Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization
Abstract Background Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base‐pair resolution, but the use of short‐read sequencing is limited by repetitive sequences, and long‐read ap...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Kévin Uguen [verfasserIn] Claire Jubin [verfasserIn] Yannis Duffourd [verfasserIn] Claire Bardel [verfasserIn] Valérie Malan [verfasserIn] Jean‐Michel Dupont [verfasserIn] Laila El Khattabi [verfasserIn] Nicolas Chatron [verfasserIn] Antonio Vitobello [verfasserIn] Pierre‐Antoine Rollat‐Farnier [verfasserIn] Céline Baulard [verfasserIn] Marc Lelorch [verfasserIn] Aurélie Leduc [verfasserIn] Emilie Tisserant [verfasserIn] Frédéric Tran Mau‐Them [verfasserIn] Vincent Danjean [verfasserIn] Marc Delepine [verfasserIn] Marianne Till [verfasserIn] Vincent Meyer [verfasserIn] Stanislas Lyonnet [verfasserIn] Anne‐laure Mosca‐Boidron [verfasserIn] Julien Thevenon [verfasserIn] Laurence Faivre [verfasserIn] Christel Thauvin‐Robinet [verfasserIn] Caroline Schluth‐Bolard [verfasserIn] Anne Boland [verfasserIn] Robert Olaso [verfasserIn] Patrick Callier [verfasserIn] Serge Romana [verfasserIn] Jean‐François Deleuze [verfasserIn] Damien Sanlaville [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2020 |
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| Schlagwörter: |
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| Übergeordnetes Werk: |
In: Molecular Genetics & Genomic Medicine - Wiley, 2014, 8(2020), 3, Seite n/a-n/a |
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| Übergeordnetes Werk: |
volume:8 ; year:2020 ; number:3 ; pages:n/a-n/a |
| Links: |
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| DOI / URN: |
10.1002/mgg3.1114 |
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| Katalog-ID: |
DOAJ02814631X |
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| 245 | 1 | 0 | |a Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization |
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| 520 | |a Abstract Background Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base‐pair resolution, but the use of short‐read sequencing is limited by repetitive sequences, and long‐read approaches are not yet validated for diagnosis. Recently, 10X Genomics proposed Chromium, a technology providing linked‐reads to reconstruct long DNA fragments and which could represent a good alternative. No study has compared short‐read to linked‐read technologies to detect SVs in a constitutional diagnostic setting yet. The aim of this work was to determine whether the 10X Genomics technology enables better detection and comprehension of SVs than short‐read WGS. Methods We included 13 patients carrying various SVs. Whole genome analyses were performed using paired‐end HiSeq X sequencing with (linked‐read strategy) or without (short‐read strategy) Chromium library preparation. Two different bioinformatic pipelines were used: Variants are called using BreakDancer for short‐read strategy and LongRanger for long‐read strategy. Variant interpretations were first blinded. Results The short‐read strategy allowed diagnosis of known SV in 10/13 patients. After unblinding, the linked‐read strategy identified 10/13 SVs, including one (patient 7) missed by the short‐read strategy. Conclusion In conclusion, regarding the results of this study, 10X Genomics solution did not improve the detection and characterization of SV. | ||
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| 700 | 0 | |a Valérie Malan |e verfasserin |4 aut | |
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| 700 | 0 | |a Nicolas Chatron |e verfasserin |4 aut | |
| 700 | 0 | |a Antonio Vitobello |e verfasserin |4 aut | |
| 700 | 0 | |a Pierre‐Antoine Rollat‐Farnier |e verfasserin |4 aut | |
| 700 | 0 | |a Céline Baulard |e verfasserin |4 aut | |
| 700 | 0 | |a Marc Lelorch |e verfasserin |4 aut | |
| 700 | 0 | |a Aurélie Leduc |e verfasserin |4 aut | |
| 700 | 0 | |a Emilie Tisserant |e verfasserin |4 aut | |
| 700 | 0 | |a Frédéric Tran Mau‐Them |e verfasserin |4 aut | |
| 700 | 0 | |a Vincent Danjean |e verfasserin |4 aut | |
| 700 | 0 | |a Marc Delepine |e verfasserin |4 aut | |
| 700 | 0 | |a Marianne Till |e verfasserin |4 aut | |
| 700 | 0 | |a Vincent Meyer |e verfasserin |4 aut | |
