Gene interactions are a potential key to personalized medicine

Gene interactions identified as personalized medicine’s missing link

“The ability to affordably sequence genomes has prompted numerous predictions about the rise of personalised medicine, however so far this has failed to come to pass. But in research published today, scientists have identified gene interactions as the key barrier to this medical revolution taking off.

Personalised medicine, where individuals are prescribed pharmaceuticals based on their own genetic makeup, has been raised as a possibility since the Human Genome Project was completed in 2003. It was thought that as more people had their genomes sequenced scientists would unearth genes responsible for predispositions to specific diseases, which would enable medication to be tailored to individuals.

However, while tens of thousands of people around the world have now had their genomes sequenced, it has not produced the clear genetic interactions initially predicted. And the reason for this is gene interactions: how different genes impact each other in the results and responses they produce.”

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Single sperm sequencing to understand meiotic recombination

Factors influencing meiotic recombination revealed by whole-genome sequencing of single sperm

Anjali Gupta Hinch, Gang Zhang, Philipp W. Becker, Daniela Moralli, Robert Hinch, Benjamin Davies, Rory Bowden, & Peter Donnelly

Science (Research Article)

Sequencing and the single sperm

During meiosis, homologous chromosomes undergo doublestrand breaks in DNA that can cross over, shuffling genetic material. However, not every double-strand break resolves in a crossover event. Hinch et al. wanted to determine the rules governing DNA recombination. They developed a method to sequence individual mouse sperm and applied it to mice carrying two different alleles of a protein involved in mammalian crossovers. A high-resolution genetic map revealed the relationships between the distribution of crossovers, proteins involved in recombination, and specific factors determining whether a double-strand break becomes a crossover.

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Liquid Biopsies help with Lung Cancer Diagnostics

Illumina-Sponsored Study Finds Liquid Biopsy Complements Tissue-Based Genotyping in Lung Cancer

NEW YORK (GenomeWeb) – The Illumina-sponsored Actionable Genome Consortium reported this week that cell-free DNA-based tumor genotyping for non-small cell lung cancer patients is concordant with tissue tumor-based genotyping most of the time and could be particularly useful in cases where acquiring a tissue biopsy is not feasible.

The group, which includes researchers from Memorial Sloan Kettering Cancer Center, Dan-Farber Cancer Center, MD Anderson Cancer Center, Grail, and Illumina, published its study this week in Annals of Oncology.

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Abbot gets clearance for Alinity Molecular Diagnostics

Abbott Receives CE Mark for Alinity Molecular Diagnostics System, Assays

“NEW YORK (GenomeWeb) – Abbott announced today that it has received CE marking for its Alinity molecular diagnostics system and assays, which are now available in countries that recognize the designation.

The firm said that its molecular system will help clinicians who are struggling to keep up with demand for infectious disease testing.

The MDx platform offers a number of initial assays, including virology testing for human immunodeficiency virus type 1, hepatitis B virus, and hepatitis C virus; sexual health-related testing for Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, and Mycoplasma genitalium, or a CT/NG/TV/MG panel; and high-risk human papillomavirus testing.“

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Walnut genome to be sequenced by UC Davis and USDA

Deciphering the Walnut Genome

“In a new study, a team of scientists at the University of California, Davis, and USDA’s Agricultural Research Service (ARS) used a unique approach to sequence the genomes of the English walnut and its wild North American relative by tapping into the capabilities of two state-of-the-art technologies: long-read DNA sequencing and optical genome mapping. The resulting genome sequences are believed to be of the highest quality ever assembled of any woody perennial.”

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Cornell sequences student genomes

What’s in Your DNA? Cornell Genomics Class Provides Students Free 23andMe Testing

“The first-ever sequencing of the human genome cost $2.7 billion. Today, the service 23andMe offers personal genome sequencing for less than $200. And for students enrolled in Cornell’s personal genomics class, it’s free.

Prof. Charles Aquadro, molecular biology and genetics, has been teaching Molecular Biology and Genetics 1290: Personal Genomics and Medicine: Why Should You Care About What’s in Your Genes for seven years now, following his hugely successful Cornell University Genetic Ancestry Project, a collaboration that traced the ancestry of over 200 Cornell undergraduates in the spring of 2011.”

