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World of Genomics: Slovenia

Article written by Bethany Hanson, Science Communications Writer.

Known for its stunning glacial lakes and historic mountain towns, we head to the beautiful Alpine nation of Slovenia for our next stop on the World of Genomics tour!

Slovenia is one of the smallest countries in Europe by size and hosts stunning Alpine landscapes. A huge 54% of Slovenia is protected land and the Škocjan Caves in the southwest hold one of the largest underground canyons in the world! Slovenia is also famous for its white show horses which are bred nowhere else: one stud farm is over 425 years old.

Their official language is Slovene, a South Slavic language similar to West Slavic Czech and Slovak. Culturally, Slovenians share many similarities with other Alpine communities such as Northern Italians and the Swiss15.  Nine out of ten Slovenians are ethnically Slovene and directly descended from 6th century settlers, who migrated to the area from the Russian plains.

The Population of Slovenia

Slovenia borders Austria, Croatia, Italy and Hungary and has a small stretch of coastline on the Adriatic Sea. The country’s topography is incredibly diverse containing the European Alps and the stunning Mediterranean coast. The only relatively flat area is northeast, and outside of the coastal area the terrain consists of huge plateaus and ridges, alongside Alpine peaks cut through with glacial valleys and basins.

The majority of Slovenians hold religious beliefs. Christianity was introduced to Slavic tribes in the 8th century with the Roman Catholic Church dominating until the late 1900s. Today, the country’s dominant religions are Roman Catholic (58%), Muslim (2.5%), Orthodox Christian (2.3%) and Protestant Christian (0.8%). However, 10.5% of Slovenians list themselves as atheist and 26.5% as agnostic or other.

Slovenia was previously part of Yugoslavia. In 1941, it was partitioned in a German invasion. Slovenian resistance groups fought against the Nazi occupation, until Ljubljana was liberated in 1945. When the British repatriated more than 10,000 civilians who had retreated with the Germans, the Yugoslavian military massacred most of them in what came to be known as the “Pits of Kočevje”.

After the war, Slovenia entered a period of rapid urban expansion. In the 1960s, the communist government began establishing industrial areas and built high density housing in an effort to bring more workers to the cities. However, following the development of efficient rail and bus systems across the 1980s, the majority of Slovenian workers still commuted in from rural areas. While on average, the population has a 50/50 rural to urban split, the people is still over-dispersed; 75% of population centres are villages with less than 200 residents.

Slovenia became an independent nation with the democratic constitution in December of 1991. The country re-oriented its political system to align closer with those of the European Union, and Slovenia became a member in 2004. Slovenia adopted the Euro three years later in 200715.

Geographic and Demographic Information

Summary statistics

  • Land area:  20,675 km2
  • Gross domestic product (GDP):
    • Total: $62.12 billion
    • Per capita:  $29, 458

Population statistics

  • Population size:  2,108,732
  • Birth rate:  8.9 per 1,000 people
  • Death rate:  10.5 per 1,000 people
  • Infant mortality rate:  1.6 per 1,000 live births
  • Average life expectancy:  81 years
  • Ethnicity:  Slovenian (94%), Bosnian and Herzegovinian (2.6%), Kosovo (0.7%), Serbian (0.6%) and Macedonian (0.5%)

Healthcare system

Slovenia’s healthcare system uses a compulsory social health insurance (SHI) policy, which covers 99% of permanent residents and offers comprehensive coverage, including family planning and cancer treatments3. Some groups, including undocumented migrants, unhoused people and the Roma population, are unable to register for SHI due to a lack of formal residency. Some programmes are in place to combat this, but don’t address all cases3.

The Health Insurance Institute of Slovenia (HIIS) acts as the single public insurer and is funded mostly by individuals’ SHI contributions. There is an option for voluntary health insurance, provided by three private companies. This is commonly used to cover SHI co-payments, which are charged for the majority of the publicly financed health services.

The Slovenian Ministry for Health (MoH) dictates regulations and infrastructure planning, and the Health Council advises the MoH on new treatments, technology and policy. The MoH and Health Council provide nearly all hospital capacity, the majority of specialist care and all tertiary care, such as surgeries. Alternatively, primary care is provided by individual municipalities1,3. Across the country 30 hospitals provide inpatient care. Of these, 27 are state run3.

Slovenian healthcare spending has increased in line with economic growth1. In 2019, health spending was lower than the EU average but higher than neighbouring countries, Croatia and Hungary, for both per capita and GDP share. Despite the high coverage of public healthcare, in 2019, private spending accounted for 27.2% of total health expenditure, much higher than the EU average of 20.3% and the highest in the region1. On the other hand, Slovenia has much lower rates of out-of-pocket spending than most of the EU3 (11.7% and 15.4%, respectively).

Slovenia, alongside many European countries, is facing a shortage of qualified healthcare professionals, in particular doctors and registered nurses. In 2018, Slovenia had 3.2 doctors per 1,000 people, which is lower than the EU average of 3.92. However, in 2022 Slovenia had more practising nurses than the EU average (10.3 and 9.2 per 1,000 respectively) but still reported shortages, especially for hospital-based care3.

