Scientists have set a new milestone by completely sequencing a human chromosome
For the first time, a group of scientists has managed to completely sequence a whole human chromosome, bridging all the gaps over the years.
Back in 2003, scientists made headlines around the world stating that the human genome was complete. When deciphered, it was noticed that there were some parts of the sequences missing known as gaps.
One of the reasons for these gaps is due to the inability of DNA sequencing machines to read genomes like how a human reads books. Instead, they first break all the 23 pairs of chromosomes, leading to billions of letters, overwhelming the machine. The broken pieces tend to overlap making it impossible to read.
Now for the first time, scientists have bridged the gaps, giving the first complete look of a human chromosome. This accomplishment was due to the result of nanopore sequencing.
Nanopore sequencing is an advanced fourth-generation DNA sequencing. Some significant advantages of nanopores include ultra-long reads, label-free, and, high throughput results.
Using nanopore sequencing, a single strand of chromosome can be completely sequenced without the need of Polymerase chain reaction (PCR). This particular technology can offer a relatively low cost genotyping and rapid processing of samples on a real-time basis.
This technology is in contrast to previously available techniques which could only read short sections one at a time. This makes it very difficult for researchers who have to piece the gaps like a puzzle. Though in most of the cases it was successful, it was tricky to patch the minute gaps.
What did the study reveal?
By reading the whole sequence, the results reveal that the gap regions in the X chromosome sequence are one of the richest regions for variation in human populations. For so many years, the field has been missing out on a lot of information that could have led to a better understanding of human biology and diseases.
The nanopore sequencing used, consists of a nanopore protein set up in an electrically resistant membrane. When current is passed through the nanopore, it is fed with the necessary genetic material which translates into a genetic sequence.
This process was previously used by biologist Miga and the team for studying DNA obtained from a rare benign tumor.
“We used an iterative process over three different sequencing platforms to polish the sequence and reach a high level of accuracy,” Miga said. “The unique markers provide an anchoring system for the ultra-long reads, and once you anchor the reads, you can use multiple data sets to call each base.”
Even with these advanced technologies, there still remained minute gaps.- most obviously in the centromere. The centromere is the structure that connects the chromatids, later into which a chromosome divides.
The gaps were resolved by looking at the results from the sequencing. It was revealed that there were slight variations in the repeats which helped the researchers to align and connect the long reads into a complete sequence for the centromere.
A major breakthrough:
“For me, the idea that we can put together a 3-megabase-size tandem repeat is just mind-blowing,” Miga said. “We can now reach these repeat regions covering millions of bases that were previously thought intractable.”
This new advancement by the scientific team has led to bridging over 29 gaps in the X chromosome reference. This a major step forward for completing the while human genome mapping. This will also help in bridging the gap and complete the sequencing of the remaining chromosomes.