Increase the accuracy of DNA sequencing by 1000 times

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Increase the accuracy of DNA sequencing by 1000 times

Increase the accuracy of DNA sequencing by 1000 times, so that rare gene mutations have nowhere to hide.

Detection of mutations from single DNA molecules has crucial applications in many fields, such as finding diagnostic, predictive and prognostic biomarkers of disease, understanding cancer evolution and somatic mosaicism, and studying infectious diseases and aging, among others. However, it is still challenging to implement at present.

Next-generation sequencing (NGS) is capable of enormous sequencing throughput, but it cannot directly sequence double-stranded DNA molecules to identify true mutations on both strands .

Single-molecule sequencing technologies (such as PacBio and nanopore sequencing) can perform overall sequencing of long fragments of DNA molecules to distinguish true mutations on the double strands, but in practical applications, the accuracy and sequencing throughput have yet to be improved.

On April 27, 2023, researchers from the Broad Institute published a research paper entitled: Single duplex DNA sequencing with CODEC detects mutations with high sensitivity in the journal Nature Genetics .

The study developed a new method for next-generation sequencing – CODEC (Concatenating Original Duplex for Error Correction) , which can increase the accuracy of next-generation sequencing by about 1000 times , thus opening up a series of application possibilities, These include detecting cancer-associated genetic mutations in tiny blood samples, monitoring cancer progression during and after treatment, and identifying genetic mutations underlying rare diseases, all at relatively low cost.

Increase the accuracy of DNA sequencing by 1000 times

Professor Viktor Adalsteinsson , corresponding author of the paper , said that the beauty of this method is that it does not revolutionize the way genes are sequenced, so it does not require new instruments or capital investment, it just adds to the existing sample preparation workflow Adding a set of simple steps to , can dramatically improve the accuracy of DNA sequencing.

The Challenges of Gene Sequencing

Next-generation sequencing (NGS) , also known as next-generation sequencing, or high-throughput sequencing, is a sequencing method in which the two single strands that make up the DNA double helix are separated and sequenced individually.

This process is fast, but cannot distinguish DNA mutations from errors introduced by the sequencing itself, which reduces its ability to accurately detect rare genetic mutations.

There is a sample preparation method called duplex sequencing , which can distinguish between true mutations and errors introduced by the sequencing process by labeling single strands of DNA, but this method is very inefficient because it independently analyzes the DNA double strands.

Each single strand of the chain is sequenced. Third-generation sequencing can sequence DNA without separating the double strands to identify rare mutations, but can also be inefficient and inaccurate.

To overcome these limitations, the research team developed a method called CODEC ( Concatenating Original Duplex for Error Correction ) , which uses specially designed adapter sequences to link one strand of the DNA duplex to the reverse complement of the second strand stand up.

These two new strands are then sequenced using next-generation sequencing (NGS) technology. This makes it possible to distinguish between true genetic mutations and errors caused by the sequencing process, and to generate highly accurate sequence data at low cost.

Increase the accuracy of DNA sequencing by 1000 times Overview of CODECs

Gene Mutation Detection

The research team used CODEC to look for mutation frequencies in sperm and age-related mutations in blood cells, as well as mutations in single molecules of DNA in tumors and other patient samples .

CODEC sequencing results showed that the mutation frequency in the sperm of a 39-year-old individual was 2.72× 10 -8 , and somatic mutations in blood cells increased with age.

CODEC detects genome-wide clonal hematopoietic mutations, clonal hematopoietic mutations from a single DNA molecule, single-mutation double-stranded from tumor genomes and liquid biopsies, microsatellite instability, 10-fold improvement in sensitivity and mutational signature, tumor-specific The reads of the mutation were reduced by 100 times.

CODECs enable more precise genetic testing and reveal biologically important genetic mutations that are often masked by errors in next-generation sequencing (NGS) .

Overall, CODEC provided 1000-fold higher sequencing accuracy than next-generation sequencing (NGS) .

Compared with double sequencing, the accuracy of CODEC in distinguishing real gene mutations from errors introduced during the sequencing process was similar, but CODE C The amount of data analysis required is only one-hundredth of that of duplex sequencing , significantly improving efficiency.

It is reported that Viktor Adalsteinsson’s team has applied for a patent for this technology and is further developing methods to improve CODEC efficiency.

He also said that it is very exciting that this technology allows us to see things that were not possible with DNA sequencing before.

Since the method was introduced in a preprint in June 2021, they have been contacted by many researchers wishing to use CODEC.

Paper link :
https://www.nature.com/articles/s41588-023-01376-0

Increase the accuracy of DNA sequencing by 1000 times

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