Large-scale study finds genetic testing technology falsely detects very rare variants

UNIVERSITY OF EXETER

Research News

 

A technology that is widely used by commercial genetic testing companies is "extremely unreliable" in detecting very rare variants, meaning results suggesting individuals carry rare disease-causing genetic variants are usually wrong, according to new research published in the BMJ.

After hearing of cases where women had surgery scheduled after wrongly being told they had very rare genetic variations in the gene BRCA1 that could significantly increase risk of breast cancer, a team at the University of Exeter conducted a large-scale analysis of the technology using data from nearly 50,000 people. They found that the technology wrongly identified the presence of very rare genetic variants in the majority of cases.

The team analysed SNP chips, which test genetic variation at hundreds-of-thousands of specific locations across the genome. While excellent at detecting common genetic variation that can increase the risk of diseases such as type 2 diabetes, geneticists have long known they are less reliable at detecting rarer variation. However, this problem is less well known outside the genetic research community, and SNP chips are widely used by commercial companies that offer genetic testing direct to consumers.

Caroline Wright, Professor in Genomic Medicine at the University of Exeter Medical School, senior author on the paper, said: "SNP chips are fantastic at detecting common genetic variants, yet we have to recognise that tests that perform well in one scenario are not necessarily applicable to others. We've confirmed that SNP chips are extremely poor at detecting very rare disease-causing genetic variants, often giving false positive results that can have profound clinical impact. These false results had been used to schedule invasive medical procedures that were both unnecessary and unwarranted."

The team compared data from SNP chips with data from the more reliable tool of next generation sequencing in 49,908 participants of UK Biobank, and an additional 21 people who shared results of their consumer genetic tests via the Personal Genome Project.

The study concluded that SNP chips performed extremely well in detecting common genetic variants. However, the rarer the variation was, the less reliable the results became. In very rare variants, present in fewer than 1 in 100,000 individuals, typical of those causing rare genetic disease, 84 per cent were false positives in UK Biobank. In the data from commercial customers, 20 of 21 individuals analysed had at least one false positive rare disease-causing variant that had been incorrectly genotyped.

Dr Leigh Jackson, Lecturer in Genomic Medicine at the University of Exeter and co-author of the paper, said: "The number of false positives on rare genetic variants produced by SNP chips was shockingly high. To be clear: a very rare, disease-causing variant detected using a SNP chip is more likely to be wrong than right. Although some consumer genomics companies perform sequencing to validate important results before releasing them to consumers, most consumers also download their "raw" SNP chip data for secondary analysis, and this raw data still contain these incorrect results. The implications of our findings are very simple: SNP chips perform poorly for detecting very rare genetic variants and the results should never be used to guide a patient's medical care, unless they have been validated."

###

The paper published today in the BMJ is entitled 'Using SNP chips to detect very rare pathogenic variants: retrospective population-based diagnostic evaluation'.

Notes to editors: For further context, see the joint statement from the Royal College of General Practitioners and the British Society for Genetic Medicine on direct to consumer genomic testing, which references the pre-print version of the paper.

Once the embargo lifts, the paper will publish at: https://www.bmj.com/content/372/bmj.n214

*Labels applied according to the Academy of Medical Sciences press release labelling system.

About the University of Exeter Medical School

The University of Exeter Medical School is part of the University of Exeter's College of Medicine and Health. Our mission is to improve the health of the South West and beyond, through the development of high quality graduates and world-leading research that has international impact.

As part of a Russell Group university, we combine this world-class research with very high levels of student satisfaction. Exeter has over 19,000 students and is ranked 12th in The Times and Sunday Times Good University Guide 2020.

The University of Exeter Medical School's Medicine course is in the top 10 in the Complete University Guide 2020.

The College's Medical Imaging programme is ranked in the top 5 in the Guardian Guide 2020 and the Complete University Guide 2020.

The University of Exeter entered the world top 20 for Biomedical and Health Sciences in the CWTS Leiden Ranking 2019, based on the percentage of publications ranked in the top 10 per cent most cited.

https://medicine.exeter.ac.uk/

For further information:

Louise Vennells
Press and Media Manager
University of Exeter Medical School
+44 (0)1392 724927 or 07768 511866
l.vennells@exeter.ac.uk

Improved use of databases could save billions of euro in health care costs

Billions of euro in health care costs - arising from osteoporosis-related bone fractures - could be saved by improved use of existing databases

LERO

Research News

 

Years of suffering and billions of euro in global health care costs, arising from osteoporosis-related bone fractures, could be eliminated using big data to target vulnerable patients, according to researchers at Lero, the Science Foundation Ireland Research Centre for Software.

