Retrotransposition disrupting EBP in a girl and her mother with X-linked dominant chondrodysplasia punctata
X-linked dominant chondrodysplasia punctata (CDPX2) is a rare congenital disorder caused by pathogenic variants in EBP on Xp11.23. We encountered a girl and her mother with CDPX2-compatible phenotypes including punctiform calcification in the neonatal period of the girl, and asymmetric limb shorteni...
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| Veröffentlicht in: | Journal of human genetics 2022-05, Vol.67 (5), p.303-306 |
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| container_title | Journal of human genetics |
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| creator | Hiraide, Takuya Masunaga, Yohei Honda, Akira Kato, Fumiko Fukuda, Tokiko Fukami, Maki Nakashima, Mitsuko Saitsu, Hirotomo Ogata, Tsutomu |
| description | X-linked dominant chondrodysplasia punctata (CDPX2) is a rare congenital disorder caused by pathogenic variants in EBP on Xp11.23. We encountered a girl and her mother with CDPX2-compatible phenotypes including punctiform calcification in the neonatal period of the girl, and asymmetric limb shortening and ichthyosis following the Blaschko lines in both subjects. Although Sanger direct sequencing failed to reveal a disease-causing variant in EBP, whole genome sequencing (WGS) followed by Manta analysis identified a ~ 4.5 kb insertion at EBP exon 2 of both subjects. The insertion was associated with the hallmarks of retrotransposition such as an antisense poly(A) tail, a target site duplication, and a consensus endonuclease cleavage site, and the inserted sequence harbored full-length SVA_F1 element with 5'- and 3'-transductions containing the Alu sequence. The results imply the relevance of retrotransposition to the human genetic diseases and the usefulness of WGS in the identification of retrotransposition. |
| doi_str_mv | 10.1038/s10038-021-01000-1 |
| format | Article |
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We encountered a girl and her mother with CDPX2-compatible phenotypes including punctiform calcification in the neonatal period of the girl, and asymmetric limb shortening and ichthyosis following the Blaschko lines in both subjects. Although Sanger direct sequencing failed to reveal a disease-causing variant in EBP, whole genome sequencing (WGS) followed by Manta analysis identified a ~ 4.5 kb insertion at EBP exon 2 of both subjects. The insertion was associated with the hallmarks of retrotransposition such as an antisense poly(A) tail, a target site duplication, and a consensus endonuclease cleavage site, and the inserted sequence harbored full-length SVA_F1 element with 5'- and 3'-transductions containing the Alu sequence. The results imply the relevance of retrotransposition to the human genetic diseases and the usefulness of WGS in the identification of retrotransposition.</description><identifier>ISSN: 1434-5161</identifier><identifier>EISSN: 1435-232X</identifier><identifier>DOI: 10.1038/s10038-021-01000-1</identifier><identifier>PMID: 34999728</identifier><language>eng</language><publisher>England: Nature Publishing Group</publisher><subject>Age ; Alopecia ; Baldness ; Calcification ; Cataracts ; Childrens health ; Chondrodystrophy ; Congenital diseases ; Conserved sequence ; Disease ; Endonuclease ; Genetic disorders ; Genetics ; Genomes ; Ichthyosis ; Insertion ; Medicine ; Neonates ; Pediatrics ; Phenotypes ; Polyadenine ; Polyadenylation ; Retrotransposition ; Skin ; Sterols ; Vertebrae ; Whole genome sequencing</subject><ispartof>Journal of human genetics, 2022-05, Vol.67 (5), p.303-306</ispartof><rights>2021. 