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The most complete view yet of the human genome has arrived, and it tackles the messy parts scientists used to skip.

The new work assembles nearly all of the repeat-rich, shape-shifting DNA that helps explain disease risk and drug response across different people.

It is not a single tidy sequence, but rather 65 complete genomes drawn from diverse ancestries and resolved with unusual clarity.

That scale and quality move the field toward practical use in precision medicine, where care adjusts to each person’s genetic wiring.

Uncovering DNA’s hidden changes

The hardest regions to read are home to structural variants. These include large insertions, deletions, inversions, duplications, and translocations that often change how genes work.

If you ignore these variants, risk models fall short, and rare disease diagnoses stall. Getting them right is the difference between a vague genetic hint and a confident clinical answer.

The study was co-led by Christine Beck of The Jackson Laboratory and UConn Health, as part of the Human Genome Structural Variation Consortium (HGSVC).

What the genome map shows

Across 130 haplotypes, the team reports closing 92 percent of the assembly gaps that lingered after earlier references and bringing 39 percent of chromosomes to telomere to telomere status.

That level of finish lets researchers track long, tangled stretches end to end instead of guessing across voids.

The experts resolved 1,852 previously intractable complex structural variants that older methods could not untie.

The team also validated 1,246 human centromeres – the control hubs needed for proper chromosome segregation in cell division. These regions long stymied assemblies because of their repeating DNA.

Sequences that rewire gene activity

The team cataloged 12,919 insertions from transposable elements, the mobile sequences that can rewire gene activity – accounting for nearly 10 percent of all structural variation detected here.

This catalog turns what used to be background noise into an interpretable signal for disease studies.

The research provides contiguous sequences for the immune related Major Histocompatibility Complex (MHC), along with other regions that influence digestion and development. Each of those regions matters directly to diagnosis or treatment decisions in clinics.

Representation matters in genetics

For many years, genetic reference data left out large parts of the world’s population. This new study was designed to address that gap by creating a more inclusive and complete resource.

Only recently has technology advanced enough to allow scientists to sequence entire genomes without the large gaps that once limited the field.

Using these tools, researchers estimate they can now capture more than 95 percent of structural variants within each genome they study.

Hard places, practical payoffs

The MHC carries dense immune variation associated with more than 100 human diseases, so fully charting it helps clinicians weigh risk with more nuance across populations.

When the reference is biased or incomplete, those associations skew toward the few ancestries that dominate the data.

The study delivers complete sequences for the following genes: SMN1 and SMN2, which are the drug targets in spinal muscular atrophy. That matters because therapies like nusinersen improve infant survival, and better maps speed diagnosis and treatment eligibility.

The researchers also finished especially stubborn parts of the Y chromosome, building on a 2023 effort that first produced a gapless Y sequence.

Closing and comparing many Ys provides cleaner baselines for fertility research and forensic work that depend on those repeats and palindromes.

Building a global genome map

This breakthrough research stands on two recent pillars. In 2022, the Telomere to Telomere Consortium published the first complete sequence of a single human genome.

This achievement proved that full chromosomes were feasible with the latest approaches.

In 2023, the Human Pangenome Reference expanded representation by assembling 47 individuals from many ancestries – a shift from a one genome yardstick to a family of references that reflect global diversity.

The genome map and health

When reference genomes miss common variations, clinical pipelines struggle. Expanding structural variant catalogs improves read mapping, variant calling, and interpretation.

Ultimately, this strengthens rare disease diagnosis and risk prediction across ancestries.

When a rearrangement sits next to a dosage-sensitive gene or flips an enhancer away from its target, the biological effect can be large, and it can be missed by short-read tools. This study makes those events visible at a scale that finally matches clinical need.

The moving parts of genomes

The new assemblies also clarify how endogenous retroviruses and other transposable elements to contribute regulatory switches.

Recent work shows that long terminal repeats from ancient viruses form distinct subfamilies with their own enhancer motifs. These motifs can rise or fall across primate lineages in ways that influence gene regulation.

At everyday scales, the finished amylase region helps connect gene dosage to diet. People from high starch diet populations tend to carry more copies of salivary amylase – an example of structural variation with clear physiological impact.

What’s next for the genome map

Open methods and shared datasets mean other teams can now reach the same level of completeness. That is essential if the benefits of precision medicine are going to reach everyone, not just those already overrepresented in genetic research.

The muscle, immune, and neurodevelopmental regions that used to be black boxes are now spelled out with far fewer interruptions. This clarity sets a new bar for reference genomes, clinical pipelines, and the science that connects DNA to health outcomes.

The study is published in the journal Nature.

