A new company offers a “gene vault” for doctors who want to add genomics to patient care.
Genomic sequencing might be more common in medicine if doctors had a simple way to send for the test and keep track of the data.
That’s the hope of Coriell Life Sciences in Camden, N.J., a startup that grew out of a partnership between the Coriell Institute for Medical Research and IBM. The company wants to facilitate the process of ordering, storing and interpreting whole-genome-sequence data for doctors. The company launched in January and is now working with different health-care providers to set up its service.
“The intent is that the doctor would order a test like any other diagnostic test they order today,” says Scott Megill, president of Coriell Life Sciences. The company would facilitate sequencing the patient’s DNA (through existing sequencing companies such as Illumina or Ion Torrent), store it in its so-called gene vault, and act as the middleman between doctors and companies that offer interpretation services. Finally, “we will return the genetic result in the human readable form back to the electronic medical record so the doctor can read it and interpret it for the patient,” says Megill.
“You need a robust software infrastructure for storing, analyzing, and presenting information,” says Jon Hirsch, who founded Syapse, a California-based company developing software to analyze biological data sets for diagnosing patients. “Until that gets built, you can generate all the data you want, but it’s not going to have any impact outside the few major centers of genomics medicine,” he says.
The company will use a board of scientific advisors to guide them to the best interpretation programs available. “No one company is in position to interpret the entire genome for its meaning,” says Michael Christman, CEO of the Coriell Institute for Medical Research. “But by having one’s sequence in the gene vault, then the physician will be able to order interpretative engines, analogous to apps for the iPhone,” he says. Doctors could order an app to analyze a patient’s genome for DNA variants linked to poor drug response at one point, and later on, order another for variants linked to heart disease.
The cloud-based workflow could help doctors in different locations take advantage of expert interpretations anywhere, says Christman. “This would allow a doctor who’s at a community clinic in Tulsa, Okla., order an interpretation of breast cancer sequences derived at Sloan Kettering,” he says.
The main function of gene promoters appears to be the integration of different gene products in their biological pathways in order to maintain homeostasis. Generally, promoters have been classified in two major classes, namely TATA and CpG. Nevertheless, many genes using the same combinatorial formation of transcription factors have different gene expression patterns. Accordingly, a group of scientists has now tried to find some fundamental questions: Why certain genes have an overall predisposition for higher gene expression levels than others? What causes such a predisposition? Is there a structural relationship of these sequences in different tissues? Is there a strong phylogenetic relationship between promoters of closely related species?
In order to gain valuable insights into different promoter regions, they obtained a series of image-based patterns allowing the identificaion of 10 generic classes of promoters. A comprehensive analysis was undertaken for promoter sequences from Arabidopsis thaliana, Drosophila melanogaster, Homo sapiensand Oryza sativa, and a more extensive analysis of tissue-specific promoters in humans. The scientists observed a clear preference for these species to use certain classes of promoters for specific biological processes. Moreover, in humans, they found that different tissues use distinct classes of promoters, reflecting an emerging promoter network. Depending on the tissue type, comparisons made between these classes of promoters reveal a complementarity between their patterns whereas some other classes of promoters have been observed to occur in competition. Furthermore, they also noticed the existence of some transitional states between these classes of promoters that may explain certain evolutionary mechanisms, which suggest a possible predisposition for specific levels of gene expression and perhaps for a different number of factors responsible for triggering gene expression. They conclusions from all this are based on comprehensive data from three different databases and a new computer model whose core is using Kappa index of coincidence.
Heidi Rehm has been using disease-targeted gene panels to diagnose patients in her clinical molecular genetics practice for a decade. Having adopted next-generation sequencing approaches two years ago, and whole-genome and whole-exome sequencing for some patients in the past year, she is a pioneer in applying genomics in the clinic.
Very good discussion on the current impact that genetic and genomic sequencing are having on clinical decisions, and a look into the future when genome analysis is much more cost effective.
