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AGBT Meets High Standards, Gets Low, Low, Low…

Advances in Genome Biology and Technology delivers cutting-edge genomics news by day, holds beachside festivities (enlivened by Flo Rida’s “Low”)…



The Advances in Genome Biology and Technology (AGBT) conference, held in the beach town of Hollywood, FL, last month, got its beachside groove back after a couple of landlocked years. Due to COVID-19, the conference took a break in 2021, and last year’s event was held inland, in Orlando, in the steamy month of June. But the four days spent on the coast at this year’s meeting brought back all the positive vibes that AGBT attendees have grown accustomed to: ocean views, dining al fresco, near-perfect weather, and above all, cutting-edge genomics research.

The conference was stacked with news and announcements on spatial biology, single-cell genomics, next-generation sequencing (NGS) and library prep innovations, and the construction of more-complete genomes and pangenomes.

Last year’s AGBT had been chock full of new NGS instrument releases and even new company launches. This year, smaller updates and iterative improvements filled the NGS news stream. The NGS companies in attendance seemed to be sending the same message: We are delivering on the promises we made last year.

Walking the walk

Illumina’s biggest splash was the news that the NovaSeq X, the instrument announced last fall at the Illumina Genomics Forum, was shipped to the company’s first customer, the Broad Institute of MIT and Harvard—a surprise to no one. Illumina also announced, with a much smaller splash, its long-anticipated long-read technology, Complete Long Reads, which relies on comparing “landmarks” on an original, long, single-molecule fragment to unmarked short reads.

Element Biosciences’ messages were hard to miss, as they were emblazoned on its team’s T-shirts. First, Element’s instrument, the AVITI, when coupled with the company’s novel pricing structure (which includes a subscription-like model for reagents), now offers a whole human genome sequence for as little as $200. Second, now that the AVITI is shipping, there is no lag time for manufacturing. Third, Element’s new cloudbreak chemistry, which uses new enzymes, has shortened the AVITI’s run time. And fourth, in a sponsored talk given by co-founder Matt Kellinger, PhD, the company did not shy away from making direct comparisons between the AVITI system and other platforms on the market—most notably, Illumina’s. In fact, Kellinger very candidly set the two side by side.

The other San Diego–based newcomer, Singular Genomics, was a bit more reserved, letting the advantages of its technology speak for itself. The company announced a new flow cell (the F3) for its G4 sequencing platform and a new kit (Max Read Kits) that will enable single-cell genomics.

Ultima Genomics, the latest entrant to the field, was even more reserved. (Indeed, the company was hard to find.) Last year, Ultima had a suite that was constantly packed. Curious onlookers swarmed an enormous instrument (UG-100) in the middle of the room to learn about the new technology. This year, there was no instrument, no suite, no onlookers. CEO Gilad Almogy, PhD, told GEN that Ultima is focused on its existing customers of the early-access plan.

AGBT is known for its intense activities during the day and at night. This year, Pacific Biosciences raised the bar on the meeting’s entertainment by sponsoring a Flo Rida concert. Although genomics experts may have been an atypical audience for the rapper, everyone embraced replacing their conversations about long reads and plex with singing and dancing for the evening.

Pacific Biosciences (PacBio) was not so reserved. From team-wide uniforms that included pink Converse shoes and tie-dyed T-shirts, to a full-blown evening concert by rapper Flo Rida, PacBio seems to be having one big party. Like Illumina, PacBio had an announcement about an instrument it introduced. In PacBio’s case, the instrument is the Revio. It started shipping the week of this year’s AGBT. Users will have to wait longer for PacBio’s short-read platform, the Onso, which will begin shipping later this year. Jonas Korlach, PhD, PacBio’s co-founder and CSO, stressed the importance of the company’s long-read technology in transcriptomics. He told GEN that that “short-read RNA-seq is completely inadequate to resolve the complexity of the transcriptome.”

Complete Genomics at AGBT 2023
At the AGBT meeting, Complete Genomics announced that it was launching two new instruments and a novel library prep kit for long fragment sequencing. During a well-attended presentation, Complete Genomics’ chief science officer, Radoje (Rade) Drmanac, PhD, explained how the company’s sequencing technology works.

The one exception to small NGS announcements was Complete Genomics, which launched a pair of new instruments at AGBT—just weeks after making waves at the J.P. Morgan Healthcare Conference with the news that its fleet of instruments is now available in the United States. One of the two machines launched at AGBT is the most high-throughput sequencing instrument in existence—the DNBSEQ-T20—which Complete says offers a whole human genome sequence for less than $100. On the other side of the spectrum is the DNBSEQ-G99, an ultra-high-speed gene sequencer offering mid- to low-range throughput that runs in 12 hours.

