Next-generation sequencing methodologies to detect low-frequency mutations: “Catch me if you can”

Error-corrected next-generation sequencing to advance nonclinical genotoxicity and carcinogenicity testing

(2023) Francesco Marchetti et al.   NATURE REVIEWS DRUG DISCOVERY

Single duplex DNA sequencing with CODEC detects mutations with high sensitivity

(2023) Jin H. Bae et al.   NATURE GENETICS

Genome‐wide detection of ultralow‐frequency substitution mutations in cultures of mouse lymphoma L5178Y cells and Caenorhabditis elegans worms by PacBio sequencing

(2022) Jaime A. Miranda et al.   ENVIRONMENTAL AND MOLECULAR MUTAGENESIS

Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing

(2022) Renato Salazar et al.   GENOME RESEARCH

Somatic genomic changes in single Alzheimer’s disease neurons

(2022) Michael B. Miller et al.   NATURE

Single-molecule, quantitative detection of low-abundance somatic mutations by high-throughput sequencing

(2022) Alexander Y. Maslov et al.   Science Advances

Massively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth

(2022) Gregory Gydush et al.   Nature Biomedical Engineering

Bias and inconsistency in the estimation of tumour mutation burden

(2022) Mohammad A. Makrooni et al.   BMC CANCER

Duplex sequencing identifies genomic features that determine susceptibility to benzo(a)pyrene-induced in vivo mutations

(2022) Danielle P. M. LeBlanc et al.   BMC GENOMICS

Cyclobutane Pyrimidine Dimer Hyperhotspots as Sensitive Indicators of Keratinocyte UV Exposure †

(2022) Alejandro Garcia‐Ruiz et al.   PHOTOCHEMISTRY AND PHOTOBIOLOGY

A quantification method of somatic mutations in normal tissues and their accumulation in pediatric patients with chemotherapy

(2022) Sho Ueda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The impact of rare germline variants on human somatic mutation processes

(2022) Mischan Vali-Pour et al.   Nature Communications

A clinically annotated post-mortem approach to study multi-organ somatic mutational clonality in normal tissues

(2022) Tom Luijts et al.   Scientific Reports

Analysis of mutations in DNA damage repair pathway gene in Chinese patients with hepatocellular carcinoma

(2022) Jiarong Li et al.   Scientific Reports

High prevalence of somatic PIK3CA and TP53 pathogenic variants in the normal mammary gland tissue of sporadic breast cancer patients revealed by duplex sequencing

(2022) Anna Kostecka et al.   npj Breast Cancer

Immunotherapy in Advanced NSCLC Without Driver Mutations: Available Therapeutic Alternatives After Progression and Future Treatment Options

(2022) Jose Luis Leal et al.   Clinical Lung Cancer

Low-level brain somatic mutations are implicated in schizophrenia

(2021) Myeong-Heui Kim et al.   BIOLOGICAL PSYCHIATRY

Hawk-Seq™ differentiates between various mutations in Salmonella typhimurium TA100 strain caused by exposure to Ames test-positive mutagens

(2021) Yuki Otsubo et al.   MUTAGENESIS

Somatic mutation landscapes at single-molecule resolution

(2021) Federico Abascal et al.   NATURE

Detection of low-frequency DNA variants by targeted sequencing of the Watson and Crick strands

(2021) Joshua D. Cohen et al.   NATURE BIOTECHNOLOGY

Author Correction: The landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing

(2021) Rachel E. Rodin et al.   NATURE NEUROSCIENCE

Somatic Mutations in “Benign” Disease

(2021) Satu Mustjoki et al.   NEW ENGLAND JOURNAL OF MEDICINE

Somatic Copy Number Alterations in Human Cancers: An Analysis of Publicly Available Data From The Cancer Genome Atlas

(2021) Luuk Harbers et al.   Frontiers in Oncology

DNA Damage Response and Repair Gene Alterations Increase Tumor Mutational Burden and Promote Poor Prognosis of Advanced Lung Cancer

(2021) Jiawei Dai et al.   Frontiers in Oncology

More attention should be paid to pregnant women who fail non-invasive prenatal screening

(2021) Bin Zhang et al.   CLINICAL BIOCHEMISTRY

Nanopore sequencing technology, bioinformatics and applications

(2021) Yunhao Wang et al.   NATURE BIOTECHNOLOGY

Calibration-free NGS quantitation of mutations below 0.01% VAF

(2021) Peng Dai et al.   Nature Communications

Patterns of somatic structural variation in human cancer genomes

(2020) Yilong Li et al.   NATURE

High tumor mutation burden is associated with DNA damage repair gene mutation in breast carcinomas

(2020) Ping Mei et al.   Diagnostic Pathology

Most noninvasive prenatal screens failing due to inadequate fetal cell free DNA are negative for trisomy when repeated

