smMIP
Single-Molecule Molecular Inversion Probes
The smMIP method uses single-molecule tagging and molecular inversion probes to detect and quantify genetic variations occurring at low frequencies (Hiatt et al., 2013). In this method, probes are used to detect targets in gDNA. After the probed targets are copied, exonuclease digestion leaves the target with a tag, which subsequently undergoes PCR amplification. Sequencing allows for high-resolution sequence reads of targets, while greater depth allows for better alignment of every unique molecular tag.
Advantages:
- Detects low-frequency targets
- Can perform single-cell sequencing or sequencing for samples with limited starting material
- Per-base error of 2.6×10-5 in clinical samples (Eboreime et al., 2016)
Disadvantages:
- PCR amplification errors
- PCR biases can underrepresent GC-rich templates
- Targets smaller than 500 bp are amplified preferentially by polymerases during PCR
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
Eboreime J., Choi S. K., Yoon S. R., Arnheim N. and Calabrese P. Estimating Exceptionally Rare Germline and Somatic Mutation Frequencies via Next Generation Sequencing. PLoS One. 2016;11:e0158340
References:
Luks V. L., Kamitaki N., Vivero M. P., et al. Lymphatic and other vascular malformative/overgrowth disorders are caused by somatic mutations in PIK3CA. J Pediatr. 2015;166:1048-1054 e1041-1045
Mirzaa G. M., Conti V., Timms A. E., et al. Characterisation of mutations of the phosphoinositide-3-kinase regulatory subunit, PIK3R2, in perisylvian polymicrogyria: a next-generation sequencing study. Lancet Neurol. 2015;14:1182-1195
Carlson K. D., Sudmant P. H., Press M. O., Eichler E. E., Shendure J. and Queitsch C. MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals. Genome Res. 2015;25:750-761
Carvill G. L., McMahon J. M., Schneider A., et al. Mutations in the GABA Transporter SLC6A1 Cause Epilepsy with Myoclonic-Atonic Seizures. Am J Hum Genet. 2015;96:808-815
Kang H. C., Baek S. T., Song S. and Gleeson J. G. Clinical and Genetic Aspects of the Segmental Overgrowth Spectrum Due to Somatic Mutations in PIK3CA. J Pediatr. 2015;167:957-962
Weren R. D., Ligtenberg M. J., Kets C. M., et al. A germline homozygous mutation in the base-excision repair gene NTHL1 causes adenomatous polyposis and colorectal cancer. Nat Genet. 2015;47:668-671
Related
History: smMIP
Revision by sbrumpton on 2017-06-21 07:50:21 - Show/Hide
Single-Molecule Molecular Inversion Probes
The smMIP method uses single-molecule tagging and molecular inversion probes to detect and quantify genetic variations occurring at low frequencies (Hiatt et al., 2013). In this method, probes are used to detect targets in gDNA. After the probed targets are copied, exonuclease digestion leaves the target with a tag, which subsequently undergoes PCR amplification. Sequencing allows for high-resolution sequence reads of targets, while greater depth allows for better alignment of every unique molecular tag.
Advantages:- Detects low-frequency targets
- Can perform single-cell sequencing or sequencing for samples with limited starting material
- Per-base error of 2.6x10-5 in clinical samples (Eboreime et al., 2016)
Disadvantages:- PCR amplification errors
- PCR biases can underrepresent GC-rich templates
- Targets smaller than 500 bp are amplified preferentially by polymerases during PCR
Reagents:Illumina Library prep and Array Kit SelectorReviews:Eboreime J., Choi S. K., Yoon S. R., Arnheim N. and Calabrese P. Estimating Exceptionally Rare Germline and Somatic Mutation Frequencies via Next Generation Sequencing. PLoS One. 2016;11:e0158340References:Luks V. L., Kamitaki N., Vivero M. P., et al. Lymphatic and other vascular malformative/overgrowth disorders are caused by somatic mutations in PIK3CA. J Pediatr. 2015;166:1048-1054 e1041-1045Mirzaa G. M., Conti V., Timms A. E., et al. Characterisation of mutations of the phosphoinositide-3-kinase regulatory subunit, PIK3R2, in perisylvian polymicrogyria: a next-generation sequencing study. Lancet Neurol. 2015;14:1182-1195Carlson K. D., Sudmant P. H., Press M. O., Eichler E. E., Shendure J. and Queitsch C. MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals. Genome Res. 2015;25:750-761Carvill G. L., McMahon J. M., Schneider A., et al. Mutations in the GABA Transporter SLC6A1 Cause Epilepsy with Myoclonic-Atonic Seizures. Am J Hum Genet. 2015;96:808-815Kang H. C., Baek S. T., Song S. and Gleeson J. G. Clinical and Genetic Aspects of the Segmental Overgrowth Spectrum Due to Somatic Mutations in PIK3CA. J Pediatr. 2015;167:957-962Weren R. D., Ligtenberg M. J., Kets C. M., et al. A germline homozygous mutation in the base-excision repair gene NTHL1 causes adenomatous polyposis and colorectal cancer. Nat Genet. 2015;47:668-671