Diversity in Clinical Genetics Remains Poorly Defined

Diversity in Clinical Genetics Remains Poorly Defined but the Clinical Genome Resource (ClinGen) Ancestry and Diversity Working Group is working to address this important issue. In clinical genetics and genomics, many approaches depend on the ability to identify genetic variation that appears to be non-randomly distributed in a population. However, genetic variation often clusters in ways that reflect how peoples’ ancestors were grouped together. These historical associations are often summarized by the terms Race, Ethnicity, and Ancestry but what these terms mean, both semantically and biologically, are still very unclear. The paper below provides no clear solutions but is an excellent introduction and discussion of this problem and the challenges we face in addressing it.

Clinical Genetics Lacks Standard Definitions and Protocols for the Collection and Use of Diversity Measures

Abstract

Genetics researchers and clinical professionals rely on diversity measures such as race, ethnicity, and ancestry (REA) to stratify study participants and patients for a variety of applications in research and precision medicine. However, there are no comprehensive, widely accepted standards or guidelines for collecting and using such data in clinical genetics practice. Two NIH-funded research consortia, the Clinical Genome Resource (ClinGen) and Clinical Sequencing Evidence-generating Research (CSER), have partnered to address this issue and report how REA are currently collected, conceptualized, and used. Surveying clinical genetics professionals and researchers (n = 448), we found heterogeneity in the way REA are perceived, defined, and measured, with variation in the perceived importance of REA in both clinical and research settings. The majority of respondents (>55%) felt that REA are at least somewhat important for clinical variant interpretation, ordering genetic tests, and communicating results to patients. However, there was no consensus on the relevance of REA, including how each of these measures should be used in different scenarios and what information they can convey in the context of human genetics. A lack of common definitions and applications of REA across the precision medicine pipeline may contribute to inconsistencies in data collection, missing or inaccurate classifications, and misleading or inconclusive results. Thus, our findings support the need for standardization and harmonization of REA data collection and use in clinical genetics and precision health research.

READ MORE …

Here’s a link to the group that published this paper: https://www.clinicalgenome.org/working-groups/ancestry/

Suggestions for Science Communications

Hyped-up science erodes trust. Here’s how researchers can fight back.

View fullsize

Science is often poorly communicated. Researchers can fight back.

By Brian Resnick, Vox

In 2018, psychology PhD student William McAuliffe co-published a paper in the prestigious journal Nature Human Behavior. The study’s conclusion — that people become less generous over time when they make decisions in an environment where they don’t know or interact with other people — was fairly nuanced.

But the university’s press department, perhaps in an attempt to make the study more attractive to news outlets, amped up the finding. The headline of the press release heralding the publication of the study read “Is big-city living eroding our nice instinct?”

From there, the study took on a new life as stories in the press appeared with headlines like “City life makes humans less kind to strangers.”

This interpretation wasn’t correct: The study was conducted in a lab, not a city. And it measured investing money, not overall kindness.

READ MORE…

Thank you for reading!

Unproven Stem Cell Therapies Earn Traction and Criticism

This an interesting article about the some of efforts in take advantage of Stem Cell therapies happening in China, and some of actions being taken to slow these efforts down to a responsible rate.

China urged to abandon plan to sell unproven cell therapies

David Cyranoski, Nature

An international stem-cell body says the country’s proposed law could put patients at risk.

An international group of stem-cell researchers is urging China to cancel draft regulations that would permit some hospitals to sell therapies developed from patients’ own cells, without approval from the nation’s drug regulator.

The International Society for Stem Cell Research (ISSCR) sent a statement outlining its concerns to Jiao Hong, director of China’s National Medical Products Administration in Beijing, on 20 May. The society, which is based in Skokie, Illinois, represents more than 4,000 scientists, clinicians and ethicists around the world.

“We are deeply concerned that China’s newly proposed regulations will provide incentives for hospitals to market unsafe and ineffective interventions directly to consumers. This has the potential to harm the people of China, undermine public health and discredit the international standing of the Chinese regenerative medicine community,” warns the statement, which was signed by society president Doug Melton.

