Exome and genome sequencing: a revolution for the discovery and diagnosis of monogenic disorders

Massively parallel DNA sequencing has revolutionized analyses of human genetic variation. From having been out of reach for individual research groups and even more so for clinical diagnostic laboratories until recently, it is now possible to analyse complete human genomes within reasonable time frames and at a reasonable cost using technologies that are becoming increasingly available. This represents a huge advance in our ability to provide correct diagnoses for patients with rare inherited disorders and their families. This paradigm shift is especially dramatic within the area of monogenic disorders. Not only can rapid and safe diagnostics of virtually all known single‐gene defects now be established, but novel causes of disease in previously unsolved cases can also be identified, illuminating novel pathways important for normal physiology. This greatly increases the capability not only to improve management of rare disorders, but also to improve understanding of pathogenetic mechanisms relevant for common, complex diseases.

[1]  A. Monaco,et al.  Cloning the gene for an inherited human disorder—chronic granulomatous disease—on the basis of its chromosomal location , 1986, Nature.

[2]  P. Shannon,et al.  Exome sequencing identifies the cause of a Mendelian disorder , 2009, Nature Genetics.

[3]  L. Tsui,et al.  Identification of the cystic fibrosis gene: genetic analysis. , 1989, Science.

[4]  C. Nusbaum,et al.  Comprehensive variation discovery in single human genomes , 2014, Nature Genetics.

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

[6]  L. Pauling,et al.  Sickle cell anemia a molecular disease. , 1949, Science.

[7]  M. Baumgartner,et al.  Lack of the mitochondrial protein acylglycerol kinase causes Sengers syndrome. , 2012, American journal of human genetics.

[8]  D. Botstein,et al.  Construction of a genetic linkage map in man using restriction fragment length polymorphisms. , 1980, American journal of human genetics.

[9]  A. Young,et al.  A polymorphic DNA marker genetically linked to Huntington's disease , 1983, Nature.

[10]  Emily H Turner,et al.  Target-enrichment strategies for next-generation sequencing , 2010, Nature Methods.

[11]  Thomas L. Casavant,et al.  First Exons and Introns - A Survey of GC Content and Gene Structure in the Human Genome , 2006, Silico Biol..

[12]  S. Hinrichs,et al.  Structural evidence for the authenticity of the human retinoblastoma gene. , 1987, Science.

[13]  L. Tsui,et al.  Erratum: Identification of the Cystic Fibrosis Gene: Cloning and Characterization of Complementary DNA , 1989, Science.

[14]  S. Henikoff,et al.  Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm , 2009, Nature Protocols.

[15]  Jonathan S Berg,et al.  Points to Consider: Ethical, Legal, and Psychosocial Implications of Genetic Testing in Children and Adolescents. , 2015, American journal of human genetics.

[16]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[17]  B. Knoppers,et al.  Whole-genome sequencing in health care , 2013, European Journal of Human Genetics.

[18]  V. Ingram Abnormal human haemoglobins. III. The chemical difference between normal and sickle cell haemoglobins. , 1959, Biochimica et biophysica acta.

[19]  Erika Check Hayden,et al.  Technology: The $1,000 genome , 2014, Nature.

[20]  I. Adzhubei,et al.  Predicting Functional Effect of Human Missense Mutations Using PolyPhen‐2 , 2013, Current protocols in human genetics.

[21]  E. Bertini,et al.  Leukoencephalopathy with thalamus and brainstem involvement and high lactate 'LTBL' caused by EARS2 mutations. , 2012, Brain : a journal of neurology.

[22]  D. Thorburn,et al.  Minimum birth prevalence of mitochondrial respiratory chain disorders in children. , 2003, Brain : a journal of neurology.

[23]  A. Monaco,et al.  Cloning the gene for the inherited disorder chronic granulomatous disease on the basis of its chromosomal location. , 1986, Cold Spring Harbor symposia on quantitative biology.

[24]  Joseph K. Pickrell,et al.  A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes , 2012, Science.

[25]  Emily H Turner,et al.  Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome , 2010, Nature Genetics.

[26]  G. Helt,et al.  Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution , 2005, Science.

[27]  M. Metzker Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[28]  International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome , 2001, Nature.

[29]  L. Tsui,et al.  Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA. , 1989, Science.

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

[31]  R. Williamson,et al.  Analysis of the beta-delta-globin gene loci in normal and Hb Lepore DNA: direct determination of gene linkage and intergene distance. , 1978, Cell.

[32]  Matthew Mort,et al.  The Human Gene Mutation Database: providing a comprehensive central mutation database for molecular diagnostics and personalised genomics , 2009, Human Genomics.

[33]  K. Veeramah,et al.  Exome sequencing reveals new causal mutations in children with epileptic encephalopathies , 2013, Epilepsia.

[34]  Robert W. Taylor,et al.  ELAC2 mutations cause a mitochondrial RNA processing defect associated with hypertrophic cardiomyopathy. , 2013, American journal of human genetics.

[35]  A. Hoischen,et al.  Neu-Laxova syndrome is a heterogeneous metabolic disorder caused by defects in enzymes of the L-serine biosynthesis pathway. , 2014, American journal of human genetics.

[36]  S. Ferdinandusse,et al.  ECHS1 mutations in Leigh disease: a new inborn error of metabolism affecting valine metabolism. , 2014, Brain : a journal of neurology.

[37]  Serafim Batzoglou,et al.  Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++ , 2010, PLoS Comput. Biol..

[38]  M. Rieder,et al.  Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations , 2011, Nature Genetics.

[39]  A. Vanderver,et al.  Novel (ovario) leukodystrophy related to AARS2 mutations , 2014, Neurology.

[40]  Matej Oresic,et al.  Exome sequencing identifies mitochondrial alanyl-tRNA synthetase mutations in infantile mitochondrial cardiomyopathy. , 2011, American journal of human genetics.

[41]  E S Lander,et al.  Homozygosity mapping: a way to map human recessive traits with the DNA of inbred children. , 1987, Science.

[42]  Mark J. P. Chaisson,et al.  Resolving the complexity of the human genome using single-molecule sequencing , 2014, Nature.

[43]  R. Williamson,et al.  Analysis of the β-δ-globin gene loci in normal and hb lepore DNA: Direct determination of gene linkage and intergene distance , 1978, Cell.

[44]  J. Lundeberg,et al.  Adenosine kinase deficiency disrupts the methionine cycle and causes hypermethioninemia, encephalopathy, and abnormal liver function. , 2011, American journal of human genetics.

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

[46]  Z. Ning,et al.  Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of GC-biased genomes , 2009, Nature Methods.

[47]  L. Vissers,et al.  Genome sequencing identifies major causes of severe intellectual disability , 2014, Nature.

[48]  Manish S. Shah,et al.  A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes , 1993, Cell.

[49]  A. Paetau,et al.  Mitochondrial phenylalanyl-tRNA synthetase mutations underlie fatal infantile Alpers encephalopathy. , 2012, Human molecular genetics.

[50]  S. Salzberg,et al.  The Transcriptional Landscape of the Mammalian Genome , 2005, Science.

[51]  J. Shendure,et al.  A general framework for estimating the relative pathogenicity of human genetic variants , 2014, Nature Genetics.

[52]  Robin Andeer,et al.  Rapid pulsed whole genome sequencing for comprehensive acute diagnostics of inborn errors of metabolism , 2014, BMC Genomics.

[53]  D. Jaffe,et al.  Molecular Diagnosis of Infantile Mitochondrial Disease with Targeted Next-Generation Sequencing , 2012, Science Translational Medicine.

[54]  Christian Gilissen,et al.  A de novo paradigm for mental retardation , 2010, Nature Genetics.

[55]  A. Fischer,et al.  Contribution of high‐throughput DNA sequencing to the study of primary immunodeficiencies , 2014, European journal of immunology.

[56]  M. Koenig,et al.  Complete cloning of the duchenne muscular dystrophy (DMD) cDNA and preliminary genomic organization of the DMD gene in normal and affected individuals , 1987, Cell.

[57]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.