Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance

dv-trio: a family-based variant calling pipeline using DeepVariant

(2020) Eddie K K Ip et al.   BIOINFORMATICS

Insights into genetics, human biology and disease gleaned from family based genomic studies

(2019) Jennifer E. Posey et al.   GENETICS IN MEDICINE

Miniaturization and optimization of 384-well compatible RNA sequencing library preparation

(2019) Madeline Y. Mayday et al.   PLoS One

Whole-genome sequencing identifies complex contributions to genetic risk by variants in genes causing monogenic systemic lupus erythematosus

(2019) Jonas Carlsson Almlöf et al.   HUMAN GENETICS

Recent developments in genetic/genomic medicine

(2019) Rachel H. Horton et al.   CLINICAL SCIENCE

Practical Guidance to Implementing Quality Management Systems in Public Health Laboratories Performing Next Generation Sequencing: Personnel, Equipment, and Process Management (Phase 1)

(2019) Rebecca J. Hutchins et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Clinical application of next-generation sequencing to the practice of neurology

(2019) Jessica Rexach et al.   LANCET NEUROLOGY

Whole-genome and targeted sequencing of drug-resistant Mycobacterium tuberculosis on the iSeq100 and MiSeq: A performance, ease-of-use, and cost evaluation

(2019) Rebecca E. Colman et al.   PLOS MEDICINE

Comparative Analysis for the Performance of Variant Calling Pipelines on Detecting the de novo Mutations in Humans

(2019) Yu Liang et al.   Frontiers in Pharmacology

Long-Read Sequencing Emerging in Medical Genetics

(2019) Tuomo Mantere et al.   Frontiers in Genetics

Targeted next generation sequencing as a tool for precision medicine

(2019) Markus Gulilat et al.   BMC Medical Genomics

Investigation of candidate genes of non-syndromic cleft lip with or without cleft palate, using both case–control and family-based association studies

(2019) Xing Ge et al.   MEDICINE

Long-read sequencing in human genetics

(2019) Florian Kraft et al.   Medizinische Genetik

Genome sequencing and implications for rare disorders

(2019) Jennifer E. Posey   Orphanet Journal of Rare Diseases

Safeguarding the future of genomic research in South Africa: Broad consent and the Protection of Personal Information Act No. 4 of 2013

(2019) C Staunton et al.   SAMJ SOUTH AFRICAN MEDICAL JOURNAL

Using linkage studies combined with whole‐exome sequencing to identify novel candidate genes for familial colorectal cancer

(2019) Claudio Toma et al.   INTERNATIONAL JOURNAL OF CANCER

Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology

(2018) Neal I. Lindeman et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

geck: trio-based comparative benchmarking of variant calls

(2018) Péter Kómár et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

appreci8: a pipeline for precise variant calling integrating 8 tools

(2018) Sarah Sandmann et al.   BIOINFORMATICS

ToTem: a tool for variant calling pipeline optimization

(2018) Nikola Tom et al.   BMC BIOINFORMATICS

CoVaCS: a consensus variant calling system

(2018) Matteo Chiara et al.   BMC GENOMICS

The Challenge of Rare Diseases

(2018) James K. Stoller   CHEST

Next-generation sequencing technologies and their application to the study and control of bacterial infections

(2018) J. Besser et al.   CLINICAL MICROBIOLOGY AND INFECTION

Exome sequencing has higher diagnostic yield compared to simulated disease-specific panels in children with suspected monogenic disorders

(2018) Oliver James Dillon et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Making new genetic diagnoses with old data: iterative reanalysis and reporting from genome-wide data in 1,133 families with developmental disorders

(2018) Caroline F Wright et al.   GENETICS IN MEDICINE

Massively parallel sequencing analysis of mucinous ovarian carcinomas: genomic profiling and differential diagnoses

(2018) Jennifer J. Mueller et al.   GYNECOLOGIC ONCOLOGY

Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines

(2018) Somak Roy et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Cloud computing for genomic data analysis and collaboration

(2018) Ben Langmead et al.   NATURE REVIEWS GENETICS

The Third Revolution in Sequencing Technology

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

Cloud computing applications for biomedical science: A perspective

(2018) Vivek Navale et al.   PLoS Computational Biology

Trio Clinical Exome Sequencing in a Patient With Multicentric Carpotarsal Osteolysis Syndrome: First Case Report in the Balkans