| 700 | 0 | |a Stanislas Lyonnet |e verfasserin |4 aut | |
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| 700 | 0 | |a Julien Thevenon |e verfasserin |4 aut | |
| 700 | 0 | |a Laurence Faivre |e verfasserin |4 aut | |
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10.1002/mgg3.1114 doi (DE-627)DOAJ02814631X (DE-599)DOAJ2bc4ee64a0974d0d8733a52a9dd35fe4 DE-627 ger DE-627 rakwb eng QH426-470 Kévin Uguen verfasserin aut Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base‐pair resolution, but the use of short‐read sequencing is limited by repetitive sequences, and long‐read approaches are not yet validated for diagnosis. Recently, 10X Genomics proposed Chromium, a technology providing linked‐reads to reconstruct long DNA fragments and which could represent a good alternative. No study has compared short‐read to linked‐read technologies to detect SVs in a constitutional diagnostic setting yet. The aim of this work was to determine whether the 10X Genomics technology enables better detection and comprehension of SVs than short‐read WGS. Methods We included 13 patients carrying various SVs. Whole genome analyses were performed using paired‐end HiSeq X sequencing with (linked‐read strategy) or without (short‐read strategy) Chromium library preparation. Two different bioinformatic pipelines were used: Variants are called using BreakDancer for short‐read strategy and LongRanger for long‐read strategy. Variant interpretations were first blinded. Results The short‐read strategy allowed diagnosis of known SV in 10/13 patients. After unblinding, the linked‐read strategy identified 10/13 SVs, including one (patient 7) missed by the short‐read strategy. Conclusion In conclusion, regarding the results of this study, 10X Genomics solution did not improve the detection and characterization of SV. 10X Genomics: Illumina bioinformatics genome sequencing structural variants Genetics Claire Jubin verfasserin aut Yannis Duffourd verfasserin aut Claire Bardel verfasserin aut Valérie Malan verfasserin aut Jean‐Michel Dupont verfasserin aut Laila El Khattabi verfasserin aut Nicolas Chatron verfasserin aut Antonio Vitobello verfasserin aut Pierre‐Antoine Rollat‐Farnier verfasserin aut Céline Baulard verfasserin aut Marc Lelorch verfasserin aut Aurélie Leduc verfasserin aut Emilie Tisserant verfasserin aut Frédéric Tran Mau‐Them verfasserin aut Vincent Danjean verfasserin aut Marc Delepine verfasserin aut Marianne Till verfasserin aut Vincent Meyer verfasserin aut Stanislas Lyonnet verfasserin aut Anne‐laure Mosca‐Boidron verfasserin aut Julien Thevenon verfasserin aut Laurence Faivre verfasserin aut Christel Thauvin‐Robinet verfasserin aut Caroline Schluth‐Bolard verfasserin aut Anne Boland verfasserin aut Robert Olaso verfasserin aut Patrick Callier verfasserin aut Serge Romana verfasserin aut Jean‐François Deleuze verfasserin aut Damien Sanlaville verfasserin aut In Molecular Genetics & Genomic Medicine Wiley, 2014 8(2020), 3, Seite n/a-n/a (DE-627)769222234 (DE-600)2734884-2 23249269 nnns volume:8 year:2020 number:3 pages:n/a-n/a https://doi.org/10.1002/mgg3.1114 kostenfrei https://doaj.org/article/2bc4ee64a0974d0d8733a52a9dd35fe4 kostenfrei https://doi.org/10.1002/mgg3.1114 kostenfrei https://doaj.org/toc/2324-9269 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_636 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2020 3 n/a-n/a |
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10.1002/mgg3.1114 doi (DE-627)DOAJ02814631X (DE-599)DOAJ2bc4ee64a0974d0d8733a52a9dd35fe4 DE-627 ger DE-627 rakwb eng QH426-470 Kévin Uguen verfasserin aut Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base‐pair resolution, but the use of short‐read sequencing is limited by repetitive sequences, and long‐read approaches are not yet validated for diagnosis. Recently, 10X Genomics proposed Chromium, a technology providing linked‐reads to reconstruct long DNA fragments and which could represent a good alternative. No study has compared short‐read to linked‐read technologies to detect SVs in a constitutional diagnostic setting yet. The aim of this work was to determine whether the 10X Genomics technology enables better detection and comprehension of SVs than short‐read WGS. Methods We included 13 patients carrying various SVs. Whole genome