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Funding for European NGS projects

European Genomics Collaborative Issues First Call for Proposals

“NEW YORK (GenomeWeb) — The European Advanced Infrastructure for Innovative Genomics (EASI-Genomics) today issued a first call for proposals for a range of projects that will be able to take advantage of the group's next-generation sequencing technologies and services.

EASI-Genomics, which is funded with €10 million ($11.3 million) under the European Union's Horizon 2020 program, is tasked with providing free access to NGS technologies and genomic services to researchers from industry and academia. It was launched earlier this year and aims to support between 150 and 300 projects over the next four years.“

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microRNA and cancer therapy

Scientists home in on microRNA processing for novel cancer therapies

“More than a decade of research on the mda-7/IL-24 gene has shown that it helps to suppress a majority of cancer types, and now scientists are focusing on how the gene drives this process by influencing microRNAs. Published this week in the journal Proceedings of the National Academy of Sciences, the findings could potentially have implications beyond cancer for a variety of cardiovascular and neurodegenerative diseases caused by the same microRNA-driven processes.”

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Great story about the application of evolutionary principles to fight cancer

A CLEVER NEW STRATEGY FOR TREATING CANCER, THANKS TO DARWIN

ROXANNE KHAMSI (WIRED)

“Even if cancer therapies kill most of the cells they target, a small subset can survive, largely thanks to genetic changes that render them resistant. In advanced-stage cancer, it’s generally a matter of when, not if, the pugnacious surviving cells will become an unstoppable force. Gatenby thought this deadly outcome might be prevented. His idea was to expose a tumor to medication intermittently, rather than in a constant assault, thereby reducing the pressure on its cells to evolve resistance.“

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Genome sequencing has been getting cheaper, but library preps haven't--until now

IDT lowers genomic barriers with targeted sequencing system

“Itegrated DNA Technologies (IDT) has introduced its rhAmpSeq targeted sequencing system, providing researchers with highly accurate, cost-effective and easy-to-use amplicon sequencing on Illumina next-generation sequencing (NGS) platforms. The rhAmpSeq chemistry enables multiplexing at impressive levels with high on-target rates and uniform coverage, delivering accurate results and accelerating projects. The system has wide-ranging applications, including human disease research and sample tracking and analysis, CRISPR genome editing analysis and agricultural biotechnology.”

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How transcription shapes the genome

The role of transcription in shaping the spatial organization of the genome

Bas van Steensel & Eileen E. M. Furlong

Nature Reviews Molecular Cell Biology (Review Article)

Abstract—The spatial organization of the genome into compartments and topologically associated domains can have an important role in the regulation of gene expression. But could gene expression conversely regulate genome organization? Here, we review recent studies that assessed the requirement of transcription and/or the transcription machinery for the establishment or maintenance of genome topology. The results reveal different requirements at different genomic scales. Transcription is generally not required for higher-level genome compartmentalization, has only moderate effects on domain organization and is not sufficient to create new domain boundaries. However, on a finer scale, transcripts or transcription does seem to have a role in the formation of subcompartments and subdomains and in stabilizing enhancer–promoter interactions. Recent evidence suggests a dynamic, reciprocal interplay between fine-scale genome organization and transcription, in which each is able to modulate or reinforce the activity of the other.

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George Smith on what's to gain from looking into the genomes of extinct furry elephants

Decoding a Mammoth with George Church

Join Harvard DNA pioneer George Church and Chris Smith in conversation as they discuss gene cloning, DNA sequencing, decoding the mammoth genome, the risks posed by fossil viruses lurking in extinct genomes, the prospects of xenotransplantation, and safety of gene therapy, and the risks of human CRISPR. The discussion was recorded on March 15th, live in front of a studio audience at the Hello Tomorrow Summit, in Paris, 2019...

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Microbiome may predict preterm births

Spontaneous Preterm Birth Clues Identified in Cervicovaginal Microbiome

NEW YORK (GenomeWeb) – A University of Pennsylvania and University of Maryland team has identified microbial community features and host immune features in the cervix and vagina that appear to coincide with spontaneous preterm birth risk.

Based on targeted sequence data and enzyme-linked immunosorbent assay (ELISA) data that provided a look at cervicovaginal microbial community members and immune protein levels, respectively, in hundreds of women with or without preterm birth, the researchers pinned down half a dozen microbial community types and identified seven taxa with apparent ties to spontaneous preterm birth.

