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BALTIMORE – Researchers from the New York Genome Center and Weill Cornell Medicine and their collaborators have demonstrated the utility of Ultima Genomics’ sequencing platform for sensitive blood-based cancer monitoring, using whole-genome error-corrected sequencing of circulating cell-free DNA (ccfDNA) at high coverage. In a preprint posted on BioRxiv last year, the researchers showed that the Ultima sequencing platform, a newcomer in the next-generation sequencing field, generates data that is sufficiently accurate to perform the sensitive mutation calling that is necessary for cancer liquid biopsy testing. Additionally, with the Ultima platform’s low sequencing cost, it is now possible to implement genome-wide duplex error-corrected sequencing for circulating tumor DNA (ctDNA) detection in a cost-effective way, they suggested, enabling the clinical adoption of de novo cancer detection and minimal residual disease (MRD) monitoring. Currently, ctDNA detection usually involves deep targeted sequencing, often informed by a patient’s tumor mutational profile. While this strategy can boost the sequencing coverage for specific targets, its outcome is also dictated by the abundance of ccfDNA in the sample. "Although, in principle, you could sequence patient-specific [targets] or cancer hotspots to, let's say, a million X," said Dan Landau, a researcher at Weill Cornell Medicine and the New York Genome Center, the senior author of the study. "In practice, after about a few thousand fragments, you're exhausting the available material, which puts a physical boundary to the approach of deep-targeted sequencing." To circumvent this problem, several years ago, Landau’s team sought to perform whole-genome sequencing (WGS) on plasma samples. "Back in 2016, we had this eureka moment: We said, 'What if we do whole-genome sequencing and aggregate signal across the tens of thousands of mutations that are found [in the plasma] genome-wide? '," he said. "That allows us to use the cumulative signal from all of these mutations together in a way that is no longer dependent on the number of genomic equivalents." In 2020, Landau’s team published a proof-of-concept study , demonstrating the value of WGS in liquid biopsy for ultra-sensitive cancer monitoring. Landau is also the scientific cofounder of C2i Genomics , a joint venture and spinout from NYGC and Weill Cornell Medicine that has been commercializing a WGS-based liquid biopsy test for solid tumor MRD detection. Despite the promise of the whole-genome approach, until recently, sequencing costs still imposed a hurdle for the wide adoption of the method, Landau said. "That put a limitation on the clinical applicability of this work." To overcome this barrier, more than a year ago, Landau’s team started to collaborate with Ultima, which emerged last year with a promise to drastically reduce sequencing costs and deliver a $100 genome. While the study authors did not disclose the exact cost of Ultima sequencing in their paper, Landau said in this study, the cost per gigabase for the Ultima platform is at least seven times less than that of Illumina sequencing, which, according to the paper, is conducted on a HiSeq X or NovaSeq platform using 2×150 paired-end chemistry. For their recent study, the researchers used the Ultima platform to perform deep sequencing at about 120X coverage on plasma samples from healthy controls, cancer patients, and patient-derived xenograft mouse models. The deep coverage boosted the sensitivity of the assay, enabling ctDNA detection in the parts-per-million range, they wrote. The researchers also performed a head-to-head comparison between matching libraries of the Ultima and Illumina platforms, which showed comparable copy number and single nucleotide variant profiles between the two technologies. "It’s a new machine, so we needed to establish that the error profiles are compatible with the very sensitive mutation calling we need in the field of liquid biopsy," Landau said. Encouraged by the results, the authors further utilized the cost advantage of Ultima sequencing by implementing duplex error-corrected sequencing at a genome-wide scale. This resulted in approximately 1,500-fold error reduction in the plasma of patient-derived xenograft mouse models and an error rate of one in 10 million in patient plasma samples. The researchers then deployed the assay to help detect resectable melanoma in blood without matching tumor sequencing data, demonstrating the assay’s ability for de novo cancer monitoring. "In the liquid biopsy space, this is really meaningful, because for the first time, we can actually get good mutational profiles from just plasma directly at the level of the entire genome," Landau noted, adding that this will allow for the de novo detection of cancer, both as part of monitoring and, in the future, for early detection. The authors have filed patent applications regarding certain aspects of the technology. "We will be discussing this with commercial partners to try and team up so we can leverage this for commercial development," Landau said. However, he did not say whether C2i Genomics will be exclusively licensing the IP. "As a clinician, this is very exciting," said Lillian Siu, a medical oncologist at the Princess Margaret Cancer Centre in Canada. The method holds a lot of promise, she added, "especially because it is likely going to be a tumor-naive assay." Because most existing liquid biopsy tests for MRD detection are tumor-informed, Siu said, clinicians need to have prior knowledge of a patient’s tumor sequence in order to achieve targeted sequencing. These include, for example, Natera's Signatera assay, Personalis's NeXT Personal assay, and NeoGenomics subsidiary Inivata's Radar assay. "If you don't know what you are looking for, then it becomes very difficult," she noted. As such, a tumor-independent approach would be "very attractive" for tumors that do not have archival samples available or are not easily resectable
