Precise detection of chromosomal translocation or inversion breakpoints by whole-genome sequencing
Structural variations (SVs), including translocations, inversions, deletions and duplications, are potentially associated with Mendelian diseases and contiguous gene syndromes. Determination of SV-related breakpoints at the nucleotide level is important to reveal the genetic causes for diseases. Who...
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| Veröffentlicht in: | Journal of human genetics 2014-12, Vol.59 (12), p.649-654 |
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| container_title | Journal of human genetics |
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| creator | Suzuki, Toshifumi Tsurusaki, Yoshinori Nakashima, Mitsuko Miyake, Noriko Saitsu, Hirotomo Takeda, Satoru Matsumoto, Naomichi |
| description | Structural variations (SVs), including translocations, inversions, deletions and duplications, are potentially associated with Mendelian diseases and contiguous gene syndromes. Determination of SV-related breakpoints at the nucleotide level is important to reveal the genetic causes for diseases. Whole-genome sequencing (WGS) by next-generation sequencers is expected to determine structural abnormalities more directly and efficiently than conventional methods. In this study, 14 SVs (9 balanced translocations, 1 inversion and 4 microdeletions) in 9 patients were analyzed by WGS with a shallow (5 × ) to moderate read coverage (20 × ). Among 28 breakpoints (as each SV has two breakpoints), 19 SV breakpoints had been determined previously at the nucleotide level by any other methods and 9 were uncharacterized. BreakDancer and Integrative Genomics Viewer determined 20 breakpoints (16 translocation, 2 inversion and 2 deletion breakpoints), but did not detect 8 breakpoints (2 translocation and 6 deletion breakpoints). These data indicate the efficacy of WGS for the precise determination of translocation and inversion breakpoints. |
| doi_str_mv | 10.1038/jhg.2014.88 |
| format | Article |
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Determination of SV-related breakpoints at the nucleotide level is important to reveal the genetic causes for diseases. Whole-genome sequencing (WGS) by next-generation sequencers is expected to determine structural abnormalities more directly and efficiently than conventional methods. In this study, 14 SVs (9 balanced translocations, 1 inversion and 4 microdeletions) in 9 patients were analyzed by WGS with a shallow (5 × ) to moderate read coverage (20 × ). Among 28 breakpoints (as each SV has two breakpoints), 19 SV breakpoints had been determined previously at the nucleotide level by any other methods and 9 were uncharacterized. BreakDancer and Integrative Genomics Viewer determined 20 breakpoints (16 translocation, 2 inversion and 2 deletion breakpoints), but did not detect 8 breakpoints (2 translocation and 6 deletion breakpoints). These data indicate the efficacy of WGS for the precise determination of translocation and inversion breakpoints.</description><identifier>ISSN: 1434-5161</identifier><identifier>EISSN: 1435-232X</identifier><identifier>DOI: 10.1038/jhg.2014.88</identifier><identifier>PMID: 25296578</identifier><language>eng</language><publisher>England: Nature Publishing Group</publisher><subject>Breakpoints ; Chromosome Breakpoints ; Chromosome Deletion ; Chromosome Inversion - genetics ; Chromosome translocations ; Genome, Human ; Genomes ; Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; Inversion ; Sequence Analysis, DNA ; Translocation, Genetic - genetics ; Whole genome sequencing</subject><ispartof>Journal of human genetics, 2014-12, Vol.59 (12), p.649-654</ispartof><rights>The Japan Society of Human Genetics 2014.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c533t-1ba174db15dc7e34039b345eca6a3915feea19ce63817441bba2a573ea5b46d43</citedby><cites>FETCH-LOGICAL-c533t-1ba174db15dc7e34039b345eca6a3915feea19ce63817441bba2a573ea5b46d43</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25296578$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Suzuki, Toshifumi</creatorcontrib><creatorcontrib>Tsurusaki, Yoshinori</creatorcontrib><creatorcontrib>Nakashima, Mitsuko</creatorcontrib><creatorcontrib>Miyake, Noriko</creatorcontrib><creatorcontrib>Saitsu, Hirotomo</creatorcontrib><creatorcontrib>Takeda, Satoru</creatorcontrib><creatorcontrib>Matsumoto, Naomichi</creatorcontrib><title>Precise detection of chromosomal translocation or inversion