The genomic landscape of pediatric myelodysplastic syndromes

Myelodysplastic syndromes (MDS) are uncommon in children and have a poor prognosis. In contrast to adult MDS, little is known about the genomic landscape of pediatric MDS. Here, we describe the somatic and germline changes of pediatric MDS using whole exome sequencing, targeted amplicon sequencing,...

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Veröffentlicht in:	Nature communications Jg. 8; H. 1; S. 1557 - 10
Hauptverfasser:	Schwartz, Jason R., Ma, Jing, Lamprecht, Tamara, Walsh, Michael, Wang, Shuoguo, Bryant, Victoria, Song, Guangchun, Wu, Gang, Easton, John, Kesserwan, Chimene, Nichols, Kim E., Mullighan, Charles G., Ribeiro, Raul C., Klco, Jeffery M.
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	London Nature Publishing Group UK 16.11.2017 Nature Publishing Group Nature Portfolio
Schlagworte:	631/67/1990/1673 631/67/69 Adult Animals Cell Line Child Children Cohort Studies Copy number Disorders Gene sequencing Genetic Predisposition to Disease - genetics Genomics - methods HEK293 Cells Heterozygosity Humanities and Social Sciences Humans Loss of Heterozygosity MAP kinase Mice Monosomy multidisciplinary Mutation Myelodysplastic syndrome Myelodysplastic syndromes Myelodysplastic Syndromes - genetics Myelodysplastic Syndromes - pathology Patients Pediatrics Proteins - genetics Ribonucleic acid RNA Science Science (multidisciplinary) Splicing Survival Analysis Tumor cells Tumor Suppressor Proteins - genetics
ISSN:	2041-1723, 2041-1723
Online-Zugang:	Volltext
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Abstract	Myelodysplastic syndromes (MDS) are uncommon in children and have a poor prognosis. In contrast to adult MDS, little is known about the genomic landscape of pediatric MDS. Here, we describe the somatic and germline changes of pediatric MDS using whole exome sequencing, targeted amplicon sequencing, and/or RNA-sequencing of 46 pediatric primary MDS patients. Our data show that, in contrast to adult MDS, Ras/MAPK pathway mutations are common in pediatric MDS (45% of primary cohort), while mutations in RNA splicing genes are rare (2% of primary cohort). Surprisingly, germline variants in SAMD9 or SAMD9L were present in 17% of primary MDS patients, and these variants were routinely lost in the tumor cells by chromosomal deletions (e.g., monosomy 7) or copy number neutral loss of heterozygosity (CN-LOH). Our data confirm that adult and pediatric MDS are separate diseases with disparate mechanisms, and that SAMD9/SAMD9L mutations represent a new class of MDS predisposition. Myelodysplastic syndromes (MDS) are uncommon in children and have poor prognosis. Here, the authors interrogate the genomic landscape of MDS, confirming adult and paediatric MDS are separate diseases with disparate mechanisms, and highlighting that SAMD9/SAMD9L mutations represent a new class of MDS predisposition.
AbstractList	Myelodysplastic syndromes (MDS) are uncommon in children and have a poor prognosis. In contrast to adult MDS, little is known about the genomic landscape of pediatric MDS. Here, we describe the somatic and germline changes of pediatric MDS using whole exome sequencing, targeted amplicon sequencing, and/or RNA-sequencing of 46 pediatric primary MDS patients. Our data show that, in contrast to adult MDS, Ras/MAPK pathway mutations are common in pediatric MDS (45% of primary cohort), while mutations in RNA splicing genes are rare (2% of primary cohort). Surprisingly, germline variants in SAMD9 or SAMD9L were present in 17% of primary MDS patients, and these variants were routinely lost in the tumor cells by chromosomal deletions (e.g., monosomy 7) or copy number neutral loss of heterozygosity (CN-LOH). Our data confirm that adult and pediatric MDS are separate diseases with disparate mechanisms, and that SAMD9/SAMD9L mutations represent a new class of MDS predisposition. Myelodysplastic syndromes (MDS) are uncommon in children and have poor prognosis. Here, the authors interrogate the genomic landscape of MDS, confirming adult and paediatric MDS are separate diseases with disparate mechanisms, and highlighting that SAMD9/SAMD9L mutations represent a new class of MDS predisposition. Myelodysplastic syndromes (MDS) are uncommon in children and have a poor prognosis. In contrast to adult MDS, little is known about the genomic landscape of pediatric MDS. Here, we describe the somatic and germline changes of pediatric MDS using whole exome sequencing, targeted amplicon sequencing, and/or RNA-sequencing of 46 pediatric primary MDS patients. Our data show that, in contrast to adult MDS, Ras/MAPK pathway mutations are common in pediatric MDS (45% of primary cohort), while mutations in RNA splicing genes are rare (2% of primary cohort). Surprisingly, germline variants in SAMD9 or SAMD9L were present in 17% of primary MDS patients, and