Exploiting the potential of next-generation sequencing in genomic medicine

Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA

(2016) Tychele N. Turner et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Exome sequencing analysis in a pair of monozygotic twins re-evaluates the genetics behind their intellectual disability and reveals a CHD2 mutation

(2016) Anna Maria Pinto et al.   BRAIN & DEVELOPMENT

Complex mode of inheritance in holoprosencephaly revealed by whole exome sequencing

(2016) C. Mouden et al.   CLINICAL GENETICS

Against all odds: blended phenotypes of three single-gene defects

(2016) Yong Li et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

MYBPH acts as modifier of cardiac hypertrophy in hypertrophic cardiomyopathy (HCM) patients

(2016) J. M. Mouton et al.   HUMAN GENETICS

Assessing similarity to primary tissue and cortical layer identity in induced pluripotent stem cell-derived cortical neurons through single-cell transcriptomics

(2016) Adam E. Handel et al.   HUMAN MOLECULAR GENETICS

Transcriptomics analysis of iPSC-derived neurons and modeling of neuropsychiatric disorders

(2016) Mingyan Lin et al.   MOLECULAR AND CELLULAR NEUROSCIENCE

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

(2016) Nicholas J. Schurch et al.   RNA

Long-read sequencing and de novo assembly of a Chinese genome

(2016) Lingling Shi et al.   Nature Communications

Personalized medicine in diabetes mellitus: current opportunities and future prospects

(2015) Jeffrey W. Kleinberger et al.   Annals of the New York Academy of Sciences

Somatic mosaicism of a CDKL5 mutation identified by next-generation sequencing

(2015) Takeshi Kato et al.   BRAIN & DEVELOPMENT

Low-level constitutional mosaicism of a de novoBRCA1 gene mutation

(2015) E Friedman et al.   BRITISH JOURNAL OF CANCER

Identification of novel hereditary cancer genes by whole exome sequencing

(2015) Anna P. Sokolenko et al.   CANCER LETTERS

Utility of whole-exome sequencing for those near the end of the diagnostic odyssey: time to address gaps in care

(2015) S.L. Sawyer et al.   CLINICAL GENETICS

Next generation sequencing in sporadic retinoblastoma patients reveals somatic mosaicism

(2015) Sara Amitrano et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Variants in RBP4 and AR genes modulate age at onset in familial amyloid polyneuropathy (FAP ATTRV30M)

(2015) Diana Santos et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Expanding the clinical, allelic and locus heterogeneity of retinal dystrophies

(2015) Nisha Patel et al.   GENETICS IN MEDICINE

Targeted Next-Generation Sequencing Analysis of 1,000 Individuals with Intellectual Disability

(2015) Detelina Grozeva et al.   HUMAN MUTATION

Next-Generation Diagnostics: Gene Panel, Exome, or Whole Genome?

(2015) Yu Sun et al.   HUMAN MUTATION

Evidence of digenic inheritance in Alport syndrome

(2015) Maria Antonietta Mencarelli et al.   JOURNAL OF MEDICAL GENETICS

The clinical application of genome-wide sequencing for monogenic diseases in Canada: Position Statement of the Canadian College of Medical Geneticists

(2015) Kym Boycott et al.   JOURNAL OF MEDICAL GENETICS

Sporadic hereditary motor and sensory neuropathies: Advances in the diagnosis using next generation sequencing technology

(2015) Chiara Fallerini et al.   JOURNAL OF THE NEUROLOGICAL SCIENCES

Unrevealed mosaicism in the next-generation sequencing era

(2015) Marzena Gajecka   MOLECULAR GENETICS AND GENOMICS

Deep phenotyping: The details of disease

(2015) Cathryn M. Delude   NATURE

Whole-genome sequencing of quartet families with autism spectrum disorder

(2015) Ryan K C Yuen et al.   NATURE MEDICINE

Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture

(2015) Anca M Paşca et al.   NATURE METHODS

DIDA: A curated and annotated digenic diseases database

(2015) Andrea M. Gazzo et al.   NUCLEIC ACIDS RESEARCH

Cancer whole-genome sequencing: present and future

(2015) H Nakagawa et al.   ONCOGENE

Targeted Next-Generation Sequencing for Clinical Diagnosis of 561 Mendelian Diseases

(2015) Yanqiu Liu et al.   PLoS One

Genome-wide association meta-analysis identifies five modifier loci of lung disease severity in cystic fibrosis

(2015) Harriet Corvol et al.   Nature Communications

Whole Genome Sequencing Reveals a De Novo SHANK3 Mutation in Familial Autism Spectrum Disorder

(2015) Sergio I. Nemirovsky et al.   PLoS One

Evaluation of an integrated clinical workflow for targeted next-generation sequencing of low-quality tumor DNA using a 51-gene enrichment panel

(2014) Ashish Choudhary et al.   BMC Medical Genomics

Autosomal dominant polycystic kidney disease caused by somatic and germline mosaicism

(2014) A.Y. Tan et al.   CLINICAL GENETICS

Introduction to RNA-Seq and its Applications to Drug Discovery and Development

(2014) Zainab Khatoon et al.   DRUG DEVELOPMENT RESEARCH

Human molecular cytogenetics: from cells to nucleotides

(2014) Mariluce Riegel   GENETICS AND MOLECULAR BIOLOGY

Mosaicism for Dominant Collagen 6 Mutations as a Cause for Intrafamilial Phenotypic Variability

(2014) Sandra Donkervoort et al.   HUMAN MUTATION

Molecular Findings Among Patients Referred for Clinical Whole-Exome Sequencing

(2014) Yaping Yang et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Clinical Exome Sequencing for Genetic Identification of Rare Mendelian Disorders

(2014) Hane Lee et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Efficient strategy for the molecular diagnosis of intellectual disability using targeted high-throughput sequencing

(2014) Claire Redin et al.   JOURNAL OF MEDICAL GENETICS

Sensitive and specific detection of EML4-ALK rearrangements in non-small cell lung cancer (NSCLC) specimens by multiplex amplicon RNA massive parallel sequencing

(2014) Evgeny A. Moskalev et al.   LUNG CANCER

Oligogenic germline mutations identified in early non-smokers lung adenocarcinoma patients

(2014) Alessandra Renieri et al.   LUNG CANCER

Genome sequencing identifies major causes of severe intellectual disability

(2014) Christian Gilissen et al.   NATURE

Technology: The $1,000 genome

(2014) Erika Check Hayden   NATURE

Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4

(2014) Pilar Ramos et al.   NATURE GENETICS

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Next Generation Sequencing and the Future of Genetic Diagnosis

(2014) Katja Lohmann et al.   Neurotherapeutics

Somatic Mutations in Cerebral Cortical Malformations

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

Detection of Clinically Relevant Genetic Variants in Autism Spectrum Disorder by Whole-Genome Sequencing

(2013) Yong-hui Jiang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Direct Conversion of Fibroblasts to Neurons by Reprogramming PTB-Regulated MicroRNA Circuits

(2013) Yuanchao Xue et al.   CELL

Unbiased next generation sequencing analysis confirms the existence of autosomal dominant Alport syndrome in a relevant fraction of cases

(2013) C. Fallerini et al.   CLINICAL GENETICS

Next generation sequencing as a useful tool in the diagnostics of mosaicism in Alport syndrome

(2013) Sonja Beicht et al.   GENE

Targeted Next-Generation Sequencing can Replace Sanger Sequencing in Clinical Diagnostics

