Sequencing individual genomes with recurrent genomic disorder deletions: an approach to characterize genes for autosomal recessive rare disease traits

[1]  J. Lupski Biology in balance: human diploid genome integrity, gene dosage, and genomic medicine. , 2022, Trends in genetics : TIG.

[2]  Jeffrey M. Weiss,et al.  Centers for Mendelian Genomics: A decade of facilitating gene discovery , 2021, medRxiv.

[3]  J. Lupski Clan genomics: From OMIM phenotypic traits to genes and biology , 2021, American journal of medical genetics. Part A.

[4]  Danny E Miller,et al.  Exome and genome sequencing for pediatric patients with congenital anomalies or intellectual disability: an evidence-based clinical guideline of the American College of Medical Genetics and Genomics (ACMG) , 2021, Genetics in Medicine.

[5]  David T. Miller,et al.  Chromosomal microarray analysis, including constitutional and neoplastic disease applications, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG) , 2021, Genetics in Medicine.

[6]  J. Rosenfeld,et al.  Clinical characterization of individuals with the distal 1q21.1 microdeletion , 2021, American journal of medical genetics. Part A.

[7]  F. Alkuraya How the human genome transformed study of rare diseases , 2021, Nature.

[8]  K. Kosaki,et al.  Biallelic loss of OTUD7A causes severe muscular hypotonia, intellectual disability, and seizures , 2020, American journal of medical genetics. Part A.

[9]  P. Stenson,et al.  The Human Gene Mutation Database (HGMD®): optimizing its use in a clinical diagnostic or research setting , 2020, Human Genetics.

[10]  A. Breman,et al.  CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels , 2020, Genetics in Medicine.

[11]  Johnathon R. Walls,et al.  Functional biology of the Steel syndrome founder allele and evidence for clan genomics derivation of COL27A1 pathogenic alleles worldwide , 2020, European Journal of Human Genetics.

[12]  Tariq Ahmad,et al.  A structural variation reference for medical and population genetics , 2020, Nature.

[13]  C. Shaw,et al.  The impact of the Turkish (TK) population variome on the genomic architecture of rare disease traits , 2020, bioRxiv.

[14]  J. Lupski,et al.  Increased TBX6 gene dosages induce congenital cervical vertebral malformations in humans and mice , 2019, Journal of Medical Genetics.

[15]  A J Agopian,et al.  Complete Sequence of the 22q11.2 Allele in 1,053 Subjects with 22q11.2 Deletion Syndrome Reveals Modifiers of Conotruncal Heart Defects. , 2019, American journal of human genetics.

[16]  E. Krüger,et al.  Report of the first patient with a homozygous OTUD7A variant responsible for epileptic encephalopathy and related proteasome dysfunction , 2019, Clinical genetics.

[17]  Michael J Bamshad,et al.  Mendelian Gene Discovery: Fast and Furious with No End in Sight. , 2019, American journal of human genetics.

[18]  E. Lemyre,et al.  Estimating the effect size of the 15Q11.2 BP1–BP2 deletion and its contribution to neurodevelopmental symptoms: recommendations for practice , 2019, Journal of Medical Genetics.

[19]  Steve D. M. Brown,et al.  Human and mouse essentiality screens as a resource for disease gene discovery , 2019, bioRxiv.

[20]  J. Rosenfeld,et al.  Reanalysis of Clinical Exome Sequencing Data. , 2019, The New England journal of medicine.

[21]  P. Stankiewicz,et al.  Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases , 2019, Genome Medicine.

[22]  C. Shaw,et al.  Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2 , 2019, Cell.

[23]  J. Lupski 2018 Victor A. McKusick Leadership Award: Molecular Mechanisms for Genomic and Chromosomal Rearrangements. , 2019, American journal of human genetics.

[24]  Justyna A. Karolak,et al.  Complex Compound Inheritance of Lethal Lung Developmental Disorders Due to Disruption of the TBX-FGF Pathway. , 2019, American journal of human genetics.

[25]  Ryan L. Collins,et al.  The mutational constraint spectrum quantified from variation in 141,456 humans , 2020, Nature.

[26]  M. Gerstein,et al.  Insights into genetics, human biology and disease gleaned from family based genomic studies , 2019, Genetics in Medicine.

[27]  J. Lupski,et al.  TBX6-associated congenital scoliosis (TACS) as a clinically distinguishable subtype of congenital scoliosis: further evidence supporting the compound inheritance and TBX6 gene dosage model , 2019, Genetics in Medicine.

[28]  Alan F. Scott,et al.  OMIM.org: leveraging knowledge across phenotype–gene relationships , 2018, Nucleic Acids Res..

[29]  J. Lupski,et al.  TBX6 compound inheritance leads to congenital vertebral malformations in humans and mice , 2018, Human molecular genetics.

[30]  Ivan K. Chinn,et al.  Identifying Genes Whose Mutant Transcripts Cause Dominant Disease Traits by Potential Gain-of-Function Alleles. , 2018, American journal of human genetics.