(2020) Jaime L. Lopes et al.   PRENATAL DIAGNOSIS

Ultra-accurate Duplex Sequencing for the assessment of pretreatment ABL1 kinase domain mutations in Ph+ ALL

(2020) Nicholas J. Short et al.   Blood Cancer Journal

SinoDuplex: An Improved Duplex Sequencing Approach to Detect Low-frequency Variants in Plasma cfDNA Samples

(2020) Yongzhe Ren et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Nivolumab in Patients with Advanced Platinum-resistant Urothelial Carcinoma: Efficacy, Safety, and Biomarker Analyses with Extended Follow-up from CheckMate 275

(2020) Matthew D. Galsky et al.   CLINICAL CANCER RESEARCH

3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing

(2020) Huy Q. Nguyen et al.   NATURE METHODS

Emerging mechanisms of cell competition

(2020) Nicholas E. Baker   NATURE REVIEWS GENETICS

Unique roles of rare variants in the genetics of complex diseases in humans

(2020) Yukihide Momozawa et al.   JOURNAL OF HUMAN GENETICS

Direct quantification of in vivo mutagenesis and carcinogenesis using duplex sequencing

(2020) Charles C. Valentine et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Challenges of Tumor Mutational Burden as an Immunotherapy Biomarker

(2020) Denis L. Jardim et al.   CANCER CELL

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution

(2019) Benjamin J Callahan et al.   NUCLEIC ACIDS RESEARCH

Tumor mutational burden quantification from targeted gene panels: major advancements and challenges

(2019) Laura Fancello et al.   Journal for ImmunoTherapy of Cancer

Genome-wide somatic mutation analysis via Hawk-Seq™ reveals mutation profiles associated with chemical mutagens

(2019) Shoji Matsumura et al.   ARCHIVES OF TOXICOLOGY

Brain somatic mutations in MTOR reveal translational dysregulations underlying intractable focal epilepsy

(2019) Jang Keun Kim et al.   JOURNAL OF CLINICAL INVESTIGATION

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

Next‐Generation Genotoxicology: Using Modern Sequencing Technologies to Assess Somatic Mutagenesis and Cancer Risk

(2019) Jesse J. Salk et al.   ENVIRONMENTAL AND MOLECULAR MUTAGENESIS

Genomic sites hypersensitive to ultraviolet radiation

(2019) Sanjay Premi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recurrent somatic mutations reveal new insights into consequences of mutagenic processes in cancer

(2019) Miranda D. Stobbe et al.   PLoS Computational Biology

Cell-free Circulating Tumor DNA Variant Allele Frequency Associates with Survival in Metastatic Cancer

(2019) Seyed Pairawan et al.   CLINICAL CANCER RESEARCH

Unraveling the role of low-frequency mutated genes in breast cancer

(2018) Eleonora Lusito et al.   BIOINFORMATICS

Highly sensitive detection of mutations in CHO cell recombinant DNA using multi-parallel single molecule real-time DNA sequencing

(2018) Joseph F. Cartwright et al.   BIOTECHNOLOGY AND BIOENGINEERING

Tumor Mutational Burden and Efficacy of Nivolumab Monotherapy and in Combination with Ipilimumab in Small-Cell Lung Cancer

(2018) Matthew D. Hellmann et al.   CANCER CELL

What Does This Mutation Mean? The Tools and Pitfalls of Variant Interpretation in Lymphoid Malignancies

(2018) Yann Guillermin et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Multiclonal tumor origin: Evidence and implications

(2018) Barbara L. Parsons   MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH

Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations

(2018) Jesse J. Salk et al.   NATURE REVIEWS GENETICS

Aging and the rise of somatic cancer-associated mutations in normal tissues

(2018) Rosa Ana Risques et al.   PLoS Genetics

Predicting response to checkpoint inhibitors in melanoma beyond PD-L1 and mutational burden

(2018) Carl Morrison et al.   Journal for ImmunoTherapy of Cancer

Somatic mutant clones colonize the human esophagus with age

(2018) Iñigo Martincorena et al.   SCIENCE

Elevated pyrimidine dimer formation at distinct genomic bases underlies promoter mutation hotspots in UV-exposed cancers

(2018) Kerryn Elliott et al.   PLoS Genetics

Tumor Mutational Burden as an Independent Predictor of Response to Immunotherapy in Diverse Cancers

(2017) Aaron M. Goodman et al.   MOLECULAR CANCER THERAPEUTICS

Analysis of mutant allele fractions in driver genes in colorectal cancer - biological and clinical insights

(2017) Rodrigo Dienstmann et al.   Molecular Oncology

Simple multiplexed PCR-based barcoding of DNA for ultrasensitive mutation detection by next-generation sequencing

