Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome
While next-generation sequencing has accelerated the discovery of human disease genes, progress has been largely limited to the “low hanging fruit” of mutations with obvious exonic coding or canonical splice site impact. In contrast, the lack of high-throughput, unbiased approaches for functional as...
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Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538549/ http://www.ncbi.nlm.nih.gov/pubmed/28630177 https://doi.org/10.1101/gr.219899.116 |
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ftpubmed:oai:pubmedcentral.nih.gov:5538549 2023-05-15T16:16:55+02:00 Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome Evrony, Gilad D. Cordero, Dwight R. Shen, Jun Partlow, Jennifer N. Yu, Timothy W. Rodin, Rachel E. Hill, R. Sean Coulter, Michael E. Lam, Anh-Thu N. Jayaraman, Divya Gerrelli, Dianne Diaz, Diana G. Santos, Chloe Morrison, Victoria Galli, Antonella Tschulena, Ulrich Wiemann, Stefan Martel, M. Jocelyne Spooner, Betty Ryu, Steven C. Elhosary, Princess C. Richardson, Jillian M. Tierney, Danielle Robinson, Christopher A. Chibbar, Rajni Diudea, Dana Folkerth, Rebecca Wiebe, Sheldon Barkovich, A. James Mochida, Ganeshwaran H. Irvine, James Lemire, Edmond G. Blakley, Patricia Walsh, Christopher A. 2017-08 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538549/ http://www.ncbi.nlm.nih.gov/pubmed/28630177 https://doi.org/10.1101/gr.219899.116 en eng Cold Spring Harbor Laboratory Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538549/ http://www.ncbi.nlm.nih.gov/pubmed/28630177 http://dx.doi.org/10.1101/gr.219899.116 © 2017 Evrony et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by/4.0/ This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/. CC-BY Research Text 2017 ftpubmed https://doi.org/10.1101/gr.219899.116 2017-08-13T00:13:41Z While next-generation sequencing has accelerated the discovery of human disease genes, progress has been largely limited to the “low hanging fruit” of mutations with obvious exonic coding or canonical splice site impact. In contrast, the lack of high-throughput, unbiased approaches for functional assessment of most noncoding variants has bottlenecked gene discovery. We report the integration of transcriptome sequencing (RNA-seq), which surveys all mRNAs to reveal functional impacts of variants at the transcription level, into the gene discovery framework for a unique human disease, microcephaly-micromelia syndrome (MMS). MMS is an autosomal recessive condition described thus far in only a single First Nations population and causes intrauterine growth restriction, severe microcephaly, craniofacial anomalies, skeletal dysplasia, and neonatal lethality. Linkage analysis of affected families, including a very large pedigree, identified a single locus on Chromosome 21 linked to the disease (LOD > 9). Comprehensive genome sequencing did not reveal any pathogenic coding or canonical splicing mutations within the linkage region but identified several nonconserved noncoding variants. RNA-seq analysis detected aberrant splicing in DONSON due to one of these noncoding variants, showing a causative role for DONSON disruption in MMS. We show that DONSON is expressed in progenitor cells of embryonic human brain and other proliferating tissues, is co-expressed with components of the DNA replication machinery, and that Donson is essential for early embryonic development in mice as well, suggesting an essential conserved role for DONSON in the cell cycle. Our results demonstrate the utility of integrating transcriptomics into the study of human genetic disease when DNA sequencing alone is not sufficient to reveal the underlying pathogenic mutation. Text First Nations PubMed Central (PMC) Genome Research 27 8 1323 1335 |
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Research Evrony, Gilad D. Cordero, Dwight R. Shen, Jun Partlow, Jennifer N. Yu, Timothy W. Rodin, Rachel E. Hill, R. Sean Coulter, Michael E. Lam, Anh-Thu N. Jayaraman, Divya Gerrelli, Dianne Diaz, Diana G. Santos, Chloe Morrison, Victoria Galli, Antonella Tschulena, Ulrich Wiemann, Stefan Martel, M. Jocelyne Spooner, Betty Ryu, Steven C. Elhosary, Princess C. Richardson, Jillian M. Tierney, Danielle Robinson, Christopher A. Chibbar, Rajni Diudea, Dana Folkerth, Rebecca Wiebe, Sheldon Barkovich, A. James Mochida, Ganeshwaran H. Irvine, James Lemire, Edmond G. Blakley, Patricia Walsh, Christopher A. Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome |
topic_facet |