Women at the center

On Tuesday evening, as the various parties in the suites were getting started, four women were honored with the inaugural Women Changing Science awards, high up on the 32nd floor of the event’s venue, the Diplomat Beach Resort Hollywood. Presented by the Rosalind Franklin Society, in conjunction with Rosalind (formerly OnRamp Bio), the honorees were Aruna Ayer, PhD, senior director, Single Cell Multiomics R&D at BD Biosciences; Julia Kennedy-Darling, PhD, vice president of innovation at Akoya Biosciences; Pardis Sabeti, PhD, an institute member at the Broad Institute and an HHMI investigator; and Yan Zhang, PhD, CEO of Mission Bio. It was a beautiful celebration of well-deserving women in genomics.

At AGBT 2023, the Rosalind Franklin Society and Rosalind
At AGBT 2023, the Rosalind Franklin Society and Rosalind, a software company, inaugurated the Women Changing Science awards program. It recognizes women who not only produce outstanding science, but who also dedicate themselves to supporting other women in the genomics community. The four winners this year were (in alphabetical order) Aruna S. Ayer, PhD, BD Biosciences; Julia Kennedy-Darling, PhD, Akoya Biosciences; Pardis Sabeti, MD, PhD, Broad Institute; and Yan Zhang, PhD, Mission Bio. In this image, award presenters flank three of the winners: Sabeti, Ayer, and Kennedy-Darling stand second, third, and fourth from the left.

Spatial: Plex vs. resolution

There were fewer spatial companies at AGBT than last year, but the fervor over the technology was undiminished. The opening session of the conference included a talk by Chris Mason, PhD, professor of physiology and biophysics at Weill Cornell Medical School about a project to create a Spatial Atlas of Human Anatomy (SAHA)—in collaboration with NanoString Technologies—with maps of 30 organs from a healthy and genetically diverse population of adults.

Jasmine Plummer, PhD at AGBT 2023
The recent AGBT meeting showcased new technology (as this article emphasizes), but the event also presented cutting-edge research. For example, speakers discussed evolutionary genomics, complete chromosome assemblies, pangenomes, and SARS-CoV-2. Many speakers participated in brief “Flash Talks,” which followed each other in rapid succession. As shown here, Jasmine Plummer, PhD, director of the Center for Spatial Omics at St. Jude Children’s Research Hospital, presented a Flash Talk on building a spatial atlas of breast cancer in women of African descent.

NanoString Technologies (AGBT’s gold sponsor) is putting its money on plex—how many transcripts its instrument can measure. The company’s big news was that one of its two spatial instruments, the CosMx, will be capable of 6,000-plex assays in 2024.

spatial biology
Akoya Biosciences delivered presentations at AGBT 2023 highlighting the PhenoCycler-Fusion. The multiomics spatial biology system was used to produce this image, which shows a breast cancer tissue microarray that was stained with 100 RNA and 100 protein moieties. Notice that RNA and protein markers were detected in the same section.

Akoya Biosciences is looking at spatial from a different angle. The company’s platform is much lower plex—100 proteins. When asked if that is sufficient, Niro Ramachandran, PhD, chief business officer for Akoya, assured GEN that it is “plenty.” Ramachandran said Akoya is happy to let the other companies work on increasing their plex because, he explained, higher plex comes with tradeoffs of time and data. Akoya hopes that researchers that have done their high-plex discovery will use the company’s instrument to uncover new biology through more-targeted questions.

Known for its spatial protein system, Akoya is moving into RNA. The first iteration of this is the incorporation of 12 RNA transcripts from the RNA-scope platform from Advanced Cell Diagnostics (ACD). In the second half of the year, the company indicated, customers will be able to run 50–100 targets.

Bruker showed off its MALDI HiPLEX-IHC imaging workflow at AGBT 2023. The workflow, which can visualize small molecules, lipids, glycans, proteins, and more from the same tissue section, was used to produce this image, a spatial multiomic overlay of a representative lipid and two proteins that were detected in a fresh-frozen sagittal mouse brain section.

Although “multi-omics” is a buzzword, many spatial companies like Akoya are working on “di-omics”: RNA and protein. An exception is Bruker, which had its mass spectrometry team at the conference show off the company’s MALDI HiPLEX-IHC Imaging system. It can visualize small molecules, lipids, glycans, proteins, and more from the same tissue section.

The German company Resolve Biosciences had a lower profile this year, having been the top sponsor in 2022. The firm announced a different approach for spatial biology researchers. It involves a service called Meridian, which processes customers’ slides on the company’s molecular cartography instrument, allowing researchers to run spatial experiments without having to use their own equipment.