[31]  C. Bole-Feysot,et al.  Whole-exome sequence analysis highlights the role of unmasked recessive mutations in copy number variants with incomplete penetrance , 2018, European Journal of Human Genetics.

[32]  G. Kirov,et al.  Medical consequences of pathogenic CNVs in adults: analysis of the UK Biobank , 2018, Journal of Medical Genetics.

[33]  Biren M. Dave,et al.  OTUD7A Regulates Neurodevelopmental Phenotypes in the 15q13.3 Microdeletion Syndrome , 2018, American journal of human genetics.

[34]  Rodney C. Samaco,et al.  Otud7a Knockout Mice Recapitulate Many Neurological Features of 15q13.3 Microdeletion Syndrome. , 2018, American journal of human genetics.

[35]  James D Stephenson,et al.  Quantifying the contribution of recessive coding variation to developmental disorders , 2017, Science.

[36]  R. Punnett,et al.  Experimental studies in the physiology of heredity , 2017, Zeitschrift für Induktive Abstammungs- und Vererbungslehre.

[37]  Donna M. Muzny,et al.  Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation , 2017, The New England journal of medicine.

[38]  Marylyn D. Ritchie,et al.  Distribution and clinical impact of functional variants in 50,726 whole-exome sequences from the DiscovEHR study , 2016, Science.

[39]  Evan E Eichler,et al.  Human adaptation and evolution by segmental duplication. , 2016, Current opinion in genetics & development.

[40]  Imran S Haque,et al.  Modeled Fetal Risk of Genetic Diseases Identified by Expanded Carrier Screening. , 2016, JAMA.

[41]  J. Lupski,et al.  Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates , 2015, PLoS genetics.

[42]  Heidi L Rehm,et al.  ClinGen--the Clinical Genome Resource. , 2015, The New England journal of medicine.

[43]  J. Lupski Structural variation mutagenesis of the human genome: Impact on disease and evolution , 2015, Environmental and molecular mutagenesis.

[44]  Tom R. Gaunt,et al.  Copy number variations and cognitive phenotypes in unselected populations. , 2015, JAMA.

[45]  J. Lupski Cognitive phenotypes and genomic copy number variations. , 2015, JAMA.

[46]  J. Lupski,et al.  TBX6 null variants and a common hypomorphic allele in congenital scoliosis. , 2015, The New England journal of medicine.

[47]  Magalie S Leduc,et al.  Molecular findings among patients referred for clinical whole-exome sequencing. , 2014, JAMA.

[48]  L. Vallée,et al.  Further delineation of eye manifestations in homozygous 15q13.3 microdeletions including TRPM1: A differential diagnosis of ceroid lipofuscinosis , 2014, American journal of medical genetics. Part A.

[49]  J. Lupski,et al.  The allelic spectrum of Charcot–Marie–Tooth disease in over 17,000 individuals with neuropathy , 2014, Molecular genetics & genomic medicine.

[50]  Adam J. Schwarz,et al.  CNVs conferring risk of autism or schizophrenia affect cognition in controls , 2013, Nature.

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

[52]  J. Rosenfeld,et al.  NAHR-mediated copy-number variants in a clinical population: Mechanistic insights into both genomic disorders and Mendelizing traits , 2013, Genome research.

[53]  P. Stankiewicz,et al.  Deletions of recessive disease genes: CNV contribution to carrier states and disease-causing alleles , 2013, Genome research.

[54]  Bradley P. Coe,et al.  Estimates of penetrance for recurrent pathogenic copy-number variations , 2012, Genetics in Medicine.

[55]  F. Zara,et al.  Homozygous c.649dupC mutation in PRRT2 worsens the BFIS/PKD phenotype with mental retardation, episodic ataxia, and absences , 2012, Epilepsia.

[56]  J. Veltman,et al.  De novo mutations in human genetic disease , 2012, Nature Reviews Genetics.

[57]  Pengfei Liu,et al.  Mechanisms for recurrent and complex human genomic rearrangements. , 2012, Current opinion in genetics & development.

[58]  Ana Cvejic,et al.  Inheritance of low-frequency regulatory SNPs and a rare null mutation in exon-junction complex subunit RBM8A causes TAR , 2012, Nature Genetics.

[59]  James N. Hughes,et al.  PRRT2 mutations cause benign familial infantile epilepsy and infantile convulsions with choreoathetosis syndrome. , 2012, American journal of human genetics.

[60]  Stephanie E. Vallee,et al.  Recurrent deletions and reciprocal duplications of 10q11.21q11.23 including CHAT and SLC18A3 are likely mediated by complex low‐copy repeats , 2012, Human mutation.

[61]  Ning Wang,et al.  Exome sequencing identifies truncating mutations in PRRT2 that cause paroxysmal kinesigenic dyskinesia , 2011, Nature Genetics.

[62]  J. Lupski,et al.  Frequency of nonallelic homologous recombination is correlated with length of homology: evidence that ectopic synapsis precedes ectopic crossing-over. , 2011, American journal of human genetics.

[63]  J. Lupski,et al.  Clan Genomics and the Complex Architecture of Human Disease , 2011, Cell.

[64]  D. Horn,et al.  Homozygous deletion of chromosome 15q13.3 including CHRNA7 causes severe mental retardation, seizures, muscular hypotonia, and the loss of KLF13 and TRPM1 potentially cause macrocytosis and congenital retinal dysfunction in siblings. , 2011, European journal of medical genetics.

[65]  M. DePristo,et al.  Variation in genome-wide mutation rates within and between human families , 2011, Nature Genetics.

[66]  E. Schröck,et al.  Homozygous loss of CHRNA7 on chromosome 15q13.3 causes severe encephalopathy with seizures and hypotonia , 2010, American journal of medical genetics. Part A.

[67]  Linda Odenthal-Hesse,et al.  PRDM9 variation strongly influences recombination hot-spot activity and meiotic instability in humans , 2010, Nature Genetics.

[68]  M. Holder,et al.  Delineation of 15q13.3 microdeletions , 2010, Clinical genetics.

[69]  D. Bittel,et al.  A 15q13.3 homozygous microdeletion associated with a severe neurodevelopmental disorder suggests putative functions of the TRPM1, CHRNA7, and other homozygously deleted genes , 2010, American journal of medical genetics. Part A.

[70]  P. Stankiewicz,et al.  Recurrent reciprocal 16p11.2 rearrangements associated with global developmental delay, behavioural problems, dysmorphism, epilepsy, and abnormal head size , 2009, Journal of Medical Genetics.

[71]  B. V. van Bon,et al.  Further delineation of the 15q13 microdeletion and duplication syndromes: a clinical spectrum varying from non-pathogenic to a severe outcome , 2009, Journal of Medical Genetics.

[72]  Manuel Corpas,et al.  DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. , 2009, American journal of human genetics.

[73]  P. Stankiewicz,et al.  Microdeletion 15q13.3: a locus with incomplete penetrance for autism, mental retardation, and psychiatric disorders , 2009, Journal of Medical Genetics.

[74]  J. Lupski,et al.  The complete genome of an individual by massively parallel DNA sequencing , 2008, Nature.

[75]  Joshua M. Korn,et al.  Association between microdeletion and microduplication at 16p11.2 and autism. , 2008, The New England journal of medicine.

[76]  J. Lupski,et al.  Genomic rearrangements and sporadic disease , 2007, Nature Genetics.

[77]  Reinhard Ullmann,et al.  Complex inheritance pattern resembling autosomal recessive inheritance involving a microdeletion in thrombocytopenia-absent radius syndrome. , 2007, American journal of human genetics.

[78]  Andrew J Sharp,et al.  Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome , 2006, Nature Genetics.

[79]  Andrew J Lees,et al.  Microdeletion encompassing MAPT at chromosome 17q21.3 is associated with developmental delay and learning disability , 2006, Nature Genetics.

[80]  R. Pfundt,et al.  A new chromosome 17q21.31 microdeletion syndrome associated with a common inversion polymorphism , 2006, Nature Genetics.

[81]  J. Lupski Genome structural variation and sporadic disease traits , 2006, Nature Genetics.

[82]  J. Lupski,et al.  T118M PMP22 mutation causes partial loss of function and HNPP‐like neuropathy , 2006, Annals of neurology.

[83]  J. Lupski,et al.  Phenotypic consequences of genetic variation at hemizygous alleles: Sotos syndrome is a contiguous gene syndrome incorporating coagulation factor twelve (FXII) deficiency , 2005, Genetics in Medicine.

[84]  J. Lupski,et al.  Novel mutations of MYO15A associated with profound deafness in consanguineous families and moderately severe hearing loss in a patient with Smith-Magenis syndrome , 2001, Human Genetics.

[85]  L. Shaffer,et al.  DNA rearrangements on both homologues of chromosome 17 in a mildly delayed individual with a family history of autosomal dominant carpal tunnel syndrome. , 1999, American journal of human genetics.

[86]  V. Perry,et al.  An 85-kb tandem triplication in the slow Wallerian degeneration (Wlds) mouse. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[87]  A. Harding,et al.  Deletions of chromosome 17p11.2 in multifocal neuropathies , 1996, Annals of neurology.

[88]  B. Trask,et al.  Evidence for a recessive PMP22 point mutation in Charcot–Marie–Tooth disease type 1A , 1993, Nature genetics.

[89]  A. Ballabio,et al.  Deletions and translocations involving the distal short arm of the human X chromosome: review and hypotheses. , 1992, Human molecular genetics.

[90]  R. Myerowitz,et al.  The major defect in Ashkenazi Jews with Tay-Sachs disease is an insertion in the gene for the alpha-chain of beta-hexosaminidase. , 1988, The Journal of biological chemistry.

[91]  N. Carter,et al.  Germline rates of de novo meiotic deletions and duplications causing several genomic disorders , 2008, Nature Genetics.

[92]  G. Serratrice,et al.  [Tomaculous neuropathy. A histopathological study and electroclinical correlates in 10 cases]. , 1987, Revue neurologique.