Category Archives: Genome

Natural selection shapes all life on Earth. As the world aroundthemchanges, organismsthatcanadapt have a better chance at reproducing. Humans are no exception and whilea fewexamples of recent evolution are known, welack a deeper understanding of how the human genome is being shaped by natural selection.

New findings published in the journalNature Human Behaviorare a smallstep in better understanding human evolution. Theresearchers behind the study aimedto understand how the natural selection of complex traits unfolded. The team looked at 870 human traits that are created by multiple genes,finding that 755 of them were altered due to natural selection in the last 2,000 to 3,000 years.

The team was led by Weichen Song from the Shanghai Jiao Tong University.The researchersused modern human genetic data from the UK Biobank and Psychiatric Genomics Consortium. They comparedthis data to ancient genomic DNA from across Europe and the Near-East, providing insights into changes in the human genome across the last 45,000 years.

The team's most intriguing finding showed that skin pigmentation, body measurement, and dietary traits were "continuously under intense selection pressure" across the time scales investigated. Pressuresforskin color are due to a balancing act of reducing ultraviolet damage, important vitamin D requirements, and heat regulation. In fact, one of the earliest Britons, the Cheddar Man, had dark skin.

Body measurement and dietary traits have also been changed by genetic factors, together with external pressures such as ecology, climate, and migration.

The team also found that certain diseases have not been phased out quite as efficiently as one would expect. The genetic factors associated with conditions such as anorexia nervosa and inflammatory bowel disease were being suppressed, but cases persisted.

While the findings are intriguing, the team considers them just a preliminary foundational step needed for more detailed work. The study is limited by the use of genomes from the UK, which predominantly included people of European ancestry. It was also limited by the ancient genomes employed.

The work also is limited by the methodology of genome-wide association studies which do not distinguish between association and causality.

The Human Genome Project was finished in 2003, so a complete analysis of the human genome is not even 20 years old many mysteries remain to be uncovered in it, and how it has been shaped by evolutionary forces.

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Natural Selection Has Changed The European Genome In The Last 3000 Years - IFLScience

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MENLO PARK, Calif., Nov. 16, 2021 (GLOBE NEWSWIRE) -- PacBio (Nasdaq: PACB), a leading provider of high-quality, highly accurate sequencing platforms, today announced the launch of the HiFiViral SARS-CoV-2 Kit a fully kitted end-to-end solution for COVID-19 surveillance, which public health laboratories can use to identify new SARS-CoV-2 variants and detect all variants circulating within a population.

The HiFiViral SARS-CoV-2 Kit is PacBios first kitted solution for genomic surveillance of COVID-19 variants. The assay leverages PacBios trusted HiFi sequencing to give researchers a more complete view of novel mutations of all types, ensuring that emerging variants are captured.

Accurate and timely detection of new variants of concern is critical to protecting public health. Our new HiFiViral SARS-CoV-2 Kit is a powerful solution that enables robust detection of new variants as they emerge without requiring periodic updates and revalidation to keep pace with the evolving SARS-CoV-2 virus, said Christian Henry, Chief Executive Officer and President of PacBio. As we look to the future and continue to invest in applications to improve human health, this solution offers a differentiated technology based on proven HiFi sequencing and helps address workflow and supply chain bottlenecks that have affected SARS-CoV-2 surveillance efforts to date, enabling laboratories to scale their testing with ease.

The HiFiViral SARS-CoV-2 workflow is a cost-effective and accurate method for viral sequencing, utilizing molecular inversion probes (MIPs) that provide significant workflow improvements over traditional polymerase chain reaction (PCR) amplicon-based methods. HiFi sequencing also enables laboratories to identify multiple virus types present within a single sample. The companion SMRT Link v10.2 software provides a simplified solution to perform quality checks on experiments and capture all types of genetic variation, which is critical information for public health surveillance efforts. Combined with the flexibility to run up to 384 samples at a time, this kit allows more labs to take advantage of powerful HiFi sequencing in the convenience of a ready-to-use kit.

With the HiFiViral SARS-CoV-2 workflow, we were able to capture mutations of all types and saw significant performance improvements over our PCR amplicon approach. The workflow itself was phenomenal. We were able to reduce the hands-on time by almost 80 percent which was a game changer for us, said Melissa Smith, Ph.D., Assistant Professor, Department of Biochemistry & Molecular Genetics, University of Louisville.

Concurrently with the HiFiViral SARS-CoV-2 kit, PacBio is releasing an enhanced end-to-end HiFi microbial whole genome assembly application and companion SMRT Link software on the Sequel IIe System. The upgrade doubles the recommended multiplexing capacity, provides 96 kitted barcodes, and migrates the application to HiFi sequencing while continuing to deliver the industrys leading standard for reference quality microbial genomes. This updated application gives public health labs a new and improved tool for investigating outbreaks in the food supply, tracking antimicrobial resistance, and fully characterizing emerging pathogen threats. Paired with the new HiFiViral SARS-CoV-2 kit, these innovations provide public health and microbial research labs a powerful menu of applications to service a broad range of use cases on their Sequel IIe systems.