10X Genomics’ Xenium has started shipping, with Yutaka Suzuki, PhD, from the Laboratory of Systems Genomics at the University of Tokyo being the first to report data. 10X also launched the Xenium Catalyst Program, where customers can send samples in. The company also teased progress on the highly anticipated  Visium HD—a higher resolution version of the firm’s widely used, slide-based Visium Spatial Gene Expression platform.

Vizgen announced that last year that it had installed 70 platforms, each of which can analyze up to 500 transcripts, with plans to reach 1,000 this year. Vizgen’s hallmark is customization—a researcher can design a fully individualized panel. That said, the company will also be launching two premade panels this year, one in neurology and one in oncology.

A newcomer to the spatial world, Pixelgen Technologies, appeared at AGBT for the first time. The company is introducing a new approach to spatial proteomics called molecular pixelation. Founded by Simon Fredriksson, PhD, CEO (and former co-founder, CEO, and CSO of the proteomics company Olink), the Stockholm-based company makes a kit that, using antibodies bound with DNA tags, creates a DNA inference mesh that can inform how proteins co-locate toward one another. This technology is uniquely situated to studying immunology because the location of the outer surface proteins of immune cells is fundamentally important for understanding their biology.

Just a kit

With big, expensive instruments getting so much attention, the front and back ends tend to stay out of the limelight. But multiple companies, such as New England Biolabs (NEB), Watchmaker Genomics, and Roche were talking about innovations in library prep such as new enzymes, RNA library prep, and nucleic acid library prep for formalin-fixed, paraffin-embedded samples. As Andrew Barry from NEB told me, “Sample prep—that’s where the fun stuff happens.”

Some companies are choosing to democratize sequencing technology by offering just a kit, rather than a large, expensive platform. 10X Genomics’ Visium is one such example. Also, the Seeker was launched by Curio Bioscience the week of AGBT (although the company were not present at the meeting). Seeker is a slide-based kit based on the Slide-Seq spatial technology developed at the Broad in 2019.

In the single-cell space, Parse Biosciences offers sc-RNA seq kits developed from the technique known as Split Pool Ligation-based Transcriptome sequencing (SPLiT-seq). At AGBT, the company announced the availability of two kits that allow more targeted scRNA-seq: a TCR kit for immune profiling applications and a Gene Capture kit, which allows more samples to be analyzed with less sequencing.

Whether attendees found themselves hearing about kits, instruments, flow cells, or price drops, or dancing at a Flo Rida concert, AGBT 2023 was one for the books. And lessons from the event should inspire the genomics community throughout the year. I cannot wait to see what will happen at AGBT 2024.

The post AGBT Meets High Standards, Gets Low, Low, Low… appeared first on GEN - Genetic Engineering and Biotechnology News.

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US Job Openings Unexpectedly Soar Above Highest Estimate Even As Number Of Quits Tumble

US Job Openings Unexpectedly Soar Above Highest Estimate Even As Number Of Quits Tumble

For those following the recent sharp drop in job openings,…



US Job Openings Unexpectedly Soar Above Highest Estimate Even As Number Of Quits Tumble

For those following the recent sharp drop in job openings, or perhaps merely fascinated by the narrative that AI will cause a margin-busting corporate revolution as millions of mid-level employees are replaced by a cheap "bullshitting" AI algorithm, then today's latest bizarro JOLTS report will come as a shock. That's because after three months of sharp declines, the BLS reported that in April the number of job openings soared by 358K from an upward revised 9.7 million to 10.1 million, the biggest increase since Dec 2022...

.... and printing not only above the median consensus which expected the trend to continue with 9.4 million job openings this month, but came higher than the highest Wall Street estimate! As shown in the chart below, the delta to median consensus print was a whopping 703K.

According to the BLS, the biggest increase in job openings was in retail trade (+209,000); health care and social assistance (+185,000); and transportation, warehousing, and utilities (+154,000)

The sudden, bizarre reversal in the job openings trend, meant that after falling to the lowest level since Sept 2021, in April the number of job openings was 4.446 million more than the number of unemployed workers, the highest since January.

Said otherwise, after dropping to just 1.64 job openings for every unemployed worker, the lowest since Nov 2021, in April there were 1.79 openings for every worker, a sharp spike back to levels that the Fed does not want to see.

To be sure, none of the above data are credible for reasons we have discussed before but the simplest one is because the response rate of the JOLTS survey is stuck at a record low 31%. Which means that only those who actually have job openings to report do so, while two-thirds of employers are either non-responsive or their mail is quietly lost in the mail.

Another reason why today's data is meaningless is that even as employers allegedly put up many more job wanted signs, the number of workers actually quitting their jobs - a proxy for those who believe they can get a better-paying job elsewhere, and thus strength of the overall job market - tumbled by 129K to 3.8 million, the lowest number since May 2021.

Even the Fed's WSJ mouthpiece Nick Timiraos ignored the stellar headline print, and instead focused on the plunge in quits, writing that the "rate of workers who are voluntarily leaving their jobs (including leisure and hospitality) is returning closer to pre-pandemic levels, a possible sign of less tight labor markets. Quits tend to rise when workers think they can receive better pay by changing jobs."

And the biggest paradox: as pointed out by Peter Tchir of Academy Securities, the seasonally adjusted JOLTS quits rate was 2.4 (we reached a "peak" of 2.4 in July 2019), while the Hires rate (also seasonally adjusted) was 3.9% just like it was 3.9 in July 2019. So allegedly there are 3,000,000 more jobs available now than then.

So what to make of this bizarro, conflicting report?

Well, after three months of drops in job openings, at a time when it is especially critical for Biden to still maintain the illusion that at least the labor market remains strong when everything else in the senile president's economy is crashing and burning, it appears that the BLS got a tap on the shoulder once again, especially when considering that the one category that will be most impacted by ChatGPT and which according to Indeed is seeing a collapse in job postings was also the one category that had the highest number of job openings.

Tyler Durden Wed, 05/31/2023 - 10:35

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The U.S. Office Sector: Further Disruption and Rightsizing May Give Way to a Golden Age

The NAIOP Research Foundation, as part of its Industry Trends meeting, recently hosted a panel discussion on what’s next for the office sector. The panelists…



The NAIOP Research Foundation, as part of its Industry Trends meeting, recently hosted a panel discussion on what’s next for the office sector. Analysts from leading service firms joined NAIOP Research Foundation Governors and office developers Greg Fuller, president and COO, Granite Properties and Paul Ciminelli, president and CEO, Ciminelli Development, to discuss problems and potential opportunities. The panelists agreed that the sector will undergo a shakeout that will include transformation, streamlining, new approaches to work and holistic solutions.

A “Broken” Market

Remote work and economic headwinds have created a negative demand shock in the office sector and a temporarily “broken” market that has not yet reached stability. Before the pandemic, office workspaces were densifying, with less square footage assigned per employee. Remote work and downsizing accelerated this trend, with tenants now needing less space per employee. Although office-using employment has rebounded from the brief pandemic-induced recession, office space demand has declined sharply. Phil Mobley, national director of office analytics at CoStar, estimated that the gap between office-using employment and previously expected demand could be as much as 400 million square feet. As supply continues to come online, vacancy rates will continue to climb over the next three years with negative absorption levels higher than during the Great Financial Recession.

According to Mobley, sublease availability is a key indicator of the market’s health, and it has more than doubled since 2019 and continues to rise. While transactions have slowed down, the ones that have taken place in the last two years have been at lower price points, but with strong fundamentals such as lower cap rates, which gives the impression of positive price growth. However, this masks some of the underlying problems that will inevitably come to light during loan maturities and price discoveries. The Mortgage Bankers Association reports that over 40 percent of office loans are maturing in the next 20 months.

The Hardest-hit Buildings

Not all markets, nor all types of office buildings are experiencing dramatic setbacks. CBRE’s Global Head of Occupier Thought Leadership, Julie Whelan, and her team conducted a study to identify the buildings that saw the most significant increase in vacancies. Their research revealed that smaller buildings (between 100,000-300,000 square feet) constructed between 1980 and 2009, located primarily in downtown areas with limited surrounding amenities and/or in high crime areas, were the most affected. Furthermore, the study found that only 10% of the buildings in the 64 markets examined accounted for 80% of the vacancies from Q1 2020 to Q1 2023.

During the pandemic, the vacancy rates of buildings in downtown markets have surpassed those of suburban areas. Specifically, 41% of buildings with the highest vacancy rates are in downtown markets, mainly in the Pacific Northwest and Northeastern regions of the United States. For instance, San Francisco’s vacancy rate has surged from 4% before the pandemic to almost 30% due to its reliance on the tech sector. Additionally, buildings located in high-crime areas (usually downtowns) and those with fewer adjacent amenities (usually suburbs) are struggling to retain tenants. However, there are opportunities to reposition or reinvent these properties, but they will require innovative public-private partnerships and community-based approaches. What surrounds office buildings, such as safe and walkable mixed-use communities, is just as crucial as what is inside them, according to Whelan.