(2013) Birgit Sikkema-Raddatz et al.   HUMAN MUTATION

Digenic inheritance in medical genetics

(2013) Alejandro A Schäffer   JOURNAL OF MEDICAL GENETICS

A genomic view of mosaicism and human disease

(2013) Leslie G. Biesecker et al.   NATURE REVIEWS GENETICS

Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders

(2013) Yaping Yang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Revealing the Complexity of a Monogenic Disease: Rett Syndrome Exome Sequencing

(2013) Elisa Grillo et al.   PLoS One

Genotyping by Genome Reducing and Sequencing for Outbred Animals

(2013) Qiang Chen et al.   PLoS One

Exome sequencing overrides formal genetics:ASPMmutations in a case study of apparent X-linked microcephalic intellectual deficit

(2012) F Ariani et al.   CLINICAL GENETICS

RNA-Seq and human complex diseases: recent accomplishments and future perspectives

(2012) Valerio Costa et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Opportunities and challenges for the integration of massively parallel genomic sequencing into clinical practice: lessons from the ClinSeq project

(2012) Leslie G. Biesecker   GENETICS IN MEDICINE

Next-generation sequencing demands next-generation phenotyping

(2012) Raoul C.M. Hennekam et al.   HUMAN MUTATION

Comparison of Next-Generation Sequencing Systems

(2012) Lin Liu et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Exome sequencing of extreme phenotypes identifies DCTN4 as a modifier of chronic Pseudomonas aeruginosa infection in cystic fibrosis

(2012) Mary J Emond et al.   NATURE GENETICS

Digenic inheritance of an SMCHD1 mutation and an FSHD-permissive D4Z4 allele causes facioscapulohumeral muscular dystrophy type 2

(2012) Richard J L F Lemmers et al.   NATURE GENETICS

Analysis of alternative cleavage and polyadenylation by 3′ region extraction and deep sequencing

(2012) Mainul Hoque et al.   NATURE METHODS

RETRACTED: Directed Conversion of Alzheimer's Disease Patient Skin Fibroblasts into Functional Neurons

(2011) Liang Qiang et al.   CELL

Targeted Next-Generation Sequencing for the Molecular Genetic Diagnostics of Cardiomyopathies

(2011) Benjamin Meder et al.   Circulation-Cardiovascular Genetics

Advances in Alport syndrome diagnosis using next-generation sequencing

(2011) Rosangela Artuso et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Direct generation of functional dopaminergic neurons from mouse and human fibroblasts

(2011) Massimiliano Caiazzo et al.   NATURE

Identification of Sequence Variants in Genetic Disease-Causing Genes Using Targeted Next-Generation Sequencing

(2011) Xiaoming Wei et al.   PLoS One

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

(2011) P. J. Shepard et al.   RNA

A Model for Neural Development and Treatment of Rett Syndrome Using Human Induced Pluripotent Stem Cells

(2010) Maria C.N. Marchetto et al.   CELL

Pluripotent stem cells in neurodegenerative and neurodevelopmental diseases

(2010) M. C. N. Marchetto et al.   HUMAN MOLECULAR GENETICS

Exome sequencing: the sweet spot before whole genomes

(2010) J. K. Teer et al.   HUMAN MOLECULAR GENETICS

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

Direct conversion of fibroblasts to functional neurons by defined factors

(2010) Thomas Vierbuchen et al.   NATURE

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Neural differentiation of human induced pluripotent stem cells follows developmental principles but with variable potency

(2010) B.-Y. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parallel sequencing used in detection of mosaic mutations: Comparison with four diagnostic DNA screening techniques

(2009) Anna Rohlin et al.   HUMAN MUTATION

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

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

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts

(2009) Joshua Z Levin et al.   GENOME BIOLOGY

The Genome Sequencer FLX™ System—Longer reads, more applications, straight forward bioinformatics and more complete data sets

(2008) Marcus Droege et al.   JOURNAL OF BIOTECHNOLOGY

The complete genome of an individual by massively parallel DNA sequencing

(2008) David A. Wheeler et al.   NATURE

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

(2008) Brian T. Wilhelm et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE