Somatic Mosaicism in the Human Genome

Mutations and Deregulation of Ras/Raf/MEK/ERK and PI3K/PTEN/Akt/mTOR Cascades

(2015) James Andrew McCubrey et al.   Oncotarget

Parental Somatic Mosaicism Is Underrecognized and Influences Recurrence Risk of Genomic Disorders

(2014) Ian M. Campbell et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Toward better understanding of artifacts in variant calling from high-coverage samples

(2014) Heng Li   BIOINFORMATICS

Subclonal variant calling with multiple samples and prior knowledge

(2014) M. Gerstung et al.   BIOINFORMATICS

An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples

(2014) V. K. Yadav et al.   BRIEFINGS IN BIOINFORMATICS

Recent advances in the study of somatic mosaicism and diseases other than cancer

(2014) Robert P Erickson   CURRENT OPINION IN GENETICS & DEVELOPMENT

The origin, mechanisms, incidence and clinical consequences of chromosomal mosaicism in humans

(2014) Tyl H. Taylor et al.   HUMAN REPRODUCTION UPDATE

Haplotype Counting by Next-Generation Sequencing for Ultrasensitive Human DNA Detection

(2014) Marija Debeljak et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Synaptic, transcriptional and chromatin genes disrupted in autism

(2014) Silvia De Rubeis et al.   NATURE

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

(2014) Yong Wang et al.   NATURE

The contribution of de novo coding mutations to autism spectrum disorder

(2014) Ivan Iossifov et al.   NATURE

Most genetic risk for autism resides with common variation

(2014) Trent Gaugler et al.   NATURE GENETICS

Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data

(2014) Fernando Amat et al.   NATURE METHODS

PI3K and cancer: lessons, challenges and opportunities

(2014) David A. Fruman et al.   NATURE REVIEWS DRUG DISCOVERY

Expanding the computational toolbox for mining cancer genomes

(2014) Li Ding et al.   NATURE REVIEWS GENETICS

Understanding nucleotide excision repair and its roles in cancer and ageing

(2014) Jurgen A. Marteijn et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Patches of Disorganization in the Neocortex of Children with Autism

(2014) Rich Stoner et al.   NEW ENGLAND JOURNAL OF MEDICINE

Somatic Mutations in Cerebral Cortical Malformations

(2014) Saumya S. Jamuar et al.   NEW ENGLAND JOURNAL OF MEDICINE

Distinct synthetic A  prion strains producing different amyloid deposits in bigenic mice

(2014) J. Stohr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Serial propagation of distinct strains of A  prions from Alzheimer's disease patients

(2014) J. C. Watts et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A de novo convergence of autism genetics and molecular neuroscience

(2014) Niklas Krumm et al.   TRENDS IN NEUROSCIENCES

Single-Cell, Genome-wide Sequencing Identifies Clonal Somatic Copy-Number Variation in the Human Brain

(2014) Xuyu Cai et al.   Cell Reports

Patterns of Somatically Acquired Amplifications and Deletions in Apparently Normal Tissues of Ovarian Cancer Patients

(2014) Leila Aghili et al.   Cell Reports

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

Precise inference of copy number alterations in tumor samples from SNP arrays

(2013) Gary K. Chen et al.   BIOINFORMATICS

CoNVEX: copy number variation estimation in exome sequencing data using HMM

(2013) Kaushalya C Amarasinghe et al.   BMC BIOINFORMATICS

Sensitive and specific detection of mosaic chromosomal abnormalities using the Parent-of-Origin-based Detection (POD) method

(2013) Joseph D Baugher et al.   BMC GENOMICS

Molecular Structure of β-Amyloid Fibrils in Alzheimer’s Disease Brain Tissue

(2013) Jun-Xia Lu et al.   CELL

The balancing act of DNA repeat expansions

(2013) Jane C Kim et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Brain somatic mutations: the dark matter of psychiatric genetics?