Additionally, Siu said, the assay’s ability to not only detect ctDNA signals more broadly but also sequence them at greater depth can increase the chance of successful MRD detection, especially when the disease burden is low. With regard to the test’s wider clinical adoption, Siu said a key factor to consider is its actionability. "I think the big question really is: ‘Can you do anything about it?’" Siu noted. "Even if we detect it, we cannot really do anything because it's too late, then, there's no point." "Hopefully, that's not the case," she added, and patients can be cured at an earlier point in their disease development. Trevor Pugh, a cancer genomics researcher at the Princess Margaret Cancer Center and the director of the genomics program at the Ontario Institute for Cancer Research (OICR), said he is excited about the study for two reasons. For one, he said, with the very low detection limit it achieved, the assay presents more opportunity for early cancer detection, enabling scientists to identify signals that were previously hard to detect with targeted sequencing. "Even if you had the best possible targeted sequencing approach in the world, if that piece of mutant DNA isn't in your sample, you're never going to find it," he explained. "To borrow the Canadian hockey analogy, this is more like putting as many pucks on the net as you possibly can, and hoping that some of them go in." Moreover, Pugh said, the study offered one of the first looks at the use of the Ultima sequencer in the context of ctDNA detection, offering insights into the new technology's performance when it comes to liquid biopsy. "Certainly, Illumina sequencing has been the mainstay, and they have also made some strides in lowering the genomic sequencing cost," he said. "This is also where new entrants, like Ultima, are so interesting." Pugh noted that his academic core lab at OICR, which is currently collaborating with both C2i Genomics and Ultima on cell-free DNA sequencing projects, is working on setting up a protocol similar to the one described in the NYGC/Weill-Cornell study. "It's certainly a method we're very interested in," he said. "We have spoken with many players in this space who are looking to set up these protocols, and we're making this available through our genomics program as a service." Still, Pugh said "the big rock to tackle" moving forward is to apply the WGS-based method toward cases beyond cancers with high mutation rates. "This proof of principle is in high mutation rate cancers because you have lots of shots on goal," he said. "There's a lot of innovation and work to be done so this can truly work pan-cancer, rather than just the cancers with high mutation rates." "I think this is a clever approach to capitalizing on advancements in the development of new sequencing technologies," said Joshua Cohen, an MD/PhD student at Johns Hopkins School of Medicine. Working in the lab of Bert Vogelstein, Cohen has also been developing high-sensitivity liquid biopsy assays for MRD detection. He also cofounded Haystack Oncology , a Johns Hopkins spinout that is commercializing a tumor-informed, patient-specific liquid biopsy test that is based on technology devised by the Vogelstein group. Cohen said one drawback of tumor-informed assays is that they require access to tumor tissue, which can be challenging for certain patients. Meanwhile, with the WGS-based approach, the requirement for sequencing coverage and accuracy can be demanding, he pointed out. "The challenge is that you are sequencing a much larger swath of real estate. There are many, many more positions that you have to interrogate," Cohen said. "You have to tease out more accurately all the positions that you're looking at — which ones are the ones that are likely to be driving a positive or negative call." In addition to benchmarking Ultima sequencing’s performance for liquid biopsy, Cohen said, another major achievement of the study is that the authors leveraged machine learning-based algorithms to correct the Ultima sequencing data, making cancer signals easily distinguishable from the noise. Still, given that Ultima is a new player in the field, Cohen said it remains to be seen how it will fare against competitors, especially Illumina. "I think it's a little premature to necessarily say which sequencing technology is going to come out ahead," he said. With Illumina responding to the competition by releasing its NovaSeq X instrument, which promises to significantly reduce sequencing costs, Cohen said he still thinks the company is "very much in the game." Moreover, Cohen said, there is still "a lot of work that needs to be done" in order to translate the technology described in this study into the commercial space, especially given that it was developed on a new sequencing platform. Even so, he said he believes the increasing competition in the NGS market is hugely advantageous to the liquid biopsy field in general. "It's beneficial across the board for the entire field for sequencing to be more affordable," he said. "That just opens the doors for all of these new technologies that are based on next-generation sequencing to be more affordable, which is really key to bringing all of these things to patients." Echoing Cohen’s opinion, Landau said he agreed that competition is a good thing for the community. "As part of the genomics community, we certainly welcome Illumina coming up with new products that are more affordable," he said. "We think that the fact that there is, for the first time, competition in this field is obviously enormously beneficial to the community at large." "This study makes the point that sequencing cost should no longer be a barrier to the clinical application of plasma deep sequencing for minimal residual disease applications," he said. "I think that these types of data may show that, long term, there is at least a very strong complementary role to whole-genome sequencing of the plasma, considering the current dominance of targeted panels in this field."

