An efficient genotyper and star-allele caller for pharmacogenomics

CYP2C8, CYP2C9, and CYP2C19 Characterization Using Next-Generation Sequencing and Haplotype Analysis

(2022) Andrea Gaedigk et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Analytical Validation of a Computational Method for Pharmacogenetic Genotyping from Clinical Whole Exome Sequencing

(2022) Reynold C. Ly et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

StellarPGx: A Nextflow pipeline for calling star alleles in cytochrome P450 genes

(2021) David Twesigomwe et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Cyrius: accurate CYP2D6 genotyping using whole-genome sequencing data

(2021) Xiao Chen et al.   PHARMACOGENOMICS JOURNAL

Fast two-stage phasing of large-scale sequence data

(2021) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

indelPost: harmonizing ambiguities in simple and complex indel alignments

(2021) Kohei Hagiwara et al.   BIOINFORMATICS

Towards population-scale long-read sequencing

(2021) Wouter De Coster et al.   NATURE REVIEWS GENETICS

Added Value of Clinical Sequencing: WGS-Based Profiling of Pharmacogenes

(2020) Sylvan M. Caspar et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Development and Analytical Validation of a 29 Gene Clinical Pharmacogenetic Genotyping Panel: Multi‐Ethnic Allele and Copy Number Variant Detection

(2020) Stuart A. Scott et al.   CTS-Clinical and Translational Science

A systematic comparison of pharmacogene star allele calling bioinformatics algorithms: a focus on CYP2D6 genotyping

(2020) David Twesigomwe et al.   npj Genomic Medicine

Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets

(2020) Emily Berger et al.   Nature Communications

Highly accurate long-read HiFi sequencing data for five complex genomes

(2020) Ting Hon et al.   Scientific Data

Pharmacogenomics Clinical Annotation Tool (Pharm CAT )

(2019) Katrin Sangkuhl et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Characterization of Reference Materials for Genetic Testing of CYP2D6 Alleles

(2019) Andrea Gaedigk et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Stargazer: a software tool for calling star alleles from next-generation sequencing data using CYP2D6 as a model

(2018) Seung-been Lee et al.   GENETICS IN MEDICINE

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

(2018) Ibrahim Numanagić et al.   Nature Communications

Pharmacogenomics: Precision Medicine and Drug Response

(2017) Richard M. Weinshilboum et al.   MAYO CLINIC PROCEEDINGS

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

(2016) Peter Edge et al.   GENOME RESEARCH

Characterization of 137 Genomic DNA Reference Materials for 28 Pharmacogenetic Genes

(2016) Victoria M. Pratt et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Fast and accurate long-range phasing in a UK Biobank cohort

(2016) Po-Ru Loh et al.   NATURE GENETICS

PGRNseq

(2016) Adam S. Gordon et al.   Pharmacogenetics and Genomics

Constellation: a tool for rapid, automated phenotype assignment of a highly polymorphic pharmacogene, CYP2D6, from whole-genome sequences

(2016) Greyson P Twist et al.   npj Genomic Medicine

Cypiripi: exact genotyping ofCYP2D6using high-throughput sequencing data

(2015) Ibrahim Numanagić et al.   BIOINFORMATICS

Pharmacogenomics in the clinic

(2015) Mary V. Relling et al.   NATURE

Toward better understanding of artifacts in variant calling from high-coverage samples

(2014) Heng Li   BIOINFORMATICS

Clinical Pharmacogenetics Implementation Consortium Guidelines for Cytochrome P450 2D6 Genotype and Codeine Therapy: 2014 Update

(2014) K R Crews et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Establishment of CYP2D6 reference samples by multiple validated genotyping platforms

(2014) H Fang et al.   PHARMACOGENOMICS JOURNAL

Origins of P450 diversity

(2013) H. Sezutsu et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

CYP2D6 update

(2012) Sarah C. Sim et al.   Pharmacogenetics and Genomics

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Characterization of 107 Genomic DNA Reference Materials for CYP2D6, CYP2C19, CYP2C9, VKORC1, and UGT1A1

(2010) Victoria M. Pratt et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

The Path to Personalized Medicine

(2010) Margaret A. Hamburg et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

CYP2D6: novel genomic structures and alleles

(2009) Whitney E. Kramer et al.   Pharmacogenetics and Genomics