A study of 36,590 patients who underwent bone mineral density scans in the West of Ireland between January 2000 and November 2018, found that many fractures are potentially preventable by identifying those at greatest risk before they fracture, and initiating proven, safe, low-cost effective interventions.

The multi-disciplinary study, led by Lero's Prof. John J. Carey, Consultant Physician in Medicine and Rheumatology, Galway University Hospital, Mary Dempsey, Mechanical Engineering and Dr Attracta Brennan, Computer Science, NUI Galway has just been published in the British Medical Journal.

The Irish dual-energy X-ray absorptiometry (DXA) Health Informatics Prediction (HIP) project on bone mineral density now plans to assess current diagnostic classification and risk prediction algorithms for osteoporosis and fractures, according to Prof. Carey.

"This will identify which predictors are most important for Irish people at risk for osteoporosis, and develop new, accurate and personalised risk prediction tools using the large, multicentre, longitudinal follow-up cohort.

"Furthermore, the dataset may be used to assess, and possibly support, the assessment and management of other chronic conditions such as cardiovascular disease, cancer and other illnesses due to the large number of variables collected in this project," he added.

Prof. Carey points out that while Ireland has one of the highest osteoporosis rates globally, currently there is no national public or government policy to address the healthcare requirements of osteoporotic fractures, with costs rising rapidly.

"In Ireland, public hospital bed days have increased by almost 50% in the past decade for osteoporotic fractures and outnumber heart attacks, cancer, diabetes and many other illnesses that receive much greater attention," he added.

"Preliminary estimates suggest the number of fragility fractures and deaths following fracture for Irish adults aged 50 years and older in 2020 was similar or greater to the numbers with COVID infection, but there is no daily report on the numbers tested, hospitalised or who die following a fracture. Use of these and other data could help close those gaps," he added.

Prof. Carey says there is a global osteoporosis health crisis, with predictions of American medical costs associated with osteoporotic-related fractures including productivity losses and caregiving expenditure to exceed $94 billion (€77.6bn) annually by 2040.

Prof. Carey said previous studies have shown, for example in 2010, approximately 43,000 European deaths were fracture-related while expenditure related to osteoporosis exceeded €37 billion.

"A modest 5% reduction in those costs would result in an annual saving of €1.85bn at 2010 prices," he added.

"We now have big datasets, similar to the one utilised in our study, available throughout the globe. Cost-effective, innovative forms of data interrogation such as AI (Artificial Intelligence) will enable the timely identification and treatment of patients vulnerable to osteoporosis fractures, providing them with better care and using precious resources efficiently. There will be many opportunities to provide better patient outcomes and save billions of euro," he added.

Prof. Carey believes this collaboration between clinicians, big data scientists, engineering and computer scientists in Ireland, Britain and China will help leverage innovation, critical thinking and international partnerships to accelerate their programme and opportunities.

Director of Lero, Professor Brian Fitzgerald, said the utilisation of AI, as envisaged by Prof Carey and his team, shows how software development initiatives can directly impact people's lives at a fundamental level. Lero is a world leader in research on connected health and human performance.

"When Lero's work can help alleviate suffering, improve patient outcomes and free up resources, then we are doing the job we were established to do, and that's very rewarding for all concerned," he added.

###

Citation: E E, Wang T, Yang L, et al The Irish dual-energy X-ray absorptiometry (DXA) Health Informatics Prediction (HIP) for Osteoporosis Project.

BMJ Open 2020;10:e040488. doi: 10.1136/bmjopen-2020-040488

Ethics approval: Before data collection, formal approval was sought and obtained for each clinical site from the local hospitals' Research Ethics Committee to process information from a retrospective cohort to explore DXA validity for Ireland.

How to improve gender equity in medicine

CANADIAN MEDICAL ASSOCIATION JOURNAL

Research News

 

Gender equity and racial diversity in medicine can promote creative solutions to complex health problems and improve the delivery of high-quality care, argue authors in an analysis in CMAJ (Canadian Medical Association Journal).

"[T]here is no excuse for not working to change the climate and environment of the medical profession so that it is welcoming of diversity," writes lead author Dr. Andrea Tricco, Knowledge Translation Program, Unity Health, and the University of Toronto, with coauthors. "The medical profession should be professional, be collegial, show mutual respect, and facilitate the full potential and contribution of all genders, races, ethnicities, religions and nationalities for the benefit of patient care."

The authors describe the root causes of gender inequity in society as well as medicine, and how to improve equity based on current evidence. Gender inequity in medicine is a long-standing problem and the time to act is now, they urge.