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We encountered a girl and her mother with CDPX2-compatible phenotypes including punctiform calcification in the neonatal period of the girl, and asymmetric limb shortening and ichthyosis following the Blaschko lines in both subjects. Although Sanger direct sequencing failed to reveal a disease-causing variant in EBP, whole genome sequencing (WGS) followed by Manta analysis identified a ~ 4.5 kb insertion at EBP exon 2 of both subjects. The insertion was associated with the hallmarks of retrotransposition such as an antisense poly(A) tail, a target site duplication, and a consensus endonuclease cleavage site, and the inserted sequence harbored full-length SVA_F1 element with 5'- and 3'-transductions containing the Alu sequence. The results imply the relevance of retrotransposition to the human genetic diseases and the usefulness of WGS in the identification of retrotransposition.</description><subject>Age</subject><subject>Alopecia</subject><subject>Baldness</subject><subject>Calcification</subject><subject>Cataracts</subject><subject>Childrens health</subject><subject>Chondrodystrophy</subject><subject>Congenital diseases</subject><subject>Conserved sequence</subject><subject>Disease</subject><subject>Endonuclease</subject><subject>Genetic disorders</subject><subject>Genetics</subject><subject>Genomes</subject><subject>Ichthyosis</subject><subject>Insertion</subject><subject>Medicine</subject><subject>Neonates</subject><subject>Pediatrics</subject><subject>Phenotypes</subject><subject>Polyadenine</subject><subject>Polyadenylation</subject><subject>Retrotransposition</subject><subject>Skin</subject><subject>Sterols</subject><subject>Vertebrae</subject><subject>Whole genome sequencing</subject><issn>1434-5161</issn><issn>1435-232X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNpdkctKBDEQRYMovn_AhQTcuInm2eleqvgCQREFdyGTZJxod9ImacS_NzrqwtW9VZwqiroA7BF8RDBrjzPBVRCmBOFqMSIrYJNwJhBl9Gn123MkSEM2wFbOLxVhVNJ1sMF413WStpvg9d6VFEvSIY8x--JjgNbnNI3Fh2d4fnoHfYAaPvvUQx0sXLgEh1i-5N2XBXxCvQ-vzkIbBx90KNAsYrAp2o889jp7DccpmKKL3gFrc91nt_uj2-Dx4vzh7Ard3F5en53cIMMbUZARUlKDOReyJVRiq61rscG119bKNKKzHZ3RpmmFZVryWSO4ns-0nHNpqWPb4HC5d0zxbXK5qMFn4_peBxenrGhDWkFZx3FFD_6hL3FKoV5XKcE6ykTbVYouKZNizsnN1Zj8oNOHIlh9RaGWUagahfqOQpE6tP-zepoNzv6N_P6efQKcO4SQ</recordid><startdate>20220501</startdate><enddate>20220501</enddate><creator>Hiraide, Takuya</creator><creator>Masunaga, Yohei</creator><creator>Honda, Akira</creator><creator>Kato, Fumiko</creator><creator>Fukuda, Tokiko</creator><creator>Fukami, Maki</creator><creator>Nakashima, Mitsuko</creator><creator>Saitsu, Hirotomo</creator><creator>Ogata, Tsutomu</creator><general>Nature Publishing Group</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0001-7178-9991</orcidid><orcidid>https://orcid.org/0000-0001-8159-3474</orcidid><orcidid>https://orcid.org/0000-0001-9971-4035</orcidid><orcidid>https://orcid.org/0000-0001-7941-1774</orcidid><orcidid>https://orcid.org/0000-0003-0723-0960</orcidid><orcidid>https://orcid.org/0000-0003-3754-5357</orcidid></search><sort><creationdate>20220501</creationdate><title>Retrotransposition disrupting EBP in a girl and her mother with X-linked dominant chondrodysplasia punctata</title><author>Hiraide, Takuya ; Masunaga, Yohei ; Honda, Akira ; Kato, Fumiko ; Fukuda, Tokiko ; Fukami, Maki ; Nakashima, Mitsuko ; Saitsu, Hirotomo ; Ogata, Tsutomu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c465t-c5772c0445781270dade80c02c0870dc659d92b26685d3a74b654afba7f47d2e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Age</topic><topic>Alopecia</topic><topic>Baldness</topic><topic>Calcification</topic><topic>Cataracts</topic><topic>Childrens health</topic><topic>Chondrodystrophy</topic><topic>Congenital diseases</topic><topic>Conserved