analyses were performed using paired‐end HiSeq X sequencing with (linked‐read strategy) or without (short‐read strategy) Chromium library preparation. Two different bioinformatic pipelines were used: Variants are called using BreakDancer for short‐read strategy and LongRanger for long‐read strategy. Variant interpretations were first blinded. Results The short‐read strategy allowed diagnosis of known SV in 10/13 patients. After unblinding, the linked‐read strategy identified 10/13 SVs, including one (patient 7) missed by the short‐read strategy. Conclusion In conclusion, regarding the results of this study, 10X Genomics solution did not improve the detection and characterization of SV. 10X Genomics: Illumina bioinformatics genome sequencing structural variants Genetics Claire Jubin verfasserin aut Yannis Duffourd verfasserin aut Claire Bardel verfasserin aut Valérie Malan verfasserin aut Jean‐Michel Dupont verfasserin aut Laila El Khattabi verfasserin aut Nicolas Chatron verfasserin aut Antonio Vitobello verfasserin aut Pierre‐Antoine Rollat‐Farnier verfasserin aut Céline Baulard verfasserin aut Marc Lelorch verfasserin aut Aurélie Leduc verfasserin aut Emilie Tisserant verfasserin aut Frédéric Tran Mau‐Them verfasserin aut Vincent Danjean verfasserin aut Marc Delepine verfasserin aut Marianne Till verfasserin aut Vincent Meyer verfasserin aut Stanislas Lyonnet verfasserin aut Anne‐laure Mosca‐Boidron verfasserin aut Julien Thevenon verfasserin aut Laurence Faivre verfasserin aut Christel Thauvin‐Robinet verfasserin aut Caroline Schluth‐Bolard verfasserin aut Anne Boland verfasserin aut Robert Olaso verfasserin aut Patrick Callier verfasserin aut Serge Romana verfasserin aut Jean‐François Deleuze verfasserin aut Damien Sanlaville verfasserin aut In Molecular Genetics & Genomic Medicine Wiley, 2014 8(2020), 3, Seite n/a-n/a (DE-627)769222234 (DE-600)2734884-2 23249269 nnns volume:8 year:2020 number:3 pages:n/a-n/a https://doi.org/10.1002/mgg3.1114 kostenfrei https://doaj.org/article/2bc4ee64a0974d0d8733a52a9dd35fe4 kostenfrei https://doi.org/10.1002/mgg3.1114 kostenfrei https://doaj.org/toc/2324-9269 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_636 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2020 3 n/a-n/a |
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10.1002/mgg3.1114 doi (DE-627)DOAJ02814631X (DE-599)DOAJ2bc4ee64a0974d0d8733a52a9dd35fe4 DE-627 ger DE-627 rakwb eng QH426-470 Kévin Uguen verfasserin aut Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base‐pair resolution, but the use of short‐read sequencing is limited by repetitive sequences, and long‐read approaches are not yet validated for diagnosis. Recently, 10X Genomics proposed Chromium, a technology providing linked‐reads to reconstruct long DNA fragments and which could represent a good alternative. No study has compared short‐read to linked‐read technologies to detect SVs in a constitutional diagnostic setting yet. The aim of this work was to determine whether the 10X Genomics technology enables better detection and comprehension of SVs than short‐read WGS. Methods We included 13 patients carrying various SVs. Whole genome analyses were performed using paired‐end HiSeq X sequencing with (linked‐read strategy) or without (short‐read strategy) Chromium library preparation. Two different bioinformatic pipelines were used: Variants are called using BreakDancer for short‐read strategy and LongRanger for long‐read strategy. Variant interpretations were first blinded. Results The short‐read strategy allowed diagnosis of known SV in 10/13 patients. After unblinding, the linked‐read strategy identified 10/13 SVs, including one (patient 7) missed by the short‐read strategy. Conclusion In conclusion, regarding the results of this study, 10X Genomics solution did not improve the detection and characterization of SV. 10X Genomics: Illumina bioinformatics genome sequencing structural variants Genetics Claire Jubin verfasserin aut Yannis Duffourd verfasserin aut Claire Bardel verfasserin aut Valérie Malan verfasserin aut Jean‐Michel Dupont verfasserin aut Laila El Khattabi verfasserin aut Nicolas Chatron verfasserin aut Antonio Vitobello verfasserin aut Pierre‐Antoine Rollat‐Farnier verfasserin aut Céline Baulard verfasserin aut Marc Lelorch verfasserin aut