"The history of gender inequity in Canadian medical leadership is long, despite women outnumbering men in medical schools now for over a quarter of a century," says coauthor Dr. Ainsley Moore, a family physician and associate professor, Department of Family Medicine, McMaster University, Hamilton, Ontario. "Only 8 of the past 152 presidents of the Canadian Medical Association were women, and it took 117 years for a woman to be appointed dean of a medical faculty, and only 8 have been appointed since. The time is ripe for addressing this systemic problem."

For racialized women, the issue of equity is even more pronounced. "The effects of systemic and structural racism have resulted in racialized women experiencing a double-jeopardy of race and gender bias, thereby exaggerating their underrepresentation in leadership positions in academic medicine," says coauthor Dr. Nazia Peer, research program manager of the Knowledge Translation Program, Unity Health.

Addressing gender equity requires a multi-pronged approach targeting the medical system as well as individual behaviours.

Solutions include

• Ensuring core principles of equity, diversity, inclusion, mutual respect, collegiality and professionalism are embedded in all policies and all stages of medicine
• Communicating gender statistics
• Getting buy-in from professional organizations at the national, provincial and local levels
• Championing structural and behavioural change from the top
• Role modelling
• Diverse search committees for hiring
• Flexible schedules, non-gendered parental leave and family-friendly policies
• Career support and peer mentoring

"Equity will only be realized when everyone -- regardless of gender and other differences -- experiences equity in pay, promotions and other opportunities. There is no better time than now to implement policies to advocate for and support equity in medicine," they conclude.

###

Listen to a podcast with Drs. Andrea Tricco and Ainsley Moore: https://www.cmaj.ca/lookup/doi/10.1503/cmaj.200951/tab-related-content.

"Advancing gender equity in medicine" is published February 16, 2021.

Ageism and sexism barring grandmothers from initiatives to save newborn lives in Global South

This is despite published research suggesting they have key roles in many cultures

BMJ

Research News

 

Ageism, sexism, and Western ideals of the nuclear family have excluded grandmothers from national and international policy initiatives to save newborn lives in the Global South, suggests an analysis published in the online journal BMJ Global Health.

This is despite published research indicating that they are a valuable and influential resource for children's health and survival in many cultures, the study author points out.

Around three out of 4 newborn deaths in the Global South occur in the first week of life--40% of them on the first day, and most of them at home.

But Initiatives to promote the survival of newborns across the Global South have primarily focused on strengthening health services and on young mothers within a nuclear family unit, to the exclusion of caregiver roles and practices within the wider family, says the author.

And extra funds invested in programmes to cut the newborn death rate have had relatively little impact.

To explore the role of the wider family in the care of newborns, and specifically that of grandmothers, the author reviewed relevant published studies of 70 different cultures in the three continents of Africa, Asia, and Latin America.

Cultures in the Global South tend to be collectivist rather than individualist, as in the West. They feature hierarchy based on age and experience, with elders as teachers of younger generations, and interdependency and shared decision-making valued over autonomy.

The studies revealed that grandmothers' knowledge is not always up to date and that some of their newborn practices may be harmful.

But where initiatives have recognised the value of grandmothers, such as in Nepal, Uttar Pradesh in India, Malawi, Burkina Faso and Senegal, these have been successful and prove that grandmothers may not be as resistant to change as is often assumed, notes the author.

The studies also revealed numerous examples of the significant role and influence of experienced older women, or grandmothers, on newborn care, both as authoritative advisors and direct caregivers within multi-generational family systems.

These roles extend from pregnancy onwards and include care of sick newborns, acting as breastfeeding coaches, and providing vital emotional and social support networks.

And across all three continents, the studies showed that grandmothers have similar core roles in newborn care, irrespective of variations in cultural practice.

"A growing body of evidence from across non-western, collectivist societies reveals the culturally designated role of these experienced, older women as newborn advisors and caregivers," writes the author.

"Unfortunately, at the global level, newborn research, policies and interventions continue to focus primarily on medical technologies and services, [and] to a lesser extent on mothers."

She adds: "While all research reviewed provides evidence of grandmothers' influence on newborn care, surprisingly, some does not explicitly recommend their inclusion in future programmes.

"Unfortunately, there is continued reluctance to explicitly involve grandmothers in interventions addressing newborn and other [mother and child health] issues.

"This appears to be related to: the often-repeated idea that grandmothers are barriers to change; a narrow perception of grandmothers focusing on their harmful traditional practices; and gender and ageist biases toward older women."

Future research should be grounded within a family systems framework that reflects collectivist cultures, argues the author.