(2018) Aleksandra Stajkovska et al.   Frontiers in Genetics

novoCaller: a Bayesian network approach for de novo variant calling from pedigree and population sequence data

(2018) Anwoy Kumar Mohanty et al.   BIOINFORMATICS

A universal SNP and small-indel variant caller using deep neural networks

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants

(2018) Fu-Yuan Zhu et al.   Plant Methods

Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines

(2018) Neha Kulkarni et al.   BMC BIOINFORMATICS

Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics

(2018) Shakuntala Baichoo et al.   BMC BIOINFORMATICS

ClinGen Variant Curation Expert Panel experiences and standardized processes for disease and gene-level specification of the ACMG/AMP guidelines for sequence variant interpretation

(2018) Edgar A. Rivera-Muñoz et al.   HUMAN MUTATION

A de novo pathogenic CSNK1E mutation identified by exome sequencing in family trios with epileptic encephalopathy

(2018) Xiaomin Chen et al.   HUMAN MUTATION

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

Family studies to find rare high risk variants in migraine

(2017) Rikke Dyhr Hansen et al.   JOURNAL OF HEADACHE AND PAIN

Guidelines for Validation of Next-Generation Sequencing–Based Oncology Panels

(2017) Lawrence J. Jennings et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer

(2017) Marilyn M. Li et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Parental influence on human germline de novo mutations in 1,548 trios from Iceland

(2017) Hákon Jónsson et al.   NATURE

The contribution of rare variants to risk of schizophrenia in individuals with and without intellectual disability

(2017) Tarjinder Singh et al.   NATURE GENETICS

Settling the score: variant prioritization and Mendelian disease

(2017) Karen Eilbeck et al.   NATURE REVIEWS GENETICS

A family-based genome-wide association study of chronic rhinosinusitis with nasal polyps implicates several genes in the disease pathogenesis

(2017) Anton Bohman et al.   PLoS One

Lessons learned from additional research analyses of unsolved clinical exome cases

(2017) Mohammad K. Eldomery et al.   Genome Medicine

A family-based genome-wide association study reveals an association of spondyloarthritis withMAPK14

(2016) Félicie Costantino et al.   ANNALS OF THE RHEUMATIC DISEASES

Advancements in Next-Generation Sequencing

(2016) Shawn E. Levy et al.   Annual Review of Genomics and Human Genetics

Next-Generation Sequencing Informatics: Challenges and Strategies for Implementation in a Clinical Environment

(2016) Somak Roy et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

Whole-exome sequencing to identify genetic risk variants underlying inhibitor development in severe hemophilia A patients

(2016) M. M. Gorski et al.   BLOOD

Genome-wide association study using family-based cohorts identifies the WLS and CCDC170/ESR1 loci as associated with bone mineral density

(2016) Benjamin H. Mullin et al.   BMC GENOMICS

A family-based, genome-wide association study of young-onset breast cancer: inherited variants and maternally mediated effects

(2016) Katie M O'Brien et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics

(2016) Sarah S. Kalia et al.   GENETICS IN MEDICINE

The sequence of sequencers: The history of sequencing DNA

(2016) James M. Heather et al.   GENOMICS

From next-generation resequencing reads to a high-quality variant data set

(2016) S P Pfeifer   HEREDITY

High Throughput Sequencing: An Overview of Sequencing Chemistry

(2016) Sheetal Ambardar et al.   INDIAN JOURNAL OF MICROBIOLOGY

FMFilter: A fast model based variant filtering tool

(2016) Mete Akgün et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Comparison of Next-Generation Sequencing Panels and Platforms for Detection and Verification of Somatic Tumor Variants for Clinical Diagnostics

(2016) Maksym Misyura et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Family-based association analyses of imputed genotypes reveal genome-wide significant association of Alzheimer’s disease with OSBPL6, PTPRG and PDCL3

(2016) C Herold et al.   MOLECULAR PSYCHIATRY

The importance of de novo mutations for pediatric neurological disease—It is not all in utero or birth trauma

