Daily Archives: October 5, 2021

Inside Line: Another epic contest between South Africa and New Zealand shows why rivalry is so precious – Telegraph.co.uk

Posted: October 5, 2021 at 4:32 am

Within two minutes, New Zealand and South Africa are into their stride and establishing their traditional attributes. What was so special about this contest, though, was how they both pushed one another beyond those strengths.

Transition has become a buzzword to describe a broken-field situation that arises from a change in possession. South Africas first try arrived from a particularly chaotic double transition.

Ardie Savea forces a clever turnover as an upright tackle on Kolisi collapses in front of him. New Zealand switch from defence to attack and attempt to capitalise by spreading the ball across their own 22.

But South Africas transition from attack to defence is sharp, too. Damian de Allende and Lukhanyo Am press and Taylor cannot control David Havilis pass. The spill is costly:

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Inside Line: Another epic contest between South Africa and New Zealand shows why rivalry is so precious - Telegraph.co.uk

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Covid:19 New Zealand falls 37 spots on global ranking of best places to be amid the pandemic – Stuff.co.nz

Posted: at 4:32 am

New Zealand has fallen from number one to 38 on a global ranking of the best places to be in a world grappling with the extra-infectious Delta strain of Covid-19.

New Zealand claimed the top spot on Bloombergs first Covid Resilience Ranking in November 2020 but has fallen behind nations in Europe, North America, the Middle East, Africa and other parts of Asia-Pacific as it battles to contain the Auckland outbreak, strives to boost vaccine uptake, and retains strict border controls.

Bloomberg

NZ has experienced a dramatic drop on the Covid Resilience Ranking, while Ireland has done the opposite.

No. 1 at the rankings inception last November, New Zealand fell nine spots from August to No. 38, the media and financial giant said. A Delta incursion after months virus-free has left the country in varying degrees of lockdown, still seeking to stamp out infections as it strives to boost vaccination levels.

Forty-two days into Aucklands lockdown, Director-General of Health Dr Ashley Bloomfield announced a spike in cases in New Zealands biggest city, saying these were expected. Of the 45 new community cases, 12 are unlinked to existing cases.

READ MORE:* Covid-19: 45 new cases in Delta community outbreak, highest number in three weeks* Ireland and Covid-19: More than 1000 cases every day but normality looms * Covid-19 NZ: How viable is New Zealands coronavirus elimination plan in the time of Delta?

Ireland, which has a similar sized population to New Zealand, has taken the opposite trajectory, climbing from about 40 in early January when it had the worst rate of infection in the world to number one on the list.

As Stuffs explainer editor Keith Lynch wrote in a recent article on Irelands handling of the virus, the country has been hard hit by the pandemic, recording more than 370,000 cases and more than 5000 deaths.

David White/Stuff

New Zealands handling of the Auckland outbreak has contributed to its fall in the ranking.

With some 90 per cent of its population aged 18 and over now vaccinated, however, it has become what the Financial Times described in August as a vaccine poster child. Despite the arrival of the Delta variant, Ireland has continued to ease restrictions in an effort to return to relative normality but is taking a cautious approach to reopening to the rest of the world.

Bloomberg attributed Irelands startling turnaround in part to a Europe-wide strategy involving limiting quarantine-free to people who were fully vaccinated or who had proved they have recovered from the virus. It also commended the country for boosting vaccination levels by bestowing more domestic freedoms on the inoculated while allowing social activity to resume safely.

Bloomberg

NZ has experienced a dramatic drop in Bloomberg's Covid Resilience Ranking.

Bloombergs Covid Resilience Ranking is designed to provide a monthly snapshot of which of the worlds 53 biggest economies are handling the virus best, with the least social and economic upheaval. Factors taken into consideration include virus containment, healthcare quality, vaccination coverage, overall mortality, GDP (gross domestic product) growth forecast, and progress towards easing border restrictions and restarting travel.

New Zealands resilience score of 59.6 per cent reflected its relatively low vaccination rate (44 per cent of the eligible population were fully vaccinated as of September 28), lockdown severity and closed borders, among other factors. New Zealand and Malaysia were judged to have the strictest lockdowns of all 53 economies on the list.