New York Genome Center Team Harnesses Ultima Genomics Platform for High-Sensitivity ctDNA Sequencing

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BALTIMORE – Researchers from the New York Genome Center and Weill Cornell Medicine and their collaborators have demonstrated the utility of Ultima Genomics’ sequencing platform for sensitive blood-based cancer monitoring, using whole-genome error-corrected sequencing of circulating cell-free DNA (ccfDNA) at high coverage. In a preprint posted on BioRxiv last year, the researchers showed that the Ultima sequencing platform, a newcomer in the next-generation sequencing field, generates data that is sufficiently accurate to perform the sensitive mutation calling that is necessary for cancer liquid biopsy testing. Additionally, with the Ultima platform’s low sequencing cost, it is now possible to implement genome-wide duplex error-corrected sequencing for circulating tumor DNA (ctDNA) detection in a cost-effective way, they suggested, enabling the clinical adoption of de novo cancer detection and minimal residual disease (MRD) monitoring. Currently, ctDNA detection usually involves deep targeted sequencing, often informed by a patient’s tumor mutational profile. While this strategy can boost the sequencing coverage for specific targets, its outcome is also dictated by the abundance of ccfDNA in the sample. "Although, in principle, you could sequence patient-specific [targets] or cancer hotspots to, let's say, a million X," said Dan Landau, a researcher at Weill Cornell Medicine and the New York Genome Center, the senior author of the study. "In practice, after about a few thousand fragments, you're exhausting the available material, which puts a physical boundary to the approach of deep-targeted sequencing." To circumvent this problem, several years ago, Landau’s team sought to perform whole-genome sequencing (WGS) on plasma samples. "Back in 2016, we had this eureka moment: We said, 'What if we do whole-genome sequencing and aggregate signal across the tens of thousands of mutations that are found [in the plasma] genome-wide? '," he said. "That allows us to use the cumulative signal from all of these mutations together in a way that is no longer dependent on the number of genomic equivalents." In 2020, Landau’s team published a proof-of-concept study , demonstrating the value of WGS in liquid biopsy for ultra-sensitive cancer monitoring. Landau is also the scientific cofounder of C2i Genomics , a joint venture and spinout from NYGC and Weill Cornell Medicine that has been commercializing a WGS-based liquid biopsy test for solid tumor MRD detection. Despite the promise of the whole-genome approach, until recently, sequencing costs still imposed a hurdle for the wide adoption of the method, Landau said. "That put a limitation on the clinical applicability of this work." To overcome this barrier, more than a year ago, Landau’s team started to collaborate with Ultima, which emerged last year with a promise to drastically reduce sequencing costs and deliver a $100 genome. While the authors did not disclose the exact cost of Ultima sequencing in their paper, Landau said in this study, the cost per gigabase for the Ultima platform is at least seven times less than that of Illumina sequencing, which, according to the paper, is conducted on a HiSeq X or NovaSeq platform using 2×150 paired-end chemistry. For their recent study, the researchers used the Ultima platform to perform deep sequencing at about 120X coverage on plasma samples from healthy controls, cancer patients, and patient-derived xenograft mouse models. The deep coverage boosted the sensitivity of the assay, enabling ctDNA detection in the parts-per-million range, they wrote. The researchers also performed a head-to-head comparison between matching libraries of the Ultima and Illumina platforms, which showed comparable copy number and single nucleotide variant profiles between the two technologies. "It’s a new machine, so we needed to establish that the error profiles are compatible with the very sensitive mutation calling we need in the field of liquid biopsy," Landau said. Encouraged by the results, the authors further utilized the cost advantage of Ultima sequencing by implementing duplex error-corrected sequencing at a genome-wide scale. This resulted in approximately 1,500-fold error reduction in the plasma of patient-derived xenograft mouse models and an error rate of one in 10 million in patient plasma samples. The researchers then deployed the assay to help detect resectable melanoma in blood without matching tumor sequencing data, demonstrating the assay’s ability for de novo cancer monitoring. "In the liquid biopsy space, this is really meaningful, because for the first time, we can actually get good mutational profiles from just plasma directly at the level of the entire genome," Landau noted, adding that this will allow for the de novo detection of cancer, both as part of monitoring and, in the future, for early detection. The authors have filed patent applications regarding certain aspects of the technology. "We will be discussing this with commercial partners to try and team up so we can leverage this for commercial development," Landau said. However, he did not say whether C2i Genomics will be exclusively licensing the IP. "As a clinician, this is very exciting," said Lillian Siu, a medical oncologist at the Princess Margaret Cancer Centre in Canada. The method holds a lot of promise, she added, "especially because it is likely going to be a tumor-naive assay." Because most existing liquid biopsy tests for MRD detection are tumor-informed, Siu said, clinicians need to have prior knowledge of a patient’s tumor sequence in order to achieve targeted sequencing. These include, for example, Natera's Signatera assay, Personalis's NeXT Personal assay, and NeoGenomics subsidiary Inivata's Radar assay. "If you don't know what you are looking for, then it becomes very difficult," she noted. As such, a tumor-independent approach would be "very attractive" for tumors that do not have archival samples available or are not easily resectable