(2016) Robert P. Erickson   MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Homozygous and hemizygous CNV detection from exome sequencing data in a Mendelian disease cohort

(2016) Tomasz Gambin et al.   NUCLEIC ACIDS RESEARCH

FamPipe: An Automatic Analysis Pipeline for Analyzing Sequencing Data in Families for Disease Studies

(2016) Ren-Hua Chung et al.   PLoS Computational Biology

cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs

(2016) Tobias Fehlmann et al.   Clinical Epigenetics

Exome sequencing establishes diagnosis of Alström syndrome in an infant presenting with non-syndromic dilated cardiomyopathy

(2015) Pamela A. Long et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Alignment of Next-Generation Sequencing Reads

(2015) Knut Reinert et al.   Annual Review of Genomics and Human Genetics

Unified representation of genetic variants

(2015) Adrian Tan et al.   BIOINFORMATICS

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Clinical application of whole-exome sequencing across clinical indications

(2015) Kyle Retterer et al.   GENETICS IN MEDICINE

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

(2015) Sue Richards et al.   GENETICS IN MEDICINE

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

(2015) Sara Goodwin et al.   GENOME RESEARCH

Socio-economic burden of rare diseases: A systematic review of cost of illness evidence

(2015) Aris Angelis et al.   HEALTH POLICY

Review of alignment and SNP calling algorithms for next-generation sequencing data

(2015) M. Mielczarek et al.   JOURNAL OF APPLIED GENETICS

High-Throughput Sequencing Technologies

(2015) Jason A. Reuter et al.   MOLECULAR CELL

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Good laboratory practice for clinical next-generation sequencing informatics pipelines

(2015) Amy S Gargis et al.   NATURE BIOTECHNOLOGY

SIFT missense predictions for genomes

(2015) Robert Vaser et al.   Nature Protocols

New insights into the performance of human whole-exome capture platforms

(2015) J. Meienberg et al.   NUCLEIC ACIDS RESEARCH

ClinVar: public archive of interpretations of clinically relevant variants

(2015) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

An analytical framework for optimizing variant discovery from personal genomes

(2015) Gareth Highnam et al.   Nature Communications

SeqMule: automated pipeline for analysis of human exome/genome sequencing data

(2015) Yunfei Guo et al.   Scientific Reports

Exome Sequencing: Current and Future Perspectives

(2015) Amanda Warr et al.   G3-Genes Genomes Genetics

Family-Based Benchmarking of Copy Number Variation Detection Software

(2015) Marcel Elie Nutsua et al.   PLoS One

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

(2015) Sohyun Hwang et al.   Scientific Reports

Next generation sequencing technology: Advances and applications

(2014) H.P.J. Buermans et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity

(2014) Brandi L Cantarel et al.   BMC BIOINFORMATICS

Linkage analysis and the study of Mendelian disease in the era of whole exome and genome sequencing

(2014) M. D. Teare et al.   Briefings in Functional Genomics

Using Mendelian Inheritance To Improve High-Throughput SNP Discovery

(2014) N. Chen et al.   GENETICS

Solving the molecular diagnostic testing conundrum for Mendelian disorders in the era of next-generation sequencing: single-gene, gene panel, or exome/genome sequencing

(2014) Yuan Xue et al.   GENETICS IN MEDICINE

Using familial information for variant filtering in high-throughput sequencing studies

(2014) Melanie Bahlo et al.   HUMAN GENETICS

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

CUSHAW3: Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding

(2014) Yongchao Liu et al.   PLoS One

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

(2014) Wan-Ping Lee et al.   PLoS One

FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units

(2014) Gang Peng et al.   PLoS Computational Biology

Evaluation and Comparison of Multiple Aligners for Next-Generation Sequencing Data Analysis

(2014) Jing Shang et al.   Biomed Research International

Exome sequencing greatly expedites the progressive research of Mendelian diseases

(2014) Xuejun Zhang   Frontiers of Medicine

A support vector machine for identification of single-nucleotide polymorphisms from next-generation sequencing data