READ MORE …

The Limits of What DNA Can Predict

Read the tweetorial, it isn’t too complex …

Want remarkably clear insights into genetics and public health with a bare minimum of reading? Well, some corners of Twitter have recently become an incredible resource if you’re interested in learning something about predictive statistics, epidemiology, genomics, and population genetics. There are no better examples of this than the tweetorials that Dr. Cecile Janssen posts. Dr. Janssen is a professor of translational epidemiology in the department of Epidemiology of the Rollins School of Public Health, Emory University, and her website, like her posts, contains insightful guides for thinking critically about DNA sequence data, heritability and health.

If you would like some key insights into predicting complex traits from DNA in a handful of tweets, follow this link: Why it is so hard to predict complex diseases and traits from DNA?

For a slightly longer read, here’s her article from WIRED on how DNA is best applied: DNA tells great stories -- about the past, not future

And a more advanced read, still aimed at a fairly general audience: Designing babies through gene editing: science or science fiction?

How to Train your Genomics Models

First open resource hosts trained machine-learning genomics models to facilitates their use and exchange

From Avsec (2019) Nature Biotechnology

A powerful new resource, one that is actually a new kind of resource, has come online and, hopefully, will help accelerate advances in genomics and the fight against many types of disease. The scale of genome data is so large that computational tools are required for every major step of acquiring, organizing, and analyzing genomes. Generating useful models from large genomic datasets, the kind you generate when studying human disease, is often difficult and time consuming and many aspects of this are now being automated using various types of machine learning approaches. Machine learning in this context can be roughly summarized as using computers to generate and evaluate huge numbers of statistical models in order to clarify relationships in datasets. To do this, the machine learning program needs to train on useful datasets. So for many cutting edge applications, the program doesn’t just need to be written but also trained—and this second step can require large amounts of time and computational resources, making the transmission and broader application of these programs less likely, until now. The Kipoi repository is the first open resource for machine learning methods in genomics, making cutting edge approaches available to clinicians and smaller labs. This resource is sure to speed the application and innovation in machine learning based genomics approaches, and hopefully we will all benefit from this new site for the free exchange of ideas.

For more information, here’s a nice summary from Technology Networks.

Here is the introduction from the original article, published in Nature Biotechnology.

Advances in machine learning, coupled with rapidly growing genome sequencing and molecular profiling datasets, are catalyzing progress in genomics1. In particular, predictive machine learning models, which are mathematical functions trained to map input data to output values, have found widespread usage. Prominent examples include calling variants from whole-genome sequencing data2,3, estimating CRISPR guide activity4,5 and predicting molecular phenotypes, including transcription factor binding, chromatin accessibility and splicing efficiency, from DNA sequence1,6,7,8,9,10,11. Once trained, these models can be probed in silico to infer quantitative relationships between diverse genomic data modalities, enabling several key applications such as the interpretation of functional genetic variants and rational design of synthetic genes.

However, despite the pivotal importance of predictive models in genomics, it is surprisingly difficult to share and exchange models effectively. In particular, there is no established standard for depositing and sharing trained models. This lack is in stark contrast to bioinformatics software and workflows, which are commonly shared through general-purpose software platforms such as the highly successful Bioconductor project12. Similarly, there exist platforms to share genomic raw data, including Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/), ArrayExpress (https://www.ebi.ac.uk/arrayexpress) and the European Nucleotide Archive (https://www.ebi.ac.uk/ena). In contrast, trained genomics models are made available via scattered channels, including code repositories, supplementary material of articles and author-maintained web pages. The lack of a standardized framework for sharing trained models in genomics hampers not only the effective use of these models—and in particular their application to new data—but also the use of existing models as building blocks to solve more complex tasks.

READ MORE …

Human Genome Reference Sequence: Summary or Example?

