Making new genetic diagnoses with old data: iterative reanalysis and reporting from genome-wide data in 1133 families with developmental disorders

Citation for published version: Wright, CF, McRae, JF, Clayton, S, Gallone, G, Aitken, S, Fitzgerald, TW, Jones, P, Prigmore, E, Rajan, D, Lord, J, Sifrim, A, Kelsell, R, Parker, MJ, Barrett, JC, Hurles, ME, FitzPatrick, DR & Firth, HV 2018, 'Making new genetic diagnoses with old data: iterative reanalysis and reporting from genome-wide data in 1,133 families with developmental disorders', Genetics in Medicine. https://doi.org/10.1038/gim.2017.246

[1]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[2]  R. Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[3]  P. Bork,et al.  A method and server for predicting damaging missense mutations , 2010, Nature Methods.

[4]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[5]  J. Shendure,et al.  Exome sequencing as a tool for Mendelian disease gene discovery , 2011, Nature Reviews Genetics.

[6]  Arthur Wuster,et al.  DeNovoGear: de novo indel and point mutation discovery and phasing , 2013, Nature Methods.

[7]  Magalie S Leduc,et al.  Clinical whole-exome sequencing for the diagnosis of mendelian disorders. , 2013, The New England journal of medicine.

[8]  K. Boycott,et al.  Rare-disease genetics in the era of next-generation sequencing: discovery to translation , 2013, Nature Reviews Genetics.

[9]  Jean-Baptiste Cazier,et al.  Choice of transcripts and software has a large effect on variant annotation , 2014, Genome Medicine.

[10]  Caroline F. Wright,et al.  DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation , 2013, Nucleic Acids Res..

[11]  Tomas W. Fitzgerald,et al.  A novel method for detecting uniparental disomy from trio genotypes identifies a significant excess in children with developmental disorders , 2014, Genome research.

[12]  Tom R. Gaunt,et al.  Mosaic structural variation in children with developmental disorders , 2015, Human molecular genetics.

[13]  Karynne E. Patterson,et al.  The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities. , 2015, American journal of human genetics.

[14]  Erwin Birnie,et al.  Is there a duty to recontact in light of new genetic technologies? A systematic review of the literature , 2014, Genetics in Medicine.

[15]  Alejandro Sifrim,et al.  Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data , 2015, The Lancet.

[16]  Caroline F. Wright,et al.  Facilitating Collaboration in Rare Genetic Disorders Through Effective Matchmaking in DECIPHER , 2015, Human mutation.

[17]  Morad Ansari,et al.  Discovery of four recessive developmental disorders using probabilistic genotype and phenotype matching among 4,125 families , 2015, Nature Genetics.

[18]  Arcadi Navarro,et al.  The European Genome-phenome Archive of human data consented for biomedical research , 2015, Nature Genetics.

[19]  Davis J. McCarthy,et al.  Factors influencing success of clinical genome sequencing across a broad spectrum of disorders , 2015, Nature Genetics.

[20]  Bale,et al.  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, Genetics in Medicine.

[21]  F. Cunningham,et al.  The Ensembl Variant Effect Predictor , 2016, Genome Biology.

[22]  W. Chung,et al.  Clinical application of whole-exome sequencing across clinical indications , 2015, Genetics in Medicine.

[23]  Caroline F. Wright,et al.  Principle of proportionality in genomic data sharing , 2015, Nature Reviews Genetics.

[24]  Andrew J. Hill,et al.  Analysis of protein-coding genetic variation in 60,706 humans , 2015, bioRxiv.

[25]  K. Helbig,et al.  Classification of Genes: Standardized Clinical Validity Assessment of Gene–Disease Associations Aids Diagnostic Exome Analysis and Reclassifications , 2017, Human mutation.

[26]  G. Bejerano,et al.  Systematic reanalysis of clinical exome data yields additional diagnoses: implications for providers , 2016, Genetics in Medicine.

[27]  Deciphering Developmental Disorders Study Prevalence and Architecture of De Novo Mutations in Developmental Disorders , 2017 .

[28]  Michael F. Wangler,et al.  Lessons learned from additional research analyses of unsolved clinical exome cases , 2017, Genome Medicine.