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Human Genome Reboot Better Reflects Global Population

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WASHINGTON, May 10 (Reuters) – Scientists on Wednesday unveiled a new accounting of the human genome that improves on its predecessor by including a rich diversity of people to better reflect the global population – a boost to ongoing efforts to identify genetic underpinnings of diseases and new ways to treat them.

This “pangenome” achievement was announced two decades after the first sequencing of the human genome, a feat that transformed biomedical research by giving scientists a reference map to analyze DNA for clues about disease-related mutations.

The new genome rundown may help clarify the contribution of genetic variation to health and disease, improve genetic testing, and guide drug discovery. It could be of particular value in understanding neurodevelopmental disorders such as schizophrenia, autism, macrocephaly, and microcephaly, as well as drug metabolism.

The work, led by the international Human Pangenome Reference Consortium of scientists funded by the U.S. government’s National Human Genome Research Institute (NHGRI), essentially was a reboot of the prior effort and solved a key deficiency – a failure to represent the genetic variations present among the world’s 8 billion people.

The previous work had significant gaps and was based largely on a single person’s DNA. The new work is a collection of nearly perfect genome assemblies for 47 people of diverse ancestries and an alignment of those individual genomes to show which parts match and which differ. Calling this a first draft, the researchers intend to increase the number of people reflected in the data to 350 by mid-2024.

“A pangenome is not just one reference genome, but a whole collection of diverse genomes. By comparing those genomes we can then build a map of not just one individual, but a whole population of variation,” said University of California, Santa Cruz genomicist Benedict Paten, co-leader of the consortium and senior author of the main research paper published in the journal Nature.

This collection comprised genomes of people including those of African, East Asian, South Asian, European, North American, South American, and Caribbean ancestry, though not yet Oceania.

“Bottom line – what we’re doing is retooling genomics to create a diverse, inclusive representation of human variation as the fundamental reference structure, and so mitigating bias. This is important if we want our research to benefit everyone equally,” Paten said.

A genome is an organism’s genetic blueprint – in this case a human – and contains the information needed for development and growth. But each person’s genome varies slightly – about 0.4% on average – from other people. These genetic differences can shed light on a person’s health, help diagnose disease, craft treatments and forecast medical outcomes.

“By building very high quality, almost complete references we’re getting a better picture for how some of the most complex regions of the genome vary. Until now, the composition of these fast-evolving regions has been largely invisible to us,” Paten said.

Researchers in 2003 unveiled what was billed as the complete sequence of the human genome, though about 8% of it had not been fully deciphered. That reference genome was a mosaic drawn from about 20 people, including 70% from one individual of mixed European and African ancestry. The first complete human genome, based on a single European individual, was published last year after scientists filled in the gaps.

Our species Homo sapiens arose in Africa roughly 300,000 years ago and later spread worldwide.

“Human ancestry is incredibly complex, and we’re all related to each other through our common history,” said Ira Hall, director of the Yale Center for Genomic Health and one of the research leaders. “And so by sampling broadly across the genetic tree of humanity, it benefits everybody. Even if some specific group isn’t explicitly included, it still is representing our common origins and provides common benefits.”

The cost of supporting the consortium will be about $40 million over five years, NHGRI said, less than the multibillion-dollar expenditure for the 2003 genome project thanks to technological advances.

Reporting by Will Dunham, Editing by Rosalba O’Brien

 

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The body of a Ugandan Olympic athlete who was set on fire by her partner is received by family

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NAIROBI, Kenya (AP) — The body of Ugandan Olympic athlete Rebecca Cheptegei — who died after being set on fire by her partner in Kenya — was received Friday by family and anti-femicide crusaders, ahead of her burial a day later.

Cheptegei’s family met with dozens of activists Friday who had marched to the Moi Teaching and Referral Hospital’s morgue in the western city of Eldoret while chanting anti-femicide slogans.

She is the fourth female athlete to have been killed by her partner in Kenya in yet another case of gender-based violence in recent years.

Viola Cheptoo, the founder of Tirop Angels – an organization that was formed in honor of athlete Agnes Tirop, who was stabbed to death in 2021, said stakeholders need to ensure this is the last death of an athlete due to gender-based violence.

“We are here to say that enough is enough, we are tired of burying our sisters due to GBV,” she said.

It was a somber mood at the morgue as athletes and family members viewed Cheptegei’s body which sustained 80% of burns after she was doused with gasoline by her partner Dickson Ndiema. Ndiema sustained 30% burns on his body and later succumbed.

Ndiema and Cheptegei were said to have quarreled over a piece of land that the athlete bought in Kenya, according to a report filed by the local chief.

