Nat Biotech: Same-day identification of pathogenic variants with ultrafast nanopore sequencing in just 8 hours

A team of researchers led by Stanford University recently demonstrated the value of rapid whole-genome sequencing in the diagnosis of critical illness

The researchers developed the process based on Oxford Nanopore's high-throughput sequencing device PromethION 48, combined with an optimized sample preparation scheme, parallel sequencing on 48 sequencing chips, and rapid data analysis, which is expected to help doctors quickly diagnose critically ill patients.

This time, 12 critically ill patients, ranging in age from 3 months to 57 years old, participated in the study.

The ultra-fast sequencing and analysis pipeline was completed in one day for all participants, and the causative genetic variant was identified in five patients

Ultra-fast sequencing workflow

Whole-genome sequencing has advantages in medical diagnosis, but the pipeline for sequencing and downstream analysis is often slow

To this end, Ashley-led research teams have developed a genome-wide nanopore sequencing pipeline that improves library preparation, uses a cloud-based module for near real-time base calling and alignment, and enables rapid variant calling (including SNPs) , indel and SV) and focused variant filtering

The researchers used Oxford Nanopore's high-throughput sequencing device PromethION 48 to carry out whole-genome sequencing

They found that calling performance for small variants was similar regardless of whether barcodes were used, and similar results were observed for structural variants

At the same time, sequencing speed did not affect the accuracy of variant calling

The research team tackled the data analysis problem by developing a cloud computing architecture (Google Cloud Platform) and parallel base calling and alignment across multiple GPUs (NVIDIA GPUs)

Application in clinical setting

To illustrate how the procedure performs in a real-world setting, the researchers specifically discussed two patients

The researchers completed variant calling in less than 7 hours and found 4.

The second patient, a 14-month-old baby girl with dystonic posture and developmental delay, was admitted to the Pediatric Intensive Care Unit after experiencing cardiac arrest and respiratory failure

For this case, the time to acquire 200 Gb of sequencing data was 2 hours and 46 minutes

"We are delighted to see the publication of this pivotal work and demonstrate the potential impact of ultrafast nanopore sequencing in critically ill patients

"Using whole genome sequencing to rapidly diagnose critically ill patients is challenging, but we have a solution," study participant Dr.

The cost of this ultra-fast method, which includes DNA extraction, library preparation, sequencing, and data analysis, is estimated to be just over $5,000, including $1,600 for the flow chip, $1,584 for the nanopore sequencing reagents, and $568 for the analysis
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Oxford Nanopore expects these costs to drop significantly as sample preparation, computing and sequencing chips improve
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Original text retrieval

Goenka, SD, Gorzynski, JE, Shafin, K.
et al.
Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing.
Nat Biotechnol (2022).
https://doi.
org/10.
1038/s41587-022- 01221-5