We are committed to supporting labs on the front line of this pandemic by providing easier, scalable, and more cost-effective solutions for pathogen surveillance. The launch of the HiFiViral SARS-CoV-2 kit, the upgrade to our microbial whole genome sequencing application, and the suite of SMRT Link companion software solutions are evidence of PacBios commitment to helping labs respond to infectious diseases today and in the future, said Henry.

The HiFiViral SARS-CoV-2 kit is currently shipping. The components for the HiFi microbial whole genome assembly application will ship this quarter.

To learn more, please visit the PacBio website: HiFiViral SARS-CoV-2 Kit and HiFi Microbial WGS application.

About Pacific Biosciences

Pacific Biosciences of California, Inc. (NASDAQ: PACB),is empowering life scientists with highly accurate long-read sequencing. The companys innovative instruments arebased onSingle Molecule, Real-Time (SMRT) Sequencing technology, whichdeliversacomprehensiveview of genomes, transcriptomes, and epigenomes,enablingaccess to the full spectrum of genetic variation in any organism. Cited in thousands of peer-reviewed publications, PacBiosequencingsystems arein use by scientists aroundthe world to drive discovery in human biomedical research, plant and animal sciences, and microbiology. For more information, please visitwww.pacb.comand follow@PacBio.

PacBio products are provided for research use only. Not for use in diagnostic procedures.

Forward-Looking Statements

This press release may contain forward-looking statements within the meaning of Section 21E of the Securities Exchange Act of 1934, as amended, and the U.S. Private Securities Litigation Reform Act of 1995, including statements relating to future availability, release dates, uses, accuracy, advantages, quality or performance of, or benefits of using, PacBio products or technologies, the suitability or utility of such products or technologies for particular applications or projects, and the expected benefits of such products or technologies, in each case in connection with use of the HiFiViral SARS-CoV-2 kit and HiFi sequencing technology for viral surveillance, variant detection and other public health efforts, such as investigating outbreaks in the food supply, tracking antimicrobial resistance and characterizing emerging pathogen threats; ability and ease for laboratories to scale testing; potential to address supply bottlenecks; and other future events. Readers are cautioned not to place undue reliance on these forward-looking statements because they are subject to known and unknown risks and uncertainties that could cause actual results to differ materially from the information expressed or implied by forward-looking statements made in this press release. Reported results should not be considered as an indication of future performance. Factors that could materially affect actual results can be found, and readers are strongly encouraged to read the full cautionary statements contained, in PacBios most recent filings with the Securities and Exchange Commission, including its most recent reports on Forms 8-K, 10-K, and 10-Q. These forward-looking statements speak only as of the date hereof, and PacBio disclaims any obligation to update these forward-looking statements, even if new information becomes available.

Contacts

Investors:Todd Friedman+1 (650) 521-8450ir@pacificbiosciences.com

Media:Kathy Lynchpr@pacificbiosciences.com

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PacBio Launches HiFiViral SARS-CoV-2 Kit and Microbial Whole Genome Sequencing Enhancements to Combat Infectious Disease and Strengthen Public Health...

SAN DIEGO, Nov. 15, 2021 (GLOBE NEWSWIRE) -- Bionano Genomics, Inc. (BNGO), pioneer of optical genome mapping (OGM) and provider of industry-leading data interpretation solutions for next-generation sequencing (NGS) and microarrays, today announced the lineup of content scheduled to be presented at the annual meeting of the Association for Molecular Pathology (AMP). The content is expected to include an oral platform presentation by Dr. Ravi Kolhe at Augusta Universty, six poster presentations, a corporate workshop and an innovation spotlight. The presentations this year span a wide range of applications, including prenatal analysis, genetic disease, hematological malignancies, solid tumor and advances in the OGM technique for detecting more clinically relevant variants, including absence of heterozygosity (AOH) and allelic imbalance. The AMP conference is being held virtually starting today, Monday, November 15 and goes until Friday, November 19, 2021.

Bionanos corporate workshop on Thursday, November 18 from 9:00am - 9:50am EST is planned to feature presentations from Dan Saul (BioDiscovery), Dr. Alex Hastie (Bionano), and Dr. Gordana Raca (Childrens Hospital LA), where theyll highlight the potential advantages of combining data from OGM and next-generation sequencing (NGS) to obtain the most comprehensive view of genome variation available.

The innovation spotlight will feature presentations from Dr. Soheil Shams (CIO), Dr. Alka Chaubey (CMO) and Dr. Adrian Dubuc from Brigham & Womens Hospital and Harvard Medical School. The content for the spotlight will cover Bionanos efforts in building a cancer knowledgebase for interpreting variants faster, the power of combining OGM and NGS data to reveal significantly more clinically relevant variants than with NGS alone and an illustration of an application of OGM as an alternative to karyotyping and FISH for revealing complex, clinically relevant structural variants in an aggressive leukemia/lymphoma subject.