Aurélie Leduc verfasserin aut Emilie Tisserant verfasserin aut Frédéric Tran Mau‐Them verfasserin aut Vincent Danjean verfasserin aut Marc Delepine verfasserin aut Marianne Till verfasserin aut Vincent Meyer verfasserin aut Stanislas Lyonnet verfasserin aut Anne‐laure Mosca‐Boidron verfasserin aut Julien Thevenon verfasserin aut Laurence Faivre verfasserin aut Christel Thauvin‐Robinet verfasserin aut Caroline Schluth‐Bolard verfasserin aut Anne Boland verfasserin aut Robert Olaso verfasserin aut Patrick Callier verfasserin aut Serge Romana verfasserin aut Jean‐François Deleuze verfasserin aut Damien Sanlaville verfasserin aut In Molecular Genetics & Genomic Medicine Wiley, 2014 8(2020), 3, Seite n/a-n/a (DE-627)769222234 (DE-600)2734884-2 23249269 nnns volume:8 year:2020 number:3 pages:n/a-n/a https://doi.org/10.1002/mgg3.1114 kostenfrei https://doaj.org/article/2bc4ee64a0974d0d8733a52a9dd35fe4 kostenfrei https://doi.org/10.1002/mgg3.1114 kostenfrei https://doaj.org/toc/2324-9269 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_636 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2020 3 n/a-n/a |
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10.1002/mgg3.1114 doi (DE-627)DOAJ02814631X (DE-599)DOAJ2bc4ee64a0974d0d8733a52a9dd35fe4 DE-627 ger DE-627 rakwb eng QH426-470 Kévin Uguen verfasserin aut Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base‐pair resolution, but the use of short‐read sequencing is limited by repetitive sequences, and long‐read approaches are not yet validated for diagnosis. Recently, 10X Genomics proposed Chromium, a technology providing linked‐reads to reconstruct long DNA fragments and which could represent a good alternative. No study has compared short‐read to linked‐read technologies to detect SVs in a constitutional diagnostic setting yet. The aim of this work was to determine whether the 10X Genomics technology enables better detection and comprehension of SVs than short‐read WGS. Methods We included 13 patients carrying various SVs. Whole genome analyses were performed using paired‐end HiSeq X sequencing with (linked‐read strategy) or without (short‐read strategy) Chromium library preparation. Two different bioinformatic pipelines were used: Variants are called using BreakDancer for short‐read strategy and LongRanger for long‐read strategy. Variant interpretations were first blinded. Results The short‐read strategy allowed diagnosis of known SV in 10/13 patients. After unblinding, the linked‐read strategy identified 10/13 SVs, including one (patient 7) missed by the short‐read strategy. Conclusion In conclusion, regarding the results of this study, 10X Genomics solution did not improve the detection and characterization of SV. 10X Genomics: Illumina bioinformatics genome sequencing structural variants Genetics Claire Jubin verfasserin aut Yannis Duffourd verfasserin aut Claire Bardel verfasserin aut Valérie Malan verfasserin aut Jean‐Michel Dupont verfasserin aut Laila El Khattabi verfasserin aut Nicolas Chatron verfasserin aut Antonio Vitobello verfasserin aut Pierre‐Antoine Rollat‐Farnier verfasserin aut Céline Baulard verfasserin aut Marc Lelorch verfasserin aut Aurélie Leduc verfasserin aut Emilie Tisserant verfasserin aut Frédéric Tran Mau‐Them verfasserin aut Vincent Danjean verfasserin aut Marc Delepine verfasserin aut Marianne Till verfasserin aut Vincent Meyer verfasserin aut Stanislas Lyonnet verfasserin aut Anne‐laure Mosca‐Boidron verfasserin aut Julien Thevenon verfasserin aut Laurence Faivre verfasserin aut Christel Thauvin‐Robinet verfasserin aut Caroline Schluth‐Bolard verfasserin aut Anne Boland verfasserin aut Robert Olaso verfasserin aut Patrick Callier verfasserin aut Serge Romana verfasserin aut Jean‐François Deleuze verfasserin aut Damien Sanlaville verfasserin aut In Molecular Genetics & Genomic Medicine Wiley, 2014 8(2020), 3, Seite n/a-n/a (DE-627)769222234 (DE-600)2734884-2 23249269 nnns volume:8 year:2020 number:3 pages:n/a-n/a https://doi.org/10.1002/mgg3.1114 kostenfrei https://doaj.org/article/2bc4ee64a0974d0d8733a52a9dd35fe4 kostenfrei https://doi.org/10.1002/mgg3.1114 kostenfrei https://doaj.org/toc/2324-9269 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_636 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2020 3 n/a-n/a |