Additionally, Siu said, the assay’s ability to not only detect ctDNA signals more broadly but also sequence them at greater depth can increase the chance of successful MRD detection, especially when the disease burden is low. With regard to the test’s wider clinical adoption, Siu said a key factor to consider is its actionability. "I think the big question really is: ‘Can you do anything about it?’" Siu noted. "Even if we detect it, we cannot really do anything because it's too late, then, there's no point." "Hopefully, that's not the case," she added, and patients can be cured at an earlier point in their disease development. Trevor Pugh, a cancer genomics researcher at the Princess Margaret Cancer Center and the director of the genomics program at the Ontario Institute for Cancer Research (OICR), said he is excited about the study for two reasons. For one, he said, with the very low detection limit it achieved, the assay presents more opportunity for early cancer detection, enabling scientists to identify signals that were previously hard to detect with targeted sequencing. "Even if you had the best possible targeted sequencing approach in the world, if that piece of mutant DNA isn't in your sample, you're never going to find it," he explained. "To borrow the Canadian hockey analogy, this is more like putting as many pucks on the net as you possibly can, and hoping that some of them go in." Moreover, Pugh said, the study offered one of the first looks at the use of the Ultima sequencer in the context of ctDNA detection, offering insights into the new technology's performance when it comes to liquid biopsy. "Certainly, Illumina sequencing has been the mainstay, and they have also made some strides in lowering the genomic sequencing cost," he said. "This is also where new entrants, like Ultima, are so interesting." Pugh noted that his academic core lab at OICR, which is currently collaborating with both C2i Genomics and Ultima on cell-free DNA sequencing projects, is working on setting up a protocol similar to the one described in the NYGC/Weill-Cornell study. "It's certainly a method we're very interested in," he said. "We have spoken with many players in this space who are looking to set up these protocols, and we're making this available through our genomics program as a service." Still, Pugh said "the big rock to tackle" moving forward is to apply the WGS-based method toward cases beyond cancers with high mutation rates. "This proof of principle is in high mutation rate cancers because you have lots of shots on goal," he said. "There's a lot of innovation and work to be done so this can truly work pan-cancer, rather than just the cancers with high mutation rates." "I think this is a clever approach to capitalizing on advancements in the development of new sequencing technologies," said Joshua Cohen, an MD/PhD student at Johns Hopkins School of Medicine. Working in the lab of Bert Vogelstein, Cohen has also been developing high-sensitivity liquid biopsy assays for MRD detection. He also cofounded Haystack Oncology , a Johns Hopkins spinout that is commercializing a tumor-informed, patient-specific liquid biopsy test that is based on technology devised by the Vogelstein group. Cohen said one drawback of tumor-informed assays is that they require access to tumor tissue, which can be challenging for certain patients. Meanwhile, with the WGS-based approach, the requirement for sequencing coverage and accuracy can be demanding, he pointed out. "The challenge is that you are sequencing a much larger swath of real estate. There are many, many more positions that you have to interrogate," Cohen said. "You have to tease out more accurately all the positions that you're looking at — which ones are the ones that are likely to be driving a positive or negative call." In addition to benchmarking Ultima sequencing’s performance for liquid biopsy, Cohen said, another major achievement of the study is that the authors leveraged machine learning-based algorithms to correct the Ultima sequencing data, making cancer signals easily distinguishable from the noise. Still, given that Ultima is a new player in the field, Cohen said it remains to be seen how it will fare against competitors, especially Illumina. "I think it's a little premature to necessarily say which sequencing technology is going to come out ahead," he said. With Illumina responding to the competition by releasing its NovaSeq X instrument, which promises to significantly reduce sequencing costs, Cohen said he still thinks the company is "very much in the game." Moreover, Cohen said, there is still "a lot of work that needs to be done" in order to translate the technology described in this study into the commercial space, especially given that it was developed on a new sequencing platform. Even so, he said he believes the increasing competition in the NGS market is hugely advantageous to the liquid biopsy field in general. "It's beneficial across the board for the entire field for sequencing to be more affordable," he said. "That just opens the doors for all of these new technologies that are based on next-generation sequencing to be more affordable, which is really key to bringing all of these things to patients." Echoing Cohen’s opinion, Landau said he agreed that competition is a good thing for the community. "As part of the genomics community, we certainly welcome Illumina coming up with new products that are more affordable," he said. "We think that the fact that there is, for the first time, competition in this field is obviously enormously beneficial to the community at large." "This study makes the point that sequencing cost should no longer be a barrier to the clinical application of plasma deep sequencing for minimal residual disease applications," he added. "I think that these types of data may show that, long term, there is at least a very strong complementary role to whole-genome sequencing of the plasma, considering the current dominance of targeted panels in this field."

NY Genome Center Team Harnesses Ultima Genomics Platform for High-Sensitivity ctDNA Sequencing

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New York Genome Center launches center to study non-coding cancer genome
Midtown medical tech company to lay off 20% of workers 
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The Centers for Medicare & Medicaid Services announced last week that it would increase its oversight of antipsychotic drug use in nursing homes around the country through off-site audits. While the usage rate of these drugs has declined in New York’s nursing homes in the past decade, community advocates continue to push for more enforcement of consequences that go beyond audits. Beginning this month, the CMS report reads, auditors will conduct targeted off-site assessments at select facilities to see whether those nursing homes are accurately assessing and coding residents with schizophrenia diagnoses. The shift comes as some nursing homes have developed a pattern, over decades, of inaccurately diagnosing patients with schizophrenia and administering antipsychotic drugs to sedate them. Antipsychotic drugs can also be used to treat the behavioral and physical changes that can come with dementia, which can include aggression, delusions, agitation and wandering. They can be dangerous, however. “They actually exacerbate a lot of the issues associated with dementia,” said Richard Mollot, executive director of the Midtown-based Long Term Care Community Coalition. “And they don’t cause Parkinson’s disease, but they cause Parkinson’s disease-like symptoms like shaking.”
Since 1991, nursing homes have been prohibited from using physical or chemical restraints on residents, Mollot added, but the use of chemical restraints has persisted. In 2011, five years after the Food and Drug Administration put “black box” warnings on two antipsychotic medications because of the mortality and morbidity risks they carried, a federal inspection found that 14% of the 2 million residents assessed during the review’s time period had at least one claim for antipsychotic drugs, and 22% of the drugs associated with the claims were not administered in compliance with CMS’ rules about unnecessary drugs. Another CMS review in 2022 found that from 2011 through 2019, about 80% of Medicare long-stay nursing home residents were prescribed a psychotropic drug. Furthermore, Mollot said, CMS rates have historically been risk-adjusted, meaning they exclude residents who have been given the drugs who have schizophrenia, Huntington’s disease or Tourette Syndrome. When those residents are accounted for, Mollot said, rates of drug use are higher. “What we’ve seen over the years is the percent of residents who have a diagnosis of schizophrenia has steadily increased,” he said. But those diagnoses can be “bogus,” given that it is unusual for someone to only develop schizophrenia in the end stages of their life, he explained. In New York drug usage rates have dropped in the past decade. Stephen Hanse, chief executive and president of the New York State Health Facilities Association, noted that New York ranks ninth-best in the country in reduced usage, according to CMS data. A report from the Long Term Care Community Coalition shows that in New York, the non-risk-adjusted rate of drug use in New York’s nursing homes hovered around 18% in 2021 and the first quarter of 2022, a drop from about 23% in 2021 but a slight increase from just under 18% in 2017 and 2018. CMS’ new guidelines to address schizophrenia diagnoses are “a good first step,” the advocacy organization said in a release. But the steps are not a substitute for monitoring and enforcement, the release said. Greater enforcement could mean improving citations, Mollot said. Currently, if a nursing home is cited for using the drugs, but the surveyor does not identify anything that would cause a resident harm or put a resident in jeopardy, “there is virtually no chance the facility will face any kind of penalty,” he said. CMS could use antipsychotic drug-use rates as the basis for investigations, he added. “I’m not saying go in and arrest them,” he said. “What I’m saying is, that should be a clue to look and see what is going on: Are residents getting inappropriate drugs? Has that drug use been reviewed by the pharmacists and by the medical director and practitioner as required by federal regulations?”
Hanse said each resident in a New York nursing home has a care plan developed by physicians and staff, a plan that can be updated as conditions change, and it could include the use of antipsychotic drugs depending on the resident’s diagnosis. The state Department of Health deploys survey teams to evaluate care plans and other aspects of how nursing homes function. Its focus on the use of these drugs has contributed to the drop in rates, Hanse said. But Mollot countered that by saying the state Health Department does a poor job of ensuring that nursing homes correct their problems once they are identified. In general “older adults and particularly [those] in nursing homes are significantly overmedicated,” said Daniel Reingold, president and chief executive of RiverSpring Health, which operates the Hebrew Home at Riverdale in the Bronx and serves about 18,000 people throughout the city. Facilities could also be inappropriately leaning on drugs to patch staffing gaps, Reingold said. Nursing homes are dealing with the same workforce shortages as the rest of the health care sector, he said, and giving a drug is cheaper than making a hire. Sometimes there is a clinical justification for antipsychotic drugs, he said, but they should not be used as a form of restraint. To reduce the usage of antipsychotics and make sure they’re being used appropriately, nursing homes should look at patients’ medication regimens upon arrival, Reingold said. “At the Hebrew Home . . . the first thing we do when people come in, particularly with diagnoses of, let’s say, Alzheimer’s, is take a look at the drugs they’re taking,” he said. “Because there are interactions that [could be] causing symptoms that are mimicking dementia.”
Reingold added that many medications geared toward older adults are not tested on older adults, whose bodies could react differently. He suggested alternate methods. The day after medical cannabis became legal in New York, the Hebrew Home began using it, he said, and saw “significant drops” in the need for narcotics, including antipsychotics, oxycontin and morphine. When asked about the CMS crackdown, Reingold did not suggest any further enforcement tactics. “Rules do not create better care,” he said. “What equals better care is greater engagement by communities and families.” —Jacqueline Neber
Mother Cabrini Health Foundation grants $165M to organizations throughout New York
The Mother Cabrini Health Foundation is committing $165 million in grants to more than 500 nonprofits in New York state, the organization announced Monday. The grants include $17 million for supporting immigrants and refugees, $14 million for increasing access to and destigmatizing mental health programs and $14 million for supporting workforce development among underserved populations, including for in-demand jobs, such as nurses and home aides. “We have these priority populations, these communities we’re really looking to support,” said Daniel Frascella, chief programs and grants officer at the foundation, “and one of the things we’ve really learned over the four years of our grant-making is the number of common issues or challenges that face these various communities.”