breakpoints by whole-genome sequencing</title><title>Journal of human genetics</title><addtitle>J Hum Genet</addtitle><description>Structural variations (SVs), including translocations, inversions, deletions and duplications, are potentially associated with Mendelian diseases and contiguous gene syndromes. Determination of SV-related breakpoints at the nucleotide level is important to reveal the genetic causes for diseases. Whole-genome sequencing (WGS) by next-generation sequencers is expected to determine structural abnormalities more directly and efficiently than conventional methods. In this study, 14 SVs (9 balanced translocations, 1 inversion and 4 microdeletions) in 9 patients were analyzed by WGS with a shallow (5 × ) to moderate read coverage (20 × ). Among 28 breakpoints (as each SV has two breakpoints), 19 SV breakpoints had been determined previously at the nucleotide level by any other methods and 9 were uncharacterized. BreakDancer and Integrative Genomics Viewer determined 20 breakpoints (16 translocation, 2 inversion and 2 deletion breakpoints), but did not detect 8 breakpoints (2 translocation and 6 deletion breakpoints). These data indicate the efficacy of WGS for the precise determination of translocation and inversion breakpoints.</description><subject>Breakpoints</subject><subject>Chromosome Breakpoints</subject><subject>Chromosome Deletion</subject><subject>Chromosome Inversion - genetics</subject><subject>Chromosome translocations</subject><subject>Genome, Human</subject><subject>Genomes</subject><subject>Genomics</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Humans</subject><subject>Inversion</subject><subject>Sequence Analysis, DNA</subject><subject>Translocation, Genetic - genetics</subject><subject>Whole genome sequencing</subject><issn>1434-5161</issn><issn>1435-232X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNpdkMtLAzEQh4MotlZP3iXgRZCtee7jKMUXCHpQ8BaS7Gy7dTepya7S_96trR48zQzz8ZvhQ-iUkiklPL9aLuZTRqiY5vkeGlPBZcI4e9v_6UUiaUpH6CjGJSGEs4wdohGTrEhllo-ReQ5g6wi4hA5sV3uHfYXtIvjWR9_qBndBu9h4q7fLgGv3CSFuBhNAv6987bqIzRp_LXwDyRycbwFH-OjB2drNj9FBpZsIJ7s6Qa-3Ny-z--Tx6e5hdv2YWMl5l1CjaSZKQ2VpM-CC8MJwIcHqVPOCygpA08JCyvOBE9QYzbTMOGhpRFoKPkEX29xV8MPt2Km2jhaaRjvwfVQ0TQUjLBdyQM__oUvfBzd8p5hgjHDJeDFQl1vKBh9jgEqtQt3qsFaUqI16NahXG_Uqzwf6bJfZmxbKP_bXNf8GvoSAhQ</recordid><startdate>20141201</startdate><enddate>20141201</enddate><creator>Suzuki, Toshifumi</creator><creator>Tsurusaki, Yoshinori</creator><creator>Nakashima, Mitsuko</creator><creator>Miyake, Noriko</creator><creator>Saitsu, Hirotomo</creator><creator>Takeda, Satoru</creator><creator>Matsumoto, Naomichi</creator><general>Nature Publishing Group</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><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>7TM</scope></search><sort><creationdate>20141201</creationdate><title>Precise detection of chromosomal translocation or inversion breakpoints by whole-genome sequencing</title><author>Suzuki, Toshifumi ; 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Determination of SV-related breakpoints at the nucleotide level is important to reveal the genetic causes for diseases. Whole-genome sequencing (WGS) by next-generation sequencers is expected to determine structural abnormalities more directly and efficiently than conventional methods. In this study, 14 SVs (9 balanced translocations, 1 inversion and 4 microdeletions) in 9 patients were analyzed by WGS with a shallow (5 × ) to moderate read coverage (20 × ). Among 28 breakpoints (as each SV has two breakpoints), 19 SV breakpoints had been determined previously at the nucleotide level by any other methods and 9 were uncharacterized. BreakDancer and Integrative Genomics Viewer determined 20 breakpoints (16 translocation, 2 inversion and 2 deletion breakpoints), but did not detect 8 breakpoints (2 translocation and 6 deletion breakpoints). 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| source | MEDLINE; Springer Nature - Complete Springer Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals |
| subjects | Breakpoints Chromosome Breakpoints Chromosome Deletion Chromosome Inversion - genetics Chromosome translocations Genome, Human Genomes Genomics High-Throughput Nucleotide Sequencing Humans Inversion Sequence Analysis, DNA Translocation, Genetic - genetics Whole genome sequencing |
| title | Precise detection of chromosomal translocation or inversion breakpoints by whole-genome sequencing |
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