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10.1002/mgg3.1114 doi (DE-627)DOAJ02814631X (DE-599)DOAJ2bc4ee64a0974d0d8733a52a9dd35fe4 DE-627 ger DE-627 rakwb eng QH426-470 Kévin Uguen verfasserin aut Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base‐pair resolution, but the use of short‐read sequencing is limited by repetitive sequences, and long‐read approaches are not yet validated for diagnosis. Recently, 10X Genomics proposed Chromium, a technology providing linked‐reads to reconstruct long DNA fragments and which could represent a good alternative. No study has compared short‐read to linked‐read technologies to detect SVs in a constitutional diagnostic setting yet. The aim of this work was to determine whether the 10X Genomics technology enables better detection and comprehension of SVs than short‐read WGS. Methods We included 13 patients carrying various SVs. Whole genome analyses were performed using paired‐end HiSeq X sequencing with (linked‐read strategy) or without (short‐read strategy) Chromium library preparation. Two different bioinformatic pipelines were used: Variants are called using BreakDancer for short‐read strategy and LongRanger for long‐read strategy. Variant interpretations were first blinded. Results The short‐read strategy allowed diagnosis of known SV in 10/13 patients. After unblinding, the linked‐read strategy identified 10/13 SVs, including one (patient 7) missed by the short‐read strategy. Conclusion In conclusion, regarding the results of this study, 10X Genomics solution did not improve the detection and characterization of SV. 10X Genomics: Illumina bioinformatics genome sequencing structural variants Genetics Claire Jubin verfasserin aut Yannis Duffourd verfasserin aut Claire Bardel verfasserin aut Valérie Malan verfasserin aut Jean‐Michel Dupont verfasserin aut Laila El Khattabi verfasserin aut Nicolas Chatron verfasserin aut Antonio Vitobello verfasserin aut Pierre‐Antoine Rollat‐Farnier verfasserin aut Céline Baulard verfasserin aut Marc Lelorch verfasserin aut Aurélie Leduc verfasserin aut Emilie Tisserant verfasserin aut Frédéric Tran Mau‐Them verfasserin aut Vincent Danjean verfasserin aut Marc Delepine verfasserin aut Marianne Till verfasserin aut Vincent Meyer verfasserin aut Stanislas Lyonnet verfasserin aut Anne‐laure Mosca‐Boidron verfasserin aut Julien Thevenon verfasserin aut Laurence Faivre verfasserin aut Christel Thauvin‐Robinet verfasserin aut Caroline Schluth‐Bolard verfasserin aut Anne Boland verfasserin aut Robert Olaso verfasserin aut Patrick Callier verfasserin aut Serge Romana verfasserin aut Jean‐François Deleuze verfasserin aut Damien Sanlaville verfasserin aut In Molecular Genetics & Genomic Medicine Wiley, 2014 8(2020), 3, Seite n/a-n/a (DE-627)769222234 (DE-600)2734884-2 23249269 nnns volume:8 year:2020 number:3 pages:n/a-n/a https://doi.org/10.1002/mgg3.1114 kostenfrei https://doaj.org/article/2bc4ee64a0974d0d8733a52a9dd35fe4 kostenfrei https://doi.org/10.1002/mgg3.1114 kostenfrei https://doaj.org/toc/2324-9269 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_636 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2020 3 n/a-n/a |
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Kévin Uguen @@aut@@ Claire Jubin @@aut@@ Yannis Duffourd @@aut@@ Claire Bardel @@aut@@ Valérie Malan @@aut@@ Jean‐Michel Dupont @@aut@@ Laila El Khattabi @@aut@@ Nicolas Chatron @@aut@@ Antonio Vitobello @@aut@@ Pierre‐Antoine Rollat‐Farnier @@aut@@ Céline Baulard @@aut@@ Marc Lelorch @@aut@@ Aurélie Leduc @@aut@@ Emilie Tisserant @@aut@@ Frédéric Tran Mau‐Them @@aut@@ Vincent Danjean @@aut@@ Marc Delepine @@aut@@ Marianne Till @@aut@@ Vincent Meyer @@aut@@ Stanislas Lyonnet @@aut@@ Anne‐laure Mosca‐Boidron @@aut@@ Julien Thevenon @@aut@@ Laurence Faivre @@aut@@ Christel Thauvin‐Robinet @@aut@@ Caroline Schluth‐Bolard @@aut@@ Anne Boland @@aut@@ Robert Olaso @@aut@@ Patrick Callier @@aut@@ Serge Romana @@aut@@ Jean‐François Deleuze @@aut@@ Damien Sanlaville @@aut@@ |
