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A new study analyzed the DNA of an entire family of four for the first time. The study was made possible by cheap sequencing from Calif.-based Complete Genomics, which offers sequencing for a mere $5,000 per genome.  (Source: ABC News)
Someday soon your family might be able to get its genome sequenced too

The Institute for Systems Biology (ISB) and the University of Luxembourg have published an intriguing new study in the journal Science, in which they detail the genome sequencing and analysis of a family of four humans.  The sequencing marks the first time a family of four has had their genomes sequenced, and follows many individual sequencing projects over the last decade.

David Galas, PhD, a corresponding author on the paper who works at the ISB, says the work offers a glimpse of how family genome sequencing could aid in identification and understanding of disease.  He states, "We were very pleased and a little surprised at how much additional information can come from examining the full genomes of the same family.  Comparing the sequences of unrelated individuals is useful, but for a family the results are more accurate. We can now see all the genetic variations, including rare ones, and can construct the inheritance of every piece of the chromosomes, which is critical to understanding the traits important to health and disease."

Currently, genome sequencing prices have been plummeting thanks to better techniques and equipment.  In 2007, the cost was around $1M USD -- in 2008 Applied Biosystems of Foster City, California sequenced the genome of a Nigerian man for only $60,000.  In 2009, Complete Genomics, based in Mountain View, California, claimed it could read entire human genomes for $5,000.  

Nonetheless, the number of complete genomes sequenced remains relatively low.  The X Prize foundation has offered a $10M USD reward to the first person or firm that can sequence 100 human genomes in less than 10 days for less than $10,000 each.

The new sequencing project at the ISB emphasizes the benefits of sequencing for the masses.  ISB and the University of Luxembourg actually partnered with Complete Genomics to complete the sequencing.

The sequencing allowed the identification of genes related to two genetic disorders that the children had -- Miller syndrome, a rare craniofacial disorder, and primary ciliary dyskinesia (PCD), a lung disease.  In the case of Miller's syndrome, the sequencing allowed the number of candidate genes (genes that might cause the disorder) to be reduced to four.

ISB President Leroy Hood, MD, PhD, comments, "An important finding is that by determining the genome sequences of an entire family one can identify many DNA sequencing errors, and thus greatly increase the accuracy of the data.  This will ultimately help us understand the role of genetic variations in the diagnosis, treatment, and prevention of disease."

Another exciting result from the study is the first direct measurement of the intergenerational mutation rate.  The researchers found that the rate works at half the rate predicted by researchers, hinting at a potentially slower pace of human microevolution.  

Concludes Professor Galas, "This estimate could have implications for how we think about genetic diversity, but more importantly the approach has the potential to increase enormously the power and impact of genetic research.  Our study illustrates the beginning of a new era in which the analysis of a family's genome can aid in the diagnosis and treatment of individual family members. We could soon find that our family's genome sequence will become a normal part of our medical records."



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RE: Next step in health
By captainentropy on 3/11/2010 6:15:45 PM , Rating: 2
be careful, epigenomics is heritable through mitosis but through the germline the majority of our chromatin is reset. Epigenetics are established and maintained by proteins, ncRNA, and miRNAs that derive from....genes. The Expression levels of those genes and activity of enzymes establishing epigenomic codes result from sequence variations in enhancers, promoters, and the coding regions themselves. So, ultimately genetics still controls epigenetics, of course notwithstanding environmental factors such as toxins, drugs, vitamins, or any compound that can modify the expression levels or activity of proteins.

I study epigenomics and I have to disagree that cancer is usually a breakdown of epigenomics (a better term to use than epigenetics). It is what governs expression, yes, but there is almost always something upstream of the epigenomic modifiers that is at fault. Take MYC, it's a transcription factor and is mutated in up to 30% of all breast cancers and 60% of all colorectal cancers. It's not a chromatin modifier but it recruits chromatin modifying activity to genes (often growth related genes) which can lead to cancer (so long as there are other mutations necessary for tumorigenesis). Epigenomic modifiers are rarely mutated in cancers though their activity often is deranged because they are being regulated by other factors.

And actually, freckles are caused by "overactive" melanocytes in the skin (compared to other melanocytes in less pigmented skin). Again, yes, epigenomic mechanisms are behind the excess melanin production but there is something directing THAT. Melanocytes are very long lived and very resistant to DNA damage and thus don't turn over fast. The keratinocyte is the major cell of the dermis and turns over rapidly. But by the time they reach the epidermis they have been enucleated and are just a husk of protein (melanocytes and keratinocytes derive from different germ layers too - neural crest vs. ectoderm). So their growth is determined by genetic programs that are maintained by epigenomics acting under direction of other factors. The partitioning of the genome into constitutive and facultative heterochromatin, and euchromatin is also epigenomic but also under direction of other factors that aren't proper epigenomic factors.

Epigenomics is simply the hammer that some arm swings. Taking away the hammer doesn't stop the arm from swinging. Don't get me wrong, epigenomics is important (I have a PhD on its study as well as postoctoral work) but epigenomics shouldn't be considered the foremost level for therapies but a companion.


RE: Next step in health
By geddarkstorm on 3/12/2010 12:50:47 PM , Rating: 2
Epigenetics is actually inheretable through the germline, and can persist for several generations. For 100 documented cases of this, see:

Jablonka et al. Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution. The Quarterly Review of Biology, 2009; 84 (2): 131 DOI: 10.1086/598822

It's a hot moving field. If you want to read up more on the current state of epigenetic research, there's http://www.sciencedaily.com/releases/2009/07/09072...

and for epigenetics involved in cancer see:

Watson et al. Generation of an epigenetic signature by chronic hypoxia in prostate cells. Human Molecular Genetics, 2009; DOI: 10.1093/hmg/ddp307

and http://www.sciencedaily.com/releases/2010/01/10012...

It's far more common than was previously believed even just a year ago.


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