Story continues

The table below outlines each presentation together with the program number for ease of location during the event.

OGM Application Area

Presentation / Poster Title

Affiliation

Genetics

G22. Comprehensive Evaluation and Validation of Amniocytes Using Optical Genome Mapping: From Sample Preparation to Reporting

Augusta University

Hematopathology

H02. Clinical Validation of Optical Genome Mapping to Replace Eosinophilic Leukemia FISH Panel

University Health Network, Toronto, Canada

H13. Comprehensive Detection of Structural Somatic Mutation in Hematological Cancers by Optical Genome Mapping

Bionano Genomics

H15. Clinical Utility of Optical Genome Mapping in Cytogenetic Analysis of Hematologic Malignancies

Augusta University

Informatics

I12. Detecting Absence of Heterozygosity Using High-Resolution Optical Genome Mapping

Bionano Genomics

Solid Tumors

ST74. Optical Genome Mapping for the Chromosomal Characterization of Solid Tumors

Augusta University

Technical Topics

TT24. Optical Genome Mapping: Optimizing Sample Types for Prenatal Testing, Constitutional Disorders, Hematological Malignancies, and Solid Tumor Profiling

Augusta University

Workshop

Topic

Date and Time

Corporate Workshop

Combining Optical Genome Mapping (OGM) with Next-Generation Sequencing (NGS) Data to Provide the Most Comprehensive Genome Analysis for Oncology Applications

Thursday, November 18th from 9:00am - 9:50am EST

We are thrilled to see the broad range of presentations featuring OGM at AMP this year, including coverage of the combination of OGM with NGS data to provide the most comprehensive picture of the genome, stated Erik Holmlin, PhD, CEO of Bionano Genomics. Our customers continue to push forward cutting-edge applications in molecular pathology and we look forward to the authors sharing their research with the AMP community.

For more details and to register for this online event please go to: https://amp21.amp.org/

About Bionano Genomics

Bionano is a provider of genome analysis solutions that can enable researchers and clinicians to reveal answers to challenging questions in biology and medicine. The Companys mission is to transform the way the world sees the genome through optical genome mapping (OGM) solutions, diagnostic services and software. The Company offers OGM solutions for applications across basic, translational and clinical research. Through its Lineagen business, the Company also provides diagnostic testing for patients with clinical presentations consistent with autism spectrum disorder and other neurodevelopmental disabilities. Through its BioDiscovery business, the Company also offers an industry-leading, platform-agnostic software solution, which integrates next-generation sequencing and microarray data designed to provide analysis, visualization, interpretation and reporting of copy number variants, single-nucleotide variants and absence of heterozygosity across the genome in one consolidated view. For more information, visit http://www.bionanogenomics.com, http://www.lineagen.com or http://www.biodiscovery.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 timing and content of the posters and presentations regarding OGM to be presented at the AMP conference; and the effectiveness and utility of OGM, including in combination with NGS and in comparison to traditional standard of care methods. 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 accuracy of customer posters and presentations to be presented; observations from studies covered by the posters and presentations may not be replicated; the ability of medical and research institutions to obtain funding to support adoption or continued use of our technologies; 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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Bionano Genomics Announces Extensive Lineup of Content to be Presented at the Annual Meeting of the Association for Molecular Pathology Featuring...

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Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae - Nature.com

After sequencing the jute genome in 2017, Bangladesh has now brought another landmark achievement in scientific research: it decoded the genomes of Ruhi, Kalbaus and freshwater dolphin, a global first.

At the same time, the country also completed sequences of the Mrigel and Catla fishes, which was however done earlier by China and India respectively.

A team led by Chittagong University Zoology Department Professor Dr Manzoorul Kibria unveiled the genome sequences of the four carps and the Gangetic freshwater dolphin after a two-year effort.

The US National Center for Biotechnology Information (NCBI) has already recognised the work and Bangladesh has the patent on it. It also preserved the sequenced data which can be accessed by any researcher around the world for further research.

The information was revealed at a webinar organised by the Palli Karma-Sahayak Foundation (PKSF) in Chattogram on Tuesday.

Dr Manzoorul Kibria, also coordinator of the Halda River Research Laboratory under the University of Chittagong, and Dr AMAM Junaid Siddiqui, professor at the Chittagong Veterinary and Animal Science University, were present at the event.

Professor Junaid Siddiqui provided technical support as a genome sequence expert to the team comprising two researchers from New Zealand and China, five students from Chittagong University, five from the Veterinary University and Premier University.

"We completed genome sequencing of Ruhi, Kalbaus and Gangetic dolphins for the first time in the world," Junaid Siddiqui told The Business Standard.

"The genome sequence of freshwater dolphins has elevated Bangladesh's position on the world stage," added the professor.