Health priorities

The leading causes of death in Slovenia in 2019 (per 100,000 people) were ischaemic heart disease (174), stroke (95.12) and respiratory cancers (60.66). Non-communicable diseases account for 9 out of the 10 leading causes of death in the country, with the exception of fall-related injuries (34.04). This mortality burden has been linked to the prevalence of behavioural risk factors, in particular dietary risk (16%), tobacco consumption (15%) and alcohol consumption (5%). However, each of these risks are lower than the EU averages of 17%, 17% and 6% respectively.

In 2019, 19% of adults in Slovenia were obese, higher than the EU average of 16 %. Furthermore 21% of Slovenian 15-year-olds were overweight in 2018, which is again a greater proportion than most EU countries report. To address this, the Slovenian government introduced a comprehensive, multidisciplinary National Nutrition and Physical Activity Strategy 2015-2025. The Strategy aims to tackle rising rates of obesity Slovenians on average lead active lifestyles, 60% work out for more than 3 hours a week. So, alongside encouraging increased activity, the programme will focus on nutritional education and behavioural risk factors.  

The COVID-19 pandemic hit Slovenia hard, with a direct coronavirus mortality rate 40% higher than the EU average. However, deaths from COVID-19 only accounted for 79% of Slovenia’s excess mortality over the pandemic1,4. This suggests a significant indirect impact from the pandemic on mortality, potentially exacerbated by common behavioural risk factors4.

The workforce shortage was a major contributing factor to the pressure the Slovenian healthcare system faced during the COVID-19 pandemic. Staff reported that they were overburdened, which in some cases resulted in lower quality care.  To address the workforce shortages, Slovenia implemented a series of policies aimed to increase staff retention and redistribute workloads. All available medical professionals, including doctors currently in specialist training, were reassigned to patient care and COVID support, all of whom received a 20% pay boost. Additionally, medical students were asked to man the free advice helpline. Those staff working in the highest risk areas received pay rises of up to 65% of their hourly rate. These policies helped support the health service through the pandemic, but longer-term investment in the medical workforce is still needed to address the COVID backlog3.

Genomic Medicine Capabilities

Genomic medicine in Slovenia began in 1958 when the National Institute of Public Health started to use karyotyping. In 1966, the Division of Medical Genetics (DMG) followed suit. The DMG developed into a tertiary care centre that provides laboratory testing, genetic counselling (starting in 1972), prenatal diagnosis (1981) and molecular genetic analysis (1993)6. Slovenia signed the Federal Act on Genetic Testing in 2009 and next-generation sequencing became available for public healthcare patients in 2018.

Direct-to-consumer genetic testing is available via both private companies and three health insurance providers, without corresponding genetic counselling7. As of 2015, this industry was not regulated and goes against international recommendations7.

Newborn screening was introduced to Slovenia in 1979, initially targeting phenylketonuria with tests for congenital hyperthyroidism added two years later. In 2000, the Slovenian healthcare system implemented selective screening for inborn errors of metabolism for patients exhibiting symptoms or with a known family history. This programme was expanded in 2018 by integrating mass spectrometry into testing. The expansion faces challenges due to the high cost per test and a lack of trained staff5. However, in the first year alone, a total of 15,064 samples were screened and four afflicted patients were identified before severe symptoms occurred. Following the pilot programme, NBS was introduced as confirmational test in hospitals across Slovenia, and the programme was considered a success5.

The University of Ljubljana runs of Genetic Counselling Clinic with three trained genetic counsellors12, which provides tertiary care for referred patients. The Slovenian Health Care System has noted an increasing demand for genetic health services, likely due to increased public awareness of hereditary diseases, especially in community care settings. However, many family physicians feel that they do not have adequate training, knowledge and confidence to perform genetic activities8.  

Slovenia does not currently require medical students to complete courses in either basic human genetics or clinical medical genetics10 as part of their training. However, Slovenia does recognise medical genetics as a distinct speciality and laboratory genetics training is available. In fact, Slovenia is ahead of neighbouring Balkan states in integrating genetic testing into everyday clinical practice10. Slovenia also recently launched a Masters & PhD program for Genomic Counselors11.

Notable Projects

  • The Slovenian Genome Project – The Slovenian Genome project was founded in 2022 and will study the genetic variability of the Slovenian population to simplify genetic diagnostics for people with rare diseases11. They will also create a series of national medico-ethical guidelines for genomic medicine. These will focus on genomic research and treatment, data management, interpretation of genetic results, biobanking and commercial genetic testing. In addition to the ethical and legal frameworks, the team has plans to create an online educational platform11. This is the first national project attempting to sequence the entire genome of Slovenes. In doing so, it joins similar international projects that seek to improve diagnostic procedures and prevent rare diseases of their citizens11.
  • Expanded Newborn Sequencing – Newborn Sequencing for inborn errors of metabolism has been available since 2000. In 2018, a pilot project was conducted in which NBS was combined with mass spectrometry. This allowed for a larger range of diseases to be tested for and is a more time- and cost-effective system. The pilot study examined 15,064 samples and identified 68 positive results, which were referred topaediatric endocrinologists at the University Children’s Hospital Ljubljana. Four cases were confirmed after further testing before severe complications arose. The pilot was a success and is being implemented in medical facilities across the country with the aim for NBS to be used as a front-line test without an indicative family history5.
  • Moderate and High Cancer Risk Population: Counselling, Mutational Screening And Prevention Strategies at the Institute of Oncology Ljubljana – A research group at the Institute of Oncology Ljubljana is investigating hereditary breast and ovarian cancer, malignant melanoma and colorectal cancer by sequencing the Slovenian population. The project will run from 2007 to 2027 and has already identified an oncogenic mutation specific to people of Slovenian descent. The project also aims to develop the infrastructure for a multidisciplinary molecular laboratory, genetic counselling clinic and outpatient care clinic for those identified as having a high polygenic risk for cancer or carrying hereditary mutations. The project has already successfully diagnosed 200 Slovenian families and resulted in publications in international journals. The team running the programme say that it has been highly successful and is enabling the implementation of clinical genomics in day-to-day medical care13.        