The top five economies on the ranking were all in Europe, with Spain, the Netherlands, Finland and Denmark trailing Ireland, while the United Arab Emirates, where more than 92 per cent of the population is vaccinated, came in at number six. France, Switzerland, Canada and Norway, which recently scrapped most remaining Covid-related restrictions, rounded out the top 10.

New Zealand, now in the bottom half of the ranking, was one of several Asia-Pacific nations to drop down, with Bloomberg saying the region is faltering in the era of vaccination.

123 rf

Spain came in at number two on the resilience ranking, trailing Ireland and just ahead of the Netherlands, Finland and Denmark.

Not only are their strict measures less effective in the face of Delta, former top rankers in the region are also grappling with how to reopen after such a long period of isolationist border curbs.

Singapore, which is moving towards a vaccine-led reopening, fell 11 places since the last ranking as a surge in cases saw some restrictions reimposed, while Hong Kong dropped two spots. Australia fell three places to number 34. Mainland China, by contrast, where more than 78 per cent of people are vaccinated, moved up two spots to number 23.

The United States, where Bloomberg said unfettered normalisation regardless of vaccine status drove a surge in cases and deaths, fell three spots to 28, while Britain climbed six places to 16.

The five bottom five spots on the list went to Southeast Asian economies: the Philippines, Vietnam, Malaysia, Thailand and Indonesia.

They were among multiple developing nations sitting in the lower half of the ranking, which Bloomberg said partly reflected the vaccine inequality World Health Organisation chief Tedros Adhanom Ghebreyesus has described as a shame on all humanity.

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COVID-19: What New Zealand can learn from Ireland’s leading vaccination campaign – Newshub

Posted: at 4:32 am

Bloomberg's Resilience Ranking is a "monthly snapshot" of where the virus is being handled the most effectively with the least social and economic upheaval. It is calculated using 12 data indicators that span virus containment, the quality of healthcare, vaccination coverage, overall mortality and progress toward restarting travel and easing border curbs.

After being named the best place to be during the pandemic in November 2020, New Zealand has now toppled 37 places - falling behind nations in Europe, the Middle East, Africa and other parts of Asia-Pacific to settle at 38.

New Zealand's fall from grace has been compounded by an ongoing struggle to stamp out the outbreak in Auckland, a region now approaching two months in lockdown. Prime Minister Jacinda Ardern said officials will scrap stay-at-home orders and look to ease restrictions at the border when 90 percent of the eligible population is vaccinated - but until then, strict controls on international travel will remain in place.

It comes as Bloomberg praises Ireland's "startling turnaround" from the beginning of the year, when it had experienced the worst outbreak in the world.

"Even as the peak summer travel season unfolded alongside delta's spread, Ireland and places like Spain, the Netherlands and Finland held down serious illness and deaths through pioneering moves to largely limit quarantine-free entry to immunized people," the report said.

"Bestowing more domestic freedoms on the inoculated helped boost vaccination levels to some of the highest in the world - over 90 percent of Ireland's adult population has received two shots - while allowing social activity to resume safely."

Despite rising case numbers caused by the highly infectious Delta variant, on July 26 the Irish government opted to open bars and restaurants to people who were fully vaccinated, or who had contracted COVID-19 in the past six months. There were more than 1000 cases that day.

Ireland has continued to gradually ease its restrictions, with cinemas and theatres allowed to increase their capacity to 60 percent as of September 6 - if all members of the audience are fully vaccinated or have recovered from the virus.

Masks continue to remain mandatory on public transport and self-isolation is still expected if someone falls ill.

But Ireland's phased reopening and return to relative freedom has not been without sacrifice, with the country continuing to record significant numbers of new cases each day. On Saturday (local time), 1586 cases were reported, with 40,046 active infections nationwide. On Sunday, 1051 new cases were recorded, with 319 people being treated in hospitals around the country. Sixty of these patients are in intensive care units.

According to Ireland's Health Protection Surveillance Centre, 17 deaths were notified between September 22 and September 28 - this number differs from Worldometers, which has recorded 40 deaths in the week to September 29.

Meanwhile, New Zealand's Government is facing mounting scrutiny with the spotlight on its response. Prominent figures have questioned whether enough is being done to lead the country out of lockdown, such as former Prime Minister Sir John Key, who launched stinging criticism at "self-congratulatory" Ardernfor locking New Zealanders away in a "smug hermit kingdom".

Currently, almost 80 percent of New Zealand's eligible population - those aged 12 and over - have received their first dose of the vaccine, but just 46 percent are fully vaccinated.

Comparatively, as of September 22, around 92 percent of adults aged 18 and over in Ireland have received at least one dose, with over 88 percent of the over-18 population now fully vaccinated.

Karina Butler, an Irish professor of paediatrics and the chair of Ireland's National Immunisation Advisory Committee, says the nation learned about the importance of dispelling misinformation after uptake of the HPV vaccine dropped dramatically in certain areas.

"We've had problems with vaccines before, for example, with the HPV vaccine. When there was dissemination of misinformation, vaccination dropped from 82 percent when it was introduced, right down to 47 percent in some areas," Butler told The AM Show on Monday.

"The experience of that helped set the groundwork for dealing with this. That was where we learned that we had to bring different people together, but also there was information about misinformation that was put out there - I think the public already knew they had to go to trusted sites to get good information about the vaccine, that was one of the things that really helped."

Butler says the COVID-19 vaccination campaign in Ireland has been fortified by a number of different experts from various sectors of the health system, covering all areas of concern. For example, women who are worried about getting vaccinated during pregnancy are able to receive accurate information from obstetricians, whose voices are represented in the rollout.

"The drive has been led by public health and with appropriate clinicians," Butler said.

"It was bringing the right voices and clinical voices to the fore so that people could listen [to] and trust the message, a single message that was given."

She believes complacency could be an issue for New Zealand, a nation that has recorded only 3995 cases and 27 deaths since the pandemic began last year. Comparatively,Ireland has recorded more than 5200 deaths and over 393,000 cases.

She says if people don't see the virus as a threat, there is less urgency to get vaccinated.

"We really dealt with tragedy all around it has hit almost every family and extended family. There's no doubt that made people realise that COVID really is a serious infection and different from the flu people did learn that lesson in a very hard way," Butler said.

She noted there are no monetary incentives in Ireland to encourage uptake of the vaccine, however public health teams are continuing to target harder-to-reach communities. She says an important element is providing information and resources in their own language to foster a greater sense of trust and unity.

Young people in Ireland have been particularly motivated by the prospect of not being able to travel abroad, Butler said. As summer approached, the younger demographic were spurred by the knowledge that if they were unvaccinated, they would be prevented from boarding a plane or eating at restaurants - which served as a "big incentive".

With summer around the corner in New Zealand, the Government hopes to introduce digital vaccine certificates sometime in November. As the nation staggers towards its golden target of 90 percent, officials have promised to do everything they can to ensure the public enjoys a "classic Kiwi summer" - hopefully without COVID-19.

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Cane returns to New Zealand squad for autumn Tests – RTE.ie

Posted: at 4:32 am

New Zealand have recalled captain Sam Cane for their northern hemisphere tour but locks Scott Barrett and Patrick Tuipulotu are returning home for family reasons.

Cane, who missed New Zealand's Rugby Championship campaign due to injury, will join up with the squad in Washington ahead of the All Blacks' meeting with the United States on 23 October.

Sam Whitelock, Dane Coles and Shannon Frizell have also been added to the squad that won the Rugby Championship alongside 20-year-old newcomer Josh Lord.

"From a physical point of view, we have come through The Rugby Championship really well," said New Zealand head coach Ian Foster.

"Therefore, we've decided to add fewer players than first anticipated for the next part of our 12-week tour."

With the squad unable to return to New Zealand from Australia due to pandemic restrictions, the All Blacks will hold a training camp on the Sunshine Coast before leaving for the United States on 17 October.

