Sequencing of a Patient with Balanced Chromosome Abnormalities and Neurodevelopmental Disease Identifies Disruption of Multiple High Risk Loci by Structural Variation
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{"title"=>"Sequencing of a patient with balanced chromosome abnormalities and neurodevelopmental disease identifies disruption of multiple high risk loci by structural variation", "type"=>"journal", "authors"=>[{"first_name"=>"Jonathon", "last_name"=>"Blake", "scopus_author_id"=>"8895172100"}, {"first_name"=>"Andrew", "last_name"=>"Riddell", "scopus_author_id"=>"8746304500"}, {"first_name"=>"Susanne", "last_name"=>"Theiss", "scopus_author_id"=>"42462528600"}, {"first_name"=>"Alexis Perez", "last_name"=>"Gonzalez", "scopus_author_id"=>"54883890400"}, {"first_name"=>"Bettina", "last_name"=>"Haase", "scopus_author_id"=>"55279420300"}, {"first_name"=>"Anna", "last_name"=>"Jauch", "scopus_author_id"=>"18836000200"}, {"first_name"=>"Johannes W.G.", "last_name"=>"Janssen", "scopus_author_id"=>"35429956700"}, {"first_name"=>"David", "last_name"=>"Ibberson", "scopus_author_id"=>"17338669100"}, {"first_name"=>"Dinko", "last_name"=>"Pavlinic", "scopus_author_id"=>"57190126732"}, {"first_name"=>"Ute", "last_name"=>"Moog", "scopus_author_id"=>"55882822300"}, {"first_name"=>"Vladimir", "last_name"=>"Benes", "scopus_author_id"=>"35197826600"}, {"first_name"=>"Heiko", "last_name"=>"Runz", "scopus_author_id"=>"6507593447"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"24625750", "sgr"=>"84898724739", "doi"=>"10.1371/journal.pone.0090894", "scopus"=>"2-s2.0-84898724739", "pui"=>"372786257", "isbn"=>"1932-6203", "issn"=>"19326203"}, "id"=>"2a1f95a7-5bc5-3969-b114-fe46c4dc1b86", "abstract"=>"Balanced chromosome abnormalities (BCAs) occur at a high frequency in healthy and diseased individuals, but cost-efficient strategies to identify BCAs and evaluate whether they contribute to a phenotype have not yet become widespread. Here we apply genome-wide mate-pair library sequencing to characterize structural variation in a patient with unclear neurodevelopmental disease (NDD) and complex de novo BCAs at the karyotype level. Nucleotide-level characterization of the clinically described BCA breakpoints revealed disruption of at least three NDD candidate genes (LINC00299, NUP205, PSMD14) that gave rise to abnormal mRNAs and could be assumed as disease-causing. However, unbiased genome-wide analysis of the sequencing data for cryptic structural variation was key to reveal an additional submicroscopic inversion that truncates the schizophrenia- and bipolar disorder-associated brain transcription factor ZNF804A as an equally likely NDD-driving gene. Deep sequencing of fluorescent-sorted wild-type and derivative chromosomes confirmed the clinically undetected BCA. Moreover, deep sequencing further validated a high accuracy of mate-pair library sequencing to detect structural variants larger than 10 kB, proposing that this approach is powerful for clinical-grade genome-wide structural variant detection. Our study supports previous evidence for a role of ZNF804A in NDD and highlights the need for a more comprehensive assessment of structural variation in karyotypically abnormal individuals and patients with neurocognitive disease to avoid diagnostic deception.", "link"=>"http://www.mendeley.com/research/sequencing-patient-balanced-chromosome-abnormalities-neurodevelopmental-disease-identifies-disruptio", "reader_count"=>24, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>4, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>1, "Student > Master"=>3, "Student > Bachelor"=>5, "Professor"=>3}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>4, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>1, "Student > Master"=>3, "Student > Bachelor"=>5, "Professor"=>3}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>11, "Medicine and Dentistry"=>4, "Neuroscience"=>1, "Arts and Humanities"=>1, "Psychology"=>2, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Neuroscience"=>{"Neuroscience"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Psychology"=>{"Psychology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>11}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Netherlands"=>1, "United Kingdom"=>1, "Germany"=>1, "Spain"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1418350"], "description"=>"<p>Phenotypic comparison of the patient to previously described individuals with structural variants affecting <i>ZNF804A</i> or <i>LINC00299</i>.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome sequencing", "genetics", "Genetic mutation", "Mutation types", "Human genetics", "Chromosomal disorders", "cytogenetics", "Genetics of disease", "Genomic medicine", "genetic testing", "neuroscience", "Developmental neuroscience", "Clinical genetics", "neurology", "Developmental and pediatric neurology", "pediatrics", "individuals", "variants", "affecting"], "article_id"=>960621, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Jonathon Blake", "Andrew Riddell", "Susanne Theiss", "Alexis Perez Gonzalez", "Bettina Haase", "Anna Jauch", "Johannes W. G. Janssen", "David Ibberson", "Dinko Pavlinic", "Ute Moog", "Vladimir Benes", "Heiko Runz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090894.t002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phenotypic_comparison_of_the_patient_to_previously_described_individuals_with_structural_variants_affecting_ZNF804A_or_LINC00299_/960621", "title"=>"Phenotypic comparison of the patient to previously described individuals with structural variants affecting <i>ZNF804A</i> or <i>LINC00299</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-13 08:41:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1418349"], "description"=>"<p>(A,B) Graphical representation of the three genes disrupted by an ∼10 kB deletion on chr 19 [del(19q13.4)] (A) and the cryptic paracentric inversion inv(2)(p32.1q32.1) in the patient. Sites of breakpoints are denoted by arrows. (C) Graphical representation of anomalous-read (red dots) fusion positions for the cryptic 2.49 Mb paracentric inversion on chromosome 2. Mate-pair library sequencing-predicted breakpoints 5′ and 3′ of the inversion were amplified with breakpoint-specific primers and validated at base-pair level by PCR and capillary sequencing. (D) mRNA-levels of ZNF804A and the housekeeping gene RPL19 were quantified by qRT-PCR from total RNA isolated from fibroblasts of the patient or a healthy male control and normalized to expression of beta-actin.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome sequencing", "genetics", "Genetic mutation", "Mutation types", "Human genetics", "Chromosomal disorders", "cytogenetics", "Genetics of disease", "Genomic medicine", "genetic testing", "neuroscience", "Developmental neuroscience", "Clinical genetics", "neurology", "Developmental and pediatric neurology", "pediatrics", "cryptic", "svs", "identifies", "disruption", "further", "neurodevelopmental", "genes", "demonstrates", "reduced", "znf804a"], "article_id"=>960620, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Jonathon Blake", "Andrew Riddell", "Susanne Theiss", "Alexis Perez Gonzalez", "Bettina Haase", "Anna Jauch", "Johannes W. G. Janssen", "David Ibberson", "Dinko Pavlinic", "Ute Moog", "Vladimir Benes", "Heiko Runz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090894.g003", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_wide_analysis_for_cryptic_SVs_identifies_disruption_of_further_neurodevelopmental_disease_candidate_genes_and_demonstrates_reduced_expression_of_ZNF804A_in_patient_cells_/960620", "title"=>"Genome-wide analysis for cryptic SVs identifies disruption of further neurodevelopmental disease candidate genes and demonstrates reduced expression of ZNF804A in patient cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-13 08:41:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1418351"], "description"=>"#<p>revision to clinical diagnostic reports in bold;</p>$<p>reported neurodevelopmental disease (NDD) genes in bold;</p>&<p>acc. to Huang et al., 2010 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090894#pone.0090894-Huang1\" target=\"_blank\">[28]</a>.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome sequencing", "genetics", "Genetic mutation", "Mutation types", "Human genetics", "Chromosomal disorders", "cytogenetics", "Genetics of disease", "Genomic medicine", "genetic testing", "neuroscience", "Developmental neuroscience", "Clinical genetics", "neurology", "Developmental and pediatric neurology", "pediatrics", "disrupted", "validated", "rearrangements"], "article_id"=>960622, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Jonathon Blake", "Andrew Riddell", "Susanne Theiss", "Alexis Perez Gonzalez", "Bettina Haase", "Anna Jauch", "Johannes W. G. Janssen", "David Ibberson", "Dinko Pavlinic", "Ute Moog", "Vladimir Benes", "Heiko Runz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090894.t001", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_disrupted_by_validated_structural_rearrangements_gt_10_kb_in_the_patient_/960622", "title"=>"Genes disrupted by validated structural rearrangements (>10 kb) in the patient.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-13 08:41:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1418348"], "description"=>"<p>(A,B) Graphical representation of the four genes within the cytogenetically visible reciprocal translocation t(2;7)(2p25.1;q33) and the pericentric inversion inv(2)(p24.1q24.2) in which structural variants disrupt protein-coding gene regions in the patient. Sites of breakpoints are denoted by arrows. (C,D) To monitor whether predicted SV-induced fusion transcripts resulted in abnormal transcripts, total RNA from three biological replicates per proband was isolated from lymphoblasts of the patient (46,XY,t(2;7); lanes 4–6) and a healthy male control individual (46,XY; lanes 1–3). For each site of structural rearrangement mRNA-levels of both, the wildtype and/or pre−/post rearrangement transcript, as well as the predicted fusion transcript were amplified with target-specific primers by RT-PCR.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome sequencing", "genetics", "Genetic mutation", "Mutation types", "Human genetics", "Chromosomal disorders", "cytogenetics", "Genetics of disease", "Genomic medicine", "genetic testing", "neuroscience", "Developmental neuroscience", "Clinical genetics", "neurology", "Developmental and pediatric neurology", "pediatrics", "characterization", "cytogenetically", "breakpoints", "identifies", "fusions", "encode", "abnormal"], "article_id"=>960619, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Jonathon Blake", "Andrew Riddell", "Susanne Theiss", "Alexis Perez Gonzalez", "Bettina Haase", "Anna Jauch", "Johannes W. G. Janssen", "David Ibberson", "Dinko Pavlinic", "Ute Moog", "Vladimir Benes", "Heiko Runz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090894.