Related Experiment Video
Updated: Aug 10, 2026
10:00
An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
Published on: May 23, 2018
Long-read, high-throughput sequencing of 10,000 human mitogenomes using the PacBio Sequel IIe
Mitchell M Holland1, Jennifer A McElhoe1, Charity A Holland1
1Forensic Science Program, Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA.
Forensic Science International. Genetics
|August 8, 2026
Summary
A new, cost-effective sequencing pipeline for human mitochondrial genomes (mitogenomes) enables high-throughput data generation for forensic and anthropological databases like EMPOP. This robust method achieves a high success rate, improving forensic investigations.
Area of Science:
- Genomics
- Forensic Science
- Molecular Anthropology
Background:
- Human mitochondrial genome (mitogenome) sequencing is crucial for molecular anthropology, medical research, and forensic science.
- Accurate mitogenome data is essential for forensic investigations, particularly for estimating coincidental match probabilities in haplotype databases.
- The European DNA Profiling group (EDNAP) Mitochondrial DNA Population database (EMPOP) is the gold standard for mitogenome data, serving as a reference and quality-control tool.
Purpose of the Study:
- To develop a user-friendly, robust, and cost-effective sequencing pipeline for human mitogenomes.
- To facilitate the generation of high-quality mitogenome sequences for upload to the EMPOP database.
- To enable high-throughput studies for creating large mitogenome databases.
Main Methods:
- Whole blood or buffy coat samples were processed.
- Mitogenomes were amplified using two overlapping long-range amplicons (approx. 8.5 kb).
- PacBio Sequel IIe instrument with a high-fidelity (HiFi) approach was used for sequencing after library preparation with SMRT bells.
Main Results:
- The pipeline processed 384 samples in up to 62 working hours.
- The cost was approximately $20 USD per sample for reagents and supplies, and $30 USD including labor.
- A success rate of ~98.2% was achieved for 10,394 total samples, with a per-amplicon success rate of ~99.2%.
Conclusions:
- The developed long-read sequencing pipeline is user-friendly, robust, and cost-effective.
- The pipeline successfully generates high-quality mitogenome data suitable for upload to EMPOP.
- This method is suitable for high-throughput studies aiming to build large, reliable mitogenome databases for forensic and anthropological applications.
Related Concept Videos
03:00Next-generation Sequencing
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.
03:21RNA-seq
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 microarray-based...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
01:05Maxam-Gilbert Sequencing
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...
01:57Sanger Sequencing
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...
02:02Genomics
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...