Pregnancy
Newborn screening by genome sequencing shown to be safe and effective
Two studies show the potential for genomic screening in newborns to address high rates of infant hospitalisation and mortality.
Presently, hundreds of genetic diseases are either preventable or treatable but currently are detected only after a child falls ill and endures a years-long “diagnostic odyssey,” often receiving diagnoses too late to achieve the best outcomes.
The first study described a novel platform with scalability and performance that will allow millions of babies to be screened and treated by genome sequencing and artificial intelligence within two weeks from birth.
Previously, medical genome sequencing was much too expensive for newborn screening. Plus, a high rate of false positive results – genome findings that falsely suggest a newborn to have a genetic disease – have been of great concern when genomes are examined without clinical context.
Previously, no method existed to translate genome results into treatment guidance in a way that most physicians could understand and put into practice.
The novel platform, BeginNGS (pronounced beginnings) solves this. It makes use of the latest genome sequencing technology to provide an affordable genome.
BeginNGS uses a combination of human and artificial intelligence tools to automate the complex process of interpreting disease risk based on genome information alone, which is critical for scaling to the 3.7 million babies born in the U.S. each year.
The study reported a 97 per cent reduction in false positives based on a method derived from human evolution. The genome variations that cause severe childhood diseases are subject to extreme natural selection called purifying hyperselection.
As a result, DNA variants that truly cause severe childhood disease are not found in genomes of elderly persons. By studying the genomes of almost half a million middle aged and elderly subjects, from the UK Biobank and Mexico City Prospective Study, researchers were able to discover those false positive DNA differences and reduce their occurrence to less than 1 in 50 subjects tested.
The computational methodology uses query federation, a method to analyse genomes remotely without data being moved or shared, which is enabled by TileDB, a database technology partner for BeginNGS.
Remarkably, after removing these DNA variants, BeginNGS retained greater than 99 percent sensitivity when compared with the gold standard method of rapid diagnostic genome sequencing.
BeginNGS used a custom-built clinical guidance system called Genome to Treatment (GTRx) to communicate a potential course of action for babies who screen positive. Many of these disorders are so rare the typical physician will rarely see them in practice.
GTRx provides practical guidance for physicians in a manner that is easy to understand. Testing of over 3,000 children with suspected genetic diseases revealed that 1 in 14 would have benefited from BeginNGS by receiving a time-to-diagnosis of 121 days earlier than compared with gold standard testing after those children developed symptoms.
In addition, testing revealed that BeginNGS would have benefited one in 13 babies who died in infancy.
“The future of newborn genetic screening lies in global collaboration and shared data resources,” says Stavros Papadopoulos, CEO and founder of TileDB.
“By connecting genetic information across international databases, we significantly enhance our ability to identify and understand rare diseases — an endeavour that transcends individual projects and geographical boundaries.
“Through TileDB’s expansion of the BeginNGS consortium and our federated query capabilities, we’re enabling more comprehensive analysis of variant datasets. For RCIGM and the families they serve, this translates directly into faster, more reliable answers during those critical early days of life.”
The second study evaluated whether BeginNGS was ready for broader expansion. In this trail, 120 babies in the neonatal intensive care unit at Rady Children’s Hospital – San Diego, received the BeginNGS screening.
Results were compared with traditional, federally mandated newborn screening and t\rapid diagnostic genome sequencing which evaluated all ~10,000 genetic diseases.
“The amazing, unexpected result of this BeginNGS trial was that nearly 30 percent of NICU babies who weren’t considered to need genome sequencing actually had genetic diseases — this is similar to the rate of diagnosis in babies who are suspected of having genetic diseases,” said Stephen Kingsmore, president and CEO of Rady Children’s Institute for Genomic Medicine
“This suggests that the health benefits of rapid whole genome sequencing apply to every baby admitted to a Level IV NICU, not just those who are currently being tested.”
Only babies who were not suspected of having genetic diseases were eligible for enrolment in the clinical trial since the trial wished to mimic screening of healthy newborns.
BeginNGS genome-based newborn screening was shown to be safe and effective. One in 24 babies tested had positive results that were likely to impact their care.
BeginNGS had no false positives, showing that the purifying hyperselection methods indeed worked in the real world. Eighty four percent of parents in the trial reported that their child’s genomic sequencing results were useful, and 80 per cent felt that participation did their child a lot of good. When compared with state newborn screening, BeginNGS had a higher true positive rate and lower false positive rate.
