This new human genome has almost no gaps
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This new human genome has almost no gaps
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Genomics
This new human genome has almost no gaps
Researchers have assembled the first telomere-to-telomere, diploid phased genome from a single human cell line
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Max Barnhart
August 6, 2026
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Twenty-three pairs of black and white chromosomes of varying lengths, with numbers or an X below each pair, displayed on a white background.
The 23 chromosome pairs in a person with XX sex chromosomes.
Credit: Shutterstock
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When the completion of the Human Genome Project was announced on June 26, 2000, scientists had managed to sequence and assemble about 92% of the human genome. The reason the earliest drafts were incomplete was because highly repetitive sequences, such as those found in centromeres and telomeres, were difficult to assemble with short reads.
Over 20 years later, thanks to the advent of long-read sequencing, scientists were able to fill in all the gaps (Science 2022, DOI: 10.1126/science.abj6987). And now, that same group of scientists has taken it one step further and assembled the first complete, telomere-to-telomere phased diploid genome from a single cell line (Cell 2026, DOI: 10.1016/j.cell.2026.06.016)
The work was led by Adam Phillippy, a genomicist at Johns Hopkins University and the US National Institutes of Health National Human Genome Research Institute.
Phillippy says the genome that his group previously released, called CHM13, was based on an unusual cell type where both chromosomes in a pair are nearly identical. But humans have two distinct sets of chromosomes, one from each genetic parent.
Previous assembly methods just “smash everything together,” Phillippy says. So assembling each chromosome in a pair individually was the real challenge.
The new genome is based on the HG002 cell line, and it’s the standard human genome reference material used by the US National Institute of Standards and Technology Genome in a Bottle consortium.
Phillippy and colleagues used long-read PacBio and Oxford Nanopore sequencing, along with Hi-C sequencing, which helps determine where DNA sequences are in proximity to each other.
“We had the first draft of it actually completed around the same time that CHM13 was finished, maybe even as early as kind of the fall of 2022, but we really spent the next number of years trying to make it as perfect and complete as possible so that it could be used as a benchmark,” Phillippy says.
In addition to creating a benchmark reference, the team has also created an analysis pipeline that should make sequencing and assembling an individual’s complete genome much easier.
“The ultimate vision is that, within say 5 years, this is something that we could routinely do in the clinic for a rare-disease patient,” Phillippy says. That could help detect causes of genetic disease that lie in highly repetitive regions, such as the region containing genes associated with spinal muscular atrophy. The cost of sequencing for such an assembly is only about $10,000, Phillippy adds.
The technique has also been used to sequence the genomes of other organisms, including the common marmoset and zebra finch. Those animals’ genomes are being published alongside the paper describing the new human genome (Cell 2026, DOI: 10.1016/j.cell.2026.07.017 and 10.1016/j.cell.2026.07.018).
But Phillippy admits that the new human genome isn’t 100% perfect, just very close. “We really are down to the order of 100 or more suspicious regions left in the genome,” he says. That includes, for example, regions of the genome containing ribosomal DNA, which contain tandem arrays of nearly identical, several-kilobase-long units.
Still, Phillippy argues that for clinical use, it’s likely not worth the effort to resolve those final missing pieces. “I think we've basically reached perfection when it comes to a single genome,” he says.
Max Barnhart is an assistant editor and life sciences reporter at C&EN.
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https://doi.org/10.47287/cen.564450.newsarticle
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Copyright ©<br>2026 American Chemical Society
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This new human genome has almost no gaps
Researchers have assembled the first telomere-to-telomere, diploid phased genome from a single human cell line
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