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Posts Tagged DNA sequencing

Boney lumps, linkage analysis and whole genome sequencing Grant Jacobs Jul 06

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We all have our lumps, the quirky features we develop with time.

Some of these are bone spurs, extra growths of bone.

These can be caused from damage to joints, like the lumpy joints seen in elderly people with arthritis. Bone spurs from differing causes can develop in many parts of the body, spine, toes, heel and hands.

Most bone spurs are associated with damage and old age, but some have genetic origins.

Figure 1A from Sobreira et al. (see References)

Figure 1A from Sobreira et al. (see Reference)

Metachondromatosis is a rare disorder that affects bone growth, where benign bone tumours produce lumps, mostly on the hands and feet.*

These lumps develop in children, with some of them reducing or resolving over time, others persisting.

Nara Sobreira and her colleagues set out to find genes that might cause this disease using a new approach that exploits sequencing of the whole genome of one patient.

Genetic changes that cause a disease can be as small a changing a single base in the roughly three billion bases in our DNA.

We have many, many differences that make us unique.

The art of locating the cause of a genetic disease is to determine which of those many changes from a lot of DNA is the one that has a role in causing the disease.

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Myriad Genetics patent of BRCA (breast cancer) genes denied Grant Jacobs Mar 30

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Myriad Genetics face a judicial ruling against their patent of the BRAC1 and BRAC2 genes.

Solution structure ensemble of BRCA1/BARD1 RING domain heterodimer. Brzovic, Rajagopal, Hoyt, King and Klevit Nat. Struct. Biol. 8:833 (2001) (Source: PDB.)

Solution structure ensemble of BRCA1/BARD1 RING domain heterodimer. Brzovic, Rajagopal, Hoyt, King and Klevit Nat. Struct. Biol. 8:833 (2001) (Source: PDB.)

Judge Sweet presented this as to centre around the issue,

Are isolated human genes and the comparison of their sequences patentable?

(Isolated here means ‘extracted in pure form’.)

His ruling goes on to say,

It is concluded that DNA’s existence in an “isolated” form alters neither this fundamental quality of DNA as it exists in the body nor the information it encodes. Therefore, the patents at issues directed to “isolated DNA” containing sequences found in nature are unsustainable as a matter of law and are deemed unpatentable subject matter under 35 U.S.C. §101.

The full ruling is available on-line as a PDF file. (165 pages.)

To my hurried reading, the Judge Sweet has indicated, no, isolated DNA sequences may not be patented just because have been isolated. Read widely this may have implications, not just for Myriad’s patents on the BRAC1 and BRAC2 genes, but for many other applications.

Chromosomal location of BRCA1. (Source wikipedia.)

Chromosomal location of BRCA1. (Source wikipedia.)

I haven’t time to explore this in detail unfortunately—the ruling runs to 156 pages!—so I welcome comments elaborating on my rushed presentation of this news. The ruling mentions a “partial grant”, so I would guess there’s details to be considered too. (Interested readers find Google News a useful source for further stories on this.)

Patently of gene sequences has been deplored by biologists and many others. It would be excellent to think that this might be the beginning of the end of what many see as legal nonsense. (The judicial ruling outlines how the use of “isolated” is used in what others perceive as a “lawyer’s trick” to get around “the prohibitions on DNA patenting of the DNA in our bodies” in the introduction.)

An interesting take on the patent posted earlier this month, points to a paper by Kepler et al who point out that read literally this patent would cover most genes, never mind just the BRCA1 gene. (The patent claims for “at least 15 nucleotides” of the BRCA1 gene; most genes would contain 15 nucleotides that matched.)

HT: Many people via twitter.

Molecular biology in museums Grant Jacobs Mar 09

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The past fifty years has seen the rise of molecular biology. Many museums have little to represent molecular biology and it’s impact on medicine, perhaps because the objects studied in molecular biology are usually visualised indirectly, whereas museum visitors traditionally go to view objects with their own eyes.

While on blogcation,1 biologist-artist Jessica Palmer continues to write posts to her blog, bioemphemera.

canterbury-museum-350px

Canterbury Museum, Christchurch, New Zealand. Note the early power poles. (Source: wikipedia.)

Recently she pointed out a conference on presenting modern modern science in museums, quoting from the call to contributions. It’s a lengthy “call”—almost a treatise!—so I will present only the initial portion (interested readers should read read the full account):

The 15th biannual conference of the European Association of Museums for the History of Medical Sciences (EAMHMS) will be held at the University of Copenhagen, 16–18 September, 2010.

This year’s conference focuses on the challenge to museums posed by contemporary developments in medical science and technology.

The image of medicine that emerges from most museum galleries and exhibitions is still dominated by pre-modern and modern understandings of an anatomical and physiological body, and by the diagnostic and therapeutical methods and instruments used to intervene with the body at the ‘molar’ and tangible level — limbs, organs, tissues, etc.

The rapid transition in the medical and health sciences and technologies over the last 50 years — towards a molecular understanding of human body in health and disease and the rise of a host of molecular and digital technologies for investigating and intervening with the body — is still largely absent in museum collections and exhibitions.

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Next Generation Sequencing workshop Grant Jacobs Dec 15

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Otago University’s sequencing facility will be hosting a two-day workshop, The Researchers Guide to Next Generation Sequencing, February 11-12th 2010. Places are limited to 20 and cost only $NZ100. Applications close 7th January. Be in quick!

More details about how to apply for the workshop on their website or their flyer (below). The flyer may take a short while to load. Move the slider bar to see the lower portion of the flyer. (If it does not download from SlideShare, you can get it from University of Otago website.)


Disclosure: Grant Jacobs does not work with the University of Otago NGS group that is hosting this meeting, but offers computational biology / bioinformatics research and support.

Metagenomics-finding organisms from their genomes Grant Jacobs Oct 20

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Scientists are surveying the genomes found in environments, a modern way to find what micro-organisms live there.

There has been an explosions of “-omics” over the last decade. Metagenomics is the moniker given to genomic, or DNA sequence, surveys of environmental samples.

Basically metagenomics involves researchers collecting DNA samples from, say, the ocean, beach sand, bioreactor sludge (ugh!), a lake, someone’s mouth, gut or lungs. The list of metagenomes at NCBI  includes some unusual, and rather clever, examples. There’s even a fossil metagenome (a topic for another article, hopefully).

A related term is the microbiome, the microbes, genetic elements (genomes), and interactions in a particular environment. The human microbiome project aims to find out about the microbes that live on and in us.

Some places microbes live in and on us

Some places microbes live in and on us

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