Some 82,788 genes have been identified in this study, of which 16,609, are of Ruhi fish, 16,597 of Catla fish, 16,607 of Mrigal fish, 17,620 of Kalbaus fish, and 18,365 genes of the freshwater dolphin, said Prof AMAM Junaid Siddiqui.

"Halda river is the only natural pure gene bank for fishes like Ruhi in Bangladesh. The modern complete genome formatting is a very effective method in scientific research which helps us conduct the physiological research of the fishes," said Dr Manjurul Kibria who led the research.

"Various comparative studies have been done to determine the genetic differences between different carp species. However, no complete genome sequencing of wild Ruhi, Catla, Mrigal and Kalbaus had been revealed before."

"As such, the research will help us with different diseases of the fishes, their capability to respond to the diseases, inbreeding problems, and other important biological processes," said Dr Manzoorul Kibria.

The research team collected specimens from a dead dolphin, weighing 70-80 kg, and some 16-17 kg Ruhi, Catla, Mrigal and Kalbaus fishes, in 2018.

Junaid Siddiqui said, "We can now also work on finding out the reasons why freshwater dolphins die frequently. We can know whether it is a genetic problem or because of water contamination."

"We will also be able to know why Halda fishes are different from others and what their characteristics are."

He added, "Several researchers from University of Andrews and various other institutes have expressed interest in working with us on further research."

The PKSF and the Integrated Development Foundation (IDF) financially supported the research project.

PKSF Managing Director Nomita Halder said, "We responded immediately upon getting a proposal from Professor Manjurul Kibria for the project."

"We did not take it simply as a project but as our social responsibility to save the Halda river."

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Bangladesh decodes genomes of freshwater dolphin, Ruhi, and Kalbaus - The Business Standard

At least 100,000 genomes of the Sars-CoV-2 virus that causes coronavirus disease (Covid-19) has been sequenced by the consortium of laboratories that keep an eye out for variants that might lead to a surge in infection. The Indian SARS-CoV-2 Genomics Consortium (INSACOG), which consists of 10 central laboratories and 28 regional ones, has sequenced 115,101 samples since January this year.

Of the total samples, over 65,000 samples were assigned lineages by the Pangolin software used by the researchers to determine which variant family they belong to. Of these, 69% of samples are known variants of interest (VOI) or variants of concern (VOC), according to the latest bulletin of the consortium.

At present, delta and its sub-lineage continue to be the dominant variant. Delta (B.1.617.2 and AY.x) continues to be the main VOC in India. No new VOI or VOC are noted and other VOC and VOI other than Delta are now negligible in sequencing data from India, the bulletin states. A previous bulletin had clarified the delta sub-lineage AY4.2 that was declared as a variant of interest by the UK was found in 0.1% of the samples. It is too low to be of a concern at the time, the bulletin from November 1 states.

The original delta variant (B1.617.2) continues to be the most dominant one in India, found in 66% of all the samples sequenced, according to data from outbreak.info, which compiles data from the global GISAID database. Delta is followed by five sub-lineages of it AY.43 (7%), AY.39 (5%), AY.44 (3%), AY.20 (3%), and AY.33 (2%).

In October-end, HT reported that there were 17 genome sequences that were being re-looked by researchers from INSACOG in order to see whether they can be classified as AY4.2. There are two mutations in the spike protein and one in the ORF region of the viral genome; if a sequence contains two of the three mutations coupled with the ones for delta variant they are considered to be AY4.2.

The scrutiny around AY.4.2 arose after the latest technical briefing by the Public Health England (PHE) upgraded the variant as being under investigation. The PHE document, dated October 22, said the key decision is based on AY.4.2 having a modestly increased growth rate and a higher secondary rate of attack the ability to pass the infection on to someone was higher than Deltas (12.4% versus 11.1%).

Among the total samples that have been assigned lineages so far this year, Alpha accounts for 6.4%, beta 0.33%, gamma 0.003%, delta 43.9%, close relatives of delta (B1.617.1 and B1.617.3) account for 8.2% of the sequences, and the AY sub-lineage of delta accounts for 10%, according to INSACOG data.

Dr Ekta Gupta, head of the regional INSACOG laboratory at the Institute of Liver and Biliary Sciences in Delhi said, So far, there is no clinical significance of the AY variants that we are seeing. These are also similar to the delta variant that a large proportion of the population has been exposed to, so these are unlikely to cause a huge surge.

Union minister of state for science and technology Dr Jitendra Singh, in a high-level review meeting on the current status of Covid-19 research, took note that over 100,000 samples have been sequenced so far and over 57,000 patient samples have been stored at five bio-repositories across the country that will be made available to researchers and private players for the development of vaccines and therapeutics.

A vaccine testing and research facility will come up at the second campus of the Rajiv Gandhi Centre for Biotechnology (RGCB) and this centre will also have a BSL-3 facility which is capable of handling airborne viruses like Covid-19. This facility will be the first of its kind in South India. The RGCB will be developed as a hub for research and testing of multiple vaccines such as cancer vaccines and those for infectious diseases, including Covid-19. This will bring huge recognition for the RGCB in the specific area of vaccine research and development, the minister said.

