Three scientists witness the ability of genetic sequencing to change medical care
Sequencing technology has greatly exceeded the expectations of Dr. Carlos Bustamante, Stephen Kingsmore and John Mattick. If you ask them at the beginning of their career, will one day we can sequence the human genome in one day, and their responses are: "Mad mad!", absolutely impossible" and "Dream not to dare miss you".
Despite the surprises of sequencing innovations, everyone is rapidly adopting next-generation sequencing (NGS) and today's group sequencing to advance their research and transformation efforts. As a professor of genetics and biomedical data science and founding director of the Stanford Center for Computer, Evolution, and Human Genomics, Dr. Bustamante is using population sequencing to understand genetic variation in ancient and ethnic subpopulations. Dr. Kingsmore recently served as president and CEO of the Rady Children's Hospital Genomics Medical Institute, where he is using sequencing to develop evidence bases for children's genomics. As Executive Director of the Garvan Medical Institute, Dr. Mattick is taking the lead in using research and clinical applications of population sequencing data.
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iCommunity talked to three doctors, Bustamante, Kingsmore and Mattick, about how their team used high-throughput human genome-wide and population sequencing to advance research and transformational research, incorporating a database of "omics" and phenotypic data. Requirements, and the challenges of translating this information into a format that is useful to the clinical environment.
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From left to right: Dr. Carlos Bustamante is Professor of Genetics and Biomedical Data Science and Founding Director of the Stanford Center for Computer, Evolution and Human Genomics; Dr. Stephen Kingsmore is President and CEO of the Radian Children's Hospital Genomics Institute; John Dr. Mattick is the Executive Director of the Garvan Medical Institute.
What is the sequencing technology when you first became a scientist?
John Mattick (JM): My first impression of sequencing was to see the bands on the autoradiogram. This is the early stage of molecular biology. We are cloning and sequencing genes. I thought at the time that we were masters. We can only read hundreds of bases from the gel, and then the strips are too close to distinguish. We assembled a sequence of 1-2 kb long, and each sequence was able to send a paper. Looking back now, this seems too primitive.
Stephen Kingsmore (SK): My sequencing experience started with radioactive p32 markers and agarose and polyacrylamide gels. A terrific sequencing reaction is 150 nucleotides, and that takes a long time.
Carlos Bustamante (CB): When I became a scientist, automated sequencing was under development, so I did some manual sequencing and then did a lot of sequencing on the first generation of sequencers. My first experience was when I was an intern at the Smithsonian Institution, and they just established a molecular systems laboratory. At that time, sequencing several genes of multiple individuals was a big project.
How does your sequencing method change as the tool improves?
CB: At the beginning, we looked at the data for each segment very valuable. When Celera began the early exome sequencing, they performed PCR on 200,000 samples and sequenced 20,000 genes from 39 individuals. I think, "This is a data set! We have been waiting for this." We stopped the work at hand and spent 4-5 years studying the 39 exons and published 8-9 articles. Papers analyze data in different ways. This mode of thinking has been subverted. Today, we use NGS to continuously generate data quickly and then worry about what it means.
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