Robust identification of mosaic variants in congenital heart disease
Mosaicism due to somatic mutations can cause multiple diseases including cancer, developmental and overgrowth syndromes, neurodevelopmental disorders, autoinflammatory diseases, and atrial fibrillation. With the increased use of next generation sequencing technology, multiple tools have been develop...
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| Veröffentlicht in: | Human genetics 2018-02, Vol.137 (2), p.183-193 |
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| creator | Manheimer, Kathryn B. Richter, Felix Edelmann, Lisa J. D’Souza, Sunita L. Shi, Lisong Shen, Yufeng Homsy, Jason Boskovski, Marko T. Tai, Angela C. Gorham, Joshua Yasso, Christopher Goldmuntz, Elizabeth Brueckner, Martina Lifton, Richard P. Chung, Wendy K. Seidman, Christine E. Seidman, J. G. Gelb, Bruce D. |
| description | Mosaicism due to somatic mutations can cause multiple diseases including cancer, developmental and overgrowth syndromes, neurodevelopmental disorders, autoinflammatory diseases, and atrial fibrillation. With the increased use of next generation sequencing technology, multiple tools have been developed to identify low-frequency variants, specifically from matched tumor-normal tissues in cancer studies. To investigate whether mosaic variants are implicated in congenital heart disease (CHD), we developed a pipeline using the cancer somatic variant caller MuTect to identify mosaic variants in whole-exome sequencing (WES) data from a cohort of parent/affected child trios (
n
= 715) and a cohort of healthy individuals (
n
= 416). This is a novel application of the somatic variant caller designed for cancer to WES trio data. We identified two cases with mosaic
KMT2D
mutations that are likely pathogenic for CHD, but conclude that, overall, mosaicism detectable in peripheral blood or saliva does not account for a significant portion of CHD etiology. |
| doi_str_mv | 10.1007/s00439-018-1871-6 |
| format | Article |
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n
= 715) and a cohort of healthy individuals (
n
= 416). This is a novel application of the somatic variant caller designed for cancer to WES trio data. We identified two cases with mosaic
KMT2D
mutations that are likely pathogenic for CHD, but conclude that, overall, mosaicism detectable in peripheral blood or saliva does not account for a significant portion of CHD etiology.</description><identifier>ISSN: 0340-6717</identifier><identifier>EISSN: 1432-1203</identifier><identifier>DOI: 10.1007/s00439-018-1871-6</identifier><identifier>PMID: 29417219</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Atrial fibrillation ; Biomedical and Life Sciences ; Biomedicine ; Cancer ; Cardiovascular disease ; Child ; Congenital diseases ; Congenital heart defects ; Coronary artery disease ; Data processing ; Development and progression ; Etiology ; Exome - genetics ; Exome Sequencing ; Fibrillation ; Gene Function ; Genetic aspects ; Genetic disorders ; Genetic Variation ; Health aspects ; Heart Defects, Congenital - genetics ; Heart Defects, Congenital - physiopathology ; Heart diseases ; High-Throughput Nucleotide Sequencing ; Human Genetics ; Humans ; Metabolic Diseases ; Molecular Medicine ; Mosaicism ; Mutation ; Neurodevelopmental disorders ; Original Investigation ; Peripheral blood ; Saliva ; Software</subject><ispartof>Human genetics, 2018-02, Vol.137 (2), p.183-193</ispartof><rights>Springer-Verlag GmbH Germany, part of Springer Nature 2018</rights><rights>COPYRIGHT 2018 Springer</rights><rights>Human Genetics is a copyright of Springer, (2018). All Rights Reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c637t-514ec2b3fc2819e77526054d418c1a22767630d19b5fe1c85c18b6fb964024933</citedby><cites>FETCH-LOGICAL-c637t-514ec2b3fc2819e77526054d418c1a22767630d19b5fe1c85c18b6fb964024933</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00439-018-1871-6$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00439-018-1871-6$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>230,314,776,780,881,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29417219$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Manheimer, Kathryn B.