Related Experiment Video
Updated: Jan 15, 2026
10:34
Ultra-long Read Sequencing for Whole Genomic DNA Analysis
Published on: March 15, 2019
23.9K
Scalable long-read nanopore HPV16 amplicon-based whole-genome sequencing
Maina K Titus1, David Giesbrecht1, Cliff I Oduor1
1Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, 02912, USA.
Scientific Reports
|October 7, 2025
Summary
We developed a portable whole genome sequencing method to analyze human papillomavirus 16 (HPV16) genetic diversity in sub-Saharan Africa. This approach aids in understanding HPV16
Area of Science:
- Genomics
- Virology
- Public Health
Background:
- Human papillomavirus 16 (HPV16) is a primary driver of cervical cancer (CC).
- Genetic variations in HPV16 are linked to CC risk.
- Sub-Saharan Africa faces a high burden of HPV-related diseases.
Purpose of the Study:
- To develop an affordable and portable amplicon-based whole genome sequencing (WGS) method for HPV16.
- To investigate HPV16 genetic diversity in sub-Saharan Africa.
- To establish a robust pipeline for HPV16 surveillance and diagnostics in low-resource settings.
Main Methods:
- Utilized Oxford Nanopore Technologies for long-read WGS.
- Applied an amplicon-based approach to HPV16 genomes.
- Benchmarked variant calling pipelines (Clair3, PEPPER-Margin DeepVariant) and performed phylogenetic analysis.
Main Results:
- Generated complete HPV16 genomes with high coverage from clinical samples.
- Identified all four major HPV16 lineages (A-D) and their sublineages.
- Demonstrated high accuracy and concordance across different analytical approaches, capturing genomic variation effectively.
Conclusions:
- The developed WGS method is accurate, affordable, and portable for HPV16 analysis.
- This approach is suitable for integration into public health surveillance and diagnostics in low-resource regions.
- Facilitates a deeper understanding of HPV16 genetic diversity and its implications for cervical cancer prevention.
Related Concept Videos
03:00Next-generation Sequencing
97.7K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
97.7K
01:57Sanger Sequencing
773.2K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
773.2K
03:21RNA-seq
11.7K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
11.7K
01:05Maxam-Gilbert Sequencing
12.6K
In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
Challenges of the Maxam-Gilbert Method
The...
12.6K