Integrating Massively Parallel Sequencing into Diagnostic Workflows and Managing the Annotation and Clinical Interpretation Challenge

Actionable, Pathogenic Incidental Findings in 1,000 Participants’ Exomes

(2013) Michael O. Dorschner et al.   AMERICAN JOURNAL OF HUMAN GENETICS

GATA2 haploinsufficiency caused by mutations in a conserved intronic element leads to MonoMAC syndrome

(2013) A. P. Hsu et al.   BLOOD

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

Risk categorization for oversight of laboratory-developed tests for inherited conditions

(2013) Kristin G. Monaghan et al.   GENETICS IN MEDICINE

Patient decisions for disclosure of secondary findings among the first 200 individuals undergoing clinical diagnostic exome sequencing

(2013) Layla Shahmirzadi et al.   GENETICS IN MEDICINE

Implementing genomic medicine in the clinic: the future is here

(2013) Teri A. Manolio et al.   GENETICS IN MEDICINE

Systematic Detection of Pathogenic Alu Element Insertions in NGS-Based Diagnostic Screens: TheBRCA1/BRCA2Example

(2013) Sylvia De Brakeleer et al.   HUMAN MUTATION

Integration of Genomic Medicine into Pathology Residency Training

(2013) Iris Schrijver et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Tafazzin splice variants and mutations in Barth syndrome

(2013) Susan M. Kirwin et al.   MOLECULAR GENETICS AND METABOLISM

Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database

(2013) Bryony A Thompson et al.   NATURE GENETICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders

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

TERT Promoter Mutations in Familial and Sporadic Melanoma

(2013) S. Horn et al.   SCIENCE

Patient Autonomy and Incidental Findings in Clinical Genomics

(2013) S. M. Wolf et al.   SCIENCE

Ethics and Genomic Incidental Findings

(2013) A. L. McGuire et al.   SCIENCE

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

(2013) Umadevi Paila et al.   PLoS Computational Biology

Recurrent De Novo Mutations in PACS1 Cause Defective Cranial-Neural-Crest Migration and Define a Recognizable Intellectual-Disability Syndrome

(2012) Janneke H.M. Schuurs-Hoeijmakers et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Centers for Mendelian Genomics: A new large-scale initiative to identify the genes underlying rare Mendelian conditions

(2012) Michael J. Bamshad et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB

(2012) Q. Xu et al.   BIOINFORMATICS

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

A Report Template for Molecular Genetic Tests Designed to Improve Communication Between the Clinician and Laboratory

(2012) Maren T. Scheuner et al.   Genetic Testing and Molecular Biomarkers

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

A Combined Functional Annotation Score for Non-Synonymous Variants

(2012) Margarida C. Lopes et al.   HUMAN HEREDITY

Feasibility of real time next generation sequencing of cancer genes linked to drug response: Results from a clinical trial

(2012) Ben Tran et al.   INTERNATIONAL JOURNAL OF CANCER

Synergistic effect of different levels of genomic data for cancer clinical outcome prediction

(2012) Dokyoon Kim et al.   JOURNAL OF BIOMEDICAL INFORMATICS

The implications of ENCODE for diagnostics

(2012) Eugene Fratkin et al.   NATURE BIOTECHNOLOGY

Assuring the quality of next-generation sequencing in clinical laboratory practice

(2012) Amy S Gargis et al.   NATURE BIOTECHNOLOGY

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility

(2012) Anton Nekrutenko et al.   NATURE REVIEWS GENETICS

Diagnostic Exome Sequencing in Persons with Severe Intellectual Disability

(2012) Joep de Ligt et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

Discovery of multi-dimensional modules by integrative analysis of cancer genomic data

(2012) Shihua Zhang et al.   NUCLEIC ACIDS RESEARCH

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

Rapid Whole-Genome Sequencing for Genetic Disease Diagnosis in Neonatal Intensive Care Units

(2012) C. J. Saunders et al.   Science Translational Medicine

Clan Genomics and the Complex Architecture of Human Disease

(2011) James R. Lupski et al.   CELL

International Rare Disease Research Consortium Commits to Aggressive Goals

(2011) Kristin Baxter et al.   Genetic Testing and Molecular Biomarkers

Deploying whole genome sequencing in clinical practice and public health: Meeting the challenge one bin at a time

(2011) Jonathan S Berg et al.   GENETICS IN MEDICINE

Next-generation sequencing in molecular diagnosis:NUBPLmutations highlight the challenges of variant detection and interpretation

(2011) Elena J. Tucker et al.   HUMAN MUTATION

Exome sequencing as a tool for Mendelian disease gene discovery

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

The Coming Explosion in Genetic Testing — Is There a Duty to Recontact?

(2011) Reed E. Pyeritz   NEW ENGLAND JOURNAL OF MEDICINE

SMART 7: recent updates to the protein domain annotation resource

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

Carrier Testing for Severe Childhood Recessive Diseases by Next-Generation Sequencing

(2011) C. J. Bell et al.   Science Translational Medicine

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

(2010) William McLaren et al.   BIOINFORMATICS

Using SIFT and PolyPhen to Predict Loss-of-Function and Gain-of-Function Mutations

(2010) Sarah E. Flanagan et al.   Genetic Testing and Molecular Biomarkers

A mutation in the 3′-UTR of the HDAC6 gene abolishing the post-transcriptional regulation mediated by hsa-miR-433 is linked to a new form of dominant X-linked chondrodysplasia

(2010) Delphine Simon et al.   HUMAN MOLECULAR GENETICS

The Human Variome Project (HVP) 2009 Forum “Towards Establishing Standards”

(2010) Heather J. Howard et al.   HUMAN MUTATION

Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome

(2010) Peter M Krawitz et al.   NATURE GENETICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Uncovering the roles of rare variants in common disease through whole-genome sequencing

(2010) Elizabeth T. Cirulli et al.   NATURE REVIEWS GENETICS

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

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

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

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

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

(2010) Elaine R Mardis   Genome Medicine

ClassifyingMLH1andMSH2variants using bioinformatic prediction, splicing assays, segregation, and tumor characteristics

(2009) Sven Arnold et al.   HUMAN MUTATION

Clinician Perspectives about Molecular Genetic Testing for Heritable Conditions and Development of a Clinician-Friendly Laboratory Report

(2009) Ira M. Lubin et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results

(2008) Sharon E. Plon et al.   HUMAN MUTATION