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Mutations in epigenetic regulation genes are a major cause of overgrowth with intellectual disability

Mutations in epigenetic regulation genes are a major cause of overgrowth with intellectual disability
Mutations in epigenetic regulation genes are a major cause of overgrowth with intellectual disability
To explore the genetic architecture of human overgrowth syndromes and human growth control, we performed experimental and bioinformatic analyses of 710 individuals with overgrowth (height and/or head circumference ≥+2 SD) and intellectual disability (OGID). We identified a causal mutation in 1 of 14 genes in 50% (353/710). This includes HIST1H1E, encoding histone H1.4, which has not been associated with a developmental disorder previously. The pathogenic HIST1H1E mutations are predicted to result in a product that is less effective in neutralizing negatively charged linker DNA because it has a reduced net charge, and in DNA binding and protein-protein interactions because key residues are truncated. Functional network analyses demonstrated that epigenetic regulation is a prominent biological process dysregulated in individuals with OGID. Mutations in six epigenetic regulation genes—NSD1, EZH2, DNMT3A, CHD8, HIST1H1E, and EED—accounted for 44% of individuals (311/710). There was significant overlap between the 14 genes involved in OGID and 611 genes in regions identified in GWASs to be associated with height (p = 6.84 × 10−8), suggesting that a common variation impacting function of genes involved in OGID influences height at a population level. Increased cellular growth is a hallmark of cancer and there was striking overlap between the genes involved in OGID and 260 somatically mutated cancer driver genes (p = 1.75 × 10−14). However, the mutation spectra of genes involved in OGID and cancer differ, suggesting complex genotype-phenotype relationships. These data reveal insights into the genetic control of human growth and demonstrate that exome sequencing in OGID has a high diagnostic yield.
0002-9297
725-736
Tatton-Brown, Katrina
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Loveday, Chey
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Yost, Shawn
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Clarke, Matthew
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Ramsay, Emma
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Zachariou, Anna
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Elliott, Anna
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Wylie, Harriet
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Ardissone, Anna
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Rittinger, Olaf
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Stewart, Fiona
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Temple, Karen
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Cole, Trevor
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Mahamdallie, Shazia
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Seal, Shiela
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Ruark, Elise
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Rahman, Nazneen
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Childhood Overgrowth Collaboration
Tatton-Brown, Katrina
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Loveday, Chey
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Yost, Shawn
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Clarke, Matthew
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Ramsay, Emma
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Zachariou, Anna
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Elliott, Anna
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Wylie, Harriet
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Ardissone, Anna
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Rittinger, Olaf
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Stewart, Fiona
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Temple, Karen
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Cole, Trevor
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Mahamdallie, Shazia
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Seal, Shiela
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Ruark, Elise
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Rahman, Nazneen
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Tatton-Brown, Katrina, Loveday, Chey, Yost, Shawn, Clarke, Matthew, Ramsay, Emma, Zachariou, Anna, Elliott, Anna, Wylie, Harriet, Ardissone, Anna, Rittinger, Olaf, Stewart, Fiona, Temple, Karen, Cole, Trevor, Mahamdallie, Shazia, Seal, Shiela, Ruark, Elise and Rahman, Nazneen , Childhood Overgrowth Collaboration (2017) Mutations in epigenetic regulation genes are a major cause of overgrowth with intellectual disability. The American Journal of Human Genetics, 100 (5), 725-736. (doi:10.1016/j.ajhg.2017.03.010).

Record type: Article

Abstract

To explore the genetic architecture of human overgrowth syndromes and human growth control, we performed experimental and bioinformatic analyses of 710 individuals with overgrowth (height and/or head circumference ≥+2 SD) and intellectual disability (OGID). We identified a causal mutation in 1 of 14 genes in 50% (353/710). This includes HIST1H1E, encoding histone H1.4, which has not been associated with a developmental disorder previously. The pathogenic HIST1H1E mutations are predicted to result in a product that is less effective in neutralizing negatively charged linker DNA because it has a reduced net charge, and in DNA binding and protein-protein interactions because key residues are truncated. Functional network analyses demonstrated that epigenetic regulation is a prominent biological process dysregulated in individuals with OGID. Mutations in six epigenetic regulation genes—NSD1, EZH2, DNMT3A, CHD8, HIST1H1E, and EED—accounted for 44% of individuals (311/710). There was significant overlap between the 14 genes involved in OGID and 611 genes in regions identified in GWASs to be associated with height (p = 6.84 × 10−8), suggesting that a common variation impacting function of genes involved in OGID influences height at a population level. Increased cellular growth is a hallmark of cancer and there was striking overlap between the genes involved in OGID and 260 somatically mutated cancer driver genes (p = 1.75 × 10−14). However, the mutation spectra of genes involved in OGID and cancer differ, suggesting complex genotype-phenotype relationships. These data reveal insights into the genetic control of human growth and demonstrate that exome sequencing in OGID has a high diagnostic yield.

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AJHG-D-16-00880 OGID manuscript 20170320 - Accepted Manuscript
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More information

Accepted/In Press date: 20 March 2017
Published date: 4 May 2017
Organisations: Human Development & Health

Identifiers

Local EPrints ID: 406933
URI: http://eprints.soton.ac.uk/id/eprint/406933
ISSN: 0002-9297
PURE UUID: 48fbe2f6-30c3-4ac1-b511-07df54ee894b
ORCID for Karen Temple: ORCID iD orcid.org/0000-0002-6045-1781

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Date deposited: 28 Mar 2017 01:06
Last modified: 16 Mar 2024 05:10

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Contributors

Author: Katrina Tatton-Brown
Author: Chey Loveday
Author: Shawn Yost
Author: Matthew Clarke
Author: Emma Ramsay
Author: Anna Zachariou
Author: Anna Elliott
Author: Harriet Wylie
Author: Anna Ardissone
Author: Olaf Rittinger
Author: Fiona Stewart
Author: Karen Temple ORCID iD
Author: Trevor Cole
Author: Shazia Mahamdallie
Author: Shiela Seal
Author: Elise Ruark
Author: Nazneen Rahman
Corporate Author: Childhood Overgrowth Collaboration

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