And initiatives to save newborn lives should "aim not only to strengthen health services, but also influential family caregivers, particularly grandmothers and the indigenous social support networks of which they are a part," she concludes.

###

Externally peer reviewed? Yes
Evidence type: Analysis
Subjects: Families

Managing crab and lobster catches could offer long-term benefits

UNIVERSITY OF PLYMOUTH

Research News

VIDEO: AN ANIMATION SHOWING HOW MANAGING CRAB AND LOBSTER CATCHES COULD OFFER LONG-TERM BENEFITS TO FISHERMEN AND THE ENVIRONMENT view more 

CREDIT: UNIVERSITY OF PLYMOUTH

The UK's commercial fishing industry is currently experiencing a number of serious challenges.

However, a study by the University of Plymouth has found that managing the density of crab and lobster pots at an optimum level increases the quality of catch, benefits the marine environment and makes the industry more sustainable in the long term.

Published today in Scientific Reports, a journal published by the Nature group, the findings are the result of an extensive and unprecedented four-year field study conducted in partnership with local fishermen off the coast of southern England.

Over a sustained period, researchers exposed sections of the seabed to differing densities of pot fishing and monitored any impacts using a combination of underwater videos and catch analysis.

They found that in areas of higher pot density, fishermen caught 19% less brown crab and 35% less European lobster, and their catches of brown crab were on average 35 grams per individual (7%) lighter.

The effect on marine species was also significant with two ecologically important reef species, Ross coral (Pentapora foliacea) and Neptune's Heart sea squirt (Phallusia mammillata), 83% and 74% less abundant respectively where pot density was higher.

Researchers say the study provides evidence of a pot fishing intensity 'threshold' and highlights that commercial pot fisheries are likely to be compatible with marine conservation when managed correctly at low, sustainable levels.

The study was carried out by academics from the University's School of Biological and Marine Sciences, with funding from Defra and the Blue Marine Foundation and working with the Lyme Bay Consultative Committee.

CAPTION

A stack of crab and lobster pots at the end of Lyme Regis harbour, ready for fishing

CREDIT

Adam Rees, University of Plymouth

It builds on an interim report published by Defra in 2019, and research published in October 2020 which used previously unseen footage to show the environmental impacts of pot fishing.

Dr Adam Rees, Post-Doctoral researcher and lead author on the current research, said: "The effects of bottom-towed fishing have been clearly shown as part of the University's long-term monitoring project in Lyme Bay. But before we started this research, very little was known about the precise impacts of pot fishing over a prolonged period. We have shown that - if left unchecked - it can pose threats but that changing ways of working can have benefits for species on the seabed and the quality and quantity of catches."

The study focussed on the Lyme Bay Reserve, a 206 km² area that has been protected from all bottom-towed fishing since 2008. It is part of the Lyme Bay and Torbay Special Area of Conservation, a 312 km² section of the English Channel that is predominantly fished by small boats operating out of towns and villages.

The University has been assessing the seabed recovery since 2008 and has previously demonstrated that several species have returned to the area since the MPA was introduced. Recommendations from this work have been included within the Government's 25-year Environment Plan, and a major UK government report into Highly Protected Marine Areas (HPMAs), led by former Defra Fisheries Minister Richard Benyon.

This latest study comes just days after the Marine Management Organisation (MMO) signalled its intent to ban bottom trawling at various offshore MPAs around the UK.

Dr Emma Sheehan, Associate Professor of Marine Ecology and one of the study's co-authors, said: "Over a decade ago, the fishing community in Lyme Bay realised that changing the way they fish was essential to the sustainability of their industry. We have worked closely with them ever since to take their concerns into account and attempt to provide them with solutions. This study is the latest part of our ongoing work to establish the best ways to both preserve their traditions and enhance the environment they work in."

Martin Attrill, Professor of Marine Ecology and senior author on the research, added: "The fishing industry is currently facing huge uncertainty. And we of course know that every fishing community is different. But with the drive to further enhance marine protection around the UK, some of the lessons we have learned in Lyme Bay could help other fleets make changes that can secure their long-term future."

CAPTION

A local fishermen involved in the project out hauling fishing gear within the Lyme Bay and Torbay Special Area of Conservation

CREDIT

Adam Rees, University of Plymouth

Tropical paper wasps babysit for neighbours

UNIVERSITY OF BRISTOL

Research News

 

IMAGE: POLISTES COLONIES OFFER WINDOWS INTO THE EVOLUTION OF COOPERATION view more 

CREDIT: P KENNEDY

[Images and video available: see notes to editors]

Wasps provide crucial support to their extended families by babysitting at neighbouring nests, according to new research by a team of biologists from the universities of Bristol, Exeter and UCL published today [15 February] in Nature Ecology and Evolution.