</creatorcontrib><creatorcontrib>Richter, Felix</creatorcontrib><creatorcontrib>Edelmann, Lisa J.</creatorcontrib><creatorcontrib>D’Souza, Sunita L.</creatorcontrib><creatorcontrib>Shi, Lisong</creatorcontrib><creatorcontrib>Shen, Yufeng</creatorcontrib><creatorcontrib>Homsy, Jason</creatorcontrib><creatorcontrib>Boskovski, Marko T.</creatorcontrib><creatorcontrib>Tai, Angela C.</creatorcontrib><creatorcontrib>Gorham, Joshua</creatorcontrib><creatorcontrib>Yasso, Christopher</creatorcontrib><creatorcontrib>Goldmuntz, Elizabeth</creatorcontrib><creatorcontrib>Brueckner, Martina</creatorcontrib><creatorcontrib>Lifton, Richard P.</creatorcontrib><creatorcontrib>Chung, Wendy K.</creatorcontrib><creatorcontrib>Seidman, Christine E.</creatorcontrib><creatorcontrib>Seidman, J. G.</creatorcontrib><creatorcontrib>Gelb, Bruce D.</creatorcontrib><title>Robust identification of mosaic variants in congenital heart disease</title><title>Human genetics</title><addtitle>Hum Genet</addtitle><addtitle>Hum Genet</addtitle><description>Mosaicism due to somatic mutations can cause multiple diseases including cancer, developmental and overgrowth syndromes, neurodevelopmental disorders, autoinflammatory diseases, and atrial fibrillation. With the increased use of next generation sequencing technology, multiple tools have been developed to identify low-frequency variants, specifically from matched tumor-normal tissues in cancer studies. To investigate whether mosaic variants are implicated in congenital heart disease (CHD), we developed a pipeline using the cancer somatic variant caller MuTect to identify mosaic variants in whole-exome sequencing (WES) data from a cohort of parent/affected child trios (
n
= 715) and a cohort of healthy individuals (
n
= 416). This is a novel application of the somatic variant caller designed for cancer to WES trio data. We identified two cases with mosaic
KMT2D
mutations that are likely pathogenic for CHD, but conclude that, overall, mosaicism detectable in peripheral blood or saliva does not account for a significant portion of CHD etiology.</description><subject>Atrial fibrillation</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedicine</subject><subject>Cancer</subject><subject>Cardiovascular disease</subject><subject>Child</subject><subject>Congenital diseases</subject><subject>Congenital heart defects</subject><subject>Coronary artery disease</subject><subject>Data processing</subject><subject>Development and progression</subject><subject>Etiology</subject><subject>Exome - genetics</subject><subject>Exome Sequencing</subject><subject>Fibrillation</subject><subject>Gene Function</subject><subject>Genetic aspects</subject><subject>Genetic disorders</subject><subject>Genetic Variation</subject><subject>Health aspects</subject><subject>Heart Defects, Congenital - genetics</subject><subject>Heart Defects, Congenital - physiopathology</subject><subject>Heart diseases</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Human Genetics</subject><subject>Humans</subject><subject>Metabolic Diseases</subject><subject>Molecular Medicine</subject><subject>Mosaicism</subject><subject>Mutation</subject><subject>Neurodevelopmental disorders</subject><subject>Original Investigation</subject><subject>Peripheral blood</subject><subject>Saliva</subject><subject>Software</subject><issn>0340-6717</issn><issn>1432-1203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNp1kk1vFSEUhonR2Gv1B7gxk7jRxVQOw8ewMWnqV5MmJlXXhGHglmYGKjCN_nuZ3lp7jYYFCec5L5yXF6HngI8AY_EmY0w72WLoW-gFtPwB2gDtSAsEdw_RBncUt1yAOEBPcr7EGJgk7DE6IJKCICA36N15HJZcGj_aULzzRhcfQxNdM8esvWmudfI6lNz40JgYtjb4oqfmwupUmtFnq7N9ih45PWX77HY_RN8-vP968qk9-_zx9OT4rDW8E6VlQK0hQ-cM6UFaIRjhmNGRQm9AEyK44B0eQQ7MWTA9M9AP3A2SU0yo7LpD9Hane7UMsx1NfXLSk7pKftbpp4raq_1K8BdqG68Vk1IQyqvAq1uBFL8vNhc1-2zsNOlg45IVSCm5EAJW9OVf6GVcUqjj3VC4WtjDH2qrJ6t8cLHea1ZRdcxuBqI9rdTRP6i6Rjv7aqp1vp7vNbzea6hMsT_KVi85q9Mv5_ss7FiTYs7Jujs_AKs1JmoXE1VjotaYqHW4F_eNvOv4nYsKkB2Qa6l-ero3_X9VfwHSzsTr</recordid><startdate>20180201</startdate><enddate>20180201</enddate><creator>Manheimer, Kathryn B.