“Genome-based newborn screening has the potential to transform health outcomes for children with certain rare diseases by accelerating their time to diagnosis and proper care,” said Tom DeFay, vice chair of BeginNGS and deputy head of diagnostics at Alexion, AstraZeneca Rare Disease.
“As a founding member of the BeginNGS Consortium, Alexion is encouraged by these Phase 2 results and remains committed to advancing health equity by helping improve diagnostics for families impacted by rare genetic and often life-threatening conditions.”
These studies pave the way for a much larger, multicentere clinical trial to formally compare BeginNGS with standard newborn screening.
That trial has started and to date is replicating the findings of the pilot study. In addition, now that computational methods exist for removal of false positives, BeginNGS is poised to expand from 412 severe childhood genetic diseases to the more than 2,000 disorders that have been suggested to be actionable early onset rare disorders for newborn screening.
Now that the feasibility of federated queries has been successfully demonstrated it will be possible to expand these to many genome biobanks worldwide to examine the incidence and prevalence of genetic diseases across the globe, allowing BeginNGS be tailored to screen each population.
Insight
Pregnancy and breastfeeding linked to higher cognitive ability in postmenopausal women
Pregnancy and breastfeeding are linked to stronger cognition in postmenopausal women, a long-term study suggests.
Greater cumulative time spent pregnant and time spent breastfeeding correlated with higher overall scores in the study, including verbal and visual memory, in later life.
Researchers analysed annual assessments of more than 7,000 women aged about 70 for up to 13 years using data from the Women’s Health Initiative Memory Study and the Women’s Health Initiative Study of Cognitive Aging.
On average, those who were pregnant for around 30.5 months were expected to have a 0.31 per cent higher global cognition score than those who had never been pregnant.
A lifetime average of 11.6 months of breastfeeding was linked to a 0.12 per cent higher global score.
Each additional month spent pregnant was associated with a 0.01-point rise in overall ability.
Each extra month of breastfeeding showed the same increase, and a 0.02-point gain in verbal and visual memory. Although small, these effects are similar to known protective factors such as not smoking and high physical activity.
The work was led by Molly Fox, an anthropology professor at the University of California, Los Angeles.
Fox said: “Any ways in which we can focus public health outreach or clinical interventions towards higher-risk populations leads to more effective and efficient efforts.”
Participants who had ever been pregnant scored, on average, 0.60 points higher than those who had never been pregnant.
Those who had breastfed scored 0.19 points higher overall and 0.27 points higher for verbal memory than those who had never breastfed.
Women are disproportionately affected by Alzheimer’s disease, a progressive condition that impairs memory and thinking skills, and this is not fully explained by life expectancy differences.
The authors say biology and social factors may both play roles.
They noted that more adult children could contribute to cognitive health by buffering stress, supporting wellbeing or encouraging healthy behaviour.
“If we can figure out, as a next step, why those reproductive patterns lead to better cognitive outcomes in old age, then we can work towards figuring out how to craft therapies, for example, new drugs, repurposed drugs or social programmes, that mimic the naturally occurring effect we observed,” said Fox.
The study team is now working to identify the mechanisms that link reproductive histories to cognitive resilience.
Wellness
Stroke prevention and treatment during and after pregnancy key to women’s health – AHA
Stroke prevention requires aggressive blood pressure control and rapid recognition of symptoms in pregnancy and postpartum, a new scientific statement urges.
The guidance details risk factors for pregnancy-related stroke and offers suggestions for prevention, rapid diagnosis, timely treatment and recovery during pregnancy and postpartum.
A stroke occurs in approximately 20 to 40 of every 100,000 pregnancies and is estimated to account for around four to six per cent of pregnancy-related deaths annually in the US.
The statement was published by the American Heart Association and endorsed by the American College of Obstetricians and Gynecologists.
Eliza Miller is chair of the writing group and associate professor of neurology at the University of Pittsburgh.
She said: “When a stroke occurs during pregnancy or the postpartum period, it can lead to serious complications for both the mother and baby, including neurological deficits, long-term disability, increased risk of future strokes and death.
“Controlling blood pressure and other stroke risks before and after delivery, responding immediately to stroke warning signs and providing timely treatment can help save lives and improve outcomes for mothers and their babies.”
There are two types of stroke: an ischaemic stroke occurs when a blood vessel supplying blood to the brain is blocked by a clot, while a haemorrhagic stroke occurs when a blood vessel ruptures and bleeds into the brain.