The foundation has given out about 2,200 grants worth almost $635 million in the four years since its founding. It received more than 1,500 letters of interest in its grants for this year, and about 46% of them were for at least $250,000. The specific dollar amounts awarded are usually based on what the organizations themselves say they need, although the foundation will occasionally make adjustments, Frascella said. Several organizations in the city received grants in the foundation’s latest round. Montefiore Medical Center received about $1.3 million overall for initiatives in workforce development, mental and behavioral health, community health, early childhood development and child and family well-being. The Catholic Foundation for Brooklyn and Queens received $2.6 million for community health and food and nutrition programs, and Manhattan groups, including Good Shepherd Services and the Inner-City Scholarship Fund, received $1 million each. Program officers will check in with the organizations periodically to see how their initiatives are going, Frascella said, and the foundation is still honing its methods for keeping track of how the groups are using their grant money. “As we continue to mature as a foundation, we can really make sure we’re tracking the right things and measuring the right things and supporting our grantees to do the same so that we can really understand the impact these dollars are having across the state,” he said. —Eddie Small
New York Genome Center launches center to study non-coding cancer genome
The New York Genome Center has launched a new facility to study the role and function of the non-coding genome in the evolution and treatment of many kinds of cancer, the center announced Thursday. The biomedical research community has traditionally lacked the technology and collaboration opportunities to study the non-coding genome, which makes up 98% of the human genome, according to a release from the New York Genome Center, which is based in SoHo. The non-coding genome affects DNA organization and structure, how RNA and proteins can access genomes, and organization within cells. The MacMillan Center for the Study of the Non-Coding Cancer Genome will bring researchers together to study how the non-coding genome influences the development, progression and treatment of breast, ovary, pancreas, gastrointestinal, lung and blood cancers. Engineers, mathematicians, technologists and biology experts will work together on the initiative. Researchers will hail from eight largely New York-based institutions: the BC Cancer Research Institute, Cold Spring Harbor Laboratory, Columbia University, Morehouse School of Medicine, Memorial Sloan Kettering Cancer Center, Northwell Health, New York University and Weill Cornell Medicine. The MacMillan Center was launched through a gift from the MacMillan Family Foundation, a charity organization on the Upper East Side. The New York Genome Center is at 101 Sixth Ave. The nonprofit launched JLABS @ NYC, an incubator that has space in that same building, in collaboration with Johnson & Johnson and the state of New York, in 2018. —J.N. Midtown medical tech company to lay off 20% of workers 
PAVmed, a medical technology firm with an office near Grand Central, has announced plans to lay off about 20% of its workforce and streamline its product portfolio, among other measures to cut costs. The company is implementing these cuts to prioritize commercialization efforts for two of its majority-owned subsidiaries, PAVmed announced last week in a release. Lucid Diagnostics is a commercial-stage cancer diagnostics company, and Veris Health is a private digital health firm focused on personalized cancer care. PAVmed said it hoped the cost-cutting steps would lower the quarterly cash burn by about 25%. “We believe these groundbreaking commercial products, with their large market opportunities, are our most valuable assets, and focusing on them provides our shareholders the greatest near and long-term value creation opportunity,” Dr. Lishan Aklog, PAVmed and Lucid’s chairman and chief executive, said in the release. Lucid makes EsoGuard, a commercially available diagnostic test aimed at detecting esophageal cancer early. The volume of tests performed at Lucid’s laboratory has grown steadily, the company said, and Lucid began submitting claims to insurers for the tests in the third quarter of last year. Lucid plans to continue to increase testing volume, shift sales attention away from recruiting and toward relationships with institutional accounts, maintain its team of nurse practitioners and continue to invest in LucidDx labs. The Veris Cancer Care Platform launched commercially last month, and the company plans to continue driving commercial adoption, delay development of some of its products, and focus its workforce on near-term commercialization efforts. PAVmed will support both firms in their commercialization efforts while pausing or halting other products in development. It will not pay annual cash bonuses, according to the release. PAVmed was founded in 2014 and raised $19 million before going public, according to Crunchbase. For the third quarter of last year, the company had operating expenses of more than $23 million and a net loss of about $26 million or 29 cents per share. —J.N. Loading…
AT A GLANCE
MENTAL ILLNESS: The number of incarcerated people living with serious mental illness in city jails rose to 1,108 people in November of last year, according to a recent report from city comptroller Brad Lander. Incarcerated individuals with serious mental illness now account for 19% of the jail population. The Department of Corrections’ dashboard shows that in November, about 10,000 people in jails missed medical appointments, up from just under 10,000 in November.’
ANONYMOUS DONATION: New York City Health + Hospitals/Bellevue has been awarded $1 million for its care of a trauma patient who had a head injury after a fall, H+H announced Friday. The donation was anonymous and recognized staff in the emergency room, intensive care unit, neurology care, rehabilitation care and social work. The funds will go toward funds and programs identified by the people who cared for the patient. NEW WEBSITE: The state has launched a website for its Master Plan on Aging educating New Yorkers on the plan, which is being coordinated by the department of health and the office for the aging. The site offers information on the recently established stakeholder advisory committee, the MPA council, and what the plan hopes to achieve. WHO'S NEWS: The "Who's News" portion of "At a Glance" is available online at  this link  and in the Health Pulse newsletter. "Who's News" is a daily update of career transitions in the local health care industry. For more information on submitting a listing, reach out to Debora Stein:  [email protected] . CONTACT US: Have a tip about news happening in the local health care industry? Want to provide feedback about our coverage? Contact the Health Pulse team at [email protected]