The findings suggest that animals should often seek to help more distant relatives if their closest kin are less in need.

Dr Patrick Kennedy, lead author and Marie Curie research fellow in the School of Biological Sciences at the University of Bristol, said: "These wasps can act like rich family members lending a hand to their second cousins. If there's not much more you can do to help your immediate family, you can turn your attention to the extended family."

By closely observing twenty thousand baby wasps and their carers on colonies around the Panama Canal, the research team could determine the usefulness of workers on colonies of different sizes. They showed that workers become less useful as the number of colony members rises, due to a surplus of help.

Andy Radford, Professor of Behavioural Ecology, also from Bristol and co-author, explained: "By helping more distant relatives who are more in need--those living next door with fewer carers--workers can pass on more copies of their genes overall. We believe that similar principles of diminishing returns might explain seemingly paradoxical acts of altruism in many other social animals."

Dr Kennedy added: "The fact that these paper wasps in Central and South America help at other colonies is really bizarre when you consider that most wasps, ants and bees are extremely hostile to outsiders. To solve this puzzling behaviour, we combined mathematical modelling with our detailed field observations."

Dr Kennedy continued: "We ended up being stung a lot. But it was worth it, because our results show that worker wasps can become redundant at home. A wasp on a colony with few larvae but lots of other workers becomes almost useless: the best thing to do is to babysit the larvae of other relatives."

Since Darwin, biologists have been trying to understand how 'altruism' evolves in animals. At first glance, acts of selflessness to help other individuals do not seem to allow individuals to pass on their genes.

Professor Radford said: "In 1964, the legendary biologist W. D. Hamilton figured out the cardinal rule of animal altruism. Lavish help on your family because they share many of your genes. Copies of your genes will triumph in the population."

But the tropical paper wasps studied by the team baffled Hamilton back in 1964. In Brazil, he was surprised to notice that Polistes wasps were leaving their close family on their home nests and flying off to help the neighbours, who are less closely related.

Previous work by co-author Seirian '@WaspWoman' Sumner, Professor of Behavioural Ecology at University College London, showed that over half the workers in a Panamanian population were helping on multiple nests. Wasps usually viciously attack outsiders, so this babysitting suggested something unusual was going on.

Professor Sumner explained: "Wasps offer amazing windows into the evolution of selflessness. There is so much going on in a wasp nest: power struggles, self-sacrifice, groups battling against the odds to survive... If we want to understand how societies evolve, we should look more deeply at wasps."

###

This fieldwork was supported by the National Geographic Society and the Smithsonian Tropical Research Institute in Panama.

Paper

'Diminishing returns drive altruists to help extended family' by P. Kennedy, S. Sumner?, P. Botha, N. J. Welton, A. D. Higginson and A. N. Radford in Nature Ecology and Evolution

Capuchin monkey genome reveals clues to its long life and large brain

UNIVERSITY OF LIVERPOOL

Research News

 

An international team of scientists has sequenced the genome of a capuchin monkey for the first time, uncovering new genetic clues about the evolution of their long lifespan and large brains.

Published in PNAS, the work was led by the University of Calgary in Canada and involved researchers at the University of Liverpool.

"Capuchins have the largest relative brain size of any monkey and can live past the age of 50, despite their small size, but their genetic underpinnings had remained unexplored until now," explains Professor Joao Pedro De Magalhaes, who researches ageing at the University of Liverpool.

The researchers developed and annotated a reference assembly for white-faced capuchin monkeys (Cebus imitator) to explore the evolution of these traits.

Through a comparative genomics approach spanning a wide diversity of mammals, they identified genes under evolutionary selection associated with longevity and brain development.

"We found signatures of positive selection on genes underlying both traits, which helps us to better understand how such traits evolve. In addition, we found evidence of genetic adaptation to drought and seasonal environments by looking at populations of capuchins from a rainforest and a seasonal dry forest," said senior author and Canada Research Chair Amanda Melin who has studied capuchin monkey behaviour and genetics for almost 20 years.

The researchers identified genes associated with DNA damage response, metabolism, cell cycle, and insulin signalling. Damage to the DNA is thought to be a major contributor to ageing and previous studies by Professor de Magalhaes and others have shown that genes involved in DNA damage responses exhibit longevity-specific selection patterns in mammals.

"Of course, because aging-related genes often play multiple roles it is impossible to be sure whether selection in these genes is related to ageing or to other life-history traits, like growth rates and developmental times, that in turn correlate with longevity," said Professor De Magalhaes.