There is no one human genome. Each person starts life with two non-identical copies of a genome, and variations both small and large begin to accumulate each time those copies are copied. And then there are the differences between individuals. If we think of the genome as a single list of bases at specific positions then point mutations—substitutions, small inserts and deletions—are easy enough to map to those position, however major structural variants—inversions, translocations and repetitive sequences—complicate how we map these mutations. Reference genomes, a consensus representation of deeply sequenced human genomes have traditionally been the basis of how we map nucleotides and variants to positions on chromosomes but long read technologies are making it increasingly apparent that structural variants are quite common and new methods for representing the human genome.

The first of the following articles lays out why a more advanced model for capturing the variation in the human genome is needed. The article after that describes how multiple genomes and their structural variation can be summarized using graphs, a computational improvement on the current linear reference genomes. The last article discusses the some of the single molecule sequencing technology bringing this issue to the fore. There are many other articles that deal with this topic, but these are a good start.

Yang, et al. (2019) One reference genome is not enough. Genome Biology

Abstract

A recent study on human structural variation indicates insufficiencies and errors in the human reference genome, GRCh38, and argues for the construction of a human pan-genome.

########################################################################################

Here’s an article describing how structural variants can be captured in a graph.

Rakocevic, et al. (2019) Fast and accurate genomic analyses using genome graphs. Nature Genetics

Abstract

The human reference genome serves as the foundation for genomics by providing a scaffold for alignment of sequencing reads, but currently only reflects a single consensus haplotype, thus impairing analysis accuracy. Here we present a graph reference genome implementation that enables read alignment across 2,800 diploid genomes encompassing 12.6 million SNPs and 4.0 million insertions and deletions (indels). The pipeline processes one whole-genome sequencing sample in 6.5 h using a system with 36 CPU cores. We show that using a graph genome reference improves read mapping sensitivity and produces a 0.5% increase in variant calling recall, with unaffected specificity. Structural variations incorporated into a graph genome can be genotyped accurately under a unified framework. Finally, we show that iterative augmentation of graph genomes yields incremental gains in variant calling accuracy. Our implementation is an important advance toward fulfilling the promise of graph genomes to radically enhance the scalability and accuracy of genomic analyses.

########################################################################################

Here’s an article describing how next-next generation sequencing is illuminating the diversity of structural variants across human populations.

Chaisson, et al. (2015) Resolving the complexity of the human genome using single-molecule sequencing. Nature

Abstract

Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing2, next-generation mapping3, microfluidics-based linked reads4, and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17.9 Mb and a scaffold N50 size of 44.8 Mb, resolving 8 chromosomal arms into single scaffolds. The de novoassembly, along with local assemblies and spanning long reads, closes 105 and extends into 72 out of 190 euchromatic gaps in the reference genome, adding 1.03 Mb of previously intractable sequence. High concordance between the assembly and paired-end sequences from 62,758 BAC clones provides strong support for the robustness of the assembly. We identify 18,210 structural variants by direct comparison of the assembly with the human reference, identifying thousands of breakpoints that, to our knowledge, have not been reported before. Many of the insertions are reflected in the transcriptome and are shared across the Asian population. We performed haplotype phasing of the assembly with short reads, long reads and linked reads from whole-genome sequencing and with short reads from 31,719 BAC clones, thereby achieving phased blocks with an N50 size of 11.6 Mb. Haplotigs assembled from single-molecule real-time reads assigned to haplotypes on phased blocks covered 89% of genes. The haplotigs accurately characterized the hypervariable major histocompatability complex region as well as demonstrating allele configuration in clinically relevant genes such as CYP2D6. This work presents the most contiguous diploid human genome assembly so far, with extensive investigation of unreported and Asian-specific structural variants, and high-quality haplotyping of clinically relevant alleles for precision medicine.

Thank you for reading!

Polygenic traits should not be used for selecting embryos

The article below is an important perspective on the troubling potential use of polygenic trait scores to select embryos, written by one of the directors of the EMBL-EBI on his blog. Polygenic traits are directly affected by several loci and typically exhibit phenotypes that have continuous distributions, such as intelligence and height. While some pretty obvious arguments can be made for why using polygenic traits for selecting embryos would be immoral, this article helps to make clear that it would also likely be an ineffective way to guarantee your child has a certain height and IQ.