Together with host immune protein levels, the microbiome data provided clues to preterm birth biology, the authors noted in its study, out in Nature Communications today. Moreover, they suggested that it may eventually be possible to develop therapeutic approaches that tap into microbiome or immune features associated with the condition.

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The Possibility of Computational DNA

Reprogrammable DNA

“Researchers from the California Institute of Technology and Harvard University have shown that it is possible to reprogram a DNA-based computer, Wired reports.

The team, led by Caltech's Erik Winfree, reports in Nature that it developed and validated a set of 355 DNA tiles that they could then reprogram into a range of six-bit algorithms. In particular, the team says it constructed 21 circuits that perform algorithms that copy, sort, elect a leader, and generate random patterns, among other tasks, with an error rate of less than 1 in 3,000. This, they add, suggests "molecular self-assembly could be a reliable algorithmic component within programmable chemical systems.“

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Motley-Fool's monthly speculation on cancer treatment stocks

3 Cancer Treatment Stocks to Buy in March

There has been tremendous progress in the battle against cancer, but it remains the second leading cause of death in the U.S., behind heart disease. That means there is plenty of work left to be done.

So which cancer-focused companies are worth watching? We asked three Motley Fool healthcare contributors to weigh in, and they called out Blueprint Medicines(NASDAQ:BPMC), Halozyme Therapeutics (NASDAQ:HALO), and Merck (NYSE:MRK). 

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What happens when a super-power, not start up, has your genome

What Will China Do With Your DNA?

China’s Fourth Magic Weapon, Part III: Bioweapons

by Steven Mosher (Epoch Times)

“Editor’s Note: In Parts I and II, Steven Mosher wrote about the Chinese Communist Party’s program to collect the DNA of all Chinese citizens. This was, he suggested, an effort to develop a fourth “magic weapon” of control over the Chinese population. The first three “magic weapons,” outlined by President Xi Jinping in a September 2014 speech, are “the People’s Liberation Army, propaganda, and United Front tactics.”

But this effort also extends beyond China’s borders. Here, in Part III, Mosher discusses ways in which the CCP is able to collect foreign DNA and how it might be able to profit from, or even weaponize, the genetic information it acquires from analyzing it.“

Chinese American scientists express concerns about profiling

Racial profiling harms science

“On behalf of the Society of Chinese Bioscientists in America (SCBA), the Chinese American Hematologist and Oncologist Network (CAHON), and the Chinese Biological Investigators Society (CBIS), we write to express our concerns about the recent political rhetoric and policies that single out students and scholars of Chinese descent working in the United States as threats to U.S. national interests [e.g., (1) and pp. 6–7 in (2)]. These developments have led to confusion, fear, and frustration among these highly dedicated professionals, who are in danger of being singled out for scape-goating, stereotyping, and racial profiling. U.S. policies must avoid targeting, as Representative Judy Chu (D–California) put it, “an entire ethnic group of people for suspicion that they're spies for China” (3).”

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Genome vs Exome sequencing in reference to cancer

Q&A With Mark B. Gerstein, PhD, on Diagnostic Genomic vs Exomic Sequencing

“Mark Gerstein, PhD, is Albert L Williams Professor of Biomedical Informatics and professor of molecular biophysics and biochemistry, and of computer science at the Yale School of Medicine in New Haven, Connecticut. He is also codirector of the Yale Program in Computational Biology & Bioinformatics.

Dr Gerstein spoke with Cancer Therapy Advisor about the diagnostic use of whole-genome compared with whole-exome next-generation sequencing to search for gene mutations that are thought to contribute to the risk of cancer and other diseases.1-3“

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Interesting Indian Genomics Advertorial

Genes2Me- Bringing New Healthcare Paradigm with Genomics

Genes2Me, India’s first diagnostic chain to bridge clinical diagnostics with genomics has reinvigorated the preventive healthcare sector in the country. Genes2Me has evolved as a game changer in the field of molecular testing by yielding health statistics of today and suitable lifestyle guidance for a healthy tomorrow. 

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Fisher makes big move buying Brammer Bio

Thermo Fisher to acquire Brammer Bio in $1.7 billion deal

(Reuters) - Thermo Fisher Scientific Inc, the world’s largest maker of scientific instruments, said on Sunday it has agreed to buy Brammer Bio in a roughly $1.7 billion cash deal.

Brammer Bio, a viral vector manufacturer for gene and cell therapies, is expected to post $250 million in revenue for 2019, Thermo Fisher said in a statement.

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