drosophila expressing a proofreading-defective DNA polymerase γ.	Samstag CL et al.	—	2018	→
Detecting Rare Mutations and DNA Damage with Sequencing-Based Methods.	Sloan DB et al.	—	2018	→
Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations.	Salk JJ et al.	—	2018	→
Extracellular vesicles and ctDNA in lung cancer: biomarker sources and therapeutic applications.	Huang C et al.	—	2018	→
fastp: an ultra-fast all-in-one FASTQ preprocessor.	Chen S et al.	—	2018	→
Host association influences variation at salivary protein genes in the bat ectoparasite Cimex adjunctus.	Talbot B et al.	—	2018	→
Impact of DNA lesion repair, replication and formation on the mutational spectra of environmental carcinogens: Aflatoxin B<sub>1</sub> as a case study.	Fedeles BI et al.	—	2018	→
Liquid biopsy in pancreatic cancer: the beginning of a new era.	Yadav DK et al.	—	2018	→
Mapping the Evolutionary Potential of RNA Viruses.	Dolan PT et al.	—	2018	→
Modernizing Human Cancer Risk Assessment of Therapeutics.	Fielden MR et al.	—	2018	→
Next-Generation Sequencing and Mutational Analysis: Implications for Genes Encoding LINC Complex Proteins.	Nagy PL et al.	—	2018	→
On statistical modeling of sequencing noise in high depth data to assess tumor evolution.	Rabadan R et al.	—	2018	→
Optimized targeted sequencing of cell-free plasma DNA from bladder cancer patients.	Christensen E et al.	—	2018	→
PHLI-seq: constructing and visualizing cancer genomic maps in 3D by phenotype-based high-throughput laser-aided isolation and sequencing.	Kim S et al.	—	2018	→
Prediction of acute myeloid leukaemia risk in healthy individuals.	Abelson S et al.	—	2018	→
Rare haplotype load as marker for lethal mutagenesis.	Gregori J et al.	—	2018	→
Selfish mutations dysregulating RAS-MAPK signaling are pervasive in aged human testes.	Maher GJ et al.	—	2018	→
Sensitive tumour detection and classification using plasma cell-free DNA methylomes.	Shen SY et al.	—	2018	→
Single-Molecule Sequencing Reveals Patterns of Preexisting Drug Resistance That Suggest Treatment Strategies in Philadelphia-Positive Leukemias.	Schmitt MW et al.	—	2018	→
Spatial Vulnerabilities of the <i>Escherichia coli</i> Genome to Spontaneous Mutations Revealed with Improved Duplex Sequencing.	Zhang X et al.	—	2018	→
Targeted genome fragmentation with CRISPR/Cas9 enables fast and efficient enrichment of small genomic regions and ultra-accurate sequencing with low DNA input (CRISPR-DS).	Nachmanson D et al.	—	2018	→
Techniques of using circulating tumor DNA as a liquid biopsy component in cancer management.	Elazezy M et al.	—	2018	→
The emerging clinical relevance of genomics in cancer medicine.	Berger MF et al.	—	2018	→
Ultra-Sensitive Mutation Detection and Genome-Wide DNA Copy Number Reconstruction by Error-Corrected Circulating Tumor DNA Sequencing.	Mansukhani S et al.	—	2018	→
Validation of a Plasma-Based Comprehensive Cancer Genotyping Assay Utilizing Orthogonal Tissue- and Plasma-Based Methodologies.	Odegaard JI et al.	—	2018	→
Advances in Circulating Tumor DNA Analysis.	Perakis S et al.	—	2017	→
Approach, Application, and Bioethics of mtDNA Sequencing in Cancer.	Qian M et al.	—	2017	→
AR-v7 liquid biopsy for treatment stratification in prostate cancer: how close are we?	Fletcher C	—	2017	→
Asymmetrical barcode adapter-assisted recovery of duplicate reads and error correction strategy to detect rare mutations in circulating tumor DNA.	Ahn J et al.	—	2017	→
Circulating-tumor DNA as an early detection and diagnostic tool.	Butler TM et al.	—	2017	→
Circulating tumour DNA sequence analysis as an alternative to multiple myeloma bone marrow aspirates.	Kis O et al.	—	2017	→