Polygenic trait scores, their value to medicine and for making predictions about humans, is being discussed very actively right now. Some of the most exciting, real-time conversations about polygenic traits and polygenic risk scores are happening on Twitter in real time. I strongly encourage you to follow Ewan Birney (@ewanbirney) and Cecile Janssens (@cecilejanssens) professor of translational epidemiology at Emory University, for her consistently clear and insightful comments on how we interpret whole genome data.

Why embryo selection for polygenic traits is wrong.

MAY 26, 2019 BY EWANBIRNEY

This week (May 20th 2019) has seen yet another splash by an American company offering a polygenic trait score on embryos including intelligence. This is wrong on a number of levels; ethically it is wrong to make this decision as an independent laboratory without broad societal buy in; scientifically it is wrong to imagine the ways we assess polygenic traits will translate into safe and effective embryo selection; for the specifics of IQ/Educational attainment trait this trait is so complex this is additionally unwise over and above any concerns.

READ MORE …

When is the right time to have your child's genome sequenced?

Every new technology will raise questions about its potential and effects, especially in regards to children. So it should be no surprise that now, as genome sequencing technology becomes cheaper, better, and more accessible to consumers, some important and sometimes impassioned conversations are going to have to happen. For some perspective, people had grave concerns about kids playing Dungeons & Dragons when it first became popular. The article below does a nice job covering some important points to consider.

Now You Can Genetically Test Your Child For Disease Risks. Should You?

Genomics is cheaper and more available then ever, but its usefulness for parents has yet to be proven…

“Most direct-to-consumer genetic testing services still require that patients be at least 18 years old. But there are workarounds. The popular at-home DNA test 23andMe requires that users be 18, but parents can order $199 kits for their offspring and send back their saliva through the mail, according to spokesman Andy Kill. (Kill says the company doesn't have statistics on how many children’s samples it has received.) And in April, the FDA ruled that 23andMe could release reports about patients’ risks for diseases, including Parkinson’s and late-onset Alzheimer’s diseases.

As testing children for genetic diseases becomes available to more parents, it is raising difficult ethical questions. For instance: Would the knowledge that your kid might get sick someday make you treat them differently? “There’s a concern that parents might connect to kids in a different way if they knew something negative about their future,” says Laventhal. Perhaps you'd be proactive by pushing your daughters to freeze their eggs at a young age, if you knew they were at risk for cancers and might undergo cancer treatments that could hurt their fertility.

“You’re going to create a lot of unnecessary stress and anxiety and make parents crazy,” adds Dr. Lainie Friedman Ross, who researches genetic testing policy at the MacLean Center for Clinical Medical Ethics at the University of Chicago. “

READ MORE …

Bold Chinese Experiment Genetically Engineers Monkeys, maybe makes them Smarter, definitely raises some ethical questions

Chinese researchers are going hard lately! Following projects that include genetically modifying embryos and letting two develop into twin human babies, and cloning primates, another envelope-pushing report comes from the Chinese Bio-Science community—this time by inserting a human version of a gene into a Rhesus Monkey. The gene MCPH1 is thought to play an important role in human brain development and contribute to the distinctively human cognitive ability. The genetically modified monkeys exhibited slower (more human-like) brain development and possibly even improved cognitive ability. This work was published by Oxford University Press on behalf of China Science Publishing & Media Ltd., which is ostensibly a peer-review journal, but not PLOS or PNAS, and it unclear if this work would be given the green light at an American University. There will certainly be debate in the press about this topic, which should be thrilling, but hopefully it will hasten a some thoughtful conclusions.

Read the original article HERE and other summaries here and here and here.

CRISPR gene drive vs CRISPR allelic drive

CRISP-based genome modifying technologies are offer a power and precision people only dreamed of not that long ago. CRISPR gene drives use guide RNAs (gDNAs) to insert gene-drive sequences, and the CRISPR allele drives do the same while also modifying undesired variants at a second position. Gene and allele drives are likely to be central to how humans modify the living environment in the future, in addition to being the starting point for endless unchecked-tech sci-fi nightmare scenarios . The following article provides a clear and helpful explanation of these technologies and some of their applications.