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A key study claiming to provide evidence of Majorana quasiparticles has received an extensive correction five years after it was published in the journal Science. Two researchers who flagged the paper as problematic say that the correction isn’t sufficient — triggering the latest dispute in a field dogged by controversy.

For decades, physicists have been compelled by the idea that ultracold electrons in microscopic devices could behave collectively to form quasiparticles resistant to noise — both environmental perturbations and the inherent atomic jostling that plagues all quantum systems. The resilience of these Majoranas could make them ideal candidates for forming qubits, the informational units in quantum computers that are analogous to bits in classical machines. Studies to prove their existence have come up short, although recent bold claims by technology giant Microsoft have drawn considerable scrutiny.

In September 2018, a team led by Charlie Marcus, a physicist at the University of Copenhagen, who also worked for Microsoft at the time, posted a manuscript to the preprint server arXiv that described a fresh approach to generate Majoranas. The researchers made nanowires of indium arsenide surrounded by a shell of aluminium. Applying a small magnetic field, they then measured electrical signals “consistent” with pairs of Majoranas, one at either end of each wire. A year and a half later, they included theoretical simulations to justify their results, and the study was published in Science.

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Two physicists — Sergey Frolov, at the University of Pittsburgh in Pennsylvania, and Vincent Mourik, now at the Research Centre Jülich in Germany — raised questions about the validity of the data, and in July 2021, Science applied an editorial expression of concern to the paper to warn readers of potential problems. Now, Science is lifting that warning, and the authors are issuing a 20-page correction to the paper’s supplementary material. News of the correction was first reported on 31 July by the technology news site The Register.

The authors say they are relieved by the outcome. “It’s not really correcting any errors,” says co-author Saulius Vaitiekėnas, a physicist at the University of Copenhagen. “We are summarizing and providing additional information.” Frolov, on the other hand, argues that the data in the paper do not give a full picture of electron behaviour in the team’s devices and calls for retraction. “I do not trust this data,” he says.

Jake Yeston, an editor at Science who oversees physical-sciences submissions, says that the journal decided not to retract the paper because there was not a “clear, community-grounded view that it’s obviously wrong”. But, Yeston says, the lack of information in the original paper was a problem, and it has now been fixed. “It shouldn’t be that a reader who wants to know what your protocol was has to go to your lab and talk to you,” he says. “That should be in the paper.”

Questioning the data

Thirteen years ago, Frolov and Mourik were authors on a different study in Science that reported evidence for Majoranas. But excitement around the result faded after researchers discovered that other mundane phenomena could mimic the quasiparticles.

When the Copenhagen team’s manuscript was posted to arXiv in 2018, Frolov and Mourik were dubious so they requested to see all of the data. E-mails reviewed by Nature show that the Copenhagen group released more data in November 2020. The pair of critics analysed the information provided and concluded that the data were incomplete and contradicted the study’s central claims. An internal inquiry by the university’s physics institute, however, found “no problems with the paper”, and that the Copenhagen team had turned over all of its data. Unsatisfied, editors at Science applied an expression of concern to the paper, and in October 2021, Yeston filed a complaint with the university to request an “independent, transparent investigation by experts.”

In June 2022, the university assembled a panel of independent physicists to undertake the effort: Sophie Guéron, at the University of Paris-Saclay; Allan MacDonald, at the University of Texas at Austin; and Pertti Hakonen, at Aalto University in Finland. They travelled to Copenhagen, conducted interviews and examined data from 60 microscopic devices (the original paper included data from 4). Their year-long investigation found no misconduct, but stated that the team’s selection of data led to “conclusions that did not adequately capture the variability of outcomes”. The excluded data, however, did not undermine the paper’s main conclusions, they said.

One sticking point for Frolov and Mourik continues to be the Copenhagen team’s choice of ‘tunnelling regime’ — the range of low electrical conductivities over which the devices were scanned. The Copenhagen researchers said they saw signs of Majoranas persisting “throughout” their chosen tunnelling regime. But Frolov and Mourik said that the extra data they received showed that the tunnelling regime was much wider, and that the telltale Majorana signs were limited to the smaller tunnelling window.

Marcus responds that his team first chose a narrow tunnelling regime to avoid noise, then looked for signs of Majoranas. The investigation panel agreed that the criteria for a tunnelling regime made “physical sense”, but said that including all the voltages would have “given a clearer, more faithful, picture of the complex behavior”. The correction includes a lengthy description of the tunnelling regime. “They just have to be transparent,” Guéron says.

MacDonald agrees, and hopes that the correction will lead to better standards for data availability.

