Bioinformatics and Computational Tools for Next-Generation Sequencing Analysis in Clinical Genetics

Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome

(2019) Wouter De Coster et al.   GENOME RESEARCH

Characterization of CCDC103 expression profiles: further insights in primary ciliary dyskinesia and in human reproduction

(2019) R. Pereira et al.   JOURNAL OF ASSISTED REPRODUCTION AND GENETICS

Long-read sequencing in human genetics

(2019) Florian Kraft et al.   Medizinische Genetik

Long-read sequencing for rare human genetic diseases

(2019) Satomi Mitsuhashi et al.   JOURNAL OF HUMAN GENETICS

High-resolution analysis of germ cells from men with sex chromosomal aneuploidies reveals normal transcriptome but impaired imprinting

(2019) Sandra Laurentino et al.   Clinical Epigenetics

Clinical and Genetic Analysis of Children with Kartagener Syndrome

(2019) Rute Pereira et al.   Cells

Genome Assembly of the A-Group Wolbachia in Nasonia oneida Using Linked-Reads Technology

(2019) Xiaozhu Wang et al.   Genome Biology and Evolution

Single-Cell RNA Sequencing Resolves Spatiotemporal Development of Pre-thymic Lymphoid Progenitors and Thymus Organogenesis in Human Embryos

(2019) Yang Zeng et al.   IMMUNITY

Recent advances in the detection of base modifications using the Nanopore sequencer

(2019) Liu Xu et al.   JOURNAL OF HUMAN GENETICS

Accurate, scalable and integrative haplotype estimation

(2019) Olivier Delaneau et al.   Nature Communications

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

(2019) Jeffrey M. Granja et al.   NATURE BIOTECHNOLOGY

Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers

(2018) Yu Fu et al.   BMC GENOMICS

Assessment of Capture and Amplicon-Based Approaches for the Development of a Targeted Next-Generation Sequencing Pipeline to Personalize Lymphoma Management

(2018) Stacy S. Hung et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

(2018) Fritz J. Sedlazeck et al.   NATURE REVIEWS GENETICS

VarAFT: a variant annotation and filtration system for human next generation sequencing data

(2018) Jean-Pierre Desvignes et al.   NUCLEIC ACIDS RESEARCH

Detecting Rare Mutations and DNA Damage with Sequencing-Based Methods

(2018) Daniel B. Sloan et al.   TRENDS IN BIOTECHNOLOGY

The Third Revolution in Sequencing Technology

(2018) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Single-Molecule Sequencing: Towards Clinical Applications

(2018) Adam Ameur et al.   TRENDS IN BIOTECHNOLOGY

De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data

(2018) Adam Ameur et al.   Genes

The European Society of Human Genetics: beginnings, early history and development over its first 25 years

(2017) Peter S Harper   EUROPEAN JOURNAL OF HUMAN GENETICS

Long-read genome sequencing identifies causal structural variation in a Mendelian disease

(2017) Jason D Merker et al.   GENETICS IN MEDICINE

Settling the score: variant prioritization and Mendelian disease

(2017) Karen Eilbeck et al.   NATURE REVIEWS GENETICS

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

(2017) Kazuma Nakano et al.   Human Cell

Impact of post-alignment processing in variant discovery from whole exome data

(2016) Shulan Tian et al.   BMC BIOINFORMATICS

VarElect: the phenotype-based variation prioritizer of the GeneCards Suite

(2016) Gil Stelzer et al.   BMC GENOMICS

Finding small somatic structural variants in exome sequencing data: a machine learning approach

(2016) Matthias Kuhn et al.   COMPUTATIONAL STATISTICS

Novel bioinformatic developments for exome sequencing

(2016) Stefan H. Lelieveld et al.   HUMAN GENETICS

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Three decades of nanopore sequencing

(2016) David Deamer et al.   NATURE BIOTECHNOLOGY

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

Library construction for next-generation sequencing: Overviews and challenges

(2016) Steven R. Head et al.   BIOTECHNIQUES

A Comparison of Base-calling Algorithms for Illumina Sequencing Technology

(2015) Ashley Cacho et al.   BRIEFINGS IN BIOINFORMATICS

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

(2015) Sara Goodwin et al.   GENOME RESEARCH

Evaluation of Hybridization Capture Versus Amplicon-Based Methods for Whole-Exome Sequencing

(2015) Eric Samorodnitsky et al.   HUMAN MUTATION

Improved data analysis for the MinION nanopore sequencer

(2015) Miten Jain et al.   NATURE METHODS

Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR

(2015) Hui Yang et al.   Nature Protocols

Machine learning applications in genetics and genomics

(2015) Maxwell W. Libbrecht et al.   NATURE REVIEWS GENETICS

A copy number variation map of the human genome

(2015) Mehdi Zarrei et al.   NATURE REVIEWS GENETICS

Next-generation sequencing to guide cancer therapy

(2015) Jeffrey Gagan et al.   Genome Medicine

Next-Generation Technologies for Multiomics Approaches Including Interactome Sequencing

(2015) Hiroyuki Ohashi et al.   Biomed Research International

Whole-genome CNV analysis: advances in computational approaches

(2015) Mehdi Pirooznia et al.   Frontiers in Genetics

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Systematic comparison of variant calling pipelines using gold standard personal exome variants

(2015) Sohyun Hwang et al.   Scientific Reports

Phevor Combines Multiple Biomedical Ontologies for Accurate Identification of Disease-Causing Alleles in Single Individuals and Small Nuclear Families