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India has sequenced over 100,000 viral genomes as part of its surveillance effort - Hindustan Times

Im about to begin revising the 14th edition of my human genetics textbook. In normal times, Id have amassed technical articles and case reports, as well as notes from meetings and interviews, choosing topics to add or ax and updating or replacing examples as the new edition takes shape.

But I havent thought much about genetics in 18 months, instead obsessively reading, listening, and writing about COVID-19 and SARS-CoV-2, terms that didnt exist when the current edition was published in September 2019. The before time.

So much has changed since I published my first COVID article on January 23, 2020.

Im relieved to focus once more on human genetics. A recent webinar from scientific publisher Elsevier, 20 Years of the Human Genome: From Sequence to Substance, has helped me get back on track and brought back memories.

Genetics Begat Genomics

I attended meetings in the mid-1980s, when gene mapping technologies had advanced enough to make sequencing the human genome a possibility, and not science fiction. Discovering the precise sequence of the DNA bases A, T, C, and G of that first human genome took a decade; today it can be done in under a day, a sequence displayable on a cell phone.

The US government-funded program to sequence the human genome began in 1990, accelerating as technologies improved. Each edition of my textbook followed the progress, starting with the first edition in 1993. The human genome was at first a chapter tacked onto the end. Then I moved it to follow molecular genetics and mutations. Now, genomics is woven into every chapter.

The final years of the effort to sequence a human genome became a contentious race between government researchers and the private company Celera Genomics. On June 26, 2000, Francis Collins, from the National Institutes of Health, and J. Craig Venter, from Celera, flanked President Clinton in the White House rose garden to announce the great sequencing the only open date on the calendar, so goes the lore. The effort supposedly ended in a tie.

The first drafts of a human genome sequence were published in February 2001. The Celera version was in Science, with 5 individuals contributing to that composite genome including Venter. Nature published the version from the International Human Genome Sequencing Consortium, which included the NIH group and used genome pieces from several de-identified individuals.

A fuller version was published in 2003, but all the gaps werent filled in until a publication on May 7, 2021. We now know that a human genome consists of 3,054,832,041 DNA base pairs.

Yet even as the first draft was nearing announcement, a global effort to catalog genetic variability had already begun, in 1999: the SNP Consortium. A single nucleotide polymorphism SNP is a place in the genome at which most people have one of the four DNA bases, but others have one of the other three. Cataloging the rarer SNPs quickly revealed that there is no one human genome. Were mostly the same, but the interesting parts of our genomes, many that impact health, differ.

The Rise, Finally, of Genomic Medicine

Last month, 20 Years of the Human Genome: From Sequence to Substance, began with remarks from Eric Green, MD, PhD, director of the National Human Genome Research Institute (NHGRI genome.gov/). He defined genomic medicine as an interdisciplinary medical specialty involving the use of genomic information. It embraces:

genetic testing

gene variants

exome and genome sequencing

DNA and RNA as biomarkers

microbiomes

big data omics: genomics, transcriptomics, epigenomics, pharmacogenomics, proteomics, and metabolomics

ethical, legal, and social implications (ELSI) of genetic and genomic research for individuals, families and communities

communication of findings

Practical applications of genome information have been a long time coming. Its 18 years out from the end of the genome project, 20 years from completion of the finished sequence, yet we are just starting to see genomic medical implementation. The most notable advances are in cancer genomics and pharmacogenomics, in rare genetic disease diagnostics, and diagnosing cases in ways that we never could have anticipated, faster and faster, Green said. He mentioned the newborn ICU, where rapid access to genomic information can now provide in days diagnoses that once took months, even years, in some cases changing and saving lives.

Dr. Green discussed 4 insights on the impact of genomic advances since the unveiling of the first draft sequences.

1. We are victims of our own success. We can generate human genome sequences easily and quickly. Getting an inventory of variants for an individual is straightforward, but understanding that list, and knowing for each variant what to do clinically or what to ignore, is not trivial. We often dont know what a list of gene variants means. Dr. Green mentioned ClinGen, an NIH-funded resource that defines the clinical relevance of genes and variants for use in precision medicine and research.

2. We have changed the relevance of genomics in our world. When I got involved at the beginning, it was just a bunch of geeky scientists like me trying to map the genome. We convinced health care professionals to come under our tent. Then we started doing genomic medicine cancer, pharmacogenomics, prenatal testing, rare disease diagnosis. Now genomics touches the health care ecosystem. Genomics is very much a part of society. Privacy, regulation, payment, all come with the responsibility of something becoming relevant.

3. We have a pervasive diversity problem in our field, from participants engaging as part of studies, to our workforce. He offered the example of the many genome-wide association studies GWAS that teased links between genome parts and traits/illnesses. A great majority of participants in GWAS in 2009 were European 96% and by 2016 it was 81%.

