Low stutter ratio by SuperFi polymerase

Yamanoi, Eisuke; Sakurada, Makoto; Ueno, Yoshio

doi:10.1016/j.fsir.2021.100201

Cited by 5 publications

(2 citation statements)

References 22 publications

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“…A recent study reduced stutter by targeted mutagenesis (Wang et al 2022), but is limited to 'G' homopolymer microsatellites that would not be compatible with the scale of capture we have achieved. Thus, stutter continues to be a challenge despite the improvements we have demonstrated, motivating further research to address it, perhaps by novel polymerases (Yamanoi et al 2021) or accessory proteins during library amplification.…”

Section: Discussionmentioning

confidence: 99%

High-fidelity, Large-scale Targeted Profiling of Microsatellites

Loh,

Shields,

Schwing

et al. 2023

Preprint

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Microsatellites are highly mutable sequences that can serve as markers for relationships among individuals or cells within a population. The accuracy and resolution of reconstructing these relationships depends on the fidelity of microsatellite profiling and the number of microsatellites profiled. However, current methods for targeted profiling of microsatellites incur significant “stutter” artifacts that interfere with accurate genotyping, and sequencing costs preclude whole-genome microsatellite profiling of a large number of samples. We developed a novel method for accurate and cost-effective targeted profiling of a panel of > 150,000 microsatellites per sample, along with a computational tool for designing large-scale microsatellite panels. Our method addresses the greatest challenge for microsatellite profiling — “stutter” artifacts — with a low-temperature hybridization capture that significantly reduces these artifacts. We also developed a computational tool for accurate genotyping of the resulting microsatellite sequencing data that uses an ensemble approach integrating three microsatellite genotyping tools, which we optimize by analysis of de novo microsatellite mutations in human trios. Altogether, our suite of experimental and computational tools enables high-fidelity, large-scale profiling of microsatellites, which may find utility in diverse applications such as lineage tracing, population genetics, ecology, and forensics.

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Section: Discussionmentioning

confidence: 99%

High-fidelity, Large-scale Targeted Profiling of Microsatellites

Loh,

Shields,

Schwing

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Electropherograms generated by CE instruments exhibit both STR alleles and artifacts that complicate data interpretation. Efforts are underway to understand and model instrumental artifacts [ [248] , [249] , [250] , [251] ] as well as biological artifacts of the PCR amplification process such as STR stutter products [ 252 , 253 ]. Machine learning approaches are being applied to classify artifacts versus alleles with the goal to eventually replace manual data interpretation with computer algorithms [ [254] , [255] , [256] , [257] ].…”

Section: Advancements In Current Practicesmentioning

confidence: 99%