(2014) Marc V. Singleton et al.   AMERICAN JOURNAL OF HUMAN GENETICS

H 3 M 2 : detection of runs of homozygosity from whole-exome sequencing data

(2014) Alberto Magi et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Library preparation methods for next-generation sequencing: Tone down the bias

(2014) Erwin L. van Dijk et al.   EXPERIMENTAL CELL RESEARCH

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Diagnostic Clinical Genome and Exome Sequencing

(2014) Leslie G. Biesecker et al.   NEW ENGLAND JOURNAL OF MEDICINE

leeHom: adaptor trimming and merging for Illumina sequencing reads

(2014) Gabriel Renaud et al.   NUCLEIC ACIDS RESEARCH

Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome

(2014) T. Zemojtel et al.   Science Translational Medicine

Choice of transcripts and software has a large effect on variant annotation

(2014) Davis J McCarthy et al.   Genome Medicine

Correction: Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes

(2014) Slavé Petrovski et al.   PLoS Genetics

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

(2013) Min Zhao et al.   BMC BIOINFORMATICS

Improved exome prioritization of disease genes through cross-species phenotype comparison

(2013) P. N. Robinson et al.   GENOME RESEARCH

QC-Chain: Fast and Holistic Quality Control Method for Next-Generation Sequencing Data

(2013) Qian Zhou et al.   PLoS One

An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis

(2013) Cristian Del Fabbro et al.   PLoS One

Understanding the limitations of next generation sequencing informatics, an approach to clinical pipeline validation using artificial data sets

(2013) Robert Daber et al.   Cancer Genetics

Interpretation of Genomic Variants Using a Unified Biological Network Approach

(2013) Ekta Khurana et al.   PLoS Computational Biology

Tools for mapping high-throughput sequencing data

(2012) Nuno A. Fonseca et al.   BIOINFORMATICS

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

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Progress in Ion Torrent semiconductor chip based sequencing

(2012) Barry Merriman et al.   ELECTROPHORESIS

Disease gene identification strategies for exome sequencing

(2012) Christian Gilissen et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Informatics and clinical genome sequencing: opening the black box

(2012) Sowmiya Moorthie et al.   GENETICS IN MEDICINE

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score, Condel

(2011) Abel González-Pérez et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Exome sequencing: Dual role as a discovery and diagnostic tool

(2011) Chee-Seng Ku et al.   ANNALS OF NEUROLOGY

Comparative analysis of algorithms for next-generation sequencing read alignment

(2011) M. Ruffalo et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Addressing challenges in the production and analysis of illumina sequencing data

(2011) Martin Kircher et al.   BMC GENOMICS

Base-calling for next-generation sequencing platforms

(2011) C. Ledergerber et al.   BRIEFINGS IN BIOINFORMATICS

Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph

(2011) Z. Li et al.   Briefings in Functional Genomics

Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies

(2011) Yong Kong   GENOMICS

Insight into the heterogeneity of breast cancer through next-generation sequencing

(2011) Hege G. Russnes et al.   JOURNAL OF CLINICAL INVESTIGATION

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

How to apply de Bruijn graphs to genome assembly

(2011) Phillip E C Compeau et al.   NATURE BIOTECHNOLOGY

Understanding the contribution of synonymous mutations to human disease

(2011) Zuben E. Sauna et al.   NATURE REVIEWS GENETICS

Exome sequencing as a tool for Mendelian disease gene discovery

(2011) Michael J. Bamshad et al.   NATURE REVIEWS GENETICS

Learning about human population history from ancient and modern genomes

(2011) Mark Stoneking et al.   NATURE REVIEWS GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Systematic Comparison of Three Methods for Fragmentation of Long-Range PCR Products for Next Generation Sequencing

(2011) Ellen Knierim et al.   PLoS One

The real cost of sequencing: higher than you think!

(2011) Andrea Sboner et al.   GENOME BIOLOGY

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Structural Variation in the Human Genome and its Role in Disease

(2010) Paweł Stankiewicz et al.   Annual Review of Medicine

SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data

(2010) H. J. Abel et al.   BIOINFORMATICS

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Third Generation DNA Sequencing: Pacific Biosciences' Single Molecule Real Time Technology

(2010) Alice McCarthy   CHEMISTRY & BIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

A window into third-generation sequencing

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

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The $1,000 genome, the $100,000 analysis?

(2010) Elaine R Mardis   Genome Medicine

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing

(2009) W.-C. Kao et al.   GENOME RESEARCH

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

(2009) K. D. Pruitt et al.   GENOME RESEARCH

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

The challenges of sequencing by synthesis

(2009) Carl W Fuller et al.   NATURE BIOTECHNOLOGY

Single-molecule sequencing of an individual human genome

(2009) Dmitry Pushkarev et al.   NATURE BIOTECHNOLOGY

Sense from sequence reads: methods for alignment and assembly

(2009) Paul Flicek et al.   NATURE METHODS

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

Human Splicing Finder: an online bioinformatics tool to predict splicing signals

(2009) François-Olivier Desmet et al.   NUCLEIC ACIDS RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

1000 Genomes project

(2008) Nayanah Siva   NATURE BIOTECHNOLOGY

Alta-Cyclic: a self-optimizing base caller for next-generation sequencing

(2008) Yaniv Erlich et al.   NATURE METHODS