Mumbai: Raymond McCauley is chair, Digital Biology at Singularity Universitya Silicon Valley think tank devoted to training leaders in exponential technologies. He is also part of the team that developed next generation DNA sequencing at Illumina, where he worked in bioinformatics, cancer sequencing, and personal genomics. In an email interview, McCauleywho is a speaker at the two-day SingularityU India Summit that begins on 7 Aprilspoke about the explosion in genomics research, gene editing tools like CRISPR-CAS9 and the consequences of bioinformatics and genetic testing on health and life insurance. Edited excerpts:
The explosion in genomics research along with the widespread adoption of DNA sequencing is accelerating the growth of the genomics market across the globe. Have we reached an inflection point?
As the price continues to drop for DNA sequencing, and all of the associated tools and services, we are seeing a larger market for those services really take off. The research market is strong, as always, and many new medical applications are driving new growth. And were actually seeing an explosion of consumer geneticspeople can use their genes to look at ancestry, optimize nutrition and athletic training, and even pick a good tasting wine.
Gene sequencing and gene editing (CRISPR CAS-9) are playing huge roles in the push toward personalized medicine and healthcare. Provide us with some applications of genomics.
Now that we are able to read and write DNA fairly cheaply, with even more advances to come, we can use this to help personalize medical care. Consider these examples. Pharmacogenomics uses genetic information to determine what drugs and dosages work for each person. This pays off quickly because taking the wrong drug, or a drug that actually causes an adverse reaction, is an expensive, and sometimes tragic, mistake. And its now cheap to read DNA. We all have hereditary tendencies for things like heart disease, neurological disease, and cancer locked away in our genes. Knowing your individual risks with chronic disease prediction, means you can be better prepared to prevent actually getting sick.
In the field of cancer diagnostics, new liquid biopsies can look at free-floating DNA in a simple blood sample, and sometimes identify cancer before it would show up on a body scan. Moreover, by genetically engineering a persons bone marrow cells, we can basically reprogram their immune system, and their circulatory system. Some new cancer treatments are based on this. Further, looking at the DNA of the collection of microbes in your gut can help with digestive disorders, weight loss, even understanding mood changes.
What are the consequences of bioinformatics and genetic testing on health and life insurance?
Being able to predict health and lifespan with genomic tools pretty much breaks insurance. It turns the information asymmetry, where actuaries know more about how long youll live, on its head. Because they can only predict how long people live on average. Theres a chance, though, for these companies to use this technology to help their clients make better decisions, and get access to better treatments, and live longer.
Could you point out some of the opportunities and consequences of, what you describe as, drag & drop genetic editing?
The first and biggest changes that come here are in industrial microbiology, where we reprogram single-celled creatures to manufacture things for us, like plastics and biofuels and even complex products like medicine and computersand also to mine and recycle these materials. It also makes it easier to do engineering and enhancement on plants and animals, for agriculture, and also on humans, for medicine and enhancement, then finally, on the environment itself. Think about using this technology to produce mosquitoes that cant pass along malaria, or to reverse greenhouse gas increases and ocean acidification.
What steps are being taken to address some of the challenges arising out of fields like bioinformatics and bioengineering like privacy and legal hurdles?
Some enlightened polities are passing laws to prevent discrimination by the government or employers based on genetic information, and to give individuals some control over who can access their information. This is particularly important for insurance, and who is allowed to access genetic databases built for different purposes.
But, policy-wise, its still the early days. Should law enforcement be allowed to scan databases built for research or health practitioners to go fishing to find someone who may have been at the scene of a crime? Should a sports team test their prospective athletes for hidden heart disease genes before signing a multi-million dollar contract? Do people have a right to not know about health problems or secrets in their family tree, and what if siblings disagree about this? Many questions remain to be resolved. And its likely that different groups and nations will come up with different best answers.
How can a country like India take advantage of genomics research?
India has more trained bioinformaticists than any other country on earth. These people, who are trained to use computers in the life sciences, and systems biologists, and biostatisticians, are the heroes of the coming biotech revolution. They keep it moving forward. Professionals here are uniquely positioned to both contribute to pushing this technology forward, and to make a huge amount of money, for themselves and the economy, while doing it. India also has a pharmaceutical industry that serves as an example to the rest of the worldwhere the entrepreneurs and the policymakers have done much figured out how to balance making money with the needs of the people to receive affordable health care.
Glossary for laypersons
1. Genome sequencing
Getting a read-out of an individual organisms entire DNA sequence. For humans, this is about 3.2 billion bases, spread across 23 chromosomes. Useful for research, and for personalized medicine. This is how we read the blueprint of life.
2. De novo sequencing
Looking at a species genome for the first time. Its always more difficult to sequence the first member of a species. This is harder, because we read DNA in short sections, and we have to figure out how all the sections connect.
3. Resequencing
Looking at an individuals DNA, when youve already got examples of that species DNA sequence, called a reference sequence, to compare it to. Sometimes, individual genes or groups of genes are targeted and sequenced, without looking at the entire genome.
4. Exome sequencing
Looking at just the genes, or portion of the DNA that codes for proteins (about 1% in humans) or the portion that is thought to be involved in regulating genes (about 10% in humans).
5. RNA sequencing
The DNA is the read-only memory of the cell, and when new proteins need to be made, the cell copies the appropriate genes DNA into RNA. All cells, from bone cells to brain cells, have basically the same DNA, but they dont always turn on, or express, the same genes. By sequencing the RNA, we get a snapshot of what proteins the different kinds of cells express at different times. We call this gene expression, or sometimes RNAseq, for short. Useful for research, and responsible for about half the research sequencing done.
6. Methylation sequencing
One way of understanding gene expression, sometimes referred to as the epigenome. Theres a level of gene regulation in DNA, where special stretches of DNA are methylated (have a special chemical group added to them), to keep nearby genes turned off. Useful for research, especially in understanding cancer, which sometimes sneakily figures out ways to change this and turn growth genes on.
7. CHIP sequencing
A special research method for finding which proteins grab which stretches of DNA, so we can understand better how the cellular machinery works together. Not done on a computer chip, but this is an acronym for Chromatin Immuno-Precipitation.
8. MicroRNA sequencing
Another research method for understanding gene expression, by looking at short pieces of RNA that float around the cell and turn off groups of genes.
9. Microbiome sequencing
Looking at the DNA in entire groups of tiny organisms, like all of the microbes in your gut, or all of the microbes in an environmental sample. Its like a population census for bacteria. New uses for this are being found in agriculture and biomanufacturing. Sometimes called metagenomics.
10. Barcode sequencing
Looking at a short stretch of DNA, to identify a species, like scanning a printed barcode in a market. Used for diagnosing infections, environmental research, and even protecting endangered species.
First Published: Fri, Apr 07 2017. 02 04 AM IST
See the original post here:
India's bioinformaticists are the heroes of the coming biotech ... - Livemint
- MOgene Announces Partnership with Intuitive Genomics to Expand Bioinformatics Capabilities - January 28th, 2013 [January 28th, 2013]
- Bioinformatics Organization - Bioinformatics.Org Wiki - January 17th, 2014 [January 17th, 2014]
- Bioinformatics Market by Application (Genomics, Molecular Phylogenetics, Metabolomics, Proteomics, Chemoinformatics ... - April 9th, 2014 [April 9th, 2014]
- Bioinformatics Master of Science - Northeastern ... - April 9th, 2014 [April 9th, 2014]
- Master of Science in Bioinformatics | AAP | JHU - April 9th, 2014 [April 9th, 2014]
- Bioinformatics - Bioinformatics.Org Wiki - April 9th, 2014 [April 9th, 2014]
