How low can you go?: Methodologic considerations in clonal hematopoiesis variant calling

A practical approach to curate clonal hematopoiesis of indeterminate potential in human genetic datasets

(2023) Caitlyn Vlasschaert et al.   BLOOD

The genetic determinants of recurrent somatic mutations in 43,693 blood genomes

(2023) Joshua S. Weinstock et al.   Science Advances

Association of Clonal Hematopoiesis of Indeterminate Potential with Worse Kidney Function and Anemia in Two Cohorts of Patients with Advanced Chronic Kidney Disease

(2022) Caitlyn Vlasschaert et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

The longitudinal dynamics and natural history of clonal haematopoiesis

(2022) Margarete A. Fabre et al.   NATURE

The Human Pangenome Project: a global resource to map genomic diversity

(2022) Ting Wang et al.   NATURE

A complete reference genome improves analysis of human genetic variation

(2022) Sergey Aganezov et al.   SCIENCE

TET2-mutant clonal hematopoiesis and risk of gout

(2022) Mridul Agrawal et al.   BLOOD

Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis

(2022) Siddhartha P. Kar et al.   NATURE GENETICS

Common and rare variant associations with clonal haematopoiesis phenotypes

(2022) Michael D. Kessler et al.   NATURE

Somatic Mutations in “Benign” Disease

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

Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis

(2021) Shuo Li et al.   Nature Communications

Association of clonal hematopoiesis with chronic obstructive pulmonary disease

(2021) Peter G. Miller et al.   BLOOD

Dnmt3a-mutated clonal hematopoiesis promotes osteoporosis

(2021) Peter Geon Kim et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Clonal hematopoiesis is associated with risk of severe Covid-19

(2021) Kelly L. Bolton et al.   Nature Communications

Accurate detection of mosaic variants in sequencing data without matched controls

(2020) Yanmei Dou et al.   NATURE BIOTECHNOLOGY

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

The evolutionary dynamics and fitness landscape of clonal hematopoiesis

(2020) Caroline J. Watson et al.   SCIENCE

Cancer therapy shapes the fitness landscape of clonal hematopoiesis

(2020) Kelly L. Bolton et al.   NATURE GENETICS

Linked-read analysis identifies mutations in single-cell DNA-sequencing data

(2019) Craig L. Bohrson et al.   NATURE GENETICS

Somatic Mutations Increase Hepatic Clonal Fitness and Regeneration in Chronic Liver Disease

(2019) Min Zhu et al.   CELL

RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues

(2019) Keren Yizhak et al.   SCIENCE

eVIDENCE: a practical variant filtering for low-frequency variants detection in cell-free DNA

(2019) Kei Mizuno et al.   Scientific Reports

Strelka2: fast and accurate calling of germline and somatic variants

(2018) Sangtae Kim et al.   NATURE METHODS

ERASE-Seq: Leveraging replicate measurements to enhance ultralow frequency variant detection in NGS data

(2018) Nick Kamps-Hughes et al.   PLoS One

A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data

(2018) Chang Xu   Computational and Structural Biotechnology Journal

Somatic mutant clones colonize the human esophagus with age

(2018) Iñigo Martincorena et al.   SCIENCE

MosaicHunter: accurate detection of postzygotic single-nucleotide mosaicism through next-generation sequencing of unpaired, trio, and paired samples

(2017) August Yue Huang et al.   NUCLEIC ACIDS RESEARCH

Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers

(2017) Maurizio Callari et al.   Genome Medicine

SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA

(2016) Can Kockan et al.   BIOINFORMATICS

Integrated digital error suppression for improved detection of circulating tumor DNA

(2016) Aaron M Newman et al.   NATURE BIOTECHNOLOGY

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

(2016) Zhongwu Lai et al.   NUCLEIC ACIDS RESEARCH

Clonal haematopoiesis harbouring AML-associated mutations is ubiquitous in healthy adults

(2016) Andrew L. Young et al.   Nature Communications

Quantifying ultra-rare pre-leukemic clones via targeted error-corrected sequencing

(2015) A L Young et al.   LEUKEMIA

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

(2015) I. Martincorena et al.   SCIENCE

Mutations in the DNA methyltransferase gene DNMT3A cause an overgrowth syndrome with intellectual disability

(2014) Katrina Tatton-Brown et al.   NATURE GENETICS

Mosaic loss of chromosome Y in peripheral blood is associated with shorter survival and higher risk of cancer

(2014) Lars A Forsberg et al.   NATURE GENETICS

Age-related mutations associated with clonal hematopoietic expansion and malignancies

(2014) Mingchao Xie et al.   NATURE MEDICINE

Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence

(2014) Giulio Genovese et al.   NEW ENGLAND JOURNAL OF MEDICINE

Age-Related Clonal Hematopoiesis Associated with Adverse Outcomes

(2014) Siddhartha Jaiswal et al.   NEW ENGLAND JOURNAL OF MEDICINE

Quantifying single nucleotide variant detection sensitivity in exome sequencing

(2013) Alison M Meynert et al.   BMC BIOINFORMATICS

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

(2013) Maura Costello et al.   NUCLEIC ACIDS RESEARCH

The Origin and Evolution of Mutations in Acute Myeloid Leukemia

(2012) John S. Welch et al.   CELL

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Detectable clonal mosaicism and its relationship to aging and cancer

(2012) Kevin B Jacobs 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

Performance comparison of exome DNA sequencing technologies

(2011) Michael J Clark et al.   NATURE BIOTECHNOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY