Tag Archives: Molecular diagnostics

Whole genome sequencing a complete island

http://commons.wikimedia.org/wiki/File:Coat_of_arms_of_Iceland.svg

http://commons.wikimedia.org/wiki/File:Coat_of_arms_of_Iceland.svg

Two days ago a groundbreaking study was published in Nature Genetics: Whole genome sequencing of 2,636 Icelanders and Genotyping of 104,220 Icelanders.

The advantage of using a small population like the Icelanders for this kind of study is that there are fewer rare variants, but sometimes also a higher occurance of some of these variants.

For the study, geenomic DNA was isolated from white blood cells and subsequent sequencing was performed on GAIIx and HiSeq instruments. The resulting reads were aligned to the human reference genome (NCBI Build 36 (hg18).

Gudbjartsson et al. then examined the data from different angles. For example, they looked for geographical dependencies for specific variants or how the data can be used to learn more about phenotypes and their underlying genomic pattern. But they also report an example “how rare variants […] can be used to analyze clinical problems”. (Gudbjartsson et. al)

Since every human being has a unique genomic pattern I think studies like this are of high importance to learn more about disease related genotypes. This will help to gain confidence in the results that we get from molecular diagnostic assays for disease treatment now and in the future.

Read the complete publication here.

GENReport: NGS Trends In Cancer Research & Clinics

GENReport_Publication growth
Enal Razvi, Ph.D. from SelectBio U.S. summarised very nicely the trends of next generation sequencing in cancer research and cancer diagnostics for Genetic Engineering & Biotechnology News.

Visit the GEN website to download the complete PDF report.

IonTorrent Upgrade

Just some days ago we discussed the dynamics in NGS and here we are with some news. Life Technologies Corporation announced that the new software v3.0 for the IonTorrent PGM consistently delivers 99.9% consensus accuracy for both short and long homopolymer regions and increases the frequency of correctly called insertions, deletions and homopolymer sequences by two-fold (Press Release LIFE).

In addition to the read accuracy also the read length increased with the launch of the new kit to 400 bp. The aim of the company is to improve their system further for microbial applications (PR LIFE).

But not only improvements in bacterial identification is on the priority list for LIFE’s RnD team but also more innovations in the area of diagnostics. A new AmpliSeq(TM) sample ID panel will increase the confidence during data analysis and a new kit is soon to be launched (PR LIFE).

I think from a customer’s perspective it is a good idea to further improve the technology in several areas since there could be some cross-linking innovations. But it also bears the risk that some competitors, focussing on a specific application, will adapt their system more quickly. But of course these are only speculations. So what is your opinion?

 

A Documentary on the Use of Sequencing Technologies in Medicine

A documentary titled “Cracking Your Genetic Code” was recently released, and it offers a glimpse on how genomics is transforming medicine. Prominent scientists are featured, including Francis Collins from the National Institute of Health and Eric Lander from the Massachusetts Institute of Technology. In the documentary we are introduced to technologies for sequencing the entire genome; Illumina is being mentioned as one of the companies with such technology. We hear real-life stories where genome sequencing and genotyping led to diagnoses and successful treatments that would not happen otherwise.

The documentary does not only present the promises that personalized medicine is bringing, it also raises important questions concerning the readiness of the society in adopting this new form of medicine. There are always pros and cons with introducing new technologies to our daily lives. It is a matter of engaging and educating the public so the society as a whole can make some informed decisions during this healthcare revolution. Cracking your Genetic Code is a great introduction to the new role of sequencing in medicine, and I hope you will share it with your colleagues and friends!