Thursday, June 19, 2014

Next Gen Sequencing Applications

Next-Generation Sequencing: Methodology and Application

Next-generation sequencing (NGS), also known as high-throughput sequencing, is the catch-all term used to describe a number of different modern sequencing technologies including:
  • Illumina (Solexa) sequencing
  • Roche 454 sequencing
  • Ion torrent: Proton / PGM sequencing
  • SOLiD sequencing
These recent technologies allow us to sequence DNA and RNA much more quickly and cheaply than the previously used Sanger sequencing, and as such have revolutionised the study of genomics and molecular biology.

Everyone knows by now that the applications of NGS or Nex-Generation Sequencing, has already proved worthy of it's time, effort and applications. Most recently, in the news:

Next-gen sequencing IDs rare infection, saves boy's life

A 14 year old boys life was saved thanks to NGS or Next Gen Sequencing.

The sample came from a 14-year-old Wisconsin boy with dangerous swelling in his brain. His doctors, not sure that he'd survive the weekend, sent the sample with the thin hope that Chiu's team might figure out what was making him sick, and solve a months-long mystery.
In just two days, using experimental genomic sequencing technology, Chiu had an answer: leptospira. It's a rare bacterial infection - so rare that it would eventually take the U.S. Centers for Disease Control four months to confirm the diagnosis - that fortunately for the boy was very treatable.

 To solve the mystery, Chiu's team used a diagnostic tool known as "next-generation sequencing," which allows scientists to very quickly read and analyze the genetic makeup of an organism. Their rapid diagnosis of Joshua was one of the first examples of using the sequencing technology in a setting outside a lab.

And, scientists say, it may be the first time the tool has saved a life. The case was written up in a paper published this month in the New England Journal of Medicine.

"I feel the diagnosis could not have been made in this boy's case without next-generation sequencing. It definitely wouldn't have been in time," said Chiu, the paper's senior author and head of the viral diagnostics laboratory at UCSF.

You can read the whole article here

Sunday, April 06, 2014

A Conversation With 23andMe’s Joanna Mountain

This interview is part of an occasional series of profiles introducing you to the people behind 23andMe’s compelling research. Early in her career, Joanna Mountain, 23andMe’s Senior Director of Research studied the language and genetic diversity in Kenya. At 23andMe, Joanna still studies the genetic diversity of Africa, most recently as part of our African Ancestry projects, but she also spends time investigating how people react to their genetic results.

“Each tiny segment of the genome has a history.”

What are you working on at 23andMe?
One of my current areas of interest is learning more about how having access to genetic test results impacts people’s lives. We wanted to know how customers reacted to their genetic risk for breast cancer, for example, and what we found is that the test results prompted people to take positive steps, including talking to their doctors and discussing the results with family members. We’re currently looking at similar research in people with genetic risk of venous thromboembolism.

Our team is also researching genetic factors that influence how people respond to medications. Preliminary findings show that people report a very short list of side effects to a variety of drugs, with the most common being hives and stomach pain. My colleague, David Hinds presented on the topic of opioid-induced vomiting at last year’s American Society of Human Genetics meeting in Boston and we expect to publish further research this year.

How does your research in Africa apply to your work at 23andMe?
I am very interested in the great depth of genetic diversity in African populations. Because our species has lived in Africa for so long, it impacts our ability to tell African Americans where their ancestors are from. Many African Americans hit a brick wall when they start researching their genealogy, but where there aren’t paper records, we hope genetics will be able to fill in the gaps.

Why are you excited about genetics?
I was first studying applied math, and there’s a lot of math in population genetics. Being able to predict what will happen over the course of generations is a cool application of math, and I was initially drawn to that.

Tell us about a recent breakthrough in genetics research that you think will have a big impact.
Today, huge numbers of people are participating in genetic research. By providing researchers with information about your health and ancestry, we can do so much. We’re getting closer to understanding human prehistory and the genetic factors and history of disease, for example. 23andMe’s customers contribute to that, and future generations will benefit in the long run.

Read the whole article here: