Since the first complete characterization of the human genome in 2003, understanding of our DNA and how it varies from person to person has become magnitudes better. We use the reference genome to search for disease variants, discover genetic functions, and act as scaffolding to sequence other large pieces of DNA. Mapping the location of our genes within chromosomes is vital to genetics. So it may surprise you to know that our current reference has many gaps.
That is, until now. In an article published by Nature on Wednesday, researchers have reached a major milestone in genetics by producing the first end-to-end (telomere-to-telomere) sequence of the human X chromosome. The researchers sequenced the 155 million base pair X chromosome, even managing to sequence highly repetitive regions that were previously not possible.
The team, led by Karen Miga of the University of California Santa Cruz Institute of Genomics, used a combination of sequencing techniques to complete the chromosome, saying the key to their success was the use of ultra-reactive nanopore sequencing. modern long. Traditional sequencing technology breaks DNA down into many small fragments, before putting them together as the world’s most complicated puzzle. This works for the most part, but if there are DNA fragments that are extremely similar to each other, the sequencing software may have a hard time fitting them in the right place. Some regions of the chromosome are made up of large amounts of repetitive DNA, and researchers in the past have been unable to obtain accurate maps of them.
“These repeat-rich sequences were once considered intractable, but we have now made great strides in sequencing technology,” Miga said in the press release.
The development of ultra long reading nanopore sequencing has since improved. By squeezing the DNA through a small pore and measuring changes in the current through the pore, The technology can read long DNA fragments accurately and with fewer gaps.
“With nanopore sequencing, we get ultra-long readings of hundreds of thousands of base pairs that can span an entire repeating region, so it avoids some of the challenges,” Miga said. However, there were still multiple gaps in the sequence that the team had to manually resolve.
A complete reference genome will now allow researchers to compare patient DNA samples with the reference and identify genetic changes that may contribute to the disease.
“We are beginning to discover that some of these regions where there were gaps in the reference sequence are actually among the richest in variation in human populations, so we have missed a lot of information that could be important in understanding human biology and disease, “said Miga.
The new sequence fixes a number of gaps in the current reference genome called the Genome Reference Consortium build 38 (GRCh38) and will aid in large-scale studies for the future. Meanwhile, Miga and the Telomere-to-Telomere consortium seek to sequence all chromosomes into a specific cell line (CHM13), opening up new opportunities for genetic research and understanding of our genome as a whole.
However, challenges remain in applying these approaches to the rest of the genome. For example, in diploid samples (samples with two copies of each chromosome per cell), it will be difficult to prevent similar regions on each chromosome from interfering with sequencing. The T2T consortium hopes to further develop existing technology to complete the entire genome.