Codon-Directed Determination of the Biological Causes of Sequence Variants in Therapeutic Proteins.	Jiang T et al.	—	2017	→
CRISPR Genome Engineering for Human Pluripotent Stem Cell Research.	Chaterji S et al.	—	2017	→
Current and Emerging Applications of Droplet Digital PCR in Oncology.	Olmedillas-López S et al.	—	2017	→
Defining, distinguishing and detecting the contribution of heterogeneous methylation to cancer heterogeneity.	Pisanic TR et al.	—	2017	→
Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller.	Xu C et al.	—	2017	→
Detection of Rare Mutations in CtDNA Using Next Generation Sequencing.	Lv X et al.	—	2017	→
Different rates of spontaneous mutation of chloroplastic and nuclear viroids as determined by high-fidelity ultra-deep sequencing.	López-Carrasco A et al.	—	2017	→
Dynamics of molecular evolution in RNA virus populations depend on sudden versus gradual environmental change.	Morley VJ et al.	—	2017	→
Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing.	Noyes NR et al.	—	2017	→
Evaluation of chemical mutagenicity using next generation sequencing: A review.	Du H et al.	—	2017	→
Facile single-stranded DNA sequencing of human plasma DNA via thermostable group II intron reverse transcriptase template switching.	Wu DC et al.	—	2017	→
Genomic Instability in Cancer: Teetering on the Limit of Tolerance.	Andor N et al.	—	2017	→
Genomic mosaicism in paternal sperm and multiple parental tissues in a Dravet syndrome cohort.	Yang X et al.	—	2017	→
Highlights from the 58th meeting of the American Society of Haematology, 1-6 December 2016, San Diego, USA.	Mazzarella L	—	2017	→
High-throughput sequencing for noninvasive disease detection in hematologic malignancies.	Scherer F et al.	—	2017	→
Incorporation of unique molecular identifiers in TruSeq adapters improves the accuracy of quantitative sequencing.	Hong J et al.	—	2017	→
Individualised multiplexed circulating tumour DNA assays for monitoring of tumour presence in patients after colorectal cancer surgery.	Ng SB et al.	—	2017	→
Liquid biopsies in lung cancer-time to implement research technologies in routine care?	Köhn L et al.	—	2017	→
Mutational spectra of aflatoxin B<sub>1</sub> in vivo establish biomarkers of exposure for human hepatocellular carcinoma.	Chawanthayatham S et al.	—	2017	→
Patient monitoring through liquid biopsies using circulating tumor DNA.	Ulz P et al.	—	2017	→
Profiling the Mismatch Tolerance of Argonaute 2 through Deep Sequencing of Sliced Polymorphic Viral RNAs.	Theotokis PI et al.	—	2017	→
Simple multiplexed PCR-based barcoding of DNA for ultrasensitive mutation detection by next-generation sequencing.	Ståhlberg A et al.	—	2017	→
Targeted Error-Suppressed Detection of Circulating Paternal DNA to Establish a Diagnosis of Gestational Trophoblastic Neoplasm.	Lavoie JM et al.	—	2017	→
Targeted error-suppressed quantification of circulating tumor DNA using semi-degenerate barcoded adapters and biotinylated baits.	Alcaide M et al.	—	2017	→
The Role of Minimal Residual Disease Testing in Myeloma Treatment Selection and Drug Development: Current Value and Future Applications.	Anderson KC et al.	—	2017	→
Ultrasensitive and high-efficiency screen of de novo low-frequency mutations by o2n-seq.	Wang K et al.	—	2017	→
Ultrasensitive detection of acute myeloid leukemia minimal residual disease using single molecule molecular inversion probes.	Waalkes A et al.	—	2017	→
Accurate Sample Assignment in a Multiplexed, Ultrasensitive, High-Throughput Sequencing Assay for Minimal Residual Disease.	Bartram J et al.	—	2016	→
A mitochondrial DNA hypomorph of cytochrome oxidase specifically impairs male fertility in Drosophila melanogaster.	Patel MR et al.	—	2016	→
