Test development, optimization and validation of a WGS pipeline for genetic disorders

[1]  Katherine R. Smith,et al.  Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study , 2022, The Lancet Neurology.

[2]  Zhiyu Peng,et al.  AutoCNV: a semiautomatic CNV interpretation system based on the 2019 ACMG/ClinGen Technical Standards for CNVs , 2021, BMC Genomics.

[3]  G. Darling,et al.  scSNV: accurate dscRNA-seq SNV co-expression analysis using duplicate tag collapsing , 2021, Genome biology.

[4]  R. Dmochowski,et al.  Foundational Statistical Principles in Medical Research: Sensitivity, Specificity, Positive Predictive Value, and Negative Predictive Value , 2021, Medicina.

[5]  Zhiyu Peng,et al.  Characterizing sensitivity and coverage of clinical WGS as a diagnostic test for genetic disorders , 2021, BMC Medical Genomics.

[6]  Daniel C. Koboldt,et al.  Best practices for variant calling in clinical sequencing , 2020, Genome medicine.

[7]  Christian R. Marshall,et al.  Best practices for the analytical validation of clinical whole-genome sequencing intended for the diagnosis of germline disease , 2020, npj Genomic Medicine.

[8]  Peixiang Ni,et al.  NGS-based spinal muscular atrophy carrier screening of 10,585 diverse couples in China: a pan-ethnic study , 2020, European journal of human genetics : EJHG.

[9]  Fei Gao,et al.  CNGBdb: China National GeneBank DataBase. , 2020, Yi chuan = Hereditas.

[10]  Zhiyu Peng,et al.  Performance characterization of PCR-free whole genome sequencing for clinical diagnosis , 2020, bioRxiv.

[11]  Fei Gao,et al.  CNSA: a data repository for archiving omics data , 2020, bioRxiv.

[12]  R. Hayeems,et al.  Determining accurate costs for genomic sequencing technologies—a necessary prerequisite , 2019, Journal of Community Genetics.

[13]  Jennifer Lu,et al.  Improved metagenomic analysis with Kraken 2 , 2019, Genome Biology.

[14]  Zhiyu Peng,et al.  AutoPVS1: An automatic classification tool for PVS1 interpretation of null variants , 2019, bioRxiv.

[15]  Le Zhang,et al.  Comprehensively benchmarking applications for detecting copy number variation , 2019, PLoS Comput. Biol..

[16]  Konrad Scheffler,et al.  ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions , 2019, bioRxiv.

[17]  J. Gagneur,et al.  MMSplice: modular modeling improves the predictions of genetic variant effects on splicing , 2019, Genome Biology.

[18]  Denise L. Perry,et al.  Clinical whole genome sequencing as a first-tier test at a resource-limited dysmorphology clinic in Mexico , 2019, npj Genomic Medicine.

[19]  David G. Knowles,et al.  Predicting Splicing from Primary Sequence with Deep Learning , 2019, Cell.

[20]  Asan,et al.  Pilot study of expanded carrier screening for 11 recessive diseases in China: results from 10,476 ethnically diverse couples , 2018, European Journal of Human Genetics.

[21]  Emily Farrow,et al.  Clinical genome sequencing in an unbiased pediatric cohort , 2018, Genetics in Medicine.

[22]  Zornitza Stark,et al.  Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases , 2018, npj Genomic Medicine.

[23]  A. Spurdle,et al.  Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort , 2018, Nucleic acids research.

[24]  S. Kingsmore,et al.  Rapid whole-genome sequencing decreases infant morbidity and cost of hospitalization , 2018, npj Genomic Medicine.

[25]  Jia Gu,et al.  fastp: an ultra-fast all-in-one FASTQ preprocessor , 2018, bioRxiv.

[26]  Asan,et al.  Rapid Targeted Next-Generation Sequencing Platform for Molecular Screening and Clinical Genotyping in Subjects with Hemoglobinopathies , 2017, EBioMedicine.

[27]  Daniele Merico,et al.  Improved diagnostic yield compared with targeted gene sequencing panels suggests a role for whole-genome sequencing as a first-tier genetic test , 2017, Genetics in Medicine.

[28]  Duy Tin Truong,et al.  Microbial strain-level population structure and genetic diversity from metagenomes , 2017, Genome research.

[29]  Valérie Lanneau,et al.  Clinical Practice Guidelines for Rare Diseases: The Orphanet Database , 2017, PloS one.

[30]  J. McPherson,et al.  Coming of age: ten years of next-generation sequencing technologies , 2016, Nature Reviews Genetics.

[31]  Steven Salzberg,et al.  Bracken: Estimating species abundance in metagenomics data , 2016, bioRxiv.

[32]  Michael Brudno,et al.  Whole-genome sequencing expands diagnostic utility and improves clinical management in paediatric medicine , 2016, npj Genomic Medicine.

[33]  Ricardo Villamarín-Salomón,et al.  ClinVar: public archive of interpretations of clinically relevant variants , 2015, Nucleic Acids Res..

[34]  Eric Boerwinkle,et al.  In silico prediction of splice-altering single nucleotide variants in the human genome , 2014, Nucleic acids research.

[35]  A. Pang,et al.  Performance of High-Throughput Sequencing for the Discovery of Genetic Variation Across the Complete Size Spectrum , 2013, G3: Genes, Genomes, Genetics.

[36]  Mauricio O. Carneiro,et al.  From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.

[37]  Joshua L. Deignan,et al.  ACMG clinical laboratory standards for next-generation sequencing , 2013, Genetics in Medicine.

[38]  A. Sivachenko,et al.  Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples , 2013, Nature Biotechnology.

[39]  Ryan M. Layer,et al.  LUMPY: a probabilistic framework for structural variant discovery , 2012, Genome Biology.

[40]  Peter Saffrey,et al.  Rapid Whole-Genome Sequencing for Genetic Disease Diagnosis in Neonatal Intensive Care Units , 2012, Science Translational Medicine.

[41]  V. Beneš,et al.  DELLY: structural variant discovery by integrated paired-end and split-read analysis , 2012, Bioinform..

[42]  Nicholas W. Wood,et al.  A robust model for read count data in exome sequencing experiments and implications for copy number variant calling , 2012, Bioinform..

[43]  M. Gerstein,et al.  CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. , 2011, Genome research.

[44]  R. Wilson,et al.  BreakDancer: An algorithm for high resolution mapping of genomic structural variation , 2009, Nature Methods.

[45]  T. Prior.  Carrier screening for spinal muscular atrophy , 2008, Genetics in Medicine.

[46]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[47]  Alan F. Scott,et al.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2002, Nucleic Acids Res..

[48]  D. Smeets,et al.  Historical prospective of human cytogenetics: from microscope to microarray. , 2004, Clinical biochemistry.

[49]  Christopher B. Burge,et al.  Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals , 2003, RECOMB '03.

[50]  D. Cooper,et al.  Human Gene Mutation Database , 1996, Human Genetics.

[51]  Claude-Alain H. Roten,et al.  Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..

[52]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[53]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..