Still searching

No group has replicated the Copenhagen team’s results, although researchers at the Institute of Science and Technology Austria (ISTA) in Klosterneuburg have studied similar nanowires. In papers published in Science and Nature, they described finding quasiparticles with electrical signals resembling those of Majoranas; however, in the end, the particles were found to be mundane and lacking the desired resilience to noise. (Nature’s news team is independent of its journal team.)

Marcus contends that the ISTA study was not an identical replication of the Copenhagen study, because, for example, it relied on a different chemical to prepare the nanowires. He says that his team would be happy to provide wires for another group to attempt a replication, but so far there have been no takers.

Much of the uncertainty around the Copenhagen group’s work stems from the messy underlying physical world: disorder from even the smallest imperfection can destroy delicate quantum states and make data selection challenging. “At present this is a fact of life for all experimental searches for Majorana particles,” the independent panel wrote in its report. “It is important that authors guard themselves against confirmation bias.”

Many researchers — with the exception of some at Microsoft — have responded to this by moving on from searches for bona-fide Majoranas to looking for phenomena that are less exotic and more stable. Marcus thinks his approach is better than the alternatives, but even he acknowledges the situation: “It would be perfectly realistic to conclude based on all of the work that people have done that even though this is beautiful physics and completely correct, as far as I’m concerned, it doesn’t really reflect a path forward in designing quantum computers, because it’s just too fragile.”

This article is reproduced with permission and was first published on August 14, 2025.

Researchers in the United States have demonstrated a new optical technology that provides the sensitivity needed to detect the vibrational motion of atoms bound within molecules (Sci. Adv., doi: 10.1126/sciadv.ady7670). The robust and accurate technique operates at room temperature, potentially providing a powerful new tool for detecting disease, monitoring industrial processes and measuring trace amounts of pollutants or hazardous compounds.

Enhancing spectral signals

Optical techniques such as Raman and infrared spectroscopy are already used to detect molecular vibrations, with the movement of atoms between quantized vibrational modes providing specific information about the structure and behavior of molecules. However, these passive measurement methods rely on extremely faint signals that can be difficult to isolate in the recorded spectra, which limits their use in many real-world conditions.

The research team, led by Ishan Barman at Johns Hopkins University, sought to devise a new solution that actively enhances and manipulates the signals generated by molecular vibrations. “Rather than trying to incrementally improve conventional methods, we asked whether we could re-engineer the very way light interacts with matter to create a fundamentally new kind of sensing,” Barman commented.

Their idea was to enclose an ensemble of the target molecules within an optical cavity formed by a pair of gold mirrors. Strong interactions are then generated between one of the cavity modes and a specific vibrational transition, which in turn created hybrid light–matter states that produce distinct peaks in the spectral response.

Numerical simulations by the team show how the presence of the molecules splits the single cavity mode into a pair of hybridized quantum states, which the researchers call “vibro-polaritons.”

Emerged hybrid states

Numerical simulations by the team show how the presence of the molecules splits the single cavity mode into a pair of hybridized quantum states, which the researchers call “vibro-polaritons.” Experiments confirmed the emergence of these hybrid states when a thin polymer film was enclosed within the cavity and when molecules in solution were injected into a cavity that had been fabricated within a microfluidic flow cell.

The researchers also demonstrated that the formation of hybrid states could be used as an indicator of molecular concentration. While the transmission spectra at low concentrations are dominated by the normal cavity modes, the coupling at higher concentrations becomes strong enough to create hybrid states that can be detected in the spectral response.

The transition to this stronger coupling regime occurs at concentrations some three times lower than is needed to detect the same molecular signal using conventional infrared spectroscopy, demonstrating the practical utility of the technique. Even so, the concentrations used in this proof-of-concept study are higher than those typically encountered in molecular sensing. Theoretical analysis suggests that the detection limit of the technique could be significantly reduced, which Barman and colleagues believe could be achieved by optimizing the design of the optical cavity.

Article Content

Polaritons are formed by the strong coupling of light and matter. When they mix together, all the matter is excited simultaneously – referred to as delocalization. This delocalization has the unique ability to relay energy between matter that is otherwise not possible.

Disordered energy is ubiquitous in nature and the universe. Disordered energy is less organized and less available to do work, such as with heat dissipation. Even in plants, disorder can ruin effective energy transfer. In the context of polaritons,  as disorder increases, it can negatively affect light-matter interactions, including polariton-enabled energy transfers. Overcoming this disorder is an important topic across many scientific fields. 

In a new study, researchers from UC San Diego designed experiments to show how disordered energy can limit the energy transfer pathway, and further demonstrated a strategy to overcome this limitation.

This work establishes a new theoretical criteria beyond which polariton formation can retain its coherent delocalization – a feature that can influence the properties of matter to control chemical reactions, with potential applications in energy technology and photonic engineering.