English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Tools annual

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools monthly

Global: Zendy Plus monthly

Presents the access of premium content as premium feature

Premium Content

Global: Zendy Plus annual

Global: Zendy Free Plan

Detection of extremely rare variant alleles, such as tumour DNA, within acomplex mixture of DNA molecules is experimentally challenging due tosequencing errors. Barcoding of target DNA molecules in library constructionfor next-generation sequencing provides a way to identify and bioinformaticallyremove polymerase induced errors. During the barcoding procedure involving $t$consecutive PCR cycles, the DNA molecules become barcoded by unique molecularidentifiers (UMI). Different library construction protocols utilise differentvalues of $t$. The effect of a larger $t$ and imperfect PCR amplifications ispoorly described.  This paper proposes a branching process with growing immigration as a modeldescribing the random outcome of $t$ cycles of PCR barcoding. Our modeldiscriminates between five different amplification rates $r_1$, $r_2$, $r_3$,$r_4$, $r$ for different types of molecules associated with the PCR barcodingprocedure. We study this model by focussing on $C_t$, the number of clusters ofmolecules sharing the same UMI, as well as $C_t(m)$, the number of UMI clustersof size $m$. Our main finding is a remarkable asymptotic pattern valid formoderately large $t$. It turns out that $E(C_t(m))/E(C_t)\approx 2^{-m}$ for$m=1,2,\ldots$, regardless of the underlying parameters $(r_1,r_2,r_3,r_4,r)$.The knowledge of the quantities $C_t$ and $C_t(m)$ as functions of theexperimental parameters $t$ and $(r_1,r_2,r_3,r_4,r)$ will help the users todraw more adequate conclusions from the outcomes of different sequencingprotocols.

Counting unique molecular identifiers in sequencing using a multitype branching process with immigration