We must address health equity issues as genomic medicine is implemented. But we risk exacerbating this problem because traditionally we know that first access to cutting edge genomic medicine is skewed to people with the best health care, and thats disproportionately people of European ancestry, Dr. Green said. The Human Pangenome Reference Center.o is compiling genome sequences that reflect all human genome variation.

4. Beyond genomics. We are in a remarkable growth phase of genomic medicine due to technology we have for sequencing DNA. But health and environmental monitoring technologies are important too, and with those we can generate other omic data to couple with genomic data.

Dr. Green suggested that we think more broadly about genomic medicine, and say decision medicine as a more precise accounting of individual variability. Precision medicine is how genomic risk affects physiology, which also reflects lifestyle and environment. Through the lens of individual genetic variants, we have a powerful opportunity to advance our understanding of human health and disease. He mentioned the NIHs All of Us cohort of a million volunteers, adding that the UK Biobank is way ahead of us.

In October 2020, on the eve of the pandemic, Dr. Green and a stellar team published 10 Bold Predictions for Human Genomics by 2030. They are:

1. Sequencing and analyzing complete human genomes will become common in research labs2. Knowing every genes function3. Considering environmental influences on genomes to predict health and disease4. Genomics will no longer use social constructs, like race, in research5. Science fairs will include more genomics projects6. Genomic testing will become as commonplace in medicine as blood tests7. It will be easy to know if a persons gene variants are clinically important8. Smartphones will display complete genome sequences unveiled 2 months later9. Advances will benefit all 10. Genomics discovery and technologies will cure more genetic diseases

At the end of the webinar, Dr. Green took a walk down memory lane 30 years ago when the idea of sequencing the human genome arose. He joked about how little attention was paid to whose genome would be sequenced.

Were the parts being sequenced from the PI (principal investigator) or the slowest post doc who couldnt run out quickly enough when they came with the hypodermic to draw blood? Someone said whoever you pick, make sure that person is normal.

We now know that everyone is a mutant in some way and it doesnt matter. Now we recognize the lack of insight and thoughts about implications of actually getting that first sequence of a human genome. Weve come a long way in terms of thinking about these things, now that we have millions of genomes sequenced, but we really werent prepared for that first one.

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Looking Back 20 Years After the Unveiling of the First Human Genome Sequence - DNA Science - PLoS Blogs

The Genome Editing market report contains a detailed focused scene in which major players (OriGene, Thermo Fisher Scientific, NEB, Integrated DNA Technologies Inc, Lonza Group Ltd., Sangamo, GenScript, Transposagen, IDT, Horizon) are profiled. Various companies engaged with the Genome Editing are studies. TheGenome Editing market research reportgives a worldwide viewpoint. This can help the end consumer to make the right decision which ultimately leads to the development of the Genome Editing market. This brand-new report covers the current COVID-19 impact on the global market. Coronavirus (COVID-19) pandemics have affected every aspect of life globally. This has brought many changes in the market conditions. Initial and future assessments of the rapidly changing market landscape and impact are included in the report.

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According to the study, the market was predicted to grow at a CAGR of approximately xx% through the forecast period to strikeUSD xx million by 2026, reaching USD xx million in 2020.

The report gives a forward-looking viewpoint on different driving and limiting factors needed for the development ofthe Genome Editing market. It provides forecasts based on how the market should be developed. Their general organization review, key financial aspects, major progress, SWOT analysis, competitive analysis, growth and strategies are studied and discussed in the Genome Editing market report.

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OriGene, Thermo Fisher Scientific, NEB, Integrated DNA Technologies Inc, Lonza Group Ltd., Sangamo, GenScript, Transposagen, IDT, Horizon, among others

(Note: Driving key market players in the Genome Editing industry are scrutinized in the report along with their financial analysis, SWOT profile, business overview, products & services, operations, and geographical locations.)

This report studies the Genome Editing market based on its classifications. In addition to this, major regions (North America, Europe, Asia Pacific, Latin America, The Middle East and Africa, etc.) are also studies via this report. This report offers a detailed examination of the market by studying aggressive factors of the Genome Editing market. It also helps in identifying the main product sectors and their forecast in the years to come.

Global Market Segmentation by Product Type:

CRISPR, TALEN, ZFN, Antisense, Other Technologies

Global Industry Segmentation by Application:

Cell Line Engineering, Animal Genetic Engineering, Plant Genetic Engineering, Other Applications

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Imperial regions are studied all over the world and the types, drivers, development, restraints, and challenges that influence the growth of the Genome Editing market are taken into consideration on these essential geologies. Research on the impact of government strategies and policies of Genome Editing market processes has also been added to give a comprehensive summary of the future of the Genome Editing market.

