A new nanopore technology for direct sequencing of long strands of DNA has resulted in the most complete human genome ever assembled with a single technology, scientists have revealed.
The research, published today in Nature Biotechnology, involved scientists the Universities of Birmingham, Nottingham, East Anglia, California, Salt Lake City, British Columbia and Toronto, as well as NIH’s National Human Genome Research Institute.
Using an emerging technology – a pocket sized, portable DNA sequencer - the scientists sequenced a complete human genome, in fragments hundreds of times larger than usual, enabling new biological insights.
The authors generated a new method for sequencing “ultra-long” sequences of DNA, more than a thousand times longer than the original reads used to generate the human genome reference sequence in 2001.
The authors have used this method to generate the longest ever read sequenced at 1,204,840 bases in length, 8,000 times longer than a typical sequencing read. Scaling the sequencing pore to the size of an adult fist, this is the equivalent to analysing a 3.85 km (2.4 mile) long rope.
This drastically reduces the complexity of piecing together the genome compared to previous techniques. The authors speculate that these reads and longer ones can be generated routinely in future, enabling human genomes as complete as the reference genome which was the subject of over 20 years of labour and more than $2bn of investment.
As well as sequencing previously uncharacterised regions of the genome, the new analysis provided greater insight into regions of the genome that are responsible for functions such as immunity and tumour growth. This in turn may have a profound impact on clinical practice, for example, detecting large genome rearrangements important in the development of cancer and in determining a person’s inherited repertoire or antibody genes.
The ability to sequence using a portable device that only costs $1,000 may put also personalised genome sequencing into the mainstream.
Professor Nick Loman, of the Institute of Microbiology and Infection at the University of Birmingham, said: “Until even just a year ago, it would have been impractically difficult to sequence a whole human genome, but thanks to recent advances and innovations such as nanopore technology we now have the ability to sequence very long fragments of the genome.
“If you imagine the process of assembling a genome together is like piecing together a jigsaw puzzle, the ability to produce extremely long sequencing reads is like finding very large pieces of the puzzle which makes the process far less complex.
“One of the most important findings of this research was that, even though the human genome reference was completed or thought to have been completed a while ago, it still contains many missing pieces and we were able to close some of those gaps in the sequence by developing a new method for developing these extremely long reads using nanopore sequencing.”
Dr Andrew Beggs, of the University of Birmingham’s Institute of Cancer and Genomic Sciences, said: “The human genome is the body’s code that tells the body how to grow and develop and all the instructions in it are similar between people, but when the instructions go wrong that’s when disease develops.
“About 20 years ago, sequencing was a very difficult task which required huge machinery and took a very long time. With the nanopore system we could rapidly get a diagnosis for cancer based on the changes in the patient’s genetic code, within 24 hours, which is something that in the past used to take days or even weeks.
“Thanks to advances using the nanopore system, I think in five to ten years we’ll be at the stage where genetic sequencing will be as ubiquitous as boiling a kettle or making a cup of tea. It will be available to us all and will lead to so-called ‘home brewed genetics’, where people will be able to take it into their own power to sequence their own genome.”
Dr Matt Loose, of the University of Nottingham’s School of Life Sciences, said: “This is a landmark for genomics – the long reads that are possible with nanopore sequencing will provide us with a much clearer picture of the overall structure and organisation of the genome than ever before.”
The study uncovered new information about the major histocompatibility complex, a region of the genome used for tissue typing before a transplant and to help scientists understand immunity. The area is particularly difficult to analyse as it contains many duplicated regions including gene families and repeated sequences. No two individuals – apart from identical twins – have the same sequence in this region in their genome.
The researchers used the ultra-long sequences generated in the project to determine the lengths of individual telomeres for the first time directly from the sequenced data.
Telomeres are the caps at the ends of each DNA strand which protect our chromosomes and play an important role in how our cells age. The older a cell, the shorter the telomeres and the disruption in the pattern of the telomeres DNA is also a significant issue found in many tumours. These regions are also difficult to study because they are highly repetitive, often appearing identical.
The international research effort used the Oxford Nanopore Technologies MinION sequencer. The sequencer, approximately the size of a mobile phone, sequences the DNA by detecting the change in current flow as single molecules of DNA pass through a nanopore – or tiny hole – in a membrane.
The MinION sequencer was developed in collaboration with Professor Loman and his PhD student Josh Quick, and the scientists recently used the technology in separate research in the field in Africa and the US to trace the spread of infectious diseases Ebola and the Zika virus. Quick, who was also involved in this latest research, was instrumental in developing the new long read method.
He said: “I had the idea of simply overloading the instrument with massive amounts of micrograms of DNA and using a technique to reduce the amount of fragmentation of these molecules. By loading those sequencing libraries into the instrument we were able to get long reads.”
To interview Professor Nick Loman, contact Emma McKinney, Communications Manager (Health Sciences), University of Birmingham call 0121 414 6681.
- Jain et al (2018). ‘Nanopore sequencing and assembly of a human genome with ultra-long reads’. Nature Biotechnology.
- The University of Birmingham is ranked amongst the world’s top 100 institutions. Its work brings people from across the world to Birmingham, including researchers, teachers and more than 5,000 international students from over 150 countries.
- The paper can be found here.
- It is estimated that 8 per cent of the human genome remains unsequenced at this time (Miga et al Nucleic Acids Research 43(20) e133).
- In 2001, the first drafts of the human genome were released, marking a significant breakthrough in the genomics healthcare revolution. However, although declared complete in 2003, it still contains over 700 gaps that have not yet been sequenced.
- In this study, researchers used a portable, biological nanopore sequencer to sequence and assemble the GM12878 human cell line genome, producing 91.2 Gb of sequence data. Using ultra-long reads of up to 882 kb each, they were able to analyze regions of the human genome that were previously intractable with state-of-the-art sequencing methods. This included detecting structural variants and epigenetic modifications in the genome, as well as closing 12 gaps in the human reference genome, GRCh38, thereby improving its accuracy.
- The study was partially supported by the Wellcome Trust, Cancer Research, the MRC, the MRC Fellowship in Microbial Bioinformatics as part of CLIMB and the NIHR Surgical Reconstruction and Microbiology Research Centre (SRMRC).