(2013) T R Insel   MOLECULAR PSYCHIATRY

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Emerging patterns of somatic mutations in cancer

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

Sturge–Weber Syndrome and Port-Wine Stains Caused by Somatic Mutation in GNAQ

(2013) Matthew D. Shirley et al.   NEW ENGLAND JOURNAL OF MEDICINE

SomatiCA: Identifying, Characterizing and Quantifying Somatic Copy Number Aberrations from Cancer Genome Sequencing Data

(2013) Mengjie Chen et al.   PLoS One

Mosaic Copy Number Variation in Human Neurons

(2013) M. J. McConnell et al.   SCIENCE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Somatic Mutation, Genomic Variation, and Neurological Disease

(2013) A. Poduri et al.   SCIENCE

The genomically mosaic brain: Aneuploidy and more in neural diversity and disease

(2013) Diane M. Bushman et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Somatic Mosaic Activating Mutations in PIK3CA Cause CLOVES Syndrome

(2012) Kyle C. Kurek et al.   AMERICAN JOURNAL OF HUMAN GENETICS

JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data

(2012) Andrew Roth et al.   BIOINFORMATICS

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain

(2012) Gilad D. Evrony et al.   CELL

Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor

(2012) Xun Xu et al.   CELL

Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm

(2012) Yong Hou et al.   CELL

Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers

(2012) Ramaswamy Govindan et al.   CELL

Mechanisms for recurrent and complex human genomic rearrangements

(2012) Pengfei Liu et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Active human retrotransposons: variation and disease

(2012) Dustin C Hancks et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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

Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells

(2012) Alexej Abyzov et al.   NATURE

De novo germline and postzygotic mutations in AKT3, PIK3R2 and PIK3CA cause a spectrum of related megalencephaly syndromes

(2012) Jean-Baptiste Rivière et al.   NATURE GENETICS

De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly

(2012) Jeong Ho Lee et al.   NATURE GENETICS

Detectable clonal mosaicism and its relationship to aging and cancer

(2012) Kevin B Jacobs et al.   NATURE GENETICS

Detectable clonal mosaicism from birth to old age and its relationship to cancer

(2012) Cathy C Laurie et al.   NATURE GENETICS

Genome-wide copy number analysis of single cells

(2012) Timour Baslan et al.   Nature Protocols

Somatic Activation of AKT3 Causes Hemispheric Developmental Brain Malformations

(2012) Annapurna Poduri et al.   NEURON

McCune-Albright syndrome and the extraskeletal manifestations of fibrous dysplasia

(2012) Michael T Collins et al.   Orphanet Journal of Rare Diseases

Extensive genetic variation in somatic human tissues

(2012) M. O'Huallachain et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Landscape of Somatic Retrotransposition in Human Cancers

(2012) E. Lee et al.   SCIENCE

Advances in Whole-Genome Genetic Testing: From Chromosomes to Microarrays

(2012) Patricia L. Crotwell et al.   Current Problems in Pediatric and Adolescent Health Care

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

(2011) David E. Larson et al.   BIOINFORMATICS

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

(2011) Valentina Boeva et al.   BIOINFORMATICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Chromosome Analysis Using Spectral Karyotyping (SKY)

(2011) George Imataka et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Valuing gene testing in children with possible neurofibromatosis 1

(2011) E Tsang et al.   CLINICAL GENETICS

Chromosomal mosaicism in human preimplantation embryos: a systematic review

(2011) Jannie van Echten-Arends et al.   HUMAN REPRODUCTION UPDATE

Somatic mutations in aging, cancer and neurodegeneration

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

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Somatic retrotransposition alters the genetic landscape of the human brain

(2011) J. Kenneth Baillie et al.   NATURE

Somatic mosaic IDH1 and IDH2 mutations are associated with enchondroma and spindle cell hemangioma in Ollier disease and Maffucci syndrome

(2011) Twinkal C Pansuriya et al.   NATURE GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

A Mosaic Activating Mutation inAKT1Associated with the Proteus Syndrome

(2011) Marjorie J. Lindhurst et al.   NEW ENGLAND JOURNAL OF MEDICINE

Direct, genome-wide assessment of DNA mutations in single cells

(2011) Michael Gundry et al.   NUCLEIC ACIDS RESEARCH

GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays

(2011) Ao Li et al.   NUCLEIC ACIDS RESEARCH

Noninvasive Prenatal Diagnosis of Fetal Trisomy 18 and Trisomy 13 by Maternal Plasma DNA Sequencing