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<?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>01000caa a22002652 4500</leader><controlfield tag="001">DOAJ02814631X</controlfield><controlfield tag="003">DE-627</controlfield><controlfield tag="005">20240414092051.0</controlfield><controlfield tag="007">cr uuu---uuuuu</controlfield><controlfield tag="008">230226s2020 xx |||||o 00| ||eng c</controlfield><datafield tag="024" ind1="7" ind2=" "><subfield code="a">10.1002/mgg3.1114</subfield><subfield code="2">doi</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-627)DOAJ02814631X</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-599)DOAJ2bc4ee64a0974d0d8733a52a9dd35fe4</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-627</subfield><subfield code="b">ger</subfield><subfield code="c">DE-627</subfield><subfield code="e">rakwb</subfield></datafield><datafield tag="041" ind1=" " ind2=" "><subfield code="a">eng</subfield></datafield><datafield tag="050" ind1=" " ind2="0"><subfield code="a">QH426-470</subfield></datafield><datafield tag="100" ind1="0" ind2=" "><subfield code="a">Kévin Uguen</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2020</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="a">Text</subfield><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="a">Computermedien</subfield><subfield code="b">c</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="a">Online-Ressource</subfield><subfield code="b">cr</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">Abstract Background Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base‐pair resolution, but the use of short‐read sequencing is limited by repetitive sequences, and long‐read approaches are not yet validated for diagnosis. Recently, 10X Genomics proposed Chromium, a technology providing linked‐reads to reconstruct long DNA fragments and which could represent a good alternative. No study has compared short‐read to linked‐read technologies to detect SVs in a constitutional diagnostic setting yet. The aim of this work was to determine whether the 10X Genomics technology enables better detection and comprehension of SVs than short‐read WGS. Methods We included 13 patients carrying various SVs. Whole genome analyses were performed using paired‐end HiSeq X sequencing with (linked‐read strategy) or without (short‐read strategy) Chromium library preparation. Two different bioinformatic pipelines were used: Variants are called using BreakDancer for short‐read strategy and LongRanger for long‐read strategy. Variant interpretations were first blinded. Results The short‐read strategy allowed diagnosis of known SV in 10/13 patients. After unblinding, the linked‐read strategy identified 10/13 SVs, including one (patient 7) missed by the short‐read strategy. 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QH426-470 Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization 10X Genomics: Illumina bioinformatics genome sequencing structural variants |
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genome sequencing in cytogenetics: comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization |
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QH426-470 |
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Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization |
| abstract |
Abstract Background Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base‐pair resolution, but the use of short‐read sequencing is limited by repetitive sequences, and long‐read approaches are not yet validated for diagnosis. Recently, 10X Genomics proposed Chromium, a technology providing linked‐reads to reconstruct long DNA fragments and which could represent a good alternative. No study has compared short‐read to linked‐read technologies to detect SVs in a constitutional diagnostic setting yet. The aim of this work was to determine whether the 10X Genomics technology enables better detection and comprehension of SVs than short‐read WGS. Methods We included 13 patients carrying various SVs. Whole genome analyses were performed using paired‐end HiSeq X sequencing with (linked‐read strategy) or without (short‐read strategy) Chromium library preparation. Two different bioinformatic pipelines were used: Variants are called using BreakDancer for short‐read strategy and LongRanger for long‐read strategy. Variant interpretations were first blinded. Results The short‐read strategy allowed diagnosis of known SV in 10/13 patients. After unblinding, the linked‐read strategy identified 10/13 SVs, including one (patient 7) missed by the short‐read strategy. Conclusion In conclusion, regarding the results of this study, 10X Genomics solution did not improve the detection and characterization of SV. |