Analysis of Base-Position Error Rate of Next-Generation Sequencing to Detect Tumor Mutations in Circulating DNA.	Pécuchet N et al.	—	2016	→
Application of Circulating Tumor DNA as a Non-Invasive Tool for Monitoring the Progression of Colorectal Cancer.	Zhou J et al.	—	2016	→
Artifactual mutations resulting from DNA lesions limit detection levels in ultrasensitive sequencing applications.	Arbeithuber B et al.	—	2016	→
Circulating cell-free DNA in hematological malignancies.	Buedts L et al.	—	2016	→
Clonal haematopoiesis harbouring AML-associated mutations is ubiquitous in healthy adults.	Young AL et al.	—	2016	→
Decreased Mitochondrial Mutagenesis during Transformation of Human Breast Stem Cells into Tumorigenic Cells.	Ahn EH et al.	—	2016	→
Development and validation of an ultra-high sensitive next-generation sequencing assay for molecular diagnosis of clinical oncology.	Liang J et al.	—	2016	→
Evaluating Cancer of the Central Nervous System Through Next-Generation Sequencing of Cerebrospinal Fluid.	Pentsova EI et al.	—	2016	→
Fragment Length of Circulating Tumor DNA.	Underhill HR et al.	—	2016	→
Genome-Wide Estimation of the Spontaneous Mutation Rate of Human Adenovirus 5 by High-Fidelity Deep Sequencing.	Risso-Ballester J et al.	—	2016	→
Genome-wide quantification of rare somatic mutations in normal human tissues using massively parallel sequencing.	Hoang ML et al.	—	2016	→
Highly heterogeneous mutation rates in the hepatitis C virus genome.	Geller R et al.	—	2016	→
Integrated digital error suppression for improved detection of circulating tumor DNA.	Newman AM et al.	—	2016	→
Mitochondrial DNA mutations increase in early stage Alzheimer disease and are inconsistent with oxidative damage.	Hoekstra JG et al.	—	2016	→
Phase 2 study of panobinostat with or without rituximab in relapsed diffuse large B-cell lymphoma.	Assouline SE et al.	—	2016	→
Polymerase specific error rates and profiles identified by single molecule sequencing.	Hestand MS et al.	—	2016	→
Statistical modeling for sensitive detection of low-frequency single nucleotide variants.	Hao Y et al.	—	2016	→
Streamlined analysis of duplex sequencing data with Du Novo.	Stoler N et al.	—	2016	→
Targeted Gene Deletion Using DNA-Free RNA-Guided Cas9 Nuclease Accelerates Adaptation of CHO Cells to Suspension Culture.	Lee N et al.	—	2016	→
Ultra-deep sequencing detects ovarian cancer cells in peritoneal fluid and reveals somatic TP53 mutations in noncancerous tissues.	Krimmel JD et al.	—	2016	→
Ultra-precise detection of mutations by droplet-based amplification of circularized DNA.	Wang K et al.	—	2016	→
Werner syndrome through the lens of tissue and tumour genomics.	Tokita M et al.	—	2016	→
Why Cockayne syndrome patients do not get cancer despite their DNA repair deficiency.	Reid-Bayliss KS et al.	—	2016	→
Accessing Genetic Information with Liquid Biopsies.	Cai X et al.	—	2015	→
Comparison of Major and Minor Viral SNPs Identified through Single Template Sequencing and Pyrosequencing in Acute HIV-1 Infection.	Iyer S et al.	—	2015	→
Detection of Ultra-Rare Mitochondrial Mutations in Breast Stem Cells by Duplex Sequencing.	Ahn EH et al.	—	2015	→
Endogenous Parkin Preserves Dopaminergic Substantia Nigral Neurons following Mitochondrial DNA Mutagenic Stress.	Pickrell AM et al.	—	2015	→
Mutation assay using single-molecule real-time (SMRT(TM)) sequencing technology.	Matsuda T et al.	—	2015	→
Rational Protein Engineering Guided by Deep Mutational Scanning.	Shin H et al.	—	2015	→
Sequencing small genomic targets with high efficiency and extreme accuracy.	Schmitt MW et al.	—	2015	→
The role of clinical genomic testing in diagnosis and discovery of pathogenic mutations.	Nagy PL et al.	—	2015	→