Following the game against the Eagles, the squad will travel to Europe to face Wales on 30 October before taking on Italy a week later.

That is followed by a Dublin Test against Ireland on 13 November, with the tour finishing in Paris and a meeting with France on 20 November.

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Grant Dalton: The stakes just raised in the America’s Cup – Stuff.co.nz

Posted: at 4:32 am

Fiona Goodall/Getty Images

Team New Zealand boss Grant Dalton, left, and his right-hand man Kevin Shoebridge have plenty to ponder for the next defence of the Americas Cup.

Grant Dalton says the growing Formula One influence on the Americas Cup emphasises Team New Zealands need to solidify their finances for the defence of the Auld Mug.

Sir Ben Ainslies Britannia syndicate confirmed a major partnership with F1 champions Mercedes-AMG Petronas on Tuesday. There is speculation the imminent return of former Cup champions Alinghi will come in a deal with F1 giants Red Bull Racing, while there have been whispers of Italians Luna Rossa getting involved with Ferrari.

The F1 teams will bring major design and development resources as the challengers look to chase down Team New Zealands winning advantage.

INEOS Britannia

World champions Mercedes come on board for AC37

Mercedes could throw as many as 50 staff at the Britannia project headed by James Allison, the chief technical officer of the F1 outfit who has played a key role in the creation of 13 constructors championship winning cars.

READ MORE:* America's Cup: British poach Luna Rossa designer, bulk up Mercedes F1 link * Sir Ben Ainslie ramps up America's Cup challenge with serious makeover* America's Cup hosting venue decision delayed

Team New Zealand boss Dalton looks with envy at the resources increasingly available to their well-funded rivals. As he tries to pin down a hosting deal to provide the financial security for the defence of the Cup, the British development is a reminder of what the champion syndicate is up against.

Congratulations to Britannia and their relationship with Mercedes, its impressive, Dalton told Stuff.

To me, it just gives context as to why we cant contemplate an under-funded campaign.

Thats because this (British) team are not only fully weaponised now as they move forward with their design process, they also have as much money as they need.

The challengers know that to beat us they have to do it differently, something that we have always done. Now, it seems we are being hung by our own success.

RICKY WILSON

The British now have Luna Rossas chief designer on board.

The British syndicate, backed by Sir James Ratcliffe, have also managed to lure Luna Rossas chief designer from their last two campaigns, Martin Fischer, into their camp another telling sign of how they are ramping up their campaign after boat frustrations in the last two Cups.

The hosting process for the next Americas Cup continues with Team New Zealand reappraising the offshore options. While Auckland remains on the table, Dalton says another home defence just isn't fundable - at the moment, emphasising at the moment.

This is going to another level now, and we wont succeed with sausage sizzles and club raffles, he said.

Team New Zealand dont have the billionaire benefactors of their rivals and a successful offshore hosting arrangement must include the venue providing a large chunk of the funding Team New Zealand wants and needs.

The hosting delay is a distraction Team New Zealand could do without as time ticks away. Dalton knows the defenders cant sit still while their challengers gather increasing resources.

Team New Zealands innovative design department is in full swing under the ongoing guidance of Dan Bernasconi. They are currently working on the 40-foot foiling monohulls that will be used for the youth and womens Americas Cup regattas to be sailed alongside the main event, hopefully in 2024.

Dalton said the words from Toto Wolff, the Mercedes F1 team principal, that the Americas Cup appeared harder to win than Formula One, were telling.

Mercedes were involved with the British challenge in Auckland, but only came on board late. Wolff believes they can now be far more influential.

I think last time around we came in more in a function of 'troubleshooting'. We weren't really part of the design process. And I don't just mean hardware. I'm talking about the process, the tools, the structure, the strategy ... we are doing it properly now."

Ainslie, who has sailed with Team New Zealand, won the Cup with Oracle, and is now into his third campaign in charge of a British challenge, sees huge gains in this Mercedes deal.

It is game-changing, he told The Telegraph in the UK.

Whether or not it will mean us winning the Cup this time around, I cant tell you right now. I hope it does. But either way, I hope that we can continue working together, because it has the capability to take us to the next level.

RICKY WILSON/Stuff

Team New Zealand's radical America's Cup-winning boat Te Rehutai is full of secrets that are central to the defence of the Auld Mug.

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Genome-Wide Association Study of Peripheral Artery Disease – DocWire News

Posted: at 4:31 am

This article was originally published here

Circ Genom Precis Med. 2021 Oct 4:CIRCGEN119002862. doi: 10.1161/CIRCGEN.119.002862. Online ahead of print.

ABSTRACT

BACKGROUND: Peripheral artery disease (PAD) affects >200 million people worldwide and is associated with high mortality and morbidity. We sought to identify genomic variants associated with PAD overall and in the contexts of diabetes and smoking status.

METHODS: We identified genetic variants associated with PAD and then meta-analyzed with published summary statistics from the Million Veterans Program and UK Biobank to replicate their findings. Next, we ran stratified genome-wide association analysis in ever smokers, never smokers, individuals with diabetes, and individuals with no history of diabetes and corresponding interaction analyses, to identify variants that modify the risk of PAD dependent on diabetic or smoking status.

RESULTS: We identified 5 genome-wide significant (Passociation 510-8) associations with PAD in 449 548 (Ncases=12 086) individuals of European ancestry near LPA, CDKN2BAS1, SH2B3-PTPN11, HDAC9, and CHRNA5 loci (which overlapped previously reported associations). Meta-analysis with variants previously association with PAD showed that 18 of 19 published variants remained genome-wide significant. In individuals with diabetes, rs116405693 at the CCSER1 locus was associated with PAD (odds ratio [95% CI], 1.51 [1.32-1.74], Pdiabetes=2.510-9, Pinteractionwithdiabetes=5.310-7). Furthermore, in smokers, rs12910984 at the CHRNA3 locus was associated with PAD (odds ratio [95% CI], 1.15 [1.11-1.19], Psmokers=9.310-10, Pinteractionwithsmoking=3.910-5).

CONCLUSIONS: Our analyses confirm the published genetic associations with PAD and identify novel variants that may influence susceptibility to PAD in the context of diabetes or smoking status.

PMID:34601942 | DOI:10.1161/CIRCGEN.119.002862

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Largest Clinical Research Study to Date Evaluating Optical Genome Mapping for Analysis of Facioscapulohumeral Muscular Dystrophy Showed Concordance…

Posted: at 4:31 am

SAN DIEGO, Sept. 29, 2021 (GLOBE NEWSWIRE) -- Bionano Genomics, Inc. (BNGO) today announced the publication of the largest clinical research study to date evaluating optical genome mapping (OGM) for facioscapulohumeral muscular dystrophy (FSHD), which concluded that OGM can be performed more quickly, accurately, and reproducibly than the current gold standard method of Southern blot analysis. This study, now available online before print in The Journal of Molecular Diagnostics, describes how OGM can be adopted as an alternative to Southern blot analysis for the identification of chromosomal abnormalities associated with FSHD, a neuromuscular disorder resulting in progressive weakness and atrophy of muscles.

FSHD is typically caused by a contraction of a D4Z4 repeat array near the telomere of chromosome 4 (chr 4) at 4q35, which activates a dormant toxic gene, DUX4, to be overexpressed in skeletal muscle. Because of its complex genotype, FSHD can often be challenging to detect using next-generation sequencing (NGS) and Southern blot analysis, which can be slow, laborious and require radioactive labeling. In this robust study of 351 participants, the authors Stence et al., validated the use of OGM with Bionanos Saphyr system to determine the size and haplotype of D4Z4 alleles to confirm a diagnosis of FSHD. The studys authors found that OGM had much higher sizing accuracy and was >99% concordant with Southern blot analysis.