sequence</topic><topic>Disease</topic><topic>Endonuclease</topic><topic>Genetic disorders</topic><topic>Genetics</topic><topic>Genomes</topic><topic>Ichthyosis</topic><topic>Insertion</topic><topic>Medicine</topic><topic>Neonates</topic><topic>Pediatrics</topic><topic>Phenotypes</topic><topic>Polyadenine</topic><topic>Polyadenylation</topic><topic>Retrotransposition</topic><topic>Skin</topic><topic>Sterols</topic><topic>Vertebrae</topic><topic>Whole genome sequencing</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hiraide, Takuya</creatorcontrib><creatorcontrib>Masunaga, Yohei</creatorcontrib><creatorcontrib>Honda, Akira</creatorcontrib><creatorcontrib>Kato, Fumiko</creatorcontrib><creatorcontrib>Fukuda, Tokiko</creatorcontrib><creatorcontrib>Fukami, Maki</creatorcontrib><creatorcontrib>Nakashima, Mitsuko</creatorcontrib><creatorcontrib>Saitsu, Hirotomo</creatorcontrib><creatorcontrib>Ogata, Tsutomu</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of human genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hiraide, Takuya</au><au>Masunaga, Yohei</au><au>Honda, Akira</au><au>Kato, Fumiko</au><au>Fukuda, Tokiko</au><au>Fukami, Maki</au><au>Nakashima, Mitsuko</au><au>Saitsu, Hirotomo</au><au>Ogata, Tsutomu</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Retrotransposition disrupting EBP in a girl and her mother with X-linked dominant chondrodysplasia punctata</atitle><jtitle>Journal of human genetics</jtitle><addtitle>J Hum Genet</addtitle><date>2022-05-01</date><risdate>2022</risdate><volume>67</volume><issue>5</issue><spage>303</spage><epage>306</epage><pages>303-306</pages><issn>1434-5161</issn><eissn>1435-232X</eissn><abstract>X-linked dominant chondrodysplasia punctata (CDPX2) is a rare congenital disorder caused by pathogenic variants in EBP on Xp11.23. We encountered a girl and her mother with CDPX2-compatible phenotypes including punctiform calcification in the neonatal period of the girl, and asymmetric limb shortening and ichthyosis following the Blaschko lines in both subjects. Although Sanger direct sequencing failed to reveal a disease-causing variant in EBP, whole genome sequencing (WGS) followed by Manta analysis identified a ~ 4.5 kb insertion at EBP exon 2 of both subjects. The insertion was associated with the hallmarks of retrotransposition such as an antisense poly(A) tail, a target site duplication, and a consensus endonuclease cleavage site, and the inserted sequence harbored full-length SVA_F1 element with 5'- and 3'-transductions containing the Alu sequence. The results imply the relevance of retrotransposition to the human genetic diseases and the usefulness of WGS in the identification of retrotransposition.</abstract><cop>England</cop><pub>Nature Publishing Group</pub><pmid>34999728</pmid><doi>10.1038/s10038-021-01000-1</doi><tpages>4</tpages><orcidid>https://orcid.org/0000-0001-7178-9991</orcidid><orcidid>https://orcid.org/0000-0001-8159-3474</orcidid><orcidid>https://orcid.org/0000-0001-9971-4035</orcidid><orcidid>https://orcid.org/0000-0001-7941-1774</orcidid><orcidid>https://orcid.org/0000-0003-0723-0960</orcidid><orcidid>https://orcid.org/0000-0003-3754-5357</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Age Alopecia Baldness Calcification Cataracts Childrens health Chondrodystrophy Congenital diseases Conserved sequence Disease Endonuclease Genetic disorders Genetics Genomes Ichthyosis Insertion Medicine Neonates Pediatrics Phenotypes Polyadenine Polyadenylation Retrotransposition Skin Sterols Vertebrae Whole genome sequencing |
| title | Retrotransposition disrupting EBP in a girl and her mother with X-linked dominant chondrodysplasia punctata |
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