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Johnson SH, Smadbeck JB, Smoley SA, Gaitatzes A, Murphy SJ, Harris FR, Drucker TM, Zenka RM, Pitel BA, Rowsey RA, Hoppman NL, Aypar U, Sukov WR, Jenkins RB, Feldman AL, Kearney HM, Vasmatzis G. SVAtools for junction detection of genome-wide chromosomal rearrangements by mate-pair sequencing (MPseq). Cancer Genet 2017; 221:1-18. [PMID: 29405991 DOI: 10.1016/j.cancergen.2017.11.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/12/2017] [Accepted: 11/27/2017] [Indexed: 01/04/2023]
Abstract
Mate-pair sequencing (MPseq), using long-insert, paired-end genomic libraries, is a powerful next-generation sequencing-based approach for the detection of genomic structural variants. SVAtools is a set of algorithms to detect both chromosomal rearrangements and large (>10 kb) copy number variants (CNVs) in genome-wide MPseq data. SVAtools can also predict gene disruptions and gene fusions, and characterize the genomic structure of complex rearrangements. To illustrate the power of SVAtools' junction detection methods to provide comprehensive molecular karyotypes, MPseq data were compared against a set of samples previously characterized by traditional cytogenetic methods. Karyotype, FISH and chromosomal microarray (CMA), performed for 29 patients in a clinical laboratory setting, collectively revealed 285 breakpoints in 87 rearrangements. The junction detection methods of SVAtools detected 87% of these breakpoints compared to 48%, 42% and 57% for karyotype, FISH and CMA respectively. Breakpoint resolution was also reported to 1 kb or less and additional genomic rearrangement complexities not appreciable by standard cytogenetic techniques were revealed. For example, 63% of CNVs detected by CMA were shown by SVAtools' junction detection to occur secondary to a rearrangement other than a simple deletion or tandem duplication. SVAtools with MPseq provides comprehensive and accurate whole-genome junction detection with improved breakpoint resolution, compared to karyotype, FISH, and CMA combined. This approach to molecular karyotyping offers considerable diagnostic potential for the simultaneous detection of both novel and recurrent genomic rearrangements in hereditary and neoplastic disorders.
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Affiliation(s)
- Sarah H Johnson
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester MN, USA
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester MN, USA
| | - Stephanie A Smoley
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Stephen J Murphy
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester MN, USA
| | - Faye R Harris
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester MN, USA
| | | | - Roman M Zenka
- Bioinformatics Systems, Mayo Clinic Rochester, MN, USA
| | - Beth A Pitel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ross A Rowsey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Umut Aypar
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - William R Sukov
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Andrew L Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Hutton M Kearney
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester MN, USA; Department of Molecular Medicine, Mayo Clinic, Rochester MN, USA.
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Santa María L, Faundes V, Curotto B, Morales P, Morales K, Aliaga S, Pugin Á, Alliende MA. Comparison of two subtelomeric assays for the screening of chromosomal rearrangements: analysis of 383 patients, literature review and further recommendations. J Appl Genet 2015; 57:63-9. [PMID: 26069167 DOI: 10.1007/s13353-015-0295-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/11/2015] [Accepted: 05/26/2015] [Indexed: 12/01/2022]
Abstract
Intellectual disability (ID) and global development delay (GDD) are caused by genetic factors such as subtelomeric rearrangements (SR) in 25 % of patients. There are several assays currently available to detect SR, but subtelomeric fluorescence in situ hybridisation (Subt-FISH) and subtelomeric multiplex ligation-dependent probe amplification (Subt-MLPA) have been the most frequently used. However, the diagnostic yield of each technique has not been compared. We reviewed the results of SR screening over a ten-year period in Chilean patients with ID/GDD using Subt-FISH and/or Subt-MLPA, compared the diagnostic yield of both tools and reviewed the corresponding literature. A total of 383 cases were included in this study, of which 53.8 % were males. The overall diagnostic yield was 8.9 % between both methods, but Subt-MLPA showed a higher performance than Subt-FISH (p = 0.002). A total of 4,181 patients with ID/GDD have been studied worldwide with Subt-MLPA and other subtelomeric assays, and 244 (5.84 %) had a pathogenic SR. It is estimated that Subt-MLPA may detect 92.6 % of the total cases with SR. The capacity of detecting tandem duplication and other critical regions, as well as the use of two MLPA kits, may explain the higher performance of this tool over Subt-FISH. Therefore, we recommend the use of this subtelomeric method as a cost-effective way to study ID/GDD patients.
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Affiliation(s)
- Lorena Santa María
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile
| | - Víctor Faundes
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile.
| | - Bianca Curotto
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile
| | - Paulina Morales
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile
| | - Karla Morales
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile.,Escuela de Tecnología Médica, Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
| | - Solange Aliaga
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile
| | - Ángela Pugin
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile
| | - María Angélica Alliende
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile
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Vanzo RJ, Martin MM, Sdano MR, Teta K, Aggarwal V, South ST. SNX8: A candidate gene for 7p22 cardiac malformations including tetralogy of fallot. Am J Med Genet A 2013; 164A:554-6. [PMID: 24311514 DOI: 10.1002/ajmg.a.36242] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 08/19/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Rena J Vanzo
- Lineagen, Inc., 423 Wakara Way, Ste 200, Salt Lake City, UT 84108, United States
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