We are pleased to be using optical genome mapping for FSHD mutation analysis because it more reliably identifies the patients mutation and simplifies the initial analysis for the laboratory, said Aaron D. Bossler, MD, PhD, FCAP, Clinical Professor and Director, Molecular Pathology Laboratory at University of Iowa Hospitals and Clinics. The extensive validation that we conducted with optical genome mapping demonstrates the power of this new technology to decrease time to result, improve standardization, and help tease out complex cases.

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OGM is well-suited for analyzing inherited genetic disorders like FSHD that require the measurement of long, intact DNA molecules for accurate sizing. The higher resolution of OGM relative to traditional techniques can enable improved detection and discrimination ability for clinically relevant variants, as was observed in this study.

The study completed by Dr. Stence and team demonstrated the superior performance of OGM over traditional molecular genetic testing for FSHD, commented Erik Holmlin, PhD, CEO of Bionano Genomics. As the largest OGM clinical study to date, the study demonstrated that using the Saphyr system to perform FSHD analysis resulted in a significantly faster turnaround time, as the OGM turnaround time was only 5 days as compared to Southern blot at 11 days. The ability to obtain accurate, reliable data more quickly allowed for the timely application of this information for the management of study participants. We believe that studies like this one could pave the way for broad adoption of OGM for a wide variety of applications in genetic disorders and cancer.

This publication is available at https://pubmed.ncbi.nlm.nih.gov/34384893/

About Bionano Genomics

Bionano is a genome analysis company providing tools and services based on its Saphyr system to scientists and clinicians conducting genetic research and patient testing; it also provides diagnostic testing for those with autism spectrum disorder (ASD) and other neurodevelopmental disabilities through its Lineagen business. Bionanos Saphyr system is a research use only platform for ultra-sensitive and ultra-specific structural variation detection that enables scientists and clinicians to accelerate the search for new diagnostics and therapeutic targets and to streamline the study of changes in chromosomes, which is known as cytogenetics. The Saphyr system is comprised of an instrument, chip consumables, reagents and a suite of data analysis tools. Bionano offers genome analysis services to provide access to data generated by the Saphyr system for researchers who prefer not to adopt the Saphyr system in their labs. Lineagen has been providing genetic testing services to families and their healthcare providers for more than nine years and has performed more than 65,000 tests for those with neurodevelopmental concerns. For more information, visit http://www.bionanogenomics.com or http://www.lineagen.com.

Forward-Looking Statements of Bionano Genomics

This press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. Words such as may, will, expect, plan, anticipate, estimate, intend and similar expressions (as well as other words or expressions referencing future events, conditions or circumstances) convey uncertainty of future events or outcomes and are intended to identify these forward-looking statements. Forward-looking statements include statements regarding our intentions, beliefs, projections, outlook, analyses or current expectations concerning, among other things: the impact of the study results discussed in this press release, including our expectations regarding the studys potential to increase adoption of OGM for analysis of FSHD or other genetic disorders; OGMs superiority in genomic analysis as compared to traditional techniques; the potential benefits resulting from a combination of OGM and NGS technologies; and the advancement of our business strategy. Each of these forward-looking statements involves risks and uncertainties. Actual results or developments may differ materially from those projected or implied in these forward-looking statements.

Factors that may cause such a difference include the risks and uncertainties associated with: the impact of the COVID-19 pandemic on our business and the global economy; general market conditions; changes in the competitive landscape and the introduction of competitive products; incompatibility between our and NGS technologies; future study results that may contradict the results of the study identified in this press release; changes in our strategic and commercial plans; our ability to obtain sufficient financing to fund our strategic plans and commercialization efforts; the ability of medical and research institutions to obtain funding to support adoption or continued use of our technologies; the loss of key members of management and our commercial team; and the risks and uncertainties associated with our business and financial condition in general, including the risks and uncertainties described in our filings with the Securities and Exchange Commission, including, without limitation, our Annual Report on Form 10-K for the year ended December 31, 2020 and in other filings subsequently made by us with the Securities and Exchange Commission. All forward-looking statements contained in this press release speak only as of the date on which they were made and are based on managements assumptions and estimates as of such date. We do not undertake any obligation to publicly update any forward-looking statements, whether as a result of the receipt of new information, the occurrence of future events or otherwise.