these variants were routinely lost in the tumor cells by chromosomal deletions (e.g., monosomy 7) or copy number neutral loss of heterozygosity (CN-LOH). Our data confirm that adult and pediatric MDS are separate diseases with disparate mechanisms, and that SAMD9/SAMD9L mutations represent a new class of MDS predisposition. Myelodysplastic syndromes (MDS) are uncommon in children and have a poor prognosis. In contrast to adult MDS, little is known about the genomic landscape of pediatric MDS. Here, we describe the somatic and germline changes of pediatric MDS using whole exome sequencing, targeted amplicon sequencing, and/or RNA-sequencing of 46 pediatric primary MDS patients. Our data show that, in contrast to adult MDS, Ras/MAPK pathway mutations are common in pediatric MDS (45% of primary cohort), while mutations in RNA splicing genes are rare (2% of primary cohort). Surprisingly, germline variants in SAMD9 or SAMD9L were present in 17% of primary MDS patients, and these variants were routinely lost in the tumor cells by chromosomal deletions (e.g., monosomy 7) or copy number neutral loss of heterozygosity (CN-LOH). Our data confirm that adult and pediatric MDS are separate diseases with disparate mechanisms, and that SAMD9/SAMD9L mutations represent a new class of MDS predisposition. Myelodysplastic syndromes (MDS) are uncommon in children and have poor prognosis. Here, the authors interrogate the genomic landscape of MDS, confirming adult and paediatric MDS are separate diseases with disparate mechanisms, and highlighting that SAMD9/SAMD9L mutations represent a new class of MDS predisposition. Myelodysplastic syndromes (MDS) are uncommon in children and have a poor prognosis. In contrast to adult MDS, little is known about the genomic landscape of pediatric MDS. Here, we describe the somatic and germline changes of pediatric MDS using whole exome sequencing, targeted amplicon sequencing, and/or RNA-sequencing of 46 pediatric primary MDS patients. Our data show that, in contrast to adult MDS, Ras/MAPK pathway mutations are common in pediatric MDS (45% of primary cohort), while mutations in RNA splicing genes are rare (2% of primary cohort). Surprisingly, germline variants in SAMD9 or SAMD9L were present in 17% of primary MDS patients, and these variants were routinely lost in the tumor cells by chromosomal deletions (e.g., monosomy 7) or copy number neutral loss of heterozygosity (CN-LOH). Our data confirm that adult and pediatric MDS are separate diseases with disparate mechanisms, and that SAMD9/SAMD9L mutations represent a new class of MDS predisposition. Myelodysplastic syndromes (MDS) are uncommon in children and have poor prognosis. Here, the authors interrogate the genomic landscape of MDS, confirming adult and paediatric MDS are separate diseases with disparate mechanisms, and highlighting that SAMD9/SAMD9L mutations represent a new class of MDS predisposition. Myelodysplastic syndromes (MDS) are uncommon in children and have a poor prognosis. In contrast to adult MDS, little is known about the genomic landscape of pediatric MDS. Here, we describe the somatic and germline changes of pediatric MDS using whole exome sequencing, targeted amplicon sequencing, and/or RNA-sequencing of 46 pediatric primary MDS patients. Our data show that, in contrast to adult MDS, Ras/MAPK pathway mutations are common in pediatric MDS (45% of primary cohort), while mutations in RNA splicing genes are rare (2% of primary cohort). Surprisingly, germline variants in SAMD9 or SAMD9L were present in 17% of primary MDS patients, and these variants were routinely lost in the tumor cells by chromosomal deletions (e.g., monosomy 7) or copy number neutral loss of heterozygosity (CN-LOH). Our data confirm that adult and pediatric MDS are separate diseases with disparate mechanisms, and that SAMD9/SAMD9L mutations represent a new class of MDS predisposition.Myelodysplastic syndromes (MDS) are uncommon in children and have a poor prognosis. In contrast to adult MDS, little is known about the genomic landscape of pediatric MDS. Here, we describe the somatic and germline changes of pediatric MDS using whole exome sequencing, targeted amplicon sequencing, and/or RNA-sequencing of 46 pediatric primary MDS patients. Our data show that, in contrast to adult MDS, Ras/MAPK pathway mutations are common in pediatric MDS (45% of primary cohort), while mutations in RNA splicing genes are rare (2% of primary cohort). Surprisingly, germline variants in SAMD9 or SAMD9L were present in 17% of primary MDS patients, and these variants were routinely lost in the tumor cells by chromosomal deletions (e.g., monosomy 7) or copy number neutral loss of heterozygosity (CN-LOH). Our data confirm that adult and pediatric MDS are separate diseases with disparate mechanisms, and that SAMD9/SAMD9L mutations represent a new class of MDS predisposition.