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Global Genome Editing Market 2021 Size Share Upcoming Trends Segmentation And Forecast To 2027 Chip Design Magazine - Chip Design Magazine

Research in translocation renal cell carcinoma (tRCC) has been limited by the rareness of the disease, explained Ziad Bakouny, MD, MSc. Current treatment practices involve therapies that have demonstrated efficacy in other forms of kidney cancer, but these options do not necessarily improve outcomes in this specific population.

If we do not understand the biology [of the disease], we are not going to be able to target it correctly, Bakouny said. Currently, extrapolating treatments from clear cell RCC has not yielded optimal outcomes. Because of this, we want to understand the biology more to be able to target the disease better, treat patients better, and ultimately get them better clinical outcomes.

In an interview withOncLive, a sister publication of Oncology Nursing News,during the 2021 Kidney Cancer Research Summit, Bakouny, a research associate at Dana-Farber Cancer Institute and resident in internal medicine at Brigham and Womens Hospital, discussed recent ongoing research into the genomic drivers and biology of tRCC that could lead to improved outcomes for patients.

Could you provide some background on the treatment of tRCC?

Bakouny: tRCC is a very rare disease that affects primarily young patients, and interestingly, females more than males. It is thought to account for 1% to 5% of all RCCs in adults, and in children, it accounts for 20% to 50% of kidney cancers. The disease is aggressive, and what we know about is actually that we do not know that much. There have been large studies on more frequent forms of kidney cancer, including clear cell RCC and papillary RCC, and because of these efforts, there is quite a bit understood about the genomic drivers of this disease.

However, rarer forms, like tRCC, have not been studied as extensively, and we do not know much about them. This contributes to the fact that we do not have many therapies that work for them. All the therapies currently used for tRCC are extrapolated from clear cell RCC, as well as from other forms of kidney cancer.

The reason it is important to understand the biology of tRCC is because it is aggressive, and patients, unfortunately, often have poor outcomes, Additionally, it disproportionately affects young patients, and there is a significant burden of disease for these young patients, particularly young women.

What were the key takeaways from this research? Did investigators identify any clinical molecular features of the disease?

Because of how rare this disease is, we realized that we could not do this on our own, in the sense that no one center anywhere across the world would have been able to get enough samples to study the molecular characteristics of the disease, in addition to the clinical characteristics. What we did was pull data from approximately 10 different data sets that were publicly available, including some of our own. We put it all together and we analyzed it, using some unorthodox methods, to be able to ask the questions about what the molecular characteristics of these tumors are, what is driving these tumors, and what therapies might work for them.

To do this, we pulled the data together and included genomic data such as DNA level analyses and mutations. We also looked at fusions because these tumors are known to be driven by a characteristic fusion involving theTFEfamily of genes. Then we looked at was transcriptomic data, as well, and wanted to know what the transcriptomic characteristics of these tumors are. Finally, we looked at clinical responses to therapies.

In the DNA-level analyses of data, we found that these tumors have a silent genomethey do not have a lot of mutations, they do not have a lot of copy number alterations. Despite that, they do seem to have some recurrent alterations that we have identified, primarily 9p21.3 deletion, which is theCDK2NAlocus that seems to be deleted in up to 20% of these tumors, as well as a few mutations that we detected in DNA damage response genes andSWI/SNFgenes. That was the mutational bucket, in fusion bucket, it is known that these tumors evolveTFE3,TFEB, andMITFgenes. What we noticed is that the pattern of how these fusions form, what they conserve as part of these genes, differs between fusions. These genes seem to conserve the C-terminal domain, the DNA binding domain, of these proteins well, but depending on the actual gene itself, there are different parts of the protein domains that are conserved in the fusion product between them, so we that was characterized.

On the transcriptomic side of things, what we found is that these tumors seem to have a distinct transcriptional signature that is different from all other forms of RCC. This is characterized by genes that are known to be targets ofTFE3. We then used cell lines to transfect the fusion into this alliance [and were then able to] deduct that the transcriptional program of these tumors appears to be induced by the fusion itself. We then asked, what is this transcriptional program and what is it characterized by? What we found is that it is characterized by activation of the NRF2 transcriptional program, and that is a program that has been known to be activated across several malignancies.

Now that we know what the genomic characteristics are, we know what the fusion looks like, and we know what the transcriptomics look like for these tumors, we are left with the clinical response. What we found is that, as expected, these NRF2-expressing tumors do not seem to respond well to targeted therapies, which explains the usually poor outcomes seen in this patient population. We used to treat clear cell RCC with targeted therapies like mTOR inhibitors and VEGF inhibitors, and because of the NRF2 activation, we see poor responses to those with tRCC. However, they [do seem to] respond well to immune checkpoint inhibitors. We used our own data, as well as data from tRCCs that were identified post hoc in the phase 3 IMmotion151 trial (NCT02420821) to show that these tumors respond well to immune checkpoint inhibitors. This is still preliminary data, but given how rare this disease is, we believe they are convincing data that patients with these tumors may do well on immune checkpoint inhibitors or immune checkpoint inhibitor-based combinations.