CONTACTSCompany Contact:Erik Holmlin, CEOBionano Genomics, Inc.+1 (858) 888-7610eholmlin@bionanogenomics.com

Investor Relations:Amy ConradJuniper Point+1 (858) 366-3243amy@juniper-point.com

Media Relations:Michael SullivanSeismic+1 (503) 799-7520michael@teamseismic.com

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Largest Clinical Research Study to Date Evaluating Optical Genome Mapping for Analysis of Facioscapulohumeral Muscular Dystrophy Showed Concordance...

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How the GOAST in the machine takes the fear out of genomics computing – The Register

Posted: at 4:31 am

Sponsored Theres nothing like a crisis to spur innovation, so its no surprise that the last couple of years has brought the issue of how HPC can power genomics research from the rarified to the mainstream.

And while much of the recent focus has been on issues that affect society on a mass scale, there has been steady progress in Precision Medicine, which aims to provide individualised prevention, diagnosis and treatment based on an individuals specific genomic and environmental backgrounds.

But this all depends on massive efforts to sequence large populations, often at a national level, to capture the genetic variation needed to enable precision treatments.

And while this is a formidable human challenge, it is also a massive technical challenge given that current technology can take over 150 hours to process a single entire genome, even when pushing GPU accelerators to the limit.

Lenovos response to this challenge is its Genomics Optimization and Stability Tool, a hardware and software combination that is up to 167 times faster than traditional environments, but which doesnt rely on specialised accelerators, and therefore comes in at up to 50 per cent lower cost.

Or to put it another way, it enables GPU level speeds, and CPU level costs. And if this makes you prick up your ears, youll want to tune into this webinar on The Role of Genomics Analytics in Precision Medicine, courtesy of Intel and Lenovo on October 13 at 1pm BST.

Youll hear about the latest trends in genomics enabled precision medicine and hear how researchers are now able to analyse an entire genome in minutes, rather than days. All without speciality hardware.

Youll also hear about lessons learned in deploying large-scale omics analytics from seasoned learners and expert panellists who have done just that.

Whether youre a data scientist, bioinformatician, researcher or IT administrator, youll come away better informed as to how GOAST has the potential to transform not just precision medicine, but also virology and agriculture.

So, if you want join Lenovo, Intel, and some of the incredible folks working at the cutting edge of genomics, head here and register now.

Sponsored by Lenovo.

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Comprehensive Genomic Features, Therapeutic Biomarkers Identified in Clear Cell Renal Cell Carcinoma – AJMC.com Managed Markets Network

Posted: at 4:31 am

Investigators reported comprehensive genomic features of patients with clear cell renal cell carcinoma, potentially giving providers a better understanding of the molecular features associated with the disease.

In a recent study, investigators reported the comprehensive genomic features of patients with clear cell renal cell carcinoma (ccRCC), which detailed the relationship between immunotherapy biomarkers and gene alterations. The analysis was published in Frontiers in Oncology.

This is the first large-scale comprehensive genomic analysis for Chinese ccRCC patients, and these results might provide a better understanding of molecular features in Chinese ccRCC patients, which can lead to an improvement in the personalized treatment for these patients, wrote the investigators.

ccRCC is the most common subtype of RCC, accounting for 70% to 85% of RCC cases, and is almost uniformly lethal and is considered critical. ccRCC often lacks sensitivity to radiation and chemotherapy and many efforts are being made to establish a biomarker-oriented therapy.

Some targeted therapies targeting vascular endothelial growth factor (VEGF) have greatly improved the prognosis of patients with ccRCC and the use of an immune checkpoint inhibitor, either alone or in combination with other medications, may also be a potential therapeutic target for patients with ccRCC.

Although some studies have reported on the genomic landscape of ccRCC, most of the data had been collected from patients from Western countries or focused on how gene alterations can help determine disease prognosis. Because of this, the genomic landscape in Chinese patients with ccRCC is in need of further investigation.