Notable Organisations 

  • Institute of Oncology Ljubljana – The Institute was established in 1938. It is a national cancer centre that provides cancer treatments, preventative care, palliative care and post-treatment rehabilitation for Slovenian patients. The centre has 290 beds, 240 doctors, 390 nurses and 265 research scientists. They also offer oncological genetic counselling. In addition to running the cancer centre, the Institute acts as a hub for many research projects, including the Slovenian Genome Project and The Cancer Registry of the Republic of Slovenia, the oldest population-based cancer registry in Europe14.
  • Centre for the Technologies of Gene and Cell Therapy – The CTGCT was founded by the Slovenian National Institute of Chemistry in September 2023 as a hub for cutting-edge research in synthetic biology, immunology and genetics. The Centre will connect Slovenian scientists to experts in the Netherlands, the UK and Germany to transfer academic knowledge to the healthcare system. The CTGCT’s research will focus on developing novel gene-based therapies for cancers and rare diseases with no effective cures. They are currently working on projects for rare neurodevelopmental disorders, cancer immunotherapies and treatments for neurodegenerative diseases.
  • The Slovenian Medical Association – Founded in 1861, the association is one of the oldest medical organisations in Central Europe. The association is made of up 65 specialist sub-divisions, 13 regional associations and 4,000 members. Members are voluntary, independent medical professionals including doctors, dentists and final year medical students. The society develops professional standards and policy, oversees the transfer of international knowledge to Slovenian doctors, promotes Slovenian research on the international stage, investigates unmet medical needs and works with patient support organisations to improve care. The society hosts the sub-division, the Slovenian Medical Genetics Association, which is responsible for running the annual Symposium of Slovenian Medical Genetics.

Notable People

  • Fran Jesenko (1875-1932) – One of Slovenia’s first geneticists, he was a botanist who specialised in plant genetics and is known for his work hybridising wheat and rye. He graduated from the University of Vienna in 1902, following which he travelled across Europe working as a tutor and studying flora. He returned to Vienna and began his work creating fertile hybrids between wheat and rye by studying their Mendelian characteristics and using backcrossing. He proposed that infertility in hybrids was caused by chromosomal incompatibility. He was a pioneer of intergeneric hybrids.
  • Franc Gubenšek (1937-2010) – A Slovenian biochemist best known for his work on neurotoxic phospholipases in snake venom. He was one of the first Slovene scientists to uncover their structure and went on to study their receptors and activation mechanisms. He co-discovered a new DNA transposable element and then further demonstrated its horizontal gene transfer between snakes and ruminants. He was also the first scientist from Slovenia to be elected as a member of the European Molecular Biology Organisation.
  • Fritz Pregl (1869-1930) – Slovenian-Austrian chemist that won the Nobel Prize for Chemistry in 1923 for his research on and improvements to quantitative organic micro-analysis. He is the only Slovenian to have won a Nobel Prize. His work on elemental analysis reduced the minimal amount of sample necessary for testing by a factor of 50. Following his passing, Pregl left funds to the Austrian Academy of Sciences to fund the Fritz Pregl Prize, which has been awarded annually since 1931. Furthermore, a square in Slovenia’s capital city, Ljubljana, is named after him. 

The Future Genomics Landscape

Slovenia has a long history of genetic research and in the last 5 years has invested funds, time and expertise into genomic medicine and precision care. Slovenia is already leading neighbouring Baltic states in integrating genomic medicine into clinical practice10. Now, with the recent expansion of newborn screening, the founding of the Centre for the Technologies of Gene and Cell and launch of the Slovenian Genome Project, Slovenia is on track to establish itself as a hub of genomic expertise.

However, the country still needs to tackle its policy-based roadblocks. Most notably, the unregulated availability of direct-to-consumer genetic testing, which does not align with EU recommendations, and the question of how genomic and precision medicine will be covered by the social health insurance plan. With multiple organisations based in Slovenia working to standardise policies to align with EU recommendations, there is hope that this will be resolved soon.

Thanks to a well-established scientific community, rapidly developing international relationships and continued investment in genomic research, Slovenia may well soon be a leader in providing accessible precision care at all stages of the diagnostic journey.  


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