"Although we should be cautious about the biological significance of our findings, it is tempting to speculate that, like in other species, changes to specific aging-related genes or pathways, could contribute to the longevity of capuchins," he added.

The team's insights were made possible thanks to the development of a new technique to isolate DNA more efficiently from primate faeces.

FecalFACS utilises an existing technique that has been developed to separate cells types in body fluids - for example to separate different cell types in blood for cancer research - and applies it to primate faecal samples.

"This is a major breakthrough because the typical way to extract DNA from faeces results in about 95-99% of the DNA coming from gut microbes and food items. A lot of money has been spent sequencing genomes from different organisms than the mammals we're actually trying to study. Because of this, when wildlife biologists have required entire genomes, they have had to rely on more pure sources of DNA, like blood, saliva, or tissue - but as you can imagine, those are very hard to come by when studying endangered animals," explained the study's lead author, Dr Joseph Orkin, who completed work on this project as a postdoctoral scholar at the University of Calgary, and in his present location at Universitat Pompeu Fabra-CSIC in Barcelona.

"FecalFACS finally provides a way to sequence whole genomes from free-ranging mammals using readily available, non-invasive samples, which could really help future conservation efforts," he added.

###

In predicting shallow but dangerous landslides, size matters

Computer models to predict areas most likely to slide confront lack of subsurface data

UNIVERSITY OF CALIFORNIA - BERKELEY

Research News

 

IMAGE: A SHALLOW LANDSLIDE TURNED INTO A DEBRIS FLOW THAT SWEPT AWAY A HOUSE IN SAUSALITO, CALIFORNIA, AT 3 A.M. ON FEB. 14, 2019. A WOMAN WAS BURIED IN THE REMAINS... view more 

CREDIT: PHOTO COURTESY OF THE CITY OF SAUSALITO

The threat of landslides is again in the news as torrential winter storms in California threaten to undermine fire-scarred hillsides and bring deadly debris flows crashing into homes and inundating roads.

But it doesn't take wildfires to reveal the landslide danger, University of California, Berkeley, researchers say. Aerial surveys using airborne laser mapping -- LiDAR (light detection and ranging) -- can provide very detailed information on the topography and vegetation that allow scientists to identify which landslide-prone areas could give way during an expected rainstorm. This is especially important for predicting where shallow landslides -- those just involving the soil mantle -- may mobilize and transform as they travel downslope into destructive debris flows.

The catch, they say, is that such information cannot yet help predict how large and potentially hazardous the landslides will be, meaning that evacuations may target lots more people than are really endangered by big slides and debris flows.

In a new paper appearing this week in the journal Proceedings of the National Academy of Sciences, the scientists, UC Berkeley geologist William Dietrich and project scientist Dino Bellugi report their latest attempt at tagging landslide-prone areas according to their likely size and hazard potential, in hopes of more precise predictions. Their model takes into account the physical aspects of hillsides -- steepness, root structures holding the slope in place and soil composition -- and the pathways water follows as it runs downslope and into the soil.

Yet, while the model is better at identifying areas prone to larger and potentially more dangerous landslides, the researchers discovered factors affecting landslide size that can't easily be determined from aerial data and must be assessed from the ground -- a daunting task, if one is concerned about the entire state of California.

The key unknowns are what the subsurface soil and underlying bedrock are like and the influence of past landslides on ground conditions.

"Our studies highlight the problem of overprediction: We have models that successfully predict the location of slides that did occur, but they end up predicting lots of places that didn't occur because of our ignorance about the subsurface," said Dietrich, UC Berkeley professor of earth and planetary science. "Our new findings point out specifically that the spatial structure of the hillslope material -- soil depth, root strength, permeability and variabilities across the slope -- play a role in the size and distribution and, therefore, the hazard itself. We are hitting a wall -- if we want to get further with landslide prediction that attempts to specify where, when and how big a landslide will be, we have to have knowledge that is really hard to get, but matters."

CAPTION

Aerial photograph of a hillslope after a rainstorm in February 2017 that generated 595 shallow landslides in a 16 square kilometer (6.4 square mile) area in the hills west of Williams, California. In the image, the landscape slopes downward from left to right. The darker brown upslope element of each scar is the landslide, while the lighter toned area downslope records the path the landslide took as it mobilized as mudflow, locally scouring and burying the grass in mud. The scale bar in lower left is 11 meters (36 feet) long.

CREDIT

Image provided by the National Center for Airborne Laser Mapping

Models key to targeted evacuations

Decades of studies by Dietrich and others have led to predictive models of where and under what rainfall conditions slopes will fail, and such models are used worldwide in conjunction with weather prediction models to pinpoint areas that could suffer slides in an oncoming storm and warn residents. But these models, triggered by a so-called "empirical rainfall thresholds," are conservative, and government agencies often end up issuing evacuation warnings for large areas to protect lives and property.