Risk factors for pregnancy-associated stroke include chronic hypertension (high blood pressure before pregnancy or diagnosed before 20 weeks), preeclampsia (a dangerous condition causing high blood pressure in pregnancy), advanced maternal age (35 years or older), diabetes, obesity, migraine with aura, infections, heart disease and clotting disorders.
Stroke disproportionately affects people of racial and ethnic minorities. A 2020 meta-analysis found that pregnant Black women are twice as likely to have a stroke compared with pregnant white women, even after adjusting for socioeconomic factors.
The statement authors emphasise that the majority of maternal strokes are preventable with earlier and more aggressive blood pressure control.
“Preeclampsia and eclampsia can occur before, during or after delivery, and the early postpartum period is actually the highest risk time for stroke.
“Very close monitoring of blood pressure is essential,” said Miller.
The statement urges all healthcare professionals who care for pregnant patients, including obstetricians, family medicine practitioners and nurses, to be trained to recognise stroke symptoms so they can promptly start treatment.
“It is crucial for women who are pregnant or have recently given birth and have symptoms of new neurological deficits or severe headache, especially if they also have elevated blood pressure, to be immediately evaluated for possible stroke,” said Miller.
The authors emphasise that pregnancy is not a reason to delay or interfere with recommended treatment for acute stroke.
Various anti-clotting medications are available that are safe for pregnant and lactating women, and mechanical thrombectomy (surgical removal of a blood clot) may be needed for patients with large-vessel blockages.
Survivors of pregnancy-associated stroke face unique challenges such as caring for an infant and require support from a multidisciplinary rehabilitation team.
Mood and sleep disorders are common after stroke and may be intensified by postpartum factors such as hormonal shifts, breastfeeding and disrupted sleep.
Miller said: “Babies depend on their mothers’ well-being, and supporting recovery after stroke, both emotionally and practically, is essential so mothers can heal and families can thrive.”
Insight
Stroke during pregnancy linked to long-term heart and mental health risks
Stroke during pregnancy and postpartum is associated with higher long-term risks of cardiovascular events and depression, a study has found.
Researchers from the University of Helsinki in Finland identified 97 female participants in Finnish healthcare registries who had an ischaemic stroke (the most common type of stroke, which occurs when a clot or blockage reduces blood flow to the brain, depriving it of oxygen and nutrients) during pregnancy or postpartum, up to three months after pregnancy.
They were matched to 280 female participants who did not have a stroke.
Researchers tracked the health of each person through registries and medical records for an average of 12 years, noting which participants later had cardiovascular events such as heart attack, stroke and heart disease or depression.
Of participants with an initial stroke, six per cent had a second stroke and seven per cent had a major cardiovascular event such as heart attack compared to zero per cent of those who were stroke-free at the start of the study.
Anna Richardt, study author from the University of Helsinki, said: “Having a stroke during pregnancy or postpartum is rare but several studies have shown it is on the rise.
“Our study sought to better understand what happens to women after a stroke during pregnancy and postpartum and found an increased risk of cardiac diseases and depression, as well as lower odds of being employed later.”
Researchers also found among participants with stroke, nine per cent had cardiac disease, including atrial fibrillation (an irregular heartbeat) or congestive heart failure (when the heart cannot pump blood effectively), compared to one per cent of those who did not have stroke.
After adjusting for age, participants with stroke had a nearly nine times greater odds of having cardiac disease.
Of participants with stroke, 19 per cent had depression compared to six per cent of those without stroke. After adjusting for age, those with stroke had nearly four times greater odds of having depression.
Researchers also reviewed employment statistics.
Of participants with stroke, 71 per cent were employed two years prior to their stroke compared to 76 per cent of those without stroke. By the end of the study, 66 per cent of those with stroke were employed compared to 78 per cent of those without stroke.
After adjusting for age, researchers found that participants with stroke had 45 per cent lower odds of being employed and nearly five times greater odds of being retired at the end of the study compared to those without stroke.
Richardt said: “Of those with stroke, 92 per cent had good functional outcomes, meaning they had either completely recovered or could manage most daily activities by the end of the study.
“Still, more than one-third of those with stroke were out of work at the end of the study.
“Our findings highlight the need for adequate stroke prevention, monitoring and rehabilitation to improve the long-term health for those who have stroke during pregnancy.”
A limitation of the study was the small number of participants with stroke since stroke during pregnancy is rare.
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