(2017) Anders Ståhlberg et al.   Nature Protocols

First-Line Nivolumab in Stage IV or Recurrent Non–Small-Cell Lung Cancer

(2017) David P. Carbone et al.   NEW ENGLAND JOURNAL OF MEDICINE

Ultrasensitive and high-efficiency screen of de novo low-frequency mutations by o2n-seq

(2017) Kaile Wang et al.   Nature Communications

Recurrent promoter mutations in melanoma are defined by an extended context-specific mutational signature

(2017) Nils Johan Fredriksson et al.   PLoS Genetics

Statistical analysis of mutant allele frequency level of circulating cell-free DNA and blood cells in healthy individuals

(2017) Ligang Xia et al.   Scientific Reports

Three decades of nanopore sequencing

(2016) David Deamer et al.   NATURE BIOTECHNOLOGY

Integrated digital error suppression for improved detection of circulating tumor DNA

(2016) Aaron M Newman et al.   NATURE BIOTECHNOLOGY

Simple, multiplexed, PCR-based barcoding of DNA enables sensitive mutation detection in liquid biopsies using sequencing

(2016) Anders Ståhlberg et al.   NUCLEIC ACIDS RESEARCH

Genome-wide quantification of rare somatic mutations in normal human tissues using massively parallel sequencing

(2016) Margaret L. Hoang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted Next Generation Sequencing Identifies Markers of Response to PD-1 Blockade

(2016) D. B. Johnson et al.   Cancer Immunology Research

Current practices and guidelines for clinical next-generation sequencing oncology testing

(2016) Samuel P. Strom et al.   Cancer Biology & Medicine

Rapid expansion of preexisting nonleukemic hematopoietic clones frequently follows induction therapy for de novo AML

(2015) T. N. Wong et al.   BLOOD

High-throughput sequencing in mutation detection: A new generation of genotoxicity tests?

(2015) Alexander Y. Maslov et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Sequencing small genomic targets with high efficiency and extreme accuracy

(2015) Michael W Schmitt et al.   NATURE METHODS

High burden and pervasive positive selection of somatic mutations in normal human skin

(2015) I. Martincorena et al.   SCIENCE

Enhancing the detection of barcoded reads in high throughput DNA sequencing data by controlling the false discovery rate

(2014) Tilo Buschmann et al.   BMC BIOINFORMATICS

Prevalence of mutations in a panel of breast cancer susceptibility genes in BRCA1/2-negative patients with early-onset breast cancer

(2014) Kara N. Maxwell et al.   GENETICS IN MEDICINE

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

Differentiation imbalance in single oesophageal progenitor cells causes clonal immortalization and field change

(2014) Maria P. Alcolea et al.   NATURE CELL BIOLOGY

Detecting ultralow-frequency mutations by Duplex Sequencing

(2014) Scott R Kennedy et al.   Nature Protocols

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Emerging patterns of somatic mutations in cancer

(2013) Ian R. Watson et al.   NATURE REVIEWS GENETICS

Impact of deleterious passenger mutations on cancer progression

(2013) C. D. McFarland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing

(2013) D. I. Lou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma

(2012) Michael Krauthammer et al.   NATURE GENETICS

Detection of ultra-rare mutations by next-generation sequencing

(2012) M. W. Schmitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Single Progenitor Population Switches Behavior to Maintain and Repair Esophageal Epithelium

(2012) D. P. Doupe et al.   SCIENCE

Universal patterns of stem cell fate in cycling adult tissues

(2011) A. M. Klein et al.   DEVELOPMENT

Prevalence of the most frequent BRCA1 mutations in Polish population

(2011) Izabela Brozek et al.   JOURNAL OF APPLIED GENETICS

Somatic mutations in aging, cancer and neurodegeneration

(2011) Scott R. Kennedy et al.   MECHANISMS OF AGEING AND DEVELOPMENT

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

Detection and quantification of rare mutations with massively parallel sequencing

(2011) I. Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Comprehensive Survey of Clonal Diversity Measures in Barrett's Esophagus as Biomarkers of Progression to Esophageal Adenocarcinoma

(2010) L. M. F. Merlo et al.   Cancer Prevention Research

A flexible and efficient template format for circular consensus sequencing and SNP detection

(2010) K. J. Travers et al.   NUCLEIC ACIDS RESEARCH

Passenger mutations as a marker of clonal cell lineages in emerging neoplasia

(2010) Jesse J. Salk et al.   SEMINARS IN CANCER BIOLOGY

The mysterious steps in carcinogenesis

(2009) D Brash et al.   BRITISH JOURNAL OF CANCER

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

Stochastic fate of p53-mutant epidermal progenitor cells is tilted toward proliferation by UV B during preneoplasia

(2009) A. M. Klein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE