Next Generation Sequencing

Sorry about the long blogging break - we have been keeping busy here at CLC getting ready for the upcoming release of Genomics Workbench 2.0 . These days we are preparing the final test rounds and fine polishing the code.

Besides being busy coding, one of our NGS specialists has been busy preparing a presentation for the upcoming Illumina Genome Analysis workshop in Malaysia. Keep an eye out for him if you are attending!

I once had the pleasure of visiting David Lambert, an expert and pioneer in ancient DNA studies. With Dave I had some of the most interesting and thought provoking discussion about biology, that I have ever had.

Now Dave and his colleagues have a new review out in TREE on New developments in ancient genomics that I can’t wait to read when I get back to work next week.

Here is the abstract:

Ancient DNA research is on the crest of a ‘third wave’ of progress due to the introduction of a new generation of DNA sequencing technologies. Here we review the advantages and disadvantages of the four new DNA sequencers that are becoming available to researchers. These machines now allow the recovery of orders of magnitude more DNA sequence data, albeit as short sequence reads. Hence, the potential reassembly of complete ancient genomes seems imminent, and when used to screen libraries of ancient sequences, these methods are cost effective. This new wealth of data is also likely to herald investigations into the functional properties of extinct genes and gene complexes and will improve our understanding of the biological basis of extinct phenotypes.

Invitrogen Corporation and Applera Corporation today announced that their Boards of Directors have approved a definitive merger agreement, under which Invitrogen will acquire all of the outstanding shares of Applera’s Applied Biosystems Group in a cash and stock transaction valued at $6.7 billion.

One of the stated rationales for the merger, is that Invitrogen and Applied Biosystems will be well positioned to compete in rapidly growing markets, such as next generation sequencing.

According to CBC, scientists have found 17 living relatives of a centuries-old “iceman” whose remains were discovered in a melting glacier in northern British Columbia, Canada, nine years ago.

Chief Diane Strand of the Champagne and Ashihik First Nations led a project to search for the young man’s living relatives. She said 241 native people from British Columbia, the Yukon and Alaska gave DNA samples for testing and the results produced 17 positive matches. All of those 17 people, and potentially their families, have the same common female ancestor as Kwaday himself.
Click here to read the full article.

From The Human Genome Organisation’s abstract on the project:

Nitrogen and carbon content in whole bone and collagen-type residue extracted from both bone and muscle indicated good preservation of proteinaceous macromolecules. Restriction enzyme analysis of mitochondrial DNA (mtDNA) determined that the British Columbia frozen remains belong to haplogroup A, one of the Native American mtDNA haplogroups. Data obtained by PCR direct sequencing of the mtDNA control region, and by sequencing the clones from overlapping PCR products were duplicated by an independent laboratory. The comparison of the mtDNA sequence with those of North American, South American, Central American, East Siberian, Greenlander and Northeast Asian populations indicates that the remains share a mtDNA type consistent with different groups of Native Americans.

Click here to read the original 2002 abstract on the “iceman”.

At the recent Bio-IT World Conference in Boston, USA, we held a competition where the lucky winner could walk away with a MacBook Air and an extensive collection of CLC bio software, including CLC Genomics Workbench.

The lucky winner was Sébastien Vachenc from Laboratoires Fournier - a Solvay Pharmaceuticals company. He was of course most thrilled when he learned he had won the first prize in the popular competition and looks forward to working with CLC Genomics Workbench, once it’s released!