</creator><creator>Richter, Felix</creator><creator>Edelmann, Lisa J.</creator><creator>D’Souza, Sunita L.</creator><creator>Shi, Lisong</creator><creator>Shen, Yufeng</creator><creator>Homsy, Jason</creator><creator>Boskovski, Marko T.</creator><creator>Tai, Angela C.</creator><creator>Gorham, Joshua</creator><creator>Yasso, Christopher</creator><creator>Goldmuntz, Elizabeth</creator><creator>Brueckner, Martina</creator><creator>Lifton, Richard P.</creator><creator>Chung, Wendy K.</creator><creator>Seidman, Christine E.</creator><creator>Seidman, J. 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G.</au><au>Gelb, Bruce D.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Robust identification of mosaic variants in congenital heart disease</atitle><jtitle>Human genetics</jtitle><stitle>Hum Genet</stitle><addtitle>Hum Genet</addtitle><date>2018-02-01</date><risdate>2018</risdate><volume>137</volume><issue>2</issue><spage>183</spage><epage>193</epage><pages>183-193</pages><issn>0340-6717</issn><eissn>1432-1203</eissn><abstract>Mosaicism due to somatic mutations can cause multiple diseases including cancer, developmental and overgrowth syndromes, neurodevelopmental disorders, autoinflammatory diseases, and atrial fibrillation. With the increased use of next generation sequencing technology, multiple tools have been developed to identify low-frequency variants, specifically from matched tumor-normal tissues in cancer studies. To investigate whether mosaic variants are implicated in congenital heart disease (CHD), we developed a pipeline using the cancer somatic variant caller MuTect to identify mosaic variants in whole-exome sequencing (WES) data from a cohort of parent/affected child trios (
n
= 715) and a cohort of healthy individuals (
n
= 416). This is a novel application of the somatic variant caller designed for cancer to WES trio data. We identified two cases with mosaic
KMT2D
mutations that are likely pathogenic for CHD, but conclude that, overall, mosaicism detectable in peripheral blood or saliva does not account for a significant portion of CHD etiology.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>29417219</pmid><doi>10.1007/s00439-018-1871-6</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
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| ispartof | Human genetics, 2018-02, Vol.137 (2), p.183-193 |
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| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_5997246 |
| source | MEDLINE; Springer Nature - Complete Springer Journals |
| subjects | Atrial fibrillation Biomedical and Life Sciences Biomedicine Cancer Cardiovascular disease Child Congenital diseases Congenital heart defects Coronary artery disease Data processing Development and progression Etiology Exome - genetics Exome Sequencing Fibrillation Gene Function Genetic aspects Genetic disorders Genetic Variation Health aspects Heart Defects, Congenital - genetics Heart Defects, Congenital - physiopathology Heart diseases High-Throughput Nucleotide Sequencing Human Genetics Humans Metabolic Diseases Molecular Medicine Mosaicism Mutation Neurodevelopmental disorders Original Investigation Peripheral blood Saliva Software |
| title | Robust identification of mosaic variants in congenital heart disease |
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