CRISPR-based 'allelic drive' allows genetic editing with selective precision and broad implications

Scientists developed a new version of a gene drive that allows the spread of specific, favorable genetic variants, also known as 'alleles,' throughout a population. The new 'allelic drive' is equipped with a guide RNA that directs CRISPR to cut undesired variants of a gene and replace it with a preferred version. Using a word processing analogy, CRISPR-based gene drives allow scientists to edit sentences of genetic information, while the new allelic drive offers letter-by-letter editing.

READ MORE …

Population Structure: A Key Concept for Understanding Genetic Variation

It is common for articles to claim that “the gene for” some trait or disease has been identified. Usually they actually mean that an association has been found between an uncommon genetic variant found in, or near, a gene and some trait or disease. These kinds of articles are becoming increasingly common because Genome-Wide Association Studies (GWAS) are becoming cheaper and more common. Though GWAS yield important insights their results can be misleading because ancestral relationships between individuals in the study can create signals that can be misinterpreted as association with the trait being studied. This phenomenon is very powerful and one reason why it is important to have a diverse group of individuals in any genetic study. Underlying ancestral relationships are known as “population structure” and serious thought is required to ensure that it doesn’t skew GWAS results. The paper below is a scientific review article (in an excellent journal with exceptional authors) and not exactly easy reading, but it was written for a broad audience and worth considering the next time you see an article discussing the identification of “the genes for” something or other, even if it appears in Genome-Media.

-RPR

Population Genetics: Why structure matters

Abstract

Great care is needed when interpreting claims about the genetic basis of human variation based on data from genome-wide association studies.

Main text

Human height is the classic example of a quantitative trait: its distribution is continuous, presumably because it is influenced by variation at a very large number of genes, most with a small effect (Fisher, 1918). Yet height is also strongly affected by the environment: average height in many countries increased during the last century and the children of immigrants are often taller than relatives in their country of origin – in both cases presumably due to changing diet and other environmental factors (Cavalli-Sforza and Bodmer, 1971; Grasgruber et al., 2016; NCD Risk Factor Collaboration, 2016). This makes it very difficult to determine the cause of geographic patterns for height, such as the ‘latitudinal cline’ seen in Europe (Figure 1).

READ MORE …



Catastrophic loss of amphibian biodiversity

Scientists Uncover the Most Devastating Disease-Afflicted Biodiversity Loss Known to Science

A recent paper published in Science revealed the shocking results of a global disease transmission assessment: A fungal disease affecting amphibians has been identified as the most devastating recorded example of biodiversity loss attributable to a single disease. The analysis was made possible by an extensive collaboration involving experts from 36 institutions.

Over the past half century, the amphibian chytridiomycosis panzootic, an infectious disease that affects amphibians worldwide, has resulted in 90 presumed extinctions as well as the decline of at least 501 amphibian species.

This fungus was identified in amphibian populations about 20 years ago as the cause of death and species extinction at a global scale. The last similar analysis that assessed global amphibian decline was published in 2007 but was mainly focused on the regions that suffered the most decline.

One of the two Cornell affiliates in the study, Prof. Kelly Zamudio, ecology and evolutionary biology, has worked in Panama, Brazil and the United States studying the effect of frog-killing chytrid fungus Batrachochytrium dendrobatidis using population genetics.

Zamudio said the idea for the global epidemiological analysis started from a conversation going around the amphibians researcher community: “How bad is this? How much have we really lost?”

