RR

Pleasure in the job puts perfection in the work!

[Greg Larssen @GregLarssen]

$BNGO - Bionano

18-Jun-2024

Slowly but surely Optical Genome Mapping is becoming mandatory and integral for new drugs discovery.

"Conservation and Faithful Representation of Circular Extrachromosomal Dna in Orthotopic Patient-Derived Medulloblastoma Xenografts"

The Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, the University of California @ San Diego, and Columbia University @ New York, publish the above paper.

In this paper the scientists argue that Extrachromosomal DNA (ecDNA) correlates with poor survival across various cancer types. As a result it is critical to ensure that the abundance and conservation of ecDNA in PDX models matches that in the tumor samples taken from the original patients so that initial phases of testing of potential new drugs is as close as possible to using those drugs in actual patients.

PDX Models = Patient-derived Xenograft models - they are models of cancer where tumor cells from patients are implanted in immunodeficient or humanized mice - they are used to model the actual human cancer so that evolutions can be monitored and documented and to facilitate the early stages of the testing of new drugs, drugs resistance studies, etc ...

Optical Genome Mapping was used to determine accurate and reliable ecDNA sequence reconstructions in the target mice.

OGM effectively cementing its role as the superior, essential, if not mandatory Quality Control tool in drug research, whether it be Stem Cells (hIPSC), gene editing (CRISPR), or, as in this study, ecDNA monitoring and reconstruction !

https://t.co/Z82ZTE9Dn1

[Greg Larssen @GregLarssen]

$BNGO - Bionano

The Mexican Society of Human Genetics has a new program of talks starting 28-Jun-2024.

Two of those talks will be about OGM :
-------------------------------------------

- Optical Genome Mapping Nomenclature (General Hospital of Mexico City, Pediatric Hospital Mexico City)

- Optical Genome Mapping (Laboratorio ColCan, Colombia)

Interesting trend inferred from this page : it looks like scientific Hackathons and Telethons aimed at solving the genetic nature of rare diseases are all turning to Optical Genome Mapping wherever they are being held, be it in Nijmegen, Holland, or Mexico City, Mexico ! Since these are typically mass events, this bodes well for OGM's expansion.

https://t.co/NnD8Qyo7I4

[Greg Larssen @GregLarssen]

$BNGO - Bionano

21-Jun-2024

German, Swedish, and U.S. universities publish the following paper in the Cell Genomics journal :

"Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci"

The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a complex genomic rearrangement (CGR). Although it has been identified as an important pathogenic DNA mutation signature in genomic disorders and cancer genomes, its architecture remains unresolved.

These scientists used a comprehensive multi-omics strategy to fully elucidate this duplication/triplication.

Bionano Optical Genome Mapping was used alongside Illumina, PacBio, and Oxford Nanopore sequencing.

https://t.co/QOu5ZeLQl2

[Greg Larssen @GregLarssen]

$BNGO - Bionano

One from left field this morning : the CEO of the National Institute of Health (NIH) Research Program tweeting about Optical Genome Mapping !!!

👍👍👍

[Greg Larssen @GregLarssen]

$BNGO - Bionano

Well, if this isn't a sign that OGM is on the up ....!

I've just come across a new scientific paper currently in the process of being peer reviewed. Imagine my surprise when reading the notes of one of the reviewers, stating :

"I would suggest the authors to discuss the Optical Genome Mapping approach in the section “CNA/CNV Detection” as well as in the other ones, since it seems one of the more promising techniques for CNA detection and some interesting results are already published, especially in the haematological context."

Way to go !!

Unfortunately the author's response to that reviewer's comment is seriously underwhelming if not catastrophically unscientific - instead of "discussing OGM" as suggested by the reviewer, the author suggests a mere 4 lines addition to the paper. Have you ever heard of the words "misplaced ego" ? 🙂

Still - it's definitely a positive that peer reviewers now ask authors to also investigate Optical Genome Mapping - it's a majorly influential shift !

https://t.co/YgkPbaqOh1

[Greg Larssen @GregLarssen]

$BNGO - Bionano

21-Jun-2024

And here is that peer reviewed paper in question. If only they'd listened properly to the reviewer and had finished the job properly !

"Insights into the Clinical, Biological and Therapeutic Impact of Copy Number Alteration in Cancer"

published by University of Western Australia, Curtin University, Perth's Children's Hospital, and the Telethon Kids Institute, all based in Perth, Western Australia, Australia.

https://t.co/HQFwGC3yBY

[Greg Larssen @GregLarssen]

$BNGO - Bionano

GenomeWeb publish as piece today on the path forward for Bionano following the approval of a Category 1 CPT code by the AMA earlier this week, titled :

"Bionano Genomics Upbeat on Further Clinical Adoption of Optical Genome Mapping With New CPT Code"

This article also reveals, incidentally, what is possibly Bionano's first VIA software marketing deal. Revvity, formerly called Perkin Elmer, will now market Bionano's VIA to its NGS sequencing customers. We're finally seeing VIA as a separate product where it can do two things : be a separate source of revenue, and, sometimes, bring NGS clients to OGM. Good !

https://t.co/ohV6Nxb4Ha

[Greg Larssen @GregLarssen]

$BNGO - Bionano

Bionano announces VIA Software Marketing Agreement with Revvity for Newborn Sequencing Research.

Interestingly, it is VIA's reporting capabilities which were the #1 selling point. Excellent !

https://t.co/hcBdvHsso6

[CiscoTrader @ciscojmd]

$BNGO 📣🛎️ PR NEWS DROP. @Bionano Announces Software Marketing Agreement with Revvity for Newborn Sequencing Research (Not an OGM adoption but pushing VIA, @EHolmlin Erik Holmlin and Gulsen Kama scrounging for revenue) #Bionano #bngo

https://t.co/yqpwCv0ddY

[Greg Larssen @GregLarssen]

$BNGO - Bionano

18-Jun-2024 (this is a good one!)

"Complex Karyotype Detection in Chronic Lymphocytic Leukemia: A Comparison of Parallel Cytogenetic Cultures Using TPA and IL2+DSP30 from a Single Center"

Hospital del Mar, Barcelona - Hospital Universitario Central de Asturias, Oviedo - Hospital Universitari Sant Joan de Reus, Reus - Hospital Universitario of Valencia, Valencia - Spain, publish the above paper where they assess and compare the best types of cell cultures to detect complex Karyotypes in Chronic Lymphocytic Leukemia (CLL).

The Conclusion is surreal : the scientists conclude, as would be expected, that Karyotyping and FISH using a combination of the two main types of cultures yields the best results but that since doing two types of cultures is also more expensive and extremely time-consuming, scientists should prioritize the use of only the IL2+DSP30 protocol which has a lesser failure rate.

OK so far.

The kicker, however : the second and, effectively, most important part of the Conclusion explains that Optical Genome Mapping does not require cultures, thus doing away will all the time consuming, variability, and unpredictability of cultures, and cost, and that, in the specific case of Chronic Lymphocytic Leukemia, CLL, it has been demonstrated that it can easily replace both Karyotyping and FISH using a rigorously produced OGM workflow !

Wow ! Thank You Spain !

https://t.co/t70pDDDcuW

[Greg Larssen @GregLarssen]

$BNGO - Bionano

19-Jun-2024

The Ruhr-University of Bochum and the University of Tübingen, Germany, publish a paper titled :

"Optical Genome Mapping Reveals Disruption of the RASGRF2 Gene in a Patient with Developmental Delay Carrying a De Novo Balanced Reciprocal Translocation"

Interestingly, despite having "OGM" in the title of the paper, this paper is actually not about OGM but, rather, about elucidating the mechanisms of balanced reciprocal translocations affecting the RASGRF2 gene and their roles in neuro-development disorders and, more widely, in other genetic disorders.

However, and this is where OGM comes into the picture, this team of clinical scientists includes the famous OGM hall-of-famer Dr Wanda Gerding who last year won the Lore Zech Prize from the German Society of Human Genetics for the best publication of 2022 (an OGM paper) and who has since contributed so much to the worldwide understanding of the possibilities which Optical Genome Mapping offers. As a result this group of scientists argue that given that a crucial aspect of understanding the effects of balanced translocations is the precise resolution of the breakpoint regions, their only choice is to use the best available technology to detect them, and that is Optical Genome Mapping !

https://t.co/vLNwrqsp08

[Greg Larssen @GregLarssen]

$BNGO - Bionano

Yessssssssssssssssssssssssssssssss !!!!

We have a Category 1 CPT code !

https://t.co/3STaeGI9JP

[Greg Larssen @GregLarssen]

$BNGO - Bionano

Hot on the heels of Bionano finally getting a Category 1 CPT code which officializes the fact that Optical Genome Mapping has gained acceptance across the medical community, we find that The Colombian Society of Genetic and Genomic Medicine includes 2 modules on OGM in the course it offers through its https://t.co/tyzU4RbbtD website.

https://t.co/Txh3pvljX1

[Greg Larssen @GregLarssen]

$BNGO - Bionano

The Bambino Gesù Children’s Hospital, the Istituto Dermopatico Dell'Immacolata, the Catholic University of the Sacred Heart, and Sapienza University, all based in Rome, Italy, publish a paper titled :

"Utility of Optical Genome Mapping In The Characterization of Paediatric Central Nervous System Tumours: Analysis of A Mono-Institutional Series of 26 Cases"

where they review the implementation of OGM in the investigation of paediatric Central Nervous System (CNS) tumors found in those four hospitals.