- Bioinformatics Organization - Bioinformatics.Org - April 9th, 2014 [April 9th, 2014]
- Bioinformatics - Wikipedia, the free encyclopedia - April 9th, 2014 [April 9th, 2014]
- Identified epigenetic factors associated with increased risk of developing cancer - April 10th, 2014 [April 10th, 2014]
- Home | Department of Computational Medicine & Bioinformatics - April 10th, 2014 [April 10th, 2014]
- Bioinformatics tool - Video - April 10th, 2014 [April 10th, 2014]
- individual assignment CADD-Bioinformatics tools - Video - April 10th, 2014 [April 10th, 2014]
- MARC travel awards announced for the 2014 Great Lakes Bioinformatics Conference - April 15th, 2014 [April 15th, 2014]
- PH genome center unveils facility powered by IBM supercomputer - April 15th, 2014 [April 15th, 2014]
- Part 1 : Introduction to Bioinformatics, PDB and EMBL-EBI - Video - April 15th, 2014 [April 15th, 2014]
- Bioinformatics - Video - April 15th, 2014 [April 15th, 2014]
- March's Bioinformatics Papers of Note - April 18th, 2014 [April 18th, 2014]
- BMC Bioinformatics - BioMed Central | The Open Access ... - April 22nd, 2014 [April 22nd, 2014]
- Bioinformaticsweb.co.nr:Open Access Bioinformatics ... - April 22nd, 2014 [April 22nd, 2014]
- Penn Bioinformatics Profiling Identifies a New Mammalian Clock Gene - April 22nd, 2014 [April 22nd, 2014]
- Bioinformatics profiling identifies a new mammalian clock gene - April 22nd, 2014 [April 22nd, 2014]
- UST Bioinformatics 2014 Project YOUTUBE - Video - April 22nd, 2014 [April 22nd, 2014]
- First Sex Determining Genes Appeared In Mammals Some 180 Million Years Ago - April 25th, 2014 [April 25th, 2014]
- Pronounce Medical Words Bioinformatics - Video - April 25th, 2014 [April 25th, 2014]
- Funding Update: NIH Bioinformatics Grants Awarded March 13, April 24, 2014 - April 25th, 2014 [April 25th, 2014]
- BIOINFORMATICS - blogspot.com - April 25th, 2014 [April 25th, 2014]
- Biology, Computers Collide in High-Demand Field of Bioinformatics - Video - April 25th, 2014 [April 25th, 2014]
- Researchers Discover Effect Of Circulating Cell Types On Cardiovascular Health - April 30th, 2014 [April 30th, 2014]
- The Genomics and Bioinformatics Group - April 30th, 2014 [April 30th, 2014]
- BIT001 Bioinformatics assignments 5 and 6 - Video - April 30th, 2014 [April 30th, 2014]
- Visual Genome Analysis Suite Bioinformatics Software Demonstration - Video - May 1st, 2014 [May 1st, 2014]
- Bioinformatics Erasing the line between biology and hacking Krystal Thomas White and Patrick Thomas - Video - May 1st, 2014 [May 1st, 2014]
- Cambridge genomics duo in the steps of Pasteur - May 2nd, 2014 [May 2nd, 2014]
- bioinformatics-phamerator - Video - May 3rd, 2014 [May 3rd, 2014]
- Metal Slug 3 Soundtrack - Bioinformatics Extendido - Video - May 3rd, 2014 [May 3rd, 2014]
- Bioinformatics approach helps researchers find new uses for old drug - May 5th, 2014 [May 5th, 2014]
- Bioinformatics Approach Helps Researchers Find New Use for Old Drug - May 5th, 2014 [May 5th, 2014]
- Biotech industry to touch $7-bn mark by FY15: Study - May 6th, 2014 [May 6th, 2014]
- Biotech industry to touch $7 bn mark by FY15-end: study - May 6th, 2014 [May 6th, 2014]
- How immune cells use steroids - May 9th, 2014 [May 9th, 2014]
- IP Update: New York University, Microsoft among Recent Bioinformatics Patent Winners - May 10th, 2014 [May 10th, 2014]
- Introduction to Bioinformatics Presenter - Video - May 10th, 2014 [May 10th, 2014]
- Dr. Jessica Schlueter Discusses Bioinformatics Research - Video - May 11th, 2014 [May 11th, 2014]
- Bioinformatics Software Carpentry Bootcamp - Session 4 - Video - May 11th, 2014 [May 11th, 2014]
- SBRI backs Eagles genomic data technology - May 12th, 2014 [May 12th, 2014]