READ MORE …

American Society of Human Genetics to expand Developing Country Awards Program

ASHG Announces Expansion to Developing Country Awards Program
25 Travel Awards Will Enhance Africa’s Participation in Scientific Dialogue

ROCKVILLE, Md. – The American Society of Human Genetics (ASHG), in collaboration with the National Human Genome Research Institute (NHGRI), is pleased to announce the addition of 25 awards to its annual Developing Country Awards Program. The new awards will enable 25 genetics trainees and/or early- to mid-career investigators from Africa who are currently working in Africa to attend the ASHG 2019 Annual Meeting, taking place October 15-19, 2019, in Houston, Texas. They will be supported by NHGRI; the Human, Heredity, and Health in Africa (H3Africa) consortium; and ASHG; and administered via the H3Africa Coordinating Center at the University of Cape Town.

“Through these awards, we hope to enhance the participation and visibility of promising African geneticists at the world’s largest genetics meeting,” said Kiran Musunuru, MD, PhD, 2019 Chair of the ASHG Program Committee. “By working to enrich the diversity of voices engaged in research worldwide, we reaffirm our commitment to global science, and we hope to grow similar partnerships in other regions in the future,” he said.

“In Africa, there is a growing research community using genomic methods in biomedical research to address the substantial disease burden,” explained Jennifer Troyer, PhD, H3Africa Program Director at NHGRI. “Over the past decade, the H3Africa Consortium and other international global health efforts have increased support for research leaders in Africa to address vital research topics there and to provide training for the next generation of African researchers, leading to the growth of genetics and genomics research on the continent,” said Dr. Troyer.

READ MORE …

Birds illustrate how genomics can make things harder, even if it makes things better

What’s in a Name? How Genome Mapping Can Make It Harder to Tell Species Apart

Rebecca Heisman, Living Bird

If you had opened a copy of the Sibley Guide to Birds when it was first published in the year 2000 and flipped to the section on wood-warblers, you would have found 13 pages devoted to members of a single genus: Dendroica, Latin for tree-dweller. Dendroica’s inhabitants included 21 colorful species—such as Magnolia, Blackburnian, and Cerulean Warblers—dear to the hearts of many birders.

Open a copy of the second edition of the Sibley Guide today, and Dendroica is nowhere to be found.

There hasn’t been a mass extinction in the intervening years. The wood-warbler species are all still there, but filed under a different genus name, Setophaga. Instead, there has been a major shift in how ornithologists sort and classify bird species, and the genus name Dendroica was a casualty.

Decisions about how North American bird species are classified and what is and is not considered a species are made every summer by a special committee of the American Ornithological Society. An AOS committee bases its judgments on the best available science. But the science is rapidly expanding. Like many other branches of biology, ornithologists are trying to make sense of a flood of new information flowing from the latest advances in genome mapping. Today, avian geneticists can dive deep into genomes to unveil the molecular differences underlying variation between birds.

READ MORE …

Nat-Geo addresses the idea of a gene

The Gene: Science's Most Powerful—and Dangerous—Idea

SIMON WORRALL, National Geographic

The gene is “one of the most powerful and dangerous ideas in the history of science,” argues Siddhartha Mukherjee in The Gene: An Intimate History . Since its discovery by Gregor Mendel, an obscure Moravian monk, the gene has been both a force for good and ill. In the 1930s, the Nazis exploited the pseudoscience of eugenics as a prelude to the Holocaust. Today, gene therapy holds out the hope of eradicating hereditary conditions like Huntington’s disease and even psychological disturbances, such as schizophrenia. [See how the DNA revolution is giving us unprecedented power.]

National Geographic caught up with the author as he was driving across the Williamsburg Bridge in New York City. Mukherjee, a professor of medicine at Columbia University who also wrote the Pulitzer Prize-winning The Emperor of All Maladies about cancer, explained why the book has deep personal roots, how the United States eagerly adopted the pseudoscience of eugenics, and why allowing individuals to make decisions about altering the genetic makeup of their children may be a dangerous thing to do.

READ MORE …

A bioengineer, a biopunk, and a biotech reporter talk about Genetic Engineering

The Future of Genetic Engineering

A bioengineer, a biopunk, and a biotech reporter square off onstage about our neobiological future.