Research |
description |
While next-generation sequencing has accelerated the discovery of human disease genes, progress has been largely limited to the “low hanging fruit” of mutations with obvious exonic coding or canonical splice site impact. In contrast, the lack of high-throughput, unbiased approaches for functional assessment of most noncoding variants has bottlenecked gene discovery. We report the integration of transcriptome sequencing (RNA-seq), which surveys all mRNAs to reveal functional impacts of variants at the transcription level, into the gene discovery framework for a unique human disease, microcephaly-micromelia syndrome (MMS). MMS is an autosomal recessive condition described thus far in only a single First Nations population and causes intrauterine growth restriction, severe microcephaly, craniofacial anomalies, skeletal dysplasia, and neonatal lethality. Linkage analysis of affected families, including a very large pedigree, identified a single locus on Chromosome 21 linked to the disease (LOD > 9). Comprehensive genome sequencing did not reveal any pathogenic coding or canonical splicing mutations within the linkage region but identified several nonconserved noncoding variants. RNA-seq analysis detected aberrant splicing in DONSON due to one of these noncoding variants, showing a causative role for DONSON disruption in MMS. We show that DONSON is expressed in progenitor cells of embryonic human brain and other proliferating tissues, is co-expressed with components of the DNA replication machinery, and that Donson is essential for early embryonic development in mice as well, suggesting an essential conserved role for DONSON in the cell cycle. Our results demonstrate the utility of integrating transcriptomics into the study of human genetic disease when DNA sequencing alone is not sufficient to reveal the underlying pathogenic mutation. |
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Text |
author |
Evrony, Gilad D. Cordero, Dwight R. Shen, Jun Partlow, Jennifer N. Yu, Timothy W. Rodin, Rachel E. Hill, R. Sean Coulter, Michael E. Lam, Anh-Thu N. Jayaraman, Divya Gerrelli, Dianne Diaz, Diana G. Santos, Chloe Morrison, Victoria Galli, Antonella Tschulena, Ulrich Wiemann, Stefan Martel, M. Jocelyne Spooner, Betty Ryu, Steven C. Elhosary, Princess C. Richardson, Jillian M. Tierney, Danielle Robinson, Christopher A. Chibbar, Rajni Diudea, Dana Folkerth, Rebecca Wiebe, Sheldon Barkovich, A. James Mochida, Ganeshwaran H. Irvine, James Lemire, Edmond G. Blakley, Patricia Walsh, Christopher A. |
author_facet |
Evrony, Gilad D. Cordero, Dwight R. Shen, Jun Partlow, Jennifer N. Yu, Timothy W. Rodin, Rachel E. Hill, R. Sean Coulter, Michael E. Lam, Anh-Thu N. Jayaraman, Divya Gerrelli, Dianne Diaz, Diana G. Santos, Chloe Morrison, Victoria Galli, Antonella Tschulena, Ulrich Wiemann, Stefan Martel, M. Jocelyne Spooner, Betty Ryu, Steven C. Elhosary, Princess C. Richardson, Jillian M. Tierney, Danielle Robinson, Christopher A. Chibbar, Rajni Diudea, Dana Folkerth, Rebecca Wiebe, Sheldon Barkovich, A. James Mochida, Ganeshwaran H. Irvine, James Lemire, Edmond G. Blakley, Patricia Walsh, Christopher A. |
author_sort |
Evrony, Gilad D. |
title |
Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome |
title_short |
Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome |
title_full |
Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome |
title_fullStr |
Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome |
title_full_unstemmed |
Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome |
title_sort |
integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor donson as the cause of microcephaly-micromelia syndrome |
publisher |
Cold Spring Harbor Laboratory Press |
publishDate |
2017 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538549/ http://www.ncbi.nlm.nih.gov/pubmed/28630177 https://doi.org/10.1101/gr.219899.116 |
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First Nations |
genre_facet |
First Nations |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538549/ http://www.ncbi.nlm.nih.gov/pubmed/28630177 http://dx.doi.org/10.1101/gr.219899.116 |
op_rights |
© 2017 Evrony et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by/4.0/ This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1101/gr.219899.116 |
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Genome Research |
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27 |
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8 |
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