Genomics and Epigenetics

The Irish Famine (or ‘Great Potato Famine’ if you live outside the Emerald Isle) killed one million people and forced another million to leave the country between 1845 and 1852. It was caused by a blight on the country’s main food stock- the Irish ‘Lumper’ potato. Now, researchers have identified the genome of the blight…

Whole genome sequencing (WGS) is becoming increasingly common. Doctors now routinely order it for patients with puzzling diseases. The NHS (National Health Service in the UK) has declared that it will sequence 100,000 genomes over the next few years. Increase WGS…increase ethical questions The direct-to-consumer company 23andme has been experimenting with whole exome sequencing (WES), and another company, DNA…

Most ‘wet lab’ biologists do not have much computer programming experience, which can make downstream analysis of next generation sequencing results a bit daunting. After the sequencing platform spits out your data, what do you do with it? That’s where Galaxy comes in. What is Galaxy? Galaxy is a bioinformatics workflow management system, created by collaboration…

“Any sufficiently advanced technology is indistinguishable from magic.” – Arthur C. Clarke In the fast-moving field of next generation sequencing, standard practices are evolving rapidly. Today, more and more labs are using Solid Phase Reversible Immobilization (SPRI) beads instead of gel purification in the preparation of libraries for sequencing. A crucial step, not for the…

For those of you who prepare your own DNA libraries, this article will cover the most critical aspects of library preparation to ensure a successful sequencing run. Previous Bite Size Bio articles have covered the basics of how 454 sequencing works, so give those a quick review if you are unfamiliar with the process. This video is also highly…

You’ve carefully collected your samples, extracted nucleic acids and made your first set of next-generation sequencing libraries. How are you going to know if the data you get back is any good and whether it will be worth the effort in learning how to do the analysis? Who is to blame? Fortunately, there are several…

You have spent days, if not weeks, at the bench setting up the treatment and control samples for that crucial experiment. You submitted your cDNA library for sequencing and after a few weeks of waiting anxiously you get back a list of differentially expressed genes. Hooray?! Hold on- not quite yet! There is something you…

Why Metagenomics? The microorganisms that we know and understand today are the ones which either cause human diseases, or are beneficial to human society in some way. From wine and cheese in food industry to the pharmaceutical industry- they are an indispensable part of our lives. Despite making good progress in understanding the microbial world,…

A commonly used technique in epigenetics is Chromatin Immunoprecipitation, or ChIP for short. This technique can show you whether a certain protein (e.g. transcription factor or histone modification) binds to DNA, when in its native conformation, namely chromatin. Insightful, but difficult This information can be very insightful, but difficult to obtain. Most protocols and suggestions…

Sanger sequencing is still a workhorse of most molecular biology labs. Even with the advent of next-generation sequencing we still need to sequence our clones and PCR products. In this article I have listed some of the tips and tricks we used in our Sanger services. (1)Dilution of BigDye: I’d expect this to be a…

Anyone who is involved in DNA sequencing in one form or fashion knows there are multiple ways to skin a cat: Sanger-based, next generation (NGS), and of course the new ion torrent sequencing technology. Which technology you use is usually dependent on the questions you’re trying to answer – and how fat your wallet is.…

As many who have worked with sequence data can tell you, the biggest bottleneck in publishing papers based on sequence data is the analysis step. Most researchers are faced with a dilemma when they receive sequence data for the first time: “do I try to use these free open source programs or do I shell…

RNA sequencing (‘RNA-seq’) has become one of the most widely used applications for Next-Generation Sequencing. RNA-seq can provide gene expression data more cheaply than microarray, at greater sensitivity, and without the biases inherent in an assay based on quantifying nucleic acid hybridization. RNA-seq can also provide data about alternative splicing, allele-specific expression, expression of non-annotated…

The Human Genome Project was successful, but hard work. The major improvements to the technology were the increases in parallelization and automation. In 2003, just as the HGP completion papers were published in Nature and Science, ABI launched the‘3730XL’. It could run 24 96-well plates per day and generate around 2 MB of sequence. Some…

It all started with proteins The earliest methods for sequencing were developed for proteins. In 1950, Pehr Edman published a paper demonstrating a label-cleavage method for protein sequencing which was later termed “Edman degradation”. Around the same time Fred Sanger was developing his own labelling and separation method which led to the sequencing of insulin.…

A revolution in 2005 The start of the NGS revolution was clearly marked in 2005 by the  publication of the complete genome sequences of two bacterium (Mycoplasma genitalium and Streptococcus pneumonia) by 454 Life Sciences Corporation in one run of their Genome Sequencer with a 96% coverage at 99.96 % accuracy (Margulies et al. 2005).…

Just before Life Technologies purchased the start-up company Ion Torrent, the fledgling company was dealing with a torrent of another kind—worldwide media interest in its new sequencing technology, which promised to bring the price of next-generation, massively parallel sequencing down to $1,000 per run. Since that dramatic announcement in the summer of 2011, Life Technologies…

The “sequencing-by-synthesis” technology now used by Illumina was originally developed by Shankar Balasubramanian and David Klenerman at the University of Cambridge. They founded the company Solexa in 1998 to commercialize their sequencing method. Illumina went on to purchase Solexa in 2007 and has built upon, and rapidly improved the original technology. Millions of reactions and…

A paradigm shift by the Big Three As we learned last week, the Human Genome Project was accomplished using the improved Sanger method and technology from Applied Biosystems (ABI). Despite the significant technical improvements to this ‘first-generation’ technology, sequencing multiple human genomes was never going to be easy without a paradigm shift. Over the last…

Next Generation DNA Sequencing (NGS) is a revolutionary new technology that provides biologists and medical scientists with the ability to collect massive amounts of DNA sequence data both rapidly and cheaply. This technology is having a huge impact on many aspects of biology and medicine because it can be applied in so many different ways.…