Back to the (New) Office

The shift to remote and hybrid work has had a significant impact on office space demand. However, many companies are realizing that returning to the office more often offers advantages. While some employers have opted for 100% remote, hybrid, or office-centric policies, Lauren Hasson, the vice president of workplace strategy at JLL, has noticed a growing number of companies that want their employees back in the office at least three days a week. Studies have shown that it is difficult to engage and mentor employees who are not physically present. Furthermore, there has been a decrease in innovation, as evidenced by a decline in patent applications. Remote job postings have decreased, but employee demand for remote work remains high. Remote job listings on LinkedIn reached their peak in early 2022 at around 20% before recently falling to 12%. However, over 50% of job applications submitted are for remote positions, indicating that many job seekers may need to accept hybrid or in-person jobs. Markets with higher costs of living, intense talent competition, and long commutes, such as Boston, San Francisco, and New York, tend to advertise a higher percentage of remote positions and have slower rates of return to the office.

Hasson has reported that companies that require employees to work in the office only one or two days a week have the highest turnover rates. Thus, companies that offer either full-time remote or full-time in-office work have a better chance of retaining their talent. However, tenants that require in-person work are offering more amenities, and flexibility while creating C-suite positions such as “Chief Workplace Experience Officer” to ensure employee satisfaction and engagement. Hasson believes that enhanced office workspace will become the ultimate recruiting tool, similar to how prospective students consider a university’s athletic facilities and campus environment. According to Hasson, the new experiential office environment, which will be fueled by innovation, creativity, employee diversity, and cutting-edge technology, will recalibrate the sector and ultimately usher in a “golden age” of work.

Developers’ Perspectives

According to Ciminelli and Fuller, the office market is going through both cyclical and structural changes. While some office properties are flourishing, others lack the necessary amenities and locations to attract employees. Fuller noted that pre-pandemic, office buildings were rarely completely occupied, with a strong occupancy rate of 72%. Currently, occupancy rates vary between 40 and 65%.

Certain buildings are structurally obsolete or not ideal for conversion, particularly when considering residential use. In some cases, it may not be feasible to convert due to the property’s floorplan or location. Furthermore, the costs associated with redevelopment have risen considerably, making it necessary to acquire properties at lower costs.

Despite the challenges ahead, Fuller and Ciminelli anticipate opportunities once the dust settles. The office market will gradually reach an equilibrium as employees return to work, albeit with more flexibility and discipline in office space utilization. Like the retail sector, the office market will undergo a rightsizing process, ultimately emerging more streamlined and beneficial for both employees and employers.

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April JOLTS report noisily shows continued deceleration

  – by New Deal democratIt is always a bad idea simply to project a current trend forward, especially with data series that are noisy and heavily revised….




 - by New Deal democrat

It is always a bad idea simply to project a current trend forward, especially with data series that are noisy and heavily revised. That was certainly on display with the April JOLTS report.

For the last several years, the jobs market has been a game of “reverse musical chairs,” where there are always more chairs than participants. Those employers whose chairs weren’t filled had to increase their wage and/or benefits offerings, or go without. This was good for labor, but certainly put pressure on prices as well. 

Because the jobs market has remained so strong, it has been unlikely that a recession would start unless the situation with job openings returned to at least close to its pre-pandemic levels. Only then could there be enough layoffs to actually be consistent with a negative monthly jobs number.

Last month, there were steep declines in job openings and hires also declined significantly. This morning’s report reversed some of those dynamics, while the overall trend of deceleration remained intact. 

Job openings (blue in the graphs below) rose 353,000 (from a March number revised higher) to 10.013 million annualized (from a peak of 12.027 million in March 2022, vs. 7 million just before the pandemic), and actual hires (red) rose 47,000 from a downwardly revised March to 6.115 million (vs. a peak of 6.843 million in November 2021 and 6 million just before the pandemic).  Voluntary quits (gold) declined -49,000 to 3.793 million (vs. a peak of 4.501 million in November 2021 and 3.5 million just before the pandemic:

All of the above remained close to 2 year lows. 

Here is the longer term view of all 3 metrics from the series inception, better to show the current situation with the historical one before the pandemic hit:

All three remain at levels higher than at any time before the pandemic hit.

Contrarily, layoffs and discharges decreased -264,000 to 1.581 million annualized, reversing last month’s big increase:

But even so, April’s number remains well above the average for the past 2 years.

Here is the longer term historical record for layoffs showing how, before the pandemic, the current level would be extremely low:

There are two overarching trends in this data:

(1) the absolute fundamentals for labor remain quite positive,
(2) but they continue to decelerate.

All of the above remains consistent with a very positive jobs report this coming Friday, but continuing to show deceleration compared with the last 12 months.

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