By Jane Metcalfe

In a new documentary that is still in production, filmmaker Cory Sheehy follows renowned bioengineer George Church and biotech reporter Antonio Regalado to China for the 2nd International Summit on Human Genome Editing. That’s where biophysicist He Jiankui made the stunning announcement that he had edited the DNA of two twin girls who were born in November 2018. Back in California, the filmmaker catches up with biohacker Josiah Zayner, whose attention-grabbing exploits—part protest, part performance art—include injecting himself with a CRISPR-Cas9 plasmid.

Watch the video here …

Cleveland Clinic Commentary for Cancer Screening

Personalizing guideline-driven cancer screening

Gautam Mankaney, MD Carol A. Burke, MD, FACG, FACP, FASGE

Cleveland Clinic Journal of Medicine (Commentary)

Reports of cancer date back thousands of years to Egyptian texts. Its existence baffled scientists until the 1950s, when Watson, Crick, and Franklin discovered the structure of DNA, laying the groundwork for identifying the genetic pathways leading to cancer. Currently, cancer is a leading global cause of death and the second leading cause of death in the United States.

In an effort to curtail cancer and its related morbidity and mortality, population-based screening programs have been implemented with tests that identify precancerous lesions and, preferably, early-stage rather than late-stage cancer.

Screening for cancer can lead to early diagnosis and prevent death from cancer, but the topic continues to provoke controversy.

READ MORE …

Illumina retaliates against BGI

Illumina Files Patent Infringement Suit Against BGI in Germany

SAN DIEGO--(BUSINESS WIRE)--Mar 29, 2019--Illumina, Inc. (NASDAQ: ILMN) today announced that it has filed a patent infringement suit against BGI Group’s subsidiary, Latvia MGI Tech SIA, in the Düsseldorf Regional Court in Germany. The complaint alleges that BGI’s sequencing products, including the BGISeq-500, MGISeq-2000, and related chemistry reagents, infringe EP 1 530 578 B1. This patent covers Illumina’s proprietary sequencing-by-synthesis chemistry.

“Illumina will not tolerate the unauthorized, infringing use of its patented technology. Illumina filed this suit to defend the substantial investments we have made in our industry leading sequencing technology, as validated in our global intellectual property portfolio. We will continue to monitor the field and file patent suits where appropriate when our patents are infringed,” said Charles Dadswell, Senior Vice President and General Counsel for Illumina.

READ MORE …

The world needs more Geneticists

Study Finds Shortage of Medical Geneticists

Genomics plays an increasingly important role in how we treat cancer. Genomic analyses can tell us who is at highest risk of developing cancer as well as how to treat someone’s cancer in the most precise and effective way possible. “Targeted drugs for cancer happen in 2 different ways,” says Michael Watson, PhD, founder and executive director of the American College of Medical Genetics and Genomics, Bethesda, Maryland. “Some drugs are molecularly targeted, so knowing the specific tumor genetics allows you to identify the best drug for the tumor. But there is also germline pharmacogenetics — someone can have a gene in their own DNA that alters how they will metabolize various drugs.” Understanding and interpreting these genetic differences factor into an oncologist’s decision regarding the best therapeutic approach to pursue.

But oncologists aren’t always trained in the newest genomic tests and technologies, which change rapidly as science in this area continues to advance at a dizzying pace. They often rely on collaboration with medical geneticists, who may work in the laboratories that run somatic cancer testing as well as serve patients clinically themselves, particularly by treating patients who may have a known genetic risk for cancer, such as disruptions in the BRCA1 or BRCA2 genes. Access to these specialist physicians will be a crucial component of cancer care in the future.

READ MORE …

Is CRISPR a National Security Threat?

National Security Implications of Gene Editing

“CRISPR-Cas9 is here and now, he pointed out. “Gene editing has a number of near term and longer term ramifications that … have implications for national security, intelligence and defense,” he said.

If the research goes clandestine, the technology could be used to modify various physiological functions in humans both before birth and perhaps key operational points or optimized points after birth, he said.

With genomic knowledge of weaknesses and susceptibilities to certain diseases, populations could be targeted in order to cause instability in societies.”

READ MORE …