ArticleNumber	1557
Author	Song, Guangchun Mullighan, Charles G. Schwartz, Jason R. Wang, Shuoguo Ribeiro, Raul C. Easton, John Ma, Jing Lamprecht, Tamara Klco, Jeffery M. Bryant, Victoria Nichols, Kim E. Kesserwan, Chimene Wu, Gang Walsh, Michael
Author_xml	– sequence: 1 givenname: Jason R. surname: Schwartz fullname: Schwartz, Jason R. organization: Department of Oncology, St. Jude Children’s Research Hospital – sequence: 2 givenname: Jing surname: Ma fullname: Ma, Jing organization: Department of Pathology, St. Jude Children’s Research Hospital – sequence: 3 givenname: Tamara surname: Lamprecht fullname: Lamprecht, Tamara organization: Department of Pathology, St. Jude Children’s Research Hospital – sequence: 4 givenname: Michael surname: Walsh fullname: Walsh, Michael organization: Department of Pathology, St. Jude Children’s Research Hospital – sequence: 5 givenname: Shuoguo surname: Wang fullname: Wang, Shuoguo organization: Department of Computational Biology, St. Jude Children’s Research Hospital – sequence: 6 givenname: Victoria surname: Bryant fullname: Bryant, Victoria organization: Department of Pathology, St. Jude Children’s Research Hospital – sequence: 7 givenname: Guangchun surname: Song fullname: Song, Guangchun organization: Department of Pathology, St. Jude Children’s Research Hospital – sequence: 8 givenname: Gang orcidid: 0000-0002-1678-5864 surname: Wu fullname: Wu, Gang organization: Department of Computational Biology, St. Jude Children’s Research Hospital – sequence: 9 givenname: John surname: Easton fullname: Easton, John organization: Department of Computational Biology, St. Jude Children’s Research Hospital – sequence: 10 givenname: Chimene surname: Kesserwan fullname: Kesserwan, Chimene organization: Department of Oncology, St. Jude Children’s Research Hospital – sequence: 11 givenname: Kim E. surname: Nichols fullname: Nichols, Kim E. organization: Department of Oncology, St. Jude Children’s Research Hospital – sequence: 12 givenname: Charles G. orcidid: 0000-0002-1871-1850 surname: Mullighan fullname: Mullighan, Charles G. organization: Department of Pathology, St. Jude Children’s Research Hospital – sequence: 13 givenname: Raul C. surname: Ribeiro fullname: Ribeiro, Raul C. organization: Department of Oncology, St. Jude Children’s Research Hospital – sequence: 14 givenname: Jeffery M. orcidid: 0000-0003-2961-6960 surname: Klco fullname: Klco, Jeffery M. email: jeffery.klco@stjude.org organization: Department of Pathology, St. Jude Children’s Research Hospital
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/29146900$$D View this record in MEDLINE/PubMed
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Snippet	Myelodysplastic syndromes (MDS) are uncommon in children and have a poor prognosis. In contrast to adult MDS, little is known about the genomic landscape of... Myelodysplastic syndromes (MDS) are uncommon in children and have poor prognosis. Here, the authors interrogate the genomic landscape of MDS, confirming adult...
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SubjectTerms	631/67/1990/1673 631/67/69 Adult Animals Cell Line Child Children Cohort Studies Copy number Disorders Gene sequencing Genetic Predisposition to Disease - genetics Genomics - methods HEK293 Cells Heterozygosity Humanities and Social Sciences Humans Loss of Heterozygosity MAP kinase Mice Monosomy multidisciplinary Mutation Myelodysplastic syndrome Myelodysplastic syndromes Myelodysplastic Syndromes - genetics Myelodysplastic Syndromes - pathology Patients Pediatrics Proteins - genetics Ribonucleic acid RNA Science Science (multidisciplinary) Splicing Survival Analysis Tumor cells Tumor Suppressor Proteins - genetics
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Title	The genomic landscape of pediatric myelodysplastic syndromes
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