How Finland is teaming up with pharma to identify genetic variants in disease

The country’s FinnGen Project seeks to use its unique population bottleneck and cohesive health records to drive genetic insights. Deep in the belly of the University of Helsinki, large metallic cylinders line a basement lab. While the setting is clinical, scientists have added a playful touch with snow-themed name tags on each of the vats. Still, the mission of the lab is serious — inside “snow queen” and “snow castle” lie genetic samples that could potentially help decode genetic variants responsible for disease.

Finland is unique

Finland came onto the world stage last year when it was named “happiest country” by Forbes. But it isn’t just their happiness scores that make the Finnish people unique.

Situated in the far northeast corner of Europe, over the last few millennia Finland has seen less immigration than other parts of Europe. This has led to Finland becoming one of the largest population bottlenecks, meaning that the Finnish gene pool is largely homogeneous.

This fact can help scientists pinpoint gene variants that are linked to specific diseases, Anu Jalanko, project manager at FinnGen, said at a media event in June. Instead of researchers sifting through billions of variants to link them to a disease or condition, they need only sift through hundreds of thousands.

“We geneticist use this fact to have an easier time to identify variants, and identify specific variants in complex situations,” Aarno Palotie, scientific director of the FinnGen Project, said at HIMSS Europe in June.

23andMe taking on Apple with pilot to gather medical data not just DNA

Dark centers of chromosomes reveal ancient DNA

Geneticists exploring the dark heart of the human genome have discovered big chunks of Neanderthal and other ancient DNA. The results open new ways to study both how chromosomes behave during cell division and how they have changed during human evolution. Centromeres sit in the middle of chromosomes, the pinched-in “waist” in the image of a chromosome from a biology textbook. The centromere anchors the fibers that pull chromosomes apart when cells divide, which means they are really important for understanding what happens when cell division goes wrong, leading to cancer or genetic defects.

But the DNA of centromeres contains lots of repeating sequences, and scientists have been unable to properly map this region.

“It’s the heart of darkness of the genome, we warn students not to go there,” said Charles Langley, professor of evolution and ecology at UC Davis. Langley is senior author on a paper describing the work published in an upcoming issue of the journal eLife.

Langley and colleagues Sasha Langley and Gary Karpen at the Lawrence Berkeley Laboratory and Karen Miga at UC Santa Cruz reasoned that there could be haplotypes – groups of genes that are inherited together in human evolution – that stretch over vast portions of our genomes, and even across the centromere.

That’s because the centromere does not participate in the “crossover” process that occurs when cells divide to form sperm or eggs. During crossover, paired chromosomes line up next to each other and their limbs cross, sometimes cutting and splicing DNA between them so that genes can be shuffled. But crossovers drop to zero near centromeres. Without that shuffling in every generation, centromeres might preserve very ancient stretches of DNA intact.

The researchers looked for inherited single nucleotide polymorphisms – inherited changes in a single letter of DNA – that would allow them to map haplotypes in the centromere.

They first showed that they could identify centromeric haplotypes, or “cenhaps,” in Drosophila fruit flies.

That finding has two implications, Langley said. Firstly, if researchers can distinguish chromosomes from each other by their centromeres, they can start to carry out functional tests to see if these differences have an impact on which piece of DNA is inherited. For example, during egg formation, four chromatids are formed from two chromosomes, but only one makes it into the egg. So scientists want to know: Are certain centromere haplotypes transmitted more often? And are some haplotypes more likely to be involved in errors?

Secondly, researchers can use centromeres to look at ancestry and evolutionary descent.

Turning to human DNA, the researchers looked at centromere sequences from the 1000 Genomes Project, a public catalog of human variation. They discovered haplotypes spanning the centromeres in all the human chromosomes.

23andMe launches predisposition test for Type 2 diabetes

At SXSW in Austin this weekend, consumer genomics company 23andMe unveiled its latest test, a predisposition report on Type 2 diabetes.

The test, which has not undergone FDA clearance and does not purport to diagnose a condition, is designed to help people understand when they’re at a higher-than-normal risk for Type 2 diabetes so they can alter their lifestyle. To assist with the latter piece, the company is leaning on its new relationship with Lark Health.

This is a significant launch from 23andMe as it’s the first polygenic test the company has offered based on its own data (at least, the first since it pulled its health tests from the market in 2013). The announcement was accompanied by a detailed whitepaper.

Why it matters

For a company like 23andMe, increasing the number of tests they offer adds a lot of value, and can have a snowball effect: the more data they collect, the more tests they can develop and the more tests they offer the more data they can collect (since new tests will drive new users to the service).

And tests like this, that are built from 23andMe’s proprietary data store, give the company a competitive advantage against consumer genomics companies without their database.

Additionally, Type 2 diabetes is a huge problem, affecting nearly one in 10 Americans and costing the healthcare system more than $327 billion a year, according to the CDC and the American Diabetes Association.

23andMe hopes that by letting more people know they’re at risk, they can prevent some number of cases before they happen.

Artificial intelligence applied to the genome identifies an unknown human ancestor

By combining deep learning algorithms and statistical methods, investigators from the Institute of Evolutionary Biology (IBE), the Centro Nacional de Anlisis Genmico (CNAG-CRG) of the Centre for Genomic Regulation (CRG) and the Institute of Genomics at the University of Tartu have identified, in the genome of Asian individuals, the footprint of a new hominid who cross bred with its ancestors tens of thousands of years ago.Modern human DNA computational analysis suggests that the extinct species was a hybrid of Neanderthals and Denisovans and cross bred with Out of Africa modern humans in Asia. This finding would explain that the hybrid found this summer in the caves of Denisova — the offspring of a Neanderthal mother and a Denisovan father — was not an isolated case, but rather was part of a more general introgression process.The study, published in Nature Communications, uses deep learning for the first time ever to account for human evolution, paving the way for the application of this technology in other questions in biology, genomics and evolution.Humans had descendants with an species that is unknown to usOne of the ways of distinguishing between two species is that while both of them may cross breed, they do not generally produce fertile descendants. However, this concept is much more complex when extinct species are involved. In fact, the story told by current human DNA blurs the lines of these limits, preserving fragments of hominids from other species, such as the Neanderthals and the Denisovans, who coexisted with modern humans more than 40,000 years ago in Eurasia.Now, investigators of the Institute of Evolutionary Biology (IBE), the Centro Nacional de Anlisis Genmico (CNAG-CRG) of the Centre for Genomic Regulation (CRG), and the University of Tartu have used deep learning algorithms to identify a new and hitherto-unknown ancestor of humans that would have interbred with modern humans tens of thousands of years ago. “About 80,000 years ago, the so-called Out of Africa occurred, when part of the human population, which already consisted of modern humans, abandoned the African continent and migrated to other continents, giving rise to all the current populations,” explained Jaume Bertranpetit, principal investigator at the IBE and head of Department at the UPF. “We know that from that time onwards, modern humans cross bred with Neanderthals in all the continents, except Africa, and with the Denisovans in Oceania and probably in South-East Asia, although the evidence of cross-breeding with a third extinct species had not been confirmed with any certainty.”