The notion that police can identify a suspect based on the tiniest drop of blood or trace of tissue has long been a staple of TV dramas, but scientists at Harvard have now taken the idea a step further. Using just a single human cell, they can reproduce an individual’s entire genome.
The researchers developed a method — dubbed MALBAC, short for Multiple Annealing and Looping-based Amplification Cycles — that requires just one cell to reproduce an entire DNA molecule.
Ray and Terry's 's insight:
As reported by KurzweilAI.net, this technique could lead to more nimble cancer treatments and enhanced prenatal screening.
LONDON (Reuters) - Up to 100,000 Britons suffering from cancer and rare diseases are to have their genetic codes fully sequenced and mapped as part of government efforts to boost drug development and improve...
Although the oomycetes and fungi are evolutionarily very distantly related, both taxa evolved biotrophy on plant hosts several times independently, giving rise to rust- and mildew-like phenotypes. Differences in host colonization and adaptation may be reflected in genome size and by gain and loss of genes. In this opinion article we combine classical knowledge with recently sequenced pathogen genomes and present new hypotheses about the convergent evolution that led to these two distinct phenotypes in obligate biotrophs.
Imagine if DNA compilation was as easy to understand as Windows or iOS. Scientific study would no longer be necessary to engineer new combinations and just about anyone could drag and drop bits of genetic code into a workable sequence.
Amirav-Drory wants to create a graphic user interface to empower people in just this way.
His new software, Genome Compiler (free and available for download at www.genomecompiler.com), converts the various parts of a DNA sequence into easy-to-understand, and easily manipulable, icons.
"A succinct, yet powerful animation titled “Synthetic Biology Explained” shows the incredible potential of this emergent field and how engineering will transform the field of genetics to produce some truly amazing technology.
With the sequencing of the human genome and the increased understanding of genes that have followed..."
The Genomics in Medicine Lecture Series is sponsored by NHGRI, in collaboration with Suburban Hospital and Johns Hopkins. Each lecture takes place at Suburban Hospital's lower level auditorium at 8600 Old Georgetown Road in Bethesda, Md.
All are welcome to the hour-long lectures, which begin at 8 a.m. on the first Friday of the month, from December 2011 through June 2012.
Plus, check out the video collection for How-To Genome Sequencing and more.
Only about two percent of the human genome contains genes. The other 98 percent has been likened to cosmology’s dark matter that fills the space between stars – there’s a lot of it, but nobody really knows what it does. Over the years scientists have put faith into the logic of evolution: if it’s there, it must serve a purpose. But a recent study shows that not all genomes are created equally. Unlike human genomes, the carnivorous bladderwort’s genome makes the most of its allotted bases having only an estimated 2 percent of non-coding DNA, or so-called “junk” DNA.
The genome of the carnivorous bladderwort plant (Utricularia gibba) is minuscule compared to the human genome – 82,000 bases versus our near 3 billion. But while it’s small, the genome is extremely efficient. About 97 percent of its genome codes for an estimated 28,500 genes and the short sequences that control those genes. The authors of a study mapping the bladderwort genome surmise that, through many generations, the non-coding portion of the carnivorous bladderwort’s genome has been systematically removed, resulting in just 3 percent of non-coding DNA.
Scientists have for the first time mapped the genomes of tapeworms, shedding light on the evolution of one of humankind's oldest parasites and revealing new possibilities for drug treatments.
DNA analysis of the tapeworms suggests that a number of existing medicines for cancer, viruses and other diseases may be able to fight serious illness caused by their larvae, which can spread through the body causing damaging cysts.
I’m sick of reading about the dangers of the genome. There are lots of popular articles I could point to, but let’s start with a recent series in Time that included eight online features and the Dec. 13 cover story, ominously titled “The DNA Dilemma.”
The series, written by Bonnie Rochman, is thoroughly reported, balanced, and full of fascinating personal stories about children whose genomes have been sequenced. It’s also timely: The primary question Rochman raises—how much information is too much information?—has been dominating commentaries about genetic testing in the medical literature.
