Short Tandem Repeat stutter model inferred from direct measurement of in vitro stutter noise

BioRxiv : the Preprint Server for Biology
Ofir RazEhud Shapiro

Abstract

Short tandem repeats (STRs) are polymorphic genomic loci valuable for various applications such as research, diagnostics and forensics. However, their polymorphic nature also introduces noise during in vitro amplification, making them difficult to analyze. Although it is possible to overcome stutter noise by using amplification-free library preparation, such protocols are presently incompatible with single cell analysis and with targeted-enrichment protocols. To address this challenge, we have designed a method for direct measurement of in vitro noise. Using a synthetic STR sequencing library, we have calibrated a Markov model for the prediction of stutter patterns at any amplification cycle. By employing this model, we have managed to genotype accurately cases of severe amplification bias, and biallelic STR signals, and validated our model for several high-fidelity PCR enzymes. Finally, we compared this model in the context of a naive STR genotyping strategy against the state-of-the-art on a benchmark of single cells, demonstrating superior accuracy.

Related Concepts

Clinical Protocols
Forensic Medicine
Polymerase Chain Reaction
Research
Patterns
Bowel Preparation
Genetic Loci
Gene Polymorphism
DNA Amplification
Analysis

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