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Thursday, November 15, 2018

Life + Arts

UH unraveling DNA


The University of Houston’s rare $500,000 ‘next generation sequencer’ has elevated Cougar researchers in Texas’ genome research community.

The results of research made possible by the sequencer have wide-reaching implications for the future of medicine.

In Assistant Professor Preethi Gunaratne’s lab alone, research is being carried out on stem cells, cancer, asthma, and other aspects of genetic regulation.

A project called Human Microbiome uses the sequencer to study bacteria-human interactions at the genetic level.

‘This technology allows us to look at diseases as never before,’ Gunaratne said.

Using the sequencer to quickly determine an individual’s genome could eventually lead to personalized medicine and risk-adjusted therapies that best suit the individual’s health needs.

The sequencer could also be used to understand the genetic errors that cause cells to turn cancerous and lead to targeted treatments that are more effective and have fewer side effects than current practices.

Manufactured by the California-based biotech company Illumina, the sequencer looks like a blue cube about the size of an oven with a few tubes, panels and a cable attatched to a lab computer.

As the sequencer deciphers samples’ genetic codes, the computer analyzes the data for researchers.

A grant from the Cullen Foundation to the University’s Institute for Molecular Design paid for the sequencer. Its findings generated seven journal publications and four research grants over the past year alone.

Additionally, other research institutions have worked with the University to take advantage of the sequencer. Scientists from Baylor College of Medicine, M.D. Anderson Cancer Center, Texas A&M and Quebec have outsourced samples to the University sequencer for their own research.

Ashley Benham, a biology graduate student in Gunaratne’s lab, said that the number of outside researchers sending their samples to the University will ‘pick up immensely once people get the preparation protocol down.’

Local researchers are enamored with the sequencer, as outsourcing genetic samples to a local lab saves money on shipping.

‘It is unbelievable how much shipping costs,’ Assistant Professor Zhenkang Xu said.

Before the University had the sequencer to analyze its own genetic samples, outsourcing one sample to another lab cost more than $3000.

Benham estimated that his research lab saved 50 percent on analyzing samples by using its own sequencer instead of relying on other laboratories’ equipment.

Sequencing genetic samples in-house also preserves accuracy. Outsourced samples can be over 20 percent inaccurate, while in-house sequencing yields 95 percent accuracy on average.

The sequencer itself works using a new technique known as ‘sequencing by synthesis.’ DNA is a double-stranded molecule composed of nucleotide bases known by their initials A, T, G and C. The order of these nucleotides comprises the genetic code or sequence.

These nucleotides pair up across the two strands of DNA, with A nucleotides matching only to T nucleotides, and G nucleotides matching only to C nucleotides.

The sequencer determines the sequence of a single strand of DNA by making its complementary strand out of fluorescently labeled nucleotides that can then be ‘read’ by the machine’s optics.

Sequencing by synthesis is a vast improvement over the older ‘sanger’ and ‘shotgun’ methods of nucleotide sequencing. Gunaratne recognized the value of the machine early on and sold John Bear, dean of the College of Natural Sciences and Mathematics, on the idea by explaining that it would allow University researchers to sequence a bacterial genome in as little as seven hours

‘The potential is huge,’ she said.


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