(2013) B. D. O'Fallon et al.   BIOINFORMATICS

Benchmarking short sequence mapping tools

(2013) Ayat Hatem et al.   BMC BIOINFORMATICS

The Next-Generation Sequencing Revolution and Its Impact on Genomics

(2013) Daniel C. Koboldt et al.   CELL

Power of Family-Based Association Designs to Detect Rare Variants in Large Pedigrees Using Imputed Genotypes

(2013) Mohamad Saad et al.   GENETIC EPIDEMIOLOGY

The utility of the traditional medical genetics diagnostic evaluation in the context of next-generation sequencing for undiagnosed genetic disorders

(2013) Vandana Shashi et al.   GENETICS IN MEDICINE

ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing

(2013) Robert C. Green et al.   GENETICS IN MEDICINE

Combined linkage analysis and exome sequencing identifies novel genes for familial goiter

(2013) Junxia Yan et al.   JOURNAL OF HUMAN GENETICS

A glimpse into past, present, and future DNA sequencing

(2013) Marcos Morey et al.   MOLECULAR GENETICS AND METABOLISM

Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders

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

ClinVar: public archive of relationships among sequence variation and human phenotype

(2013) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

Increased Protein Stability of CDKN1C Causes a Gain-of-Function Phenotype in Patients with IMAGe Syndrome

(2013) Naoki Hamajima et al.   PLoS One

WHEN CLOUD COMPUTING MEETS BIOINFORMATICS: A REVIEW

(2013) SHUIGENG ZHOU et al.   Journal of Bioinformatics and Computational Biology

Five Years of GWAS Discovery

(2012) Peter M. Visscher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Tools for mapping high-throughput sequencing data

(2012) Nuno A. Fonseca et al.   BIOINFORMATICS

Exome sequencing generates high quality data in non-target regions

(2012) Yan Guo et al.   BMC GENOMICS

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

(2012) Pablo Cingolani et al.   FLY

Applications of targeted gene capture and next-generation sequencing technologies in studies of human deafness and other genetic disabilities

(2012) Xi Lin et al.   HEARING RESEARCH

The role of large pedigrees in an era of high-throughput sequencing

(2012) Ellen M. Wijsman   HUMAN GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

SIFT web server: predicting effects of amino acid substitutions on proteins

(2012) Ngak-Leng Sim et al.   NUCLEIC ACIDS RESEARCH

A Comprehensive Evaluation of Alignment Algorithms in the Context of RNA-Seq

(2012) Robert Lindner et al.   PLoS One

Linkage Analysis in the Next-Generation Sequencing Era

(2011) Joan E. Bailey-Wilson et al.   HUMAN HEREDITY

Genome-wide linkage analysis of 972 bipolar pedigrees using single-nucleotide polymorphisms

(2011) J A Badner et al.   MOLECULAR PSYCHIATRY

Variation in genome-wide mutation rates within and between human families

(2011) Donald F Conrad et al.   NATURE GENETICS

Family-based designs for genome-wide association studies

(2011) Jurg Ott et al.   NATURE REVIEWS GENETICS

Whole-Exome Re-Sequencing in a Family Quartet Identifies POP1 Mutations As the Cause of a Novel Skeletal Dysplasia

(2011) Evgeny A. Glazov et al.   PLoS Genetics

Consensus Statement: Chromosomal Microarray Is a First-Tier Clinical Diagnostic Test for Individuals with Developmental Disabilities or Congenital Anomalies

(2010) David T. Miller et al.   AMERICAN JOURNAL OF HUMAN GENETICS

SeqAnt: A web service to rapidly identify and annotate DNA sequence variations

(2010) Amol Shetty et al.   BMC BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Public data archives for genomic structural variation

(2010) Deanna M Church et al.   NATURE GENETICS

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

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

Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing

(2010) J. C. Roach et al.   SCIENCE

The Role of Family-Based Designs in Genome-Wide Association Studies

(2010) Nan M. Laird et al.   STATISTICAL SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Next-Generation Sequencing: From Basic Research to Diagnostics

(2009) K. V. Voelkerding et al.   CLINICAL CHEMISTRY

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

Family-based genome-wide association studies

(2009) Beben Benyamin et al.   PHARMACOGENOMICS

Yield of additional metabolic studies in neurodevelopmental disorders

(2008) Hannelie M. Engbers et al.   ANNALS OF NEUROLOGY