Cheptegei competed in the women’s marathon at the Paris Olympics less than a month before the attack. She finished in 44th place.

Cheptegei’s father, Joseph, said that the body will make a brief stop at their home in the Endebess area before proceeding to Bukwo in eastern Uganda for a night vigil and burial on Saturday.

“We are in the final part of giving my daughter the last respect,” a visibly distraught Joseph said.

He told reporters last week that Ndiema was stalking and threatening Cheptegei and the family had informed police.

Kenya’s high rates of violence against women have prompted marches by ordinary citizens in towns and cities this year.

Four in 10 women or an estimated 41% of dating or married Kenyan women have experienced physical or sexual violence perpetrated by their current or most recent partner, according to the Kenya Demographic and Health Survey 2022.

The Canadian Press. All rights reserved.

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The ancient jar smashed by a 4-year-old is back on display at an Israeli museum after repair

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TEL AVIV, Israel (AP) — A rare Bronze-Era jar accidentally smashed by a 4-year-old visiting a museum was back on display Wednesday after restoration experts were able to carefully piece the artifact back together.

Last month, a family from northern Israel was visiting the museum when their youngest son tipped over the jar, which smashed into pieces.

Alex Geller, the boy’s father, said his son — the youngest of three — is exceptionally curious, and that the moment he heard the crash, “please let that not be my child” was the first thought that raced through his head.

The jar has been on display at the Hecht Museum in Haifa for 35 years. It was one of the only containers of its size and from that period still complete when it was discovered.

The Bronze Age jar is one of many artifacts exhibited out in the open, part of the Hecht Museum’s vision of letting visitors explore history without glass barriers, said Inbal Rivlin, the director of the museum, which is associated with Haifa University in northern Israel.

It was likely used to hold wine or oil, and dates back to between 2200 and 1500 B.C.

Rivlin and the museum decided to turn the moment, which captured international attention, into a teaching moment, inviting the Geller family back for a special visit and hands-on activity to illustrate the restoration process.

Rivlin added that the incident provided a welcome distraction from the ongoing war in Gaza. “Well, he’s just a kid. So I think that somehow it touches the heart of the people in Israel and around the world,“ said Rivlin.

Roee Shafir, a restoration expert at the museum, said the repairs would be fairly simple, as the pieces were from a single, complete jar. Archaeologists often face the more daunting task of sifting through piles of shards from multiple objects and trying to piece them together.

Experts used 3D technology, hi-resolution videos, and special glue to painstakingly reconstruct the large jar.

Less than two weeks after it broke, the jar went back on display at the museum. The gluing process left small hairline cracks, and a few pieces are missing, but the jar’s impressive size remains.

The only noticeable difference in the exhibit was a new sign reading “please don’t touch.”

The Canadian Press. All rights reserved.

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B.C. sets up a panel on bear deaths, will review conservation officer training

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VICTORIA – The British Columbia government is partnering with a bear welfare group to reduce the number of bears being euthanized in the province.

Nicholas Scapillati, executive director of Grizzly Bear Foundation, said Monday that it comes after months-long discussions with the province on how to protect bears, with the goal to give the animals a “better and second chance at life in the wild.”

Scapillati said what’s exciting about the project is that the government is open to working with outside experts and the public.

“So, they’ll be working through Indigenous knowledge and scientific understanding, bringing in the latest techniques and training expertise from leading experts,” he said in an interview.

B.C. government data show conservation officers destroyed 603 black bears and 23 grizzly bears in 2023, while 154 black bears were killed by officers in the first six months of this year.

Scapillati said the group will publish a report with recommendations by next spring, while an independent oversight committee will be set up to review all bear encounters with conservation officers to provide advice to the government.

Environment Minister George Heyman said in a statement that they are looking for new ways to ensure conservation officers “have the trust of the communities they serve,” and the panel will make recommendations to enhance officer training and improve policies.

Lesley Fox, with the wildlife protection group The Fur-Bearers, said they’ve been calling for such a committee for decades.

“This move demonstrates the government is listening,” said Fox. “I suspect, because of the impending election, their listening skills are potentially a little sharper than they normally are.”

Fox said the partnership came from “a place of long frustration” as provincial conservation officers kill more than 500 black bears every year on average, and the public is “no longer tolerating this kind of approach.”

“I think that the conservation officer service and the B.C. government are aware they need to change, and certainly the public has been asking for it,” said Fox.

Fox said there’s a lot of optimism about the new partnership, but, as with any government, there will likely be a lot of red tape to get through.

“I think speed is going to be important, whether or not the committee has the ability to make change and make change relatively quickly without having to study an issue to death, ” said Fox.

This report by The Canadian Press was first published Sept. 9, 2024.

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