OGM was concordant with the technology currently in use in those hospitals, Microarray, but also provided additional causative information and performed better in high complexity prognostication.

https://t.co/SCyHg9jrQk

[Greg Larssen @GregLarssen]

$BNGO - Bionano

18-Jun-2024

A brilliant example of OGM's use - aiding the discovery of new drugs.

Seven (7) U.S. and Canadian university medical centers publish a poster titled :

"Drug Screening in Patient-Derived Models of Posterior Fossa A Ependymoma (PFA-EPN) Reveals Novel Pharmacological Vulnerabilities"

where these clinical scientists are attempting to find new therapeutic targets for a specific type of paediatric brain tumor (PFA-EPN) which currently only has a survival rate of 33% even after brain surgery and radiation therapy, the current SOC treatment paths. Elucidating the right targets would enable them to design new drugs which might improve the outcome for these patients.

The scientists used Optical Genome Mapping to fully characterize tissue samples from affected patients and OGM actually revealed previously undescribed structural variants and duplications affecting genes encoding proteins responsible for signalling and transcription. OGM provided these scientists with new clues on drugs which they want to validate on larger cohorts.

The 7 organizations involved
--------------------------------
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA,

- Rady Children’s Institute for Genomic Medicine, San Diego, CA

- University of Pittsburgh, PA

- Boston Children’s Hospital, MA

- Columbia University Medical Center @ New York City, NY

- Hospital for Sick Children, University of Toronto, Toronto, Canada

- Texas Children’s Hospital, Houston, TX

https://t.co/UTacAN8U6j

[CiscoTrader @ciscojmd]

$BNGO 📣🛎️ @bionano PR News Drop: Bionano Laboratories Announces New Category I CPT Code for OGM Use in Hematological Malignancy Analysis (Erik Holmlin saw it was posted on X, and was made aware its existence so he dropped the news.)… True Story #BNGO @EHolmlin

https://t.co/Go8FGpMEEp

[Greg Larssen @GregLarssen]

$BNGO - Bionano

14-Jun-2024

The University of Sheffield, UK, publishes a paper titled :

"Culture-acquired genetic variation in human pluripotent stem cells: Twenty years on"

where they review the last 20 years of "unwanted structural variants" acquired through the use of Human Pluripotent Stem Cells (hPSC). They argue that the understanding of the consequences of culture-acquired variants for specific applications in cell therapy or research is still elusive, and concerning, and that this has galvanized the efforts to reduce uncertainty in the manufacturing of hPSC cells.

In a way this study is slightly behind other studies on the same subject, such as those that have clearly identified Optical Genome Mapping as a necessary Quality Control technology, but it still adds to the body of studies raising the alarm about the need to thoroughly monitor hPSC cells for unwanted structural variants.

This studies twice mentions Optical Genome Mapping as one of the technologies expected to facilitate easy and affordable high-resolution Quality Control monitoring of hPSC genomes.

https://t.co/oPjxABP3dg

[Greg Larssen @GregLarssen]

$BNGO - Bionano

12-Jun-2024 - (Preprint)

I like this one - "the power of word of mouth".

Clinical scientists from the Guangxi Medical University, Guangxi, China, submit a preprint study titled :

"The cryptic complex rearrangements involving the DMD gene causing completely opposite manifestations: etiologic clues revealed by optical genome mapping"

This is a classic example of the power of published studies. After reading multiple studies about Optical Genome Mapping, these scientists decided to use it to elucidate further the pathogenicity of complex rearrangements involving Duchenne Muscular Dystrophy (DMD) with unknown breakpoints, a mechanism which is still poorly understood.

The scientists' conclusion : "OGM provides valuable insights into the etiological analysis of Duchenne and Becker muscular dystrophy (DMD/BMD) and enhances our understanding of the cryptic effects of complex rearrangements."

https://t.co/M5y6kGhndg

[Greg Larssen @GregLarssen]

$BNGO - Bionano

Hartley Taylor Medical Communications, Kirkham, UK, has on its website the details of a meet on Monday, June 17th, in York, Northern England, called "Yorkshire Myeloid Update Day".

It will have a 30-minutes Optical Genome Mapping session.

https://t.co/AojbOJIOwC

[Greg Larssen @GregLarssen]

$BNGO - Bionano

13-Jun-2024

The Research Council of Finland has awarded funding to Tuomo Mantere, University of Oulu, Finland for its OGM research project titled :

"Deciphering the Structural Variant landscape of Acute Myeloid Leukemia by integrated Optical Genome Mapping and transcriptome analysis"

The funding runs from 2024 to 2028.

https://t.co/guTbOosRjy