Cargando…
A simple and accurate SNP scoring strategy based on typeIIS restriction endonuclease cleavage and matrix-assisted laser desorption/ionization mass spectrometry
BACKGROUND: We describe the development of a novel matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF)-based single nucleotide polymorphism (SNP) scoring strategy, termed Restriction Fragment Mass Polymorphism (RFMP) that is suitable for genotyping variations in a simple, accurate...
Autores principales: | , , , , , , , , , |
---|---|
Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2008
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2442615/ https://www.ncbi.nlm.nih.gov/pubmed/18538037 http://dx.doi.org/10.1186/1471-2164-9-276 |
_version_ | 1782156713194946560 |
---|---|
author | Hong, Sun Pyo Ji, Seung Il Rhee, Hwanseok Shin, Soo Kyeong Hwang, Sun Young Lee, Seung Hwan Lee, Soong Deok Oh, Heung-Bum Yoo, Wangdon Kim, Soo-Ok |
author_facet | Hong, Sun Pyo Ji, Seung Il Rhee, Hwanseok Shin, Soo Kyeong Hwang, Sun Young Lee, Seung Hwan Lee, Soong Deok Oh, Heung-Bum Yoo, Wangdon Kim, Soo-Ok |
author_sort | Hong, Sun Pyo |
collection | PubMed |
description | BACKGROUND: We describe the development of a novel matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF)-based single nucleotide polymorphism (SNP) scoring strategy, termed Restriction Fragment Mass Polymorphism (RFMP) that is suitable for genotyping variations in a simple, accurate, and high-throughput manner. The assay is based on polymerase chain reaction (PCR) amplification and mass measurement of oligonucleotides containing a polymorphic base, to which a typeIIS restriction endonuclease recognition was introduced by PCR amplification. Enzymatic cleavage of the products leads to excision of oligonucleotide fragments representing base variation of the polymorphic site whose masses were determined by MALDI-TOF MS. RESULTS: The assay represents an improvement over previous methods because it relies on the direct mass determination of PCR products rather than on an indirect analysis, where a base-extended or fluorescent report tag is interpreted. The RFMP strategy is simple and straightforward, requiring one restriction digestion reaction following target amplification in a single vessel. With this technology, genotypes are generated with a high call rate (99.6%) and high accuracy (99.8%) as determined by independent sequencing. CONCLUSION: The simplicity, accuracy and amenability to high-throughput screening analysis should make the RFMP assay suitable for large-scale genotype association study as well as clinical genotyping in laboratories. |
format | Text |
id | pubmed-2442615 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-24426152008-07-02 A simple and accurate SNP scoring strategy based on typeIIS restriction endonuclease cleavage and matrix-assisted laser desorption/ionization mass spectrometry Hong, Sun Pyo Ji, Seung Il Rhee, Hwanseok Shin, Soo Kyeong Hwang, Sun Young Lee, Seung Hwan Lee, Soong Deok Oh, Heung-Bum Yoo, Wangdon Kim, Soo-Ok BMC Genomics Methodology Article BACKGROUND: We describe the development of a novel matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF)-based single nucleotide polymorphism (SNP) scoring strategy, termed Restriction Fragment Mass Polymorphism (RFMP) that is suitable for genotyping variations in a simple, accurate, and high-throughput manner. The assay is based on polymerase chain reaction (PCR) amplification and mass measurement of oligonucleotides containing a polymorphic base, to which a typeIIS restriction endonuclease recognition was introduced by PCR amplification. Enzymatic cleavage of the products leads to excision of oligonucleotide fragments representing base variation of the polymorphic site whose masses were determined by MALDI-TOF MS. RESULTS: The assay represents an improvement over previous methods because it relies on the direct mass determination of PCR products rather than on an indirect analysis, where a base-extended or fluorescent report tag is interpreted. The RFMP strategy is simple and straightforward, requiring one restriction digestion reaction following target amplification in a single vessel. With this technology, genotypes are generated with a high call rate (99.6%) and high accuracy (99.8%) as determined by independent sequencing. CONCLUSION: The simplicity, accuracy and amenability to high-throughput screening analysis should make the RFMP assay suitable for large-scale genotype association study as well as clinical genotyping in laboratories. BioMed Central 2008-06-09 /pmc/articles/PMC2442615/ /pubmed/18538037 http://dx.doi.org/10.1186/1471-2164-9-276 Text en Copyright © 2008 Hong et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Article Hong, Sun Pyo Ji, Seung Il Rhee, Hwanseok Shin, Soo Kyeong Hwang, Sun Young Lee, Seung Hwan Lee, Soong Deok Oh, Heung-Bum Yoo, Wangdon Kim, Soo-Ok A simple and accurate SNP scoring strategy based on typeIIS restriction endonuclease cleavage and matrix-assisted laser desorption/ionization mass spectrometry |
title | A simple and accurate SNP scoring strategy based on typeIIS restriction endonuclease cleavage and matrix-assisted laser desorption/ionization mass spectrometry |
title_full | A simple and accurate SNP scoring strategy based on typeIIS restriction endonuclease cleavage and matrix-assisted laser desorption/ionization mass spectrometry |
title_fullStr | A simple and accurate SNP scoring strategy based on typeIIS restriction endonuclease cleavage and matrix-assisted laser desorption/ionization mass spectrometry |
title_full_unstemmed | A simple and accurate SNP scoring strategy based on typeIIS restriction endonuclease cleavage and matrix-assisted laser desorption/ionization mass spectrometry |
title_short | A simple and accurate SNP scoring strategy based on typeIIS restriction endonuclease cleavage and matrix-assisted laser desorption/ionization mass spectrometry |
title_sort | simple and accurate snp scoring strategy based on typeiis restriction endonuclease cleavage and matrix-assisted laser desorption/ionization mass spectrometry |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2442615/ https://www.ncbi.nlm.nih.gov/pubmed/18538037 http://dx.doi.org/10.1186/1471-2164-9-276 |
work_keys_str_mv | AT hongsunpyo asimpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry AT jiseungil asimpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry AT rheehwanseok asimpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry AT shinsookyeong asimpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry AT hwangsunyoung asimpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry AT leeseunghwan asimpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry AT leesoongdeok asimpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry AT ohheungbum asimpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry AT yoowangdon asimpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry AT kimsoook asimpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry AT hongsunpyo simpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry AT jiseungil simpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry AT rheehwanseok simpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry AT shinsookyeong simpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry AT hwangsunyoung simpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry AT leeseunghwan simpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry AT leesoongdeok simpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry AT ohheungbum simpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry AT yoowangdon simpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry AT kimsoook simpleandaccuratesnpscoringstrategybasedontypeiisrestrictionendonucleasecleavageandmatrixassistedlaserdesorptionionizationmassspectrometry |