Nested Machine Learning Facilitates Increased Sequence Content for Large-Scale Automated High Resolution Melt Genotyping

Scientific Reports
Stephanie I FraleySamuel Yang

Abstract

High Resolution Melt (HRM) is a versatile and rapid post-PCR DNA analysis technique primarily used to differentiate sequence variants among only a few short amplicons. We recently developed a one-vs-one support vector machine algorithm (OVO SVM) that enables the use of HRM for identifying numerous short amplicon sequences automatically and reliably. Herein, we set out to maximize the discriminating power of HRM + SVM for a single genetic locus by testing longer amplicons harboring significantly more sequence information. Using universal primers that amplify the hypervariable bacterial 16 S rRNA gene as a model system, we found that long amplicons yield more complex HRM curve shapes. We developed a novel nested OVO SVM approach to take advantage of this feature and achieved 100% accuracy in the identification of 37 clinically relevant bacteria in Leave-One-Out-Cross-Validation. A subset of organisms were independently tested. Those from pure culture were identified with high accuracy, while those tested directly from clinical blood bottles displayed more technical variability and reduced accuracy. Our findings demonstrate that long sequences can be accurately and automatically profiled by HRM with a novel nested SVM approach and...Continue Reading

References

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Citations

Feb 7, 2017·Scientific Reports·Nadya AndiniSamuel Yang
Apr 3, 2019·Annual Review of Analytical Chemistry·Dong Jin ShinTza-Huei Wang
Apr 17, 2020·Journal of Clinical Microbiology·April AralarStephanie I Fraley
May 27, 2021·Environmental Science and Pollution Research International·Ishnoor KaurIsrat Jahan Bulbul
May 25, 2021·Computer Methods and Programs in Biomedicine·Fatma Ozge Ozkok, Mete Celik

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Methods Mentioned

BETA
genotyping
PCR

Software Mentioned

ClustalOmega
OVO SVM
OVO
OVA LOOCV
BLAST
LOOCV
Bioedit
LAM
SVM

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