Revealing comprehensive genomic features is of great importance for understanding ccRCC and developing new therapeutic lines for patients with ccRCC, the investigators said.

The investigators analyzed genomic profiling of DNA of Chinese patients with ccRCC, who had undergone next-generation sequencing (NGS) between January 2017 and March 2020. In total, 880 patients with ccRCC and NGS data were included in the analysis. Immunohistochemistry staining for programmed death-ligand 1 (PD-L1) expression was also conducted for 460 patients of those patients.

PD-L1 expression is associated with improved overall response rates and longer progression-free survival in patients with metastatic RCC who are being administered immunotherapy.

Among the patients, 95.8% harbored at least 1 pathogenic mutation, with somatic alterations for VHL being the most commonly detected mutation among the samples (59.7%). Mutations in PBRM1 were detected in 18.0% of samples and SETD2 alteration were identified in 12.2% of samples. BAP1 alterations were found in 10.2% of samples and TP53 mutations were found in 9.4%.

When comparing the results to the Center Genome Atlas database, the investigators found a higher mutation frequency of VHL (50.0% vs 59.7%; P < .001) and TP53 (3.5% vs 9.4%; P < .001) among the Chinese cohort. Additionally, the Chinese cohort had a lower mutation frequency of PBRM1 than the database (18.0% vs 31.0%; P < .001).

VHL is a tumor suppressor gene that plays a prominent role in cellular oxygen sensing of ccRCC as well as the tumorigenesis that is associated with the disease. Inactivation of VHL is not associated with anti-VEGF receptor inhibitors, but it may help providers predict the effectiveness of hypoxia-inducible factor-2 inhibitors in ccRCC.

Of the patients who were evaluated for expression of PD-L1, 139 (30.2%) were positive for PD-L1 expression. Five (0.7%) patients were classified as microsatellite instability-high. Moreover, 5.9% (n = 52) of the patients were identified to carry pathogenic or likely pathogenic germline mutations for 22 cancer predisposition genes.

The retrospective nature of the analysis was listed as a study limitation as it prevented the investigators from eliminating a potential selection bias. Another limitation involved the lack of information on the cancer subtypes, treatment histories, and survival outcomes of the patients.

Thus, the effect of the biomarkers on treatment decisions and its correlation with survival outcomes need to be further confirmed in further studies, the investigators suggested.

Reference

Huang J, Cai W, Cai B, et al. Comprehensive genomic landscape in Chinese clear cell renal cell carcinoma patients. Front Oncol. Published online September 9, 2021. doi: 10.3389/fonc.2021.697219

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Comprehensive Genomic Features, Therapeutic Biomarkers Identified in Clear Cell Renal Cell Carcinoma - AJMC.com Managed Markets Network

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In vivo structure and dynamics of the SARS-CoV-2 RNA genome – DocWire News

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Nat Commun. 2021 Sep 28;12(1):5695. doi: 10.1038/s41467-021-25999-1.

ABSTRACT

The dynamics of SARS-CoV-2 RNA structure and their functional relevance are largely unknown. Here we develop a simplified SPLASH assay and comprehensively map the in vivo RNA-RNA interactome of SARS-CoV-2 genome across viral life cycle. We report canonical and alternative structures including 5-UTR and 3-UTR, frameshifting element (FSE) pseudoknot and genome cyclization in both cells and virions. We provide direct evidence of interactions between Transcription Regulating Sequences, which facilitate discontinuous transcription. In addition, we reveal alternative short and long distance arches around FSE. More importantly, we find that within virions, while SARS-CoV-2 genome RNA undergoes intensive compaction, genome domains remain stable but with strengthened demarcation of local domains and weakened global cyclization. Taken together, our analysis reveals the structural basis for the regulation of replication, discontinuous transcription and translational frameshifting, the alternative conformations and the maintenance of global genome organization during the whole life cycle of SARS-CoV-2, which we anticipate will help develop better antiviral strategies.

PMID:34584097 | DOI:10.1038/s41467-021-25999-1

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In vivo structure and dynamics of the SARS-CoV-2 RNA genome - DocWire News

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