Dietrich, who directs the Eel River Critical Zone Observatory -- a decade-long project to analyze how water moves all the way from the tree canopy through the soil and bedrock and into streams -- is trying to improve landslide size prediction models based on the physics of slopes. Airborne laser imaging using LiDAR can provide submeter-scale detail, not only of vegetation, but also of the ground under the vegetation, allowing precise measurements of slopes and a good estimate of the types of vegetation on the slopes.

Slopes fail during rainstorms, he said, because the water pressure in the soil -- the pore pressure -- pushes soil particles apart, making them buoyant. The buoyancy reduces the friction holding the soil particles against gravity, and once the mass of the slide is enough to snap the roots holding the soil in place, the slope slumps. Shallow slides may involve only the top portion of the soil, or scour down to bedrock and push everything below it downslope, creating deadly debris flows that can travel several meters per second.

Each wet year along the Pacific Coast, homes are swept away and lives lost from large landslides, though the threat is worldwide. As illustrated by a landslide in Sausalito exactly two years ago, landslides can originate just a short distance upslope and mobilize as a debris flow traveling meters per second before striking a house. The size of the initial landslide will influence the depth and speed of the flow and the distance it can travel downslope into canyons, Dietrich said.

With earlier computer models, Dietrich and his colleagues were able to pinpoint more precisely the places on hillslopes that would suffer landslides. In 2015, for example, Bellugi and Dietrich used their computer model to predict shallow landslides on a well-studied hillslope in Coos Bay, Oregon, during a sequence of landslide-triggering rainstorms, based solely on these physical measures. Those models employed LiDAR data to calculate steepness and how water would flow downslope and affect pore pressure inside the slope; the seasonal history of rainfall in the area, which helps assess how much groundwater is present; and estimates of the soil and root strength.

In the new paper, Bellugi and David Milledge of Newcastle University in Newcastle upon Tyne in the United Kingdom tested the landslide prediction model on two very different landscapes: a very steep, deeply etched and forested hillside in Oregon, and a smooth, grassy, gently sloped glacial valley in England's storied Lake District.

Surprisingly, they found that the distribution of small and large shallow landslides were quite similar across both landscapes and could be predicted if they took into account one extra piece of information: the variability of hillslope strength across these hillsides. They discovered that small slides can turn into major slides if the conditions -- soil strength, root strength and pore pressure -- do not vary sufficiently over short distances. Essentially, small slides can propagate across the slope and become larger by connecting isolated slide-prone areas, even if they're separated by more solid slope.

"These areas that are susceptible to shallow landslides, even though you may be able to define them, may coalesce, if close enough to each other. Then you can have a big landslide that encompasses some of these little patches of low strength," Bellugi said. "These patches of low strength may be separated by areas that are strong -- they may be densely forested or less steep or drier -- but if they are not well separated, then those areas can coalesce and make a giant landslide."

"On hillsides, there are trees and topography, and we can see them and quantify them," Dietrich added. "But starting from the surface and going down into the ground, there is a lot that we need in models that we can't now quantify over large areas: the spatial variation in soil depth and root strength and the influence of groundwater flow, which can emerge from the underlying bedrock and influence soil pore pressure."

Getting such detailed information across an entire slope is a herculean effort, Dietrich said. On the Oregon and Lake District slopes, researchers walked or scanned the entire area to map vegetation, soil composition and depth, and past slides meter by meter, and then painstakingly estimated root strength, all of which is impractical for most slopes.

"What this says is that to predict the size of a landslide and a size distribution, we have a significant barrier that is going to be hard to cross -- but we need to -- which is to be able to characterize the subsurface material properties," Dietrich said. "Dino's paper says that the spatial structure of the subsurface matters."

The researchers' previous field studies found, for example, that fractured bedrock can allow localized subsurface water flow and undermine otherwise stable slopes, something not observable -- yet -- by aerial surveys.

They urge more intensive research on steep hillsides to be able to predict these subsurface features. This could include more drilling, installing hydrologic monitoring equipment and application of other geophysical tools, including cone penetrometers, which can be used to map soil susceptible to failure.

###

Other co-authors of the paper are Lauren Larsen and Kurt Cuffey, UC Berkeley professors of geography.

The work was supported by a Gordon and Betty Moore Foundation Data Driven Discovery Investigator Award to Bellugi and Larsen. Dietrich is supported by a National Science Foundation grant for the Eel River Critical Zone Observatory (EAR-1331940). Cuffey was supported by the Martin Family Foundation.