But this is the wrong question, or at least one that’s becoming increasingly irrelevant.
Ray and Terry's 's insight:
With the wealth of genetic information (at a reasonable price) available to the public, there are ethical questions that arise. Some might panic about individuals having too much information about their own DNA, but this author suggests that we can handle it.
For the first time, researchers have sequenced DNA molecules without the need for the standard pre-sequencing workflow known as library preparation.
Using this approach, the researchers generated sequence data using considerably less DNA than is required using standard methods, even down to less than one nanogram of DNA; 500 times less DNA than is needed by standard practices.
Pathologists take note! Human whole-genome sequencing of tumors was the source of information for making treatment decisions in a recently published study.
We may have sequenced the human and other species’ genomes, but we are still nowhere near predicting how this creates a living, breathing organism. Here’s why:
In 2001, the Human Genome Project gave us an almost complete draft of the 3 billion letters in our DNA. We joined an elite club of species that have had their genome sequenced, one that is growing with every passing month. As our technologies and understanding advance, will we eventually be able to look at a pile of raw DNA sequence and glean all the workings of the organism it belongs to? Just as physicists can use the laws of mechanics to predict the motion of an object, can biologists use fundamental ideas in genetics and molecular biology to predict the traits and flaws of a body based solely on its genes? Could we pop a genome into a black box, and print out the image of a human? Or a fly? Or a mouse? Not easily. In complex organisms, some traits can be traced back to specific genes. If, for instance, you’re looking at a specific variant of the MC1R gene, chances are you’ve got a mammal in front of you, and it has red hair. Indeed, people have predicted that some Neanderthals were red-heads for precisely this reason. But beyond that, predicting if something is a mouse or a whale or a armadillo, we still can't do it.
Bernhard Palsson from the University of California, San Diego agrees. “Sequencing a woolly mammoth will not predict its properties,” he says. “But you might be able to do a lot better with bacteria.” Their simpler and smaller genomes should in theory make it easier to predict the basic features of their metabolism, or whether they grow using oxygen or not. But even though we can sequence a bacterial genome in under a day, and for just $80, we would still struggle to determine important traits, like how good a disease-causing microbe is at infecting its host.
Finding all the genes even in a small genome is hard. Earlier this year, scientists discovered a new gene in a flu virus whose genome consists of just 14,000 letters (small enough to fit into 100 tweets), and had been sequenced again and again. So it should be unsurprising that our own genome, with 3 billion letters, is full of errors and gaps, despite ostensibly being “complete”. In May, another group showed that the reference human genome is missing a gene that may have shaped the evolution of our large brains. “There’s no genome that is completely understood even in terms of the genes within it,” says Markus Covert from Stanford University. “Typically, no function is known for a fourth to a fifth of the genes, even in smaller genomes.”
“With all the things cancer is trying to do to kill our patient, how does it remember it is cancer?” he asked his rapt TEDx audience. Bradner says that the answer lies in epigenetics, the programs that manage the genome.
The Pediatric Cancer Genome Project was launched in 2010 and represents the world’s most significant investment in attempting to understand the genetic origins of various forms of childhood cancers.
A newly identified form of DNA—small circles of non-repetitive sequences—may be widespread in somatic cells of mice and humans, according to a study in this week’s issue of Science. These extrachromosomal bits of DNA, dubbed microDNA, may be the byproducts of microdeletions in chromosomes, meaning that cells all over the body may have their own constellation of missing pieces of DNA.
Genome-sequencing studies indicate that all humans carry many genetic variants predicted to cause loss of function (LoF) of protein-coding genes, suggesting unexpected redundancy in the human genome. It is estimated that human genomes typically contain ~100 genuine LoF variants with ~20 genes completely inactivated. A recent paper in Science describes some of these rare and likely deleterious LoF alleles, including 26 known and 21 predicted severe disease–causing variants, as well as common LoF variants in nonessential genes.
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