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nucleotide_level_characterization_of_cytogenetically_visible_breakpoints_identifies_gene_fusions_that_encode_for_abnormal_transcripts_/960619", "title"=>"Nucleotide-level characterization of cytogenetically visible breakpoints identifies gene fusions that encode for abnormal transcripts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-13 08:41:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1418365", "https://ndownloader.figshare.com/files/1418366", "https://ndownloader.figshare.com/files/1418367", "https://ndownloader.figshare.com/files/1418368"], "description"=>"<div><p>Balanced chromosome abnormalities (BCAs) occur at a high frequency in healthy and diseased individuals, but cost-efficient strategies to identify BCAs and evaluate whether they contribute to a phenotype have not yet become widespread. Here we apply genome-wide mate-pair library sequencing to characterize structural variation in a patient with unclear neurodevelopmental disease (NDD) and complex <i>de novo</i> BCAs at the karyotype level. Nucleotide-level characterization of the clinically described BCA breakpoints revealed disruption of at least three NDD candidate genes (<i>LINC00299</i>, <i>NUP205</i>, <i>PSMD14</i>) that gave rise to abnormal mRNAs and could be assumed as disease-causing. However, unbiased genome-wide analysis of the sequencing data for cryptic structural variation was key to reveal an additional submicroscopic inversion that truncates the schizophrenia- and bipolar disorder-associated brain transcription factor <i>ZNF804A</i> as an equally likely NDD-driving gene. Deep sequencing of fluorescent-sorted wild-type and derivative chromosomes confirmed the clinically undetected BCA. Moreover, deep sequencing further validated a high accuracy of mate-pair library sequencing to detect structural variants larger than 10 kB, proposing that this approach is powerful for clinical-grade genome-wide structural variant detection. Our study supports previous evidence for a role of <i>ZNF804A</i> in NDD and highlights the need for a more comprehensive assessment of structural variation in karyotypically abnormal individuals and patients with neurocognitive disease to avoid diagnostic deception.</p></div>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome sequencing", "genetics", "Genetic mutation", "Mutation types", "Human genetics", "Chromosomal disorders", "cytogenetics", "Genetics of disease", "Genomic medicine", "genetic testing", "neuroscience", "Developmental neuroscience", "Clinical genetics", "neurology", "Developmental and pediatric neurology", "pediatrics", "chromosome", "abnormalities", "neurodevelopmental", "identifies", "disruption", "loci"], "article_id"=>960636, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Jonathon Blake", "Andrew Riddell", "Susanne Theiss", "Alexis Perez Gonzalez", "Bettina Haase", "Anna Jauch", "Johannes W. G. Janssen", "David Ibberson", "Dinko Pavlinic", "Ute Moog", "Vladimir Benes", "Heiko Runz"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0090894.s001", "https://dx.doi.org/10.1371/journal.pone.0090894.s002", "https://dx.doi.org/10.1371/journal.pone.0090894.s003", "https://dx.doi.org/10.1371/journal.pone.0090894.s004"], "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequencing_of_a_Patient_with_Balanced_Chromosome_Abnormalities_and_Neurodevelopmental_Disease_Identifies_Disruption_of_Multiple_High_Risk_Loci_by_Structural_Variation_/960636", "title"=>"Sequencing of a Patient with Balanced Chromosome Abnormalities and Neurodevelopmental Disease Identifies Disruption of Multiple High Risk Loci by Structural Variation", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-03-13 08:41:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1418347"], "description"=>"<p>(A) Chromosomes 2 and 7 of the patient as visualized by GTG-banding. Breakpoint positions of BCAs reported from clinical analyses at karyotype level are indicated in red. (B,C) Graphical representation of anomalous-read (red dots) fusion positions for t(2;7) (B) and the paracentric inv(2) (C). Based on mate-pair library sequencing-identified gap positions primers were designed to amplify and validate anomalous regions by PCR and capillary sequencing at base-pair level. (D) Validation of re-annotated t(2;7) breakpoint positions by FISH with BAC-probes binding immediately adjacent to re-defined translocation sites.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome sequencing", "genetics", "Genetic mutation", "Mutation types", "Human genetics", "Chromosomal disorders", "cytogenetics", "Genetics of disease", "Genomic medicine", "genetic testing", "neuroscience", "Developmental neuroscience", "Clinical genetics", "neurology", "Developmental and pediatric neurology", "pediatrics", "characterization", "clinically-identified", "chromosome", "abnormality"], "article_id"=>960618, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Jonathon Blake", "Andrew Riddell", "Susanne Theiss", "Alexis Perez Gonzalez", "Bettina Haase", "Anna Jauch", "Johannes W. G. Janssen", "David Ibberson", "Dinko Pavlinic", "Ute Moog", "Vladimir Benes", "Heiko Runz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090894.g001", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Base_pair_level_characterization_of_clinically_identified_de_novo_balanced_chromosome_abnormality_BCAs_/960618", "title"=>"Base-pair level characterization of clinically-identified <i>de novo</i> balanced chromosome abnormality (BCAs).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-13 08:41:40"}

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Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Computational biology", "average_usage"=>[341, 529]}, {"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[292, 461]}]}
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