| abstractGer |
Abstract Background Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base‐pair resolution, but the use of short‐read sequencing is limited by repetitive sequences, and long‐read approaches are not yet validated for diagnosis. Recently, 10X Genomics proposed Chromium, a technology providing linked‐reads to reconstruct long DNA fragments and which could represent a good alternative. No study has compared short‐read to linked‐read technologies to detect SVs in a constitutional diagnostic setting yet. The aim of this work was to determine whether the 10X Genomics technology enables better detection and comprehension of SVs than short‐read WGS. Methods We included 13 patients carrying various SVs. Whole genome analyses were performed using paired‐end HiSeq X sequencing with (linked‐read strategy) or without (short‐read strategy) Chromium library preparation. Two different bioinformatic pipelines were used: Variants are called using BreakDancer for short‐read strategy and LongRanger for long‐read strategy. Variant interpretations were first blinded. Results The short‐read strategy allowed diagnosis of known SV in 10/13 patients. After unblinding, the linked‐read strategy identified 10/13 SVs, including one (patient 7) missed by the short‐read strategy. Conclusion In conclusion, regarding the results of this study, 10X Genomics solution did not improve the detection and characterization of SV. |
| abstract_unstemmed |
Abstract Background Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base‐pair resolution, but the use of short‐read sequencing is limited by repetitive sequences, and long‐read approaches are not yet validated for diagnosis. Recently, 10X Genomics proposed Chromium, a technology providing linked‐reads to reconstruct long DNA fragments and which could represent a good alternative. No study has compared short‐read to linked‐read technologies to detect SVs in a constitutional diagnostic setting yet. The aim of this work was to determine whether the 10X Genomics technology enables better detection and comprehension of SVs than short‐read WGS. Methods We included 13 patients carrying various SVs. Whole genome analyses were performed using paired‐end HiSeq X sequencing with (linked‐read strategy) or without (short‐read strategy) Chromium library preparation. Two different bioinformatic pipelines were used: Variants are called using BreakDancer for short‐read strategy and LongRanger for long‐read strategy. Variant interpretations were first blinded. Results The short‐read strategy allowed diagnosis of known SV in 10/13 patients. After unblinding, the linked‐read strategy identified 10/13 SVs, including one (patient 7) missed by the short‐read strategy. Conclusion In conclusion, regarding the results of this study, 10X Genomics solution did not improve the detection and characterization of SV. |
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Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization |
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Claire Jubin Yannis Duffourd Claire Bardel Valérie Malan Jean‐Michel Dupont Laila El Khattabi Nicolas Chatron Antonio Vitobello Pierre‐Antoine Rollat‐Farnier Céline Baulard Marc Lelorch Aurélie Leduc Emilie Tisserant Frédéric Tran Mau‐Them Vincent Danjean Marc Delepine Marianne Till Vincent Meyer Stanislas Lyonnet Anne‐laure Mosca‐Boidron Julien Thevenon Laurence Faivre Christel Thauvin‐Robinet Caroline Schluth‐Bolard Anne Boland Robert Olaso Patrick Callier Serge Romana Jean‐François Deleuze Damien Sanlaville |
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Claire Jubin Yannis Duffourd Claire Bardel Valérie Malan Jean‐Michel Dupont Laila El Khattabi Nicolas Chatron Antonio Vitobello Pierre‐Antoine Rollat‐Farnier Céline Baulard Marc Lelorch Aurélie Leduc Emilie Tisserant Frédéric Tran Mau‐Them Vincent Danjean Marc Delepine Marianne Till Vincent Meyer Stanislas Lyonnet Anne‐laure Mosca‐Boidron Julien Thevenon Laurence Faivre Christel Thauvin‐Robinet Caroline Schluth‐Bolard Anne Boland Robert Olaso Patrick Callier Serge Romana Jean‐François Deleuze Damien Sanlaville |
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| score |
7.3987894 |