CMS crackdown on antipsychotic drugs in nursing homes brings push for more enforcement

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New Center to Shine Light on the Dark Genome
NEW YORK, Jan. 19, 2023 /PRNewswire/ -- The New York Genome Center (NYGC) announced the launch of the MacMillan Center for the Study of the Non-Coding Cancer Genome (MCSNCG) today, a major new initiative in cancer research to study the role and function of the non-coding genome and epigenome in the evolution, progression, and treatment of multiple cancer types, including breast, ovary, pancreas, gastrointestinal, lung, and hematologic cancers. The study of the non-coding "dark" genome allows for insight into the evolution, progression, and treatment of multiple cancer types, including breast, ovary, pancreas, gastrointestinal, lung, and hematologic cancers. Tom Maniatis, PhD, NYGC's Evnin Family Scientific Director and CEO, commented: "This Center, with its leading-edge multidisciplinary approach –– bringing together experts in genomics, engineering, mathematics, computational biology, and cancer biology –– will dramatically advance the understanding of the role of the non-coding genome in cancer." The non-coding "dark" genome constitutes 98% of the human genome and it plays an essential regulatory role across all molecular layers of biological complexity (i.e. genome, epigenome, transcriptome, proteome), influencing DNA organization and structure, genome accessibility to regulatory proteins and RNA, and intracellular organelle organization. The molecular mechanisms by which cell functions are carried out hold extraordinary promise for understanding how cellular identity is encoded in individual cell types and cell states; how cells are altered by intercellular interactions within the microenvironment, including immune cells; and how they are disrupted in various disease states, most specifically in cancer. While extraordinary progress has been made through individual, gene-focused research projects, the biomedical research community has historically lacked the technology and collaborative framework to systematically study the causality of the non-coding genome in cancer. Therefore, foundational questions regarding the role of the non-coding genome in the development and progression of many cancer types remain unanswered. Established by a generous gift from the MacMillan Family Foundation, the MCSNCG will seek to answer these questions through an inter-institutional, multi-disciplinary research program that brings together engineers, data scientists, mathematicians, technologists and biological experts. This range of expertise from the NYGC's collaborative network will allow the MCSNCG to engage in coordinated efforts to understand how behavior is encoded in cells and unravel the intricacy of intercellular interactions involved in the development of cancerous cells, metastasis, and drug resistance. Education and Outreach to promote diversity and representation in genomics and cancer research, engage the broader scientific community, and educate the public on the value and benefit of this important work is another critical component of the Center. To that end, the MCSNCG will offer internship and post-baccalaureate training opportunities, workshops and seminars for both scientific and public audiences, and will broadly disseminate the Center's scientific findings through the publication of protocols, analytic methods, genomic data, and discoveries. To maximize the impact of this research, the MCSNCG will also leverage existing regional cancer and genomic technology research initiatives anchored by the NYGC collaborative network such as the Polyethnic-1000  (P-1000) initiative. The researchers of the P-1000 initiative study cancer genomes of under-represented minority populations with the goal of understanding the role of genetic diversity in cancer, improving the application and outcome of precision medicine for these populations, and addressing the stark ethnic disparities in cancer research and diagnosis. Samuel Aparicio, FRCPath PhD, FRSC, NYGC's Senior Scientific Director of Cancer Genomics, says, "Decoding causality is fundamental to providing interpretable quantitative explanations of elements of the non-coding genome in cancer. Biological problems of this nature require cross-cutting programs where investigators with a broad range of expertise are supported to collaborate and focus on building new measurement methods and computational frameworks to understand the complex dynamics of cancer biology." The NYGC and the MacMillan Family Foundation share a mutual commitment to meaningfully and measurably advancing our understanding of cancer biology by innovating and applying new technologies, methodologies, and analytics. This new collaborative initiative brings together leading researchers from eight institutions including the BC Cancer Research Institute, Cold Spring Harbor Laboratory, Columbia University, Morehouse School of Medicine, Memorial Sloan Kettering Cancer Center, Northwell Health, New York University, and Weill Cornell Medicine. About the New York Genome Center
The New York Genome Center (NYGC) is an independent, nonprofit academic research institution that serves as a multi-institutional hub for collaborative genomic research. Leveraging our strengths in technology development, computational biology, and whole-genome sequencing, our mission is to advance genomic science and its application to novel biomedical discoveries. NYGC's areas of focus include the development of computational and experimental genomic methods and disease-focused research to advance the understanding of the genetic basis of cancer, neurodegenerative disease, and neuropsychiatric disease. During the pandemic, the NYGC worked with its hospital and academic partners to advance COVID-19 research, monitoring viral variants and exploring the genetic basis of severe disease. We are committed to prioritizing diversity, equity, and inclusion, which is fundamental to promoting greater collaboration, innovation, and discovery. About the MacMillan Family Foundation
The mission of the MacMillan Family Foundation is to support organizations that help strengthen and enrich our society in three major areas: cancer and medical research, education, and the arts. In addition, through its community grants program, the Foundation supports local, grass-roots organizations and services that seek to maintain and enhance the health, education, and well-being of the communities where it operates. The MacMillan Family Foundation was founded in January 2003 by Duncan and Nancy MacMillan. The MacMillans were early signers of the Giving Pledge. Duncan serves as Chairman of the Foundation, and Nancy serves as its President. Media Contact

The New York Genome Center Launches the MacMillan Center for the Study of the Non-Coding Cancer Genome

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The New York Genome Center Launches the MacMillan Center for the Study of the Non-Coding Cancer Genome

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NEW YORK -- -- BioLegend , Inc. and the New York Genome Center announced today that they have entered into an exclusive worldwide license and collaborative research agreement for CITE-seq ™ technology for use in the research field .

BioLegend® and New York Genome Center® Enter into Exclusive Global License and Research Agreement for CITE-seq™, a Novel Technique for Multidimensional Single Cell Analysis

Technion Israel Institute of Technology is a scientific-technological university and a center of applied research.

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The New York Genome Center (NYGC) is an independent, nonprofit academic research institution whose mission is to apply its strengths in whole genome sequencing, analytics, and the development of genomic tools to advance research and patient care for those suffering from neurological diseases and cancer.

Date	Round	Amount	Investors	Valuation Valuations are submitted by companies, mined from state filings or news, provided by VentureSource, or based on a comparables valuation model.	Revenue	Sources
2/4/2019	Grant	$6M	ALS Association, and Tow Foundation		0 FY undefined	1
9/25/2013	Unattributed VC		Subscribe to see more		0 FY undefined	10

Date	2/4/2019	9/25/2013
Round	Grant	Unattributed VC
Amount	$6M
Investors	ALS Association, and Tow Foundation	Subscribe to see more
Valuation
Revenue	0 FY undefined	0 FY undefined
Sources	1	10

First funding	Last Funding	Investor	Rounds	Type	Location
2/4/2019	2/4/2019	ALS Association	1 Grant	Non-Profit Foundation	DC
00/00/0000	00/00/0000	Tow Foundation	Subscribe to see more	Non-Profit Foundation	Connecticut
00/00/0000	00/00/0000	Partnership Fund for New York City	Subscribe to see more	Venture Capital	New York

First funding	2/4/2019	00/00/0000	00/00/0000
Last Funding	2/4/2019	00/00/0000	00/00/0000
Investor	ALS Association	Tow Foundation	Partnership Fund for New York City
Rounds	1 Grant	Subscribe to see more	Subscribe to see more
Board Seats
Type	Non-Profit Foundation	Non-Profit Foundation	Venture Capital
Location	DC	Connecticut	New York

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