What are some next steps for this research?

I am excited that through our study, and from multiple other studies that have been done in this space, we now have a firmer grasp on what the genomics of these tumors are and what the drivers are. What remains to be understood is how these interplay with each other. For instance, what is the fusion doing with theCDKN2Aloss? How are they cooperating to drive the pathogenesis of these tumors?

The next step that I am excited about is figuring out the underlying biology and following up on some of the signals that we have seen on how [these factors] interact with each other to drive tumor pathogenesis. The hope is that with a more granular understanding of these tumors, we will be able to develop specific therapies that target the pathogenic processes and be able to improve the outcomes of these patients, which is still a huge unmet clinical need.

Are there any recent therapeutic developments in tRCC, that should be highlighted that you want to discuss?

Unfortunately, the main therapeutic developments are the ones I previously mentioned as part of our study and others. These therapeutic developments are using the treatments we already have for RCC and seeing how they do in tRCC. This alludes to some of our own work that was just mentioned about how immune checkpoint inhibitors might do well in these tumors. There is corroborating data from other studies that have shown similar things, and right now, that is the most exciting space, in terms something that is clinically actionable. That said, the next steps are targeting the underlying biology of disease. That is what may drive improvement in the outcomes of patients with these tumors.

This article was originally published on OncLive as Research Efforts Seek to Understand Biology, Genomic Driver of Translocation RCC

Read more from the original source:
Understanding Translocation RCC Biology, Genomic Drivers May Provide Answers Needed for Better Targeted Treatments Options - http://www.oncnursingnews.com/

Remains of a young woman who lived approximately 50,000 years ago were unearthed by experts. Examination of her remains proved that she was a 'hybrid' ancestor to modern humans that experts never saw before.Not until lately when academics discovered proof that the young woman was not alone.

In the year 2019 a project work that explored the tangled disaster of humankind's prehistoric times, investigators utilized artificial intelligence (AI) to find an unidentified human progenitor life form that people today experienced and that has liaisons with on the lengthy journey out of Africa thousands of years ago.

"The so-called Out of Africa emerged roughly 80,000 years back, since component of the living organism inhabitants which more or less comprised of homo sapiens, decided to abandon the African territory and transitioned towards other regions giving a boost to all existing population," clarified by Universitat Pompeu Fabra in Spain, Jaume Bertranpetit also known to be a evolutionary biologist.

(Photo : Photo by MICHAEL TEWELDE/AFP via Getty Images)TOPSHOT - A picture taken on August 28, 2019 shows a 3.8 million-year-old skull of an early human, known as 'MRD' and belonging to the species Australopithecus anamensis, displayed during its presentation in Addis Ababa.

As human beings carved their way into the continent of Eurasia, they carved out another direction into which resulted to mating with old and extinct early humans from the other races.

Prior to the recent time wherein such sporadic potential participants were supposed to include Neanderthals and Denisovans, although of which being unidentified till the year of 2010.

However, owing to depth understanding techniques combing through some kind of complicated array of historical and present human genetic sequence, a third ex from such an antiquity was found in Eurasian DNA in this investigation.

Employing a scientific approach known as Bayesian inference, the investigators discovered indications of a 'third introgression' or also called a 'ghost' ancient community through which homo sapiens mated amid the African migration.

Under the perspective of pattern recognition, it was a type of hypothetical confirmation of forms of the young lady's 'composite' discovered in 2018. Nevertheless, there is plenty more work that can be done, and the study initiatives actually are really not specifically linked.

"Our idea agrees with the hybridized specimens identified lately in Denisova, although we cannot rule out certain theories at this moment," stated by genomicist Mayukh Mondal from the University of Tartu in Estonia in a news release at the time of discovery. Mayukh also happens to be one of the team's members.

Also read: Geologist's Disneyland: Iran's Hormuz Island Made of Edible Soil and Enchanting Salt Caves

A further group of experts discovered traces of a 'definite third interbreeding event' alongside Denisovans and Neanderthals in the year 2018, and other studies outline the history for how these fossilsintersected and mated in more precision than it has ever been.

And although there is still a lot of study to be performed in this area, such type of AI evaluation is a very novel approach in the context of human lineage, and the existing fossil data is incredibly limited.

However, the researcher's discovery reveals not simply a long-forgotten phase of gene flow but a dalliance that, illuminates background of the study.

"We assumed we'd attempt to discover these wide convergence points in the genomic, check which seem to be Neanderthal and which are Denisovan, and see if they represent the complete context," Bertranpetit informed Smithsonian.

"Since it occurs, even when the Neanderthal and Denisovan sections are removed, and there is something in the DNA that is quite different."

Also read: World's Oldest Prehistoric Crab Perfectly Preserved in Amber for 100 Million Years

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Teenage Girl From 50,000 Years Ago Carries Never-Before-Seen Hybrid Genome - Nature World News