(2011) Eric Z. Chen et al.   PLoS One

DNA repair deficiency in neurodegeneration

(2011) Dennis Kjølhede Jeppesen et al.   PROGRESS IN NEUROBIOLOGY

An Activating Mutation of AKT2 and Human Hypoglycemia

(2011) K. Hussain et al.   SCIENCE

Somatic mosaicism in healthy human tissues

(2011) Subhajyoti De   TRENDS IN GENETICS

Mosaic Uniparental Disomies and Aneuploidies as Large Structural Variants of the Human Genome

(2010) Benjamín Rodríguez-Santiago et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Monozygotic twins discordant for neurofibromatosis 1

(2010) Lee Kaplan et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Somatic mosaicism in a case of apparently sporadic Creutzfeldt-Jakob disease carrying a de novo D178N mutation in the PRNP gene

(2010) A. Alzualde et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS

An integrated Bayesian analysis of LOH and copy number data

(2010) Paola MV Rancoita et al.   BMC BIOINFORMATICS

Mechanisms of mosaicism, chimerism and uniparental disomy identified by single nucleotide polymorphism array analysis

(2010) Laura K. Conlin et al.   HUMAN MOLECULAR GENETICS

Somatic gene mutation and human disease other than cancer: An update

(2010) Robert P. Erickson   MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH

Evaluating genome-scale approaches to eukaryotic DNA replication

(2010) David M. Gilbert   NATURE REVIEWS GENETICS

Mechanisms of trinucleotide repeat instability during human development

(2010) Cynthia T. McMurray   NATURE REVIEWS GENETICS

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Mutations inGNA11in Uveal Melanoma

(2010) Catherine D. Van Raamsdonk et al.   NEW ENGLAND JOURNAL OF MEDICINE

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

MixHMM: Inferring Copy Number Variation and Allelic Imbalance Using SNP Arrays and Tumor Samples Mixed with Stromal Cells

(2010) Zongzhi Liu et al.   PLoS One

Mitotic Recombination in Patients with Ichthyosis Causes Reversion of Dominant Mutations in KRT10

(2010) K. A. Choate et al.   SCIENCE

Human RECQ helicases: Roles in DNA metabolism, mutagenesis and cancer biology

(2010) Raymond J. Monnat   SEMINARS IN CANCER BIOLOGY

Revertant mosaicism in skin: natural gene therapy

(2010) Joey E. Lai-Cheong et al.   TRENDS IN MOLECULAR MEDICINE

Cytogenetic contribution to uniparental disomy (UPD)

(2010) Thomas Liehr   Molecular Cytogenetics

Human interphase chromosomes: a review of available molecular cytogenetic technologies

(2010) Svetlana G Vorsanova et al.   Molecular Cytogenetics

Continuous and Periodic Expansion of CAG Repeats in Huntington's Disease R6/1 Mice

(2010) Linda Møllersen et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Mechanics of T cell receptor gene rearrangement

(2009) Michael S Krangel   CURRENT OPINION IN IMMUNOLOGY

Copy number variation and mosaicism

(2009) A.J. Notini et al.   CYTOGENETIC AND GENOME RESEARCH

Sensitive and accurate detection of copy number variants using read depth of coverage

(2009) S. Yoon et al.   GENOME RESEARCH

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

L1 retrotransposition in human neural progenitor cells

(2009) Nicole G. Coufal et al.   NATURE

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

Chromosome instability is common in human cleavage-stage embryos

(2009) Evelyne Vanneste et al.   NATURE MEDICINE

DNA Damage, Aging, and Cancer

(2009) Jan H.J. Hoeijmakers   NEW ENGLAND JOURNAL OF MEDICINE

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

(2009) Peter J. A. Cock et al.   NUCLEIC ACIDS RESEARCH

DNA polymerase   and   proofreading suppress discrete mutator and cancer phenotypes in mice

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

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing

(2009) Murim Choi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Somatic mosaicism for copy number variation in differentiated human tissues

(2008) Arkadiusz Piotrowski et al.   HUMAN MUTATION

Tuberous sclerosis

(2008) Paolo Curatolo et al.   LANCET

Tissue-specific accelerated aging in nucleotide excision repair deficiency

(2008) Laura J. Niedernhofer   MECHANISMS OF AGEING AND DEVELOPMENT

Impact of whole genome amplification on analysis of copy number variants

(2008) T. J. Pugh et al.   NUCLEIC ACIDS RESEARCH