Researchers at Berkeley can take advantage of new technology that allows them to conduct, for just a few thousand dollars, experiments that once cost millions.
Students in Berkeley Connect Computational Biology recently got a special opportunity to visit the Genomic Sequencing Lab (GSL) in Stanley Hall. Facilities Director Shana McDevitt gave them an orientation to the compact but cutting-edge lab. The GSL provides Next-Generation Sequencing (NGS) on Illumina’s HiSeq and MiSeq technologies, as well as on PacBio platforms. They also offer Illumina Array Services and Biospecimen processing. What this means, in lay-person’s terms: the lab makes DNA and RNA processing accessible and affordable for the UC community, as well researchers from other institutions and from industry.
Genomic sequencing refers to the process of determining the order of nucleotide bases in a DNA molecule, similar to spelling out the order of letters in a word. The bacterial genome is a single circular strand of DNA, and can be as small as 130,000 base pairs in length. In contrast, the human genome is made up of over 3 billion base pairs spread out over 23 pairs of chromosomes. Choice of which sequencing platform to use is informed by experimental factors such as genome size and number of samples in experiment.
Genomic sequencing does not reveal much by itself. The Genome News Network compares a sequence to “a book written without capitalization or punctuation, without breaks between words, sentences, or paragraphs, and with strings of nonsense letters scattered between and even within sentences.” Once samples have been sequenced, the data must then be processed by computational algorithms to determine their biological context: which part of the genome they come from, which genes are active, what is the 3D structure of the chromosome, etc.
Despite the painstaking process, sequencing has seen many advancements in recent decades. The first human genome was sequenced by The Human Genome Project for $2.7 billion in 2003. Since then, the cost has dropped from around $10 million in 2008 to $1000 today. Illumina strives to drive down the sequencing cost even further, but the cost of integrating sequencing into primary care check-ups may to be too high to implement just yet.
Check out these links to learn more about genome sequencing and what lies ahead:
posted by Gloria Choi
Berkeley Connect Communications Assistant
(with thanks to Amanda Mok, Berkeley Connect Fellow in Computational Biology, for technical assistance)