Nature Search

Chiral DNA sequences as commutable controls for clinical genomics

Any DNA sequence can be represented by a chiral partner sequence – an exact copy arranged in reverse nucleotide order. Here, the authors show that chiral DNA sequence pairs share important properties and show the utility of synthetic chiral sequences (sequins) as controls for clinical genomics.

Ira W. Deveson
Bindu Swapna Madala
Tim R. Mercer
ResearchOpen Access22 Mar 2019
Nature Communications

Volume: 10, P: 1-13
Chimeric synthetic reference standards enable cross-validation of positive and negative controls in SARS-CoV-2 molecular tests

Bindu Swapna Madala
Andre L. M. Reis
Tim R. Mercer
ResearchOpen Access29 Jan 2021
Scientific Reports

Volume: 11, P: 1-8
A universal molecular control for DNA, mRNA and protein expression

Multi-omics analyses powerfully combine gene expression and translation, however no available controls can be used across these techniques. Here the authors develop pREF, a universal control construct designed for use in DNA, RNA and protein analyses.

Helen M. Gunter
Scott E. Youlten
Tim R. Mercer
ResearchOpen Access20 Mar 2024
Nature Communications

Volume: 15, P: 1-13
Library adaptors with integrated reference controls improve the accuracy and reliability of nanopore sequencing

Adding library adaptors to DNA samples is an essential step in preparing samples for next-generation sequencing. Here, Gunter et al. describe the development of Control Library Adaptors (CAPTORs), that correct sequencing errors and normalise quantitative biases in Nanopore libraries.

Helen M. Gunter
Scott E. Youlten
Tim R. Mercer
ResearchOpen Access28 Oct 2022
Nature Communications

Volume: 13, P: 1-11
Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology

Reliable detection of mutations below 0.5% variant allele frequency remains a key challenge for circulating tumor DNA sequencing assays.

Ira W. Deveson
Binsheng Gong
Joshua Xu
Research12 Apr 2021
Nature Biotechnology

Volume: 39, P: 1115-1128
A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features

Standard units of measurement are required for a quantitative description of the genome. Here, the authors present a universal synthetic DNA ladder that can measure genetic abundance in next-generation sequencing libraries.

Andre L. M. Reis
Ira W. Deveson
Tim R. Mercer
ResearchOpen Access17 Jul 2020
Nature Communications

Volume: 11, P: 1-11
Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

Recommendations are given on optimal read coverage and selection of calling algorithm to maximize the reproducibility of cancer mutation detection in whole-genome or whole-exome sequencing.

Wenming Xiao
Luyao Ren
Leming Shi
Research09 Sept 2021
Nature Biotechnology

Volume: 39, P: 1141-1150
Use of synthetic DNA spike-in controls (sequins) for human genome sequencing

Here, the authors describe the use of synthetic DNA spike-ins, called sequins, as internal quantitative and qualitative controls throughout the sequencing workflow. They detail their application in whole-genome and targeted human genome sequencing.

James Blackburn
Ted Wong
Tim R. Mercer
Protocols19 Jun 2019
Nature Protocols

Volume: 14, P: 2119-2151

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