A primer on precision medicine informatics

College of American Pathologists' Laboratory Standards for Next-Generation Sequencing Clinical Tests

(2015) Nazneen Aziz et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

Clinical Actionability Enhanced through Deep Targeted Sequencing of Solid Tumors

(2015) K. Chen et al.   CLINICAL CHEMISTRY

Actionable exomic incidental findings in 6503 participants: challenges of variant classification

(2015) Laura M. Amendola et al.   GENOME RESEARCH

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response

(2015) Himisha Beltran et al.   JAMA Oncology

Implementing individualized medicine into the medical practice

(2014) Konstantinos N. Lazaridis et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS

Refining the structure and content of clinical genomic reports

(2014) Michael O. Dorschner et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS

Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling

(2014) Stephen J. Salipante et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Clinical Relevance of KRAS-Mutated Subclones Detected with Picodroplet Digital PCR in Advanced Colorectal Cancer Treated with Anti-EGFR Therapy

(2014) P. Laurent-Puig et al.   CLINICAL CANCER RESEARCH

Genomic cloud computing: legal and ethical points to consider

(2014) Edward S Dove et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Reporting Incidental Findings in Clinical Whole Exome Sequencing: Incorporation of the 2013 ACMG Recommendations into Current Practices of Genetic Counseling

(2014) Lacey A. Smith et al.   Journal of Genetic Counseling

Clinical Integration of Next Generation Sequencing: Coverage and Reimbursement Challenges

(2014) Patricia A. Deverka et al.   JOURNAL OF LAW MEDICINE & ETHICS

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

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

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine

(2014) Eliezer M Van Allen et al.   NATURE MEDICINE

Accurate de novo and transmitted indel detection in exome-capture data using microassembly

(2014) Giuseppe Narzisi et al.   NATURE METHODS

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Performance comparison of SNP detection tools with illumina exome sequencing data—an assessment using both family pedigree information and sample-matched SNP array data

(2014) Ming Yi et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Davis J McCarthy et al.   Genome Medicine

Unraveling the clonal hierarchy of somatic genomic aberrations

(2014) Davide Prandi et al.   GENOME BIOLOGY

Bioinformatics for precision medicine in oncology: principles and application to the SHIVA clinical trial

(2014) Nicolas Servant et al.   Frontiers in Genetics

A comparative analysis of algorithms for somatic SNV detection in cancer

(2013) Nicola D. Roberts et al.   BIOINFORMATICS

Dramatic Response Induced by Vemurafenib in aBRAFV600E-Mutated Lung Adenocarcinoma

(2013) Solange Peters et al.   JOURNAL OF CLINICAL ONCOLOGY

Reporting results from whole-genome and whole-exome sequencing in clinical practice: a proposal for Canada?

(2013) Ma'n H Zawati et al.   JOURNAL OF MEDICAL GENETICS

Towards Precision Medicine: Advances in Computational Approaches for the Analysis of Human Variants

(2013) Thomas A. Peterson et al.   JOURNAL OF MOLECULAR BIOLOGY

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

(2013) Garrett M Frampton et al.   NATURE BIOTECHNOLOGY

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

The power of a crowd

(2013) Daniel Evanko   NATURE METHODS

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

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

Variant Callers for Next-Generation Sequencing Data: A Comparison Study

(2013) Xiangtao Liu et al.   PLoS One

Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers

(2013) Qingguo Wang et al.   Genome Medicine

Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data

(2013) Lauren M. Bragg et al.   PLoS Computational Biology

EXCAVATOR: detecting copy number variants from whole-exome sequencing data

(2013) Alberto Magi et al.   GENOME BIOLOGY

Discovery and Statistical Genotyping of Copy-Number Variation from Whole-Exome Sequencing Depth

(2012) Menachem Fromer et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package

(2012) Mohamed El-Kalioby et al.   BMC BIOINFORMATICS

A Panel of Four miRNAs Accurately Differentiates Malignant from Benign Indeterminate Thyroid Lesions on Fine Needle Aspiration

(2012) X. M. Keutgen et al.   CLINICAL CANCER RESEARCH

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

(2012) Pablo Cingolani et al.   FLY

Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia

(2012) Catherine C. Smith et al.   NATURE

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

(2012) Amy S Gargis et al.   NATURE BIOTECHNOLOGY

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV

(2011) Jarupon Fah Sathirapongsasuti et al.   BIOINFORMATICS

ChimeraScan: a tool for identifying chimeric transcription in sequencing data

(2011) Matthew K. Iyer et al.   BIOINFORMATICS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

The genomic complexity of primary human prostate cancer

(2011) Michael F. Berger et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study

(2011) S. Roychowdhury et al.   Science Translational Medicine

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

(2011) Andrew McPherson et al.   PLoS Computational Biology

Wearable Sensors and Systems

(2010) Paolo Bonato   IEEE ENGINEERING IN MEDICINE AND BIOLOGY MAGAZINE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Anaplastic Lymphoma Kinase Inhibition in Non–Small-Cell Lung Cancer

(2010) Eunice L. Kwak et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data

(2010) Andrea Sboner et al.   GENOME BIOLOGY

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS