Identification of novel FMR1 variants by massively parallel sequencing in developmentally delayed males

Fragile X syndrome (FXS), the most common inherited form of developmental delay, is typically caused by CGG‐repeat expansion in FMR1. However, little attention has been paid to sequence variants in FMR1. Through the use of pooled‐template massively parallel sequencing, we identified 130 novel FMR1 sequence variants in a population of 963 developmentally delayed males without CGG‐repeat expansion mutations. Among these, we identified a novel missense change, p.R138Q, which alters a conserved residue in the nuclear localization signal of FMRP. We have also identified three promoter mutations in this population, all of which significantly reduce in vitro levels of FMR1 transcription. Additionally, we identified 10 noncoding variants of possible functional significance in the introns and 3′‐untranslated region of FMR1, including two predicted splice site mutations. These findings greatly expand the catalog of known FMR1 sequence variants and suggest that FMR1 sequence variants may represent an important cause of developmental delay. © 2010 Wiley‐Liss, Inc.

[1]  Mary Goldman,et al.  The UCSC Genome Browser database: update 2011 , 2010, Nucleic Acids Res..

[2]  D. Cutler,et al.  Array-Based FMR1 Sequencing and Deletion Analysis in Patients with a Fragile X Syndrome–Like Phenotype , 2010, PloS one.

[3]  David Haussler,et al.  The UCSC Genome Browser database: update 2010 , 2009, Nucleic Acids Res..

[4]  Detlef Weigel,et al.  Deep sequencing to reveal new variants in pooled DNA samples , 2009, Human mutation.

[5]  Michael E Zwick,et al.  Combining Microarray‐based Genomic Selection (MGS) with the Illumina Genome Analyzer Platform to Sequence Diploid Target Regions , 2009, Annals of human genetics.

[6]  Ken Chen,et al.  VarScan: variant detection in massively parallel sequencing of individual and pooled samples , 2009, Bioinform..

[7]  Sangsoo Kim,et al.  The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. , 2009, Genome research.

[8]  Justin C. Fay,et al.  Quantification of rare allelic variants from pooled genomic DNA , 2009, Nature Methods.

[9]  Max Ingman,et al.  SNP frequency estimation using massively parallel sequencing of pooled DNA , 2009, European Journal of Human Genetics.

[10]  Emily H Turner,et al.  Targeted Capture and Massively Parallel Sequencing of Twelve Human Exomes , 2009, Nature.

[11]  Timothy B. Stockwell,et al.  Evaluation of next generation sequencing platforms for population targeted sequencing studies , 2009, Genome Biology.

[12]  Dawei Li,et al.  The diploid genome sequence of an Asian individual , 2008, Nature.

[13]  R. Durbin,et al.  Mapping Quality Scores Mapping Short Dna Sequencing Reads and Calling Variants Using P

, 2022 .

[14]  Nancy F. Hansen,et al.  Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry , 2008, Nature.

[15]  S. Ceman,et al.  Fragile X Mental Retardation Protein FMRP Binds mRNAs in the Nucleus , 2008, Molecular and Cellular Biology.

[16]  Hanlee P. Ji,et al.  Next-generation DNA sequencing , 2008, Nature Biotechnology.

[17]  Juliane C. Dohm,et al.  Substantial biases in ultra-short read data sets from high-throughput DNA sequencing , 2008, Nucleic acids research.

[18]  S. Warren,et al.  Mosaic FMR1 deletion causes fragile X syndrome and can lead to molecular misdiagnosis: A case report and review of the literature , 2008, American journal of medical genetics. Part A.

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

[20]  J. Stephenson.  1000 Genomes Project , 2008 .

[21]  Doron Betel,et al.  The microRNA.org resource: targets and expression , 2007, Nucleic Acids Res..

[22]  Timothy B. Stockwell,et al.  The Diploid Genome Sequence of an Individual Human , 2007, PLoS biology.

[23]  Hanlee P. Ji,et al.  Multigene amplification and massively parallel sequencing for cancer mutation discovery , 2007, Proceedings of the National Academy of Sciences.

[24]  Juliane Hoyer,et al.  Diagnostic yield of various genetic approaches in patients with unexplained developmental delay or mental retardation , 2006, American journal of medical genetics. Part A.

[25]  Terrence S. Furey,et al.  The UCSC Genome Browser Database: update 2006 , 2005, Nucleic Acids Res..

[26]  D. Haussler,et al.  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.

[27]  Modesto Orozco,et al.  PMUT: a web-based tool for the annotation of pathological mutations on proteins , 2005, Bioinform..

[28]  J. Fallon,et al.  AP-2α selectively regulates fragile X mental retardation-1 gene transcription during embryonic development , 2005 .

[29]  S. Eddy,et al.  Kissing complex RNAs mediate interaction between the Fragile-X mental retardation protein KH2 domain and brain polyribosomes. , 2005, Genes & development.

[30]  A. Gabrielian,et al.  The roles of Sp1, Sp3, USF1/USF2 and NRF-1 in the regulation and three-dimensional structure of the Fragile X mental retardation gene promoter. , 2005, The Biochemical journal.

[31]  J. Fallon,et al.  AP-2alpha selectively regulates fragile X mental retardation-1 gene transcription during embryonic development. , 2005, Human molecular genetics.

[32]  P. Thomas,et al.  Coding single-nucleotide polymorphisms associated with complex vs. Mendelian disease: evolutionary evidence for differences in molecular effects. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[33]  Anton J. Enright,et al.  Human MicroRNA Targets , 2004, PLoS biology.

[34]  Mariette Schrier,et al.  Transport kinetics of FMRP containing the I304N mutation of severe fragile X syndrome in neurites of living rat PC12 cells , 2004, Experimental Neurology.

[35]  J. Mandel,et al.  Five years of molecular diagnosis of Fragile X syndrome (1997–2001): A collaborative study reporting 95% of the activity in France , 2004, American journal of medical genetics. Part A.

[36]  Karen T. Smith,et al.  Occupancy and synergistic activation of the FMR1 promoter by Nrf-1 and Sp1 in vivo. , 2004, Human molecular genetics.

[37]  P. Hagerman,et al.  Redistribution of transcription start sites within the FMR1 promoter region with expansion of the downstream CGG-repeat element. , 2004, Human molecular genetics.

[38]  T. Saijo,et al.  Single-strand conformation polymorphism analysis of the FMR1 gene in autistic and mentally retarded children in Japan. , 2004, The journal of medical investigation : JMI.

[39]  A. Pastore,et al.  The N-terminus of the fragile X mental retardation protein contains a novel domain involved in dimerization and RNA binding. , 2003, Biochemistry.

[40]  Steven Henikoff,et al.  SIFT: predicting amino acid changes that affect protein function , 2003, Nucleic Acids Res..

[41]  PREVALENCE OF THE FRAGILE X SYNDROME IN YUGOSLAV PATIENTS WITH NON-SPECIFIC MENTAL RETARDATION , 2003, Journal of neurogenetics.

[42]  P. Bork,et al.  Human non-synonymous SNPs: server and survey. , 2002, Nucleic acids research.

[43]  K. Pavelić,et al.  Screening for fragile X syndrome: results from a school for mentally retarded children , 2002, Acta paediatrica.

[44]  S. Phadke,et al.  Molecular screening of FRAXA and FRAXE in Indian patients with unexplained mental retardation. , 2002, Genetic testing.

[45]  K. Usdin,et al.  Interaction of the Transcription Factors USF1, USF2, and α-Pal/Nrf-1 with the FMR1 Promoter , 2001, The Journal of Biological Chemistry.

[46]  X. Estivill,et al.  Rare variants in the promoter of the fragile X syndrome gene (FMR1). , 2000, Molecular and cellular probes.

[47]  J. Mandel,et al.  A novel RNA-binding nuclear protein that interacts with the fragile X mental retardation (FMR1) protein. , 1999, Human molecular genetics.

[48]  J. Mallolas,et al.  Single-strand conformation polymorphism analysis in the FMR1 gene. , 1999, American journal of medical genetics.

[49]  C. Sismani,et al.  Molecular screening of fragile X (FRAXA) and FRAXE mental retardation syndromes in the Hellenic population of Greece and Cyprus: incidence, genetic variation, and stability. , 1999, American journal of medical genetics.

[50]  K. Brøndum‐Nielsen,et al.  Mutational analysis of the FMR1 gene in 118 mentally retarded males suspected of fragile X syndrome: absence of prevalent mutations , 1998, Human Genetics.

[51]  B. Oostra,et al.  In vitro reactivation of the FMR1 gene involved in fragile X syndrome. , 1998, Human molecular genetics.

[52]  J. Mandel,et al.  Analysis of Domains Affecting Intracellular Localization of the FMRP Protein , 1997, Neurobiology of Disease.

[53]  D. Absher,et al.  FMRP associates with polyribosomes as an mRNP, and the I304N mutation of severe fragile X syndrome abolishes this association. , 1997, Molecular cell.

[54]  S. Hersch,et al.  Fragile X Mental Retardation Protein: Nucleocytoplasmic Shuttling and Association with Somatodendritic Ribosomes , 1997, The Journal of Neuroscience.

[55]  David Haussler,et al.  Improved splice site detection in Genie , 1997, RECOMB '97.

[56]  Shuan-yow Li,et al.  Novel point mutation within intron 10 of FMR‐1 gene causing fragile X syndrome , 1997, Human mutation.

[57]  B. Cullen,et al.  A nuclear role for the Fragile X mental retardation protein. , 1996, The EMBO journal.

[58]  R. Kooy,et al.  Severe mental retardation and macroorchidism without mutation in the FMR1 gene. , 1996, American journal of medical genetics.

[59]  S. Warren,et al.  The fragile X mental retardation protein is a ribonucleoprotein containing both nuclear localization and nuclear export signals. , 1996, Human molecular genetics.

[60]  Point mutation analysis of the FMR-1 gene in autism. , 1996, Molecular psychiatry.

[61]  J. Mandel,et al.  Alternative splicing of exon 14 determines nuclear or cytoplasmic localisation of fmr1 protein isoforms. , 1996, Human molecular genetics.

[62]  D. Nelson,et al.  Intragenic loss of function mutations demonstrate the primary role of FMR1 in fragile X syndrome , 1995, Nature Genetics.

[63]  B. Oostra,et al.  No apparent involvement of the FMR1 gene in five patients with phenotypic manifestations of the fragile X syndrome. , 1994, American journal of medical genetics.

[64]  E. Eichler,et al.  Human and murine FMR-1: alternative splicing and translational initiation downstream of the CGG–repeat , 1993, Nature Genetics.

[65]  W. Hwu,et al.  In vitro DNA methylation inhibits FMR-1 promoter. , 1993, Biochemical and Biophysical Research Communications - BBRC.

[66]  Edwin Reyniers,et al.  A point mutation in the FMR-1 gene associated with fragile X mental retardation , 1993, Nature Genetics.

[67]  J. Sutcliffe,et al.  DNA methylation represses FMR-1 transcription in fragile X syndrome. , 1992, Human molecular genetics.

[68]  J. Sutcliffe,et al.  Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome , 1991, Cell.