Commuters are inhaling unacceptably high levels of carcinogens

Twenty minutes or longer in the car also raises risk of birth defects

UNIVERSITY OF CALIFORNIA - RIVERSIDE

Research News

 

IMAGE: DRIVER EXERCISING EXTREME CAUTION IN HIS CAR. view more 

CREDIT: STAN LIM/UCR

A new study finds that California's commuters are likely inhaling chemicals at levels that increase the risk for cancer and birth defects.

As with most chemicals, the poison is in the amount. Under a certain threshold of exposure, even known carcinogens are not likely to cause cancer. Once you cross that threshold, the risk for disease increases.

Governmental agencies tend to regulate that threshold in workplaces. However, private spaces such as the interior of our cars and living rooms are less studied and less regulated.

Benzene and formaldehyde -- both used in automobile manufacturing -- are known to cause cancer at or above certain levels of exposure and are Prop. 65-listed chemicals.

New UC Riverside research shows that the average commuter in California is exceeding the threshold for exposure, breathing in unsustainably high levels of both chemicals.

Both benzene and formaldehyde are carcinogens, and benzene carries the additional risk of reproductive and developmental toxicity.

"These chemicals are very volatile, moving easily from plastics and textiles to the air that you breathe," said David Volz, UCR professor of environmental toxicology.

The study, published in the journal Environment International, calculated the daily dose of benzene and formaldehyde being inhaled by drivers with commutes of at least 20 minutes per day.

It found that up to 90% of the population in Los Angeles, San Diego, Orange, Santa Clara, and Alameda counties have at least a 10% chance of exceeding cancer risk from inhaling the chemicals, based on having 30-minute average commute times.

"Of course, there is a range of exposure that depends on how long you're in the car, and how much of the compounds your car is emitting," said Aalekhya Reddam, a graduate student in the Volz laboratory, and lead author of the study.

Previously, Volz and Reddam studied commuter exposure to a flame retardant called TDCIPP or chlorinated tris, and found that longer commute times increased exposure to that carcinogen as well.

They set out on this study wanting to understand the risk of that compound relative to other chemicals introduced during car manufacturing.

Reddam advises commuters to keep the windows open during their rides if possible. "At least with some air flow, you'd be diluting the concentration of these chemicals inside your car," she said.

Benzene is used to produce synthetic fibers, and formaldehyde is a binder in plastics. "There should be alternatives to these chemicals to achieve the same goals during vehicle manufacturing," Volz said. "If so, these should be used."

###

USA

Corn belt farmland has lost a third of its carbon-rich soil

UMass Amherst researchers used remote sensing to quantify the previously underestimated erosion

UNIVERSITY OF MASSACHUSETTS AMHERST

Research News

 

More than one-third of the Corn Belt in the Midwest - nearly 100 million acres - has completely lost its carbon-rich topsoil, according to University of Massachusetts Amherst research that indicates the U.S. Department of Agricultural has significantly underestimated the true magnitude of farmland erosion.

In a paper published in the Proceedings of the National Academy of Sciences, researchers led by UMass Amherst graduate student Evan Thaler, along with professors Isaac Larsen and Qian Yu in the department of geosciences, developed a method using satellite imagery to map areas in agricultural fields in the Corn Belt of the Midwestern U.S. that have no remaining A-horizon soil. The A-horizon is the upper portion of the soil that is rich in organic matter, which is critical for plant growth because of its water and nutrient retention properties. The researchers then used high-resolution elevation data to extrapolate the satellite measurements across the Corn Belt and the true magnitude of erosion.

Productive agricultural soils are vital for producing food for a growing global population and for sustaining rural economies. However, degradation of soil quality by erosion reduces crop yields. Thaler and his colleagues estimate that erosion of the A-horizon has reduced corn and soybean yields by about 6%, leading to nearly $3 billion in annual economic losses for farmers across the Midwest.

The A-horizon has primarily been lost on hilltops and ridgelines, which indicates that tillage erosion - downslope movement of soil by repeated plowing - is a major driver of soil loss in the Midwest. Notably, tillage erosion is not included in national assessments of soil loss and the research highlights the urgent need to include tillage erosion in the soil erosion models that are used in the U.S. and to incentivize adoption of no-till farming methods.

Further, their research suggests erosion has removed nearly 1.5 petagrams of carbon from hillslopes. Restoration of organic carbon to the degraded soils by switching from intensive conventional agricultural practices to soil-regenerative practices, has potential to sequester carbon dioxide from the atmosphere while restoring soil productivity.

###