- Bioinformatics firm SolveBio Seeks to Build Business on Providing Painless Access to Curated Data - May 16th, 2014 [May 16th, 2014]
- Szilak Lab Bioinformatics and Molecule Design, HUNGARY (MIT-LS 2014) - Video - May 16th, 2014 [May 16th, 2014]
- Happy birthday Prof Usman from bioinformatics team - Video - May 16th, 2014 [May 16th, 2014]
- KARUNYA BIOINFORMATICS - Video - May 18th, 2014 [May 18th, 2014]
- Global Market for Biomarkers to Reach $53.6 Billion in 2018; Bioinformatics to Move at 17.4% CAGR - May 20th, 2014 [May 20th, 2014]
- Careers in Bioinformatics and Precision Medicine - Career Development Week - Video - May 21st, 2014 [May 21st, 2014]
- Big Data Lets Cancer Researchers Put Old Drugs to New Uses - May 22nd, 2014 [May 22nd, 2014]
- Fugeneio The Fest - Fugeitorium - Bioinformatics Experience in 3D - Video - May 22nd, 2014 [May 22nd, 2014]
- The Hyve - OpenSource Bioinformatics - Video - May 24th, 2014 [May 24th, 2014]
- DNA sequences on the go, with an app born in a Singapore lab - May 29th, 2014 [May 29th, 2014]
- :: 29, May 2014 :: POCKET SCIENCE: NEW MOBILE APPLICATION ENABLES DNA ANALYSIS ON THE GO - May 29th, 2014 [May 29th, 2014]
- Bioinformatics Market is Expected to Grow at a CAGR of over 23.0% from 2014 to 2020 New Report Published By Grand View ... - May 29th, 2014 [May 29th, 2014]
- Professor Bud Mishra, PhD Joins the Science Advisory Board of InSilico Medicine Engaged in Aging Research for Drug ... - May 30th, 2014 [May 30th, 2014]
- A holistic view on bioinformatics market - Video - June 1st, 2014 [June 1st, 2014]
- Viral Safety Testing using an advanced next generation sequencing and bioinformatics platform - Video - June 1st, 2014 [June 1st, 2014]
- Balti and Bioinformatics - Tom Connor - CLIMB - Video - June 2nd, 2014 [June 2nd, 2014]
- Global Bioinformatics Market All Set to Register a CAGR of 21.2% According to The Newly Added Report at Analyze Future - June 4th, 2014 [June 4th, 2014]
- Bioinformatics basic database and tools - Video - June 4th, 2014 [June 4th, 2014]
- Bioinformatics Market Reports by Analyze Future - Video - June 4th, 2014 [June 4th, 2014]
- Bioinformatics | Johns Hopkins University Engineering for ... - June 6th, 2014 [June 6th, 2014]
- Global Bioinformatics Market Report by Truemarketresearch - Video - June 7th, 2014 [June 7th, 2014]
- A Web-Based System for Automatic Bioinformatics Data Classification - Video - June 12th, 2014 [June 12th, 2014]
- Bioinformatics Welcome Video - Video - June 12th, 2014 [June 12th, 2014]
- Bioinformatics Services: Surfing the Data Wave - Video - June 12th, 2014 [June 12th, 2014]
- 4th International Conference on Proteomics & Bioinformatics - Video - June 12th, 2014 [June 12th, 2014]
- Institute of Bioinformatics featured on Rajyasabha TV - Video - June 14th, 2014 [June 14th, 2014]
- Global Bioinformatics Market - Analysis, Opportunities, Segmentation and Forecast, 2013 - 2020 - Video - June 21st, 2014 [June 21st, 2014]
- 6/18/14 Bioinformatics: Computer Technology & Biological Info on Across The Fence - Video - June 21st, 2014 [June 21st, 2014]
- JAX, Frasergen announce cancer genomics facility in Hubei Province, China - June 22nd, 2014 [June 22nd, 2014]
- UK-Colombia alliance on global food security - June 22nd, 2014 [June 22nd, 2014]
- Global Bioinformatics Market Size, Trends, Analysis, Report, Growth, Forecast 2013 - 2020 - Video - June 23rd, 2014 [June 23rd, 2014]
- Aging Accelerates Genomic Changes, Signaling Challenges for Personalized Medicine - June 24th, 2014 [June 24th, 2014]
- Researchers treat incarceration as a disease epidemic, discover small changes help - June 26th, 2014 [June 26th, 2014]
- Atul Butte, MD, discusses bioinformatics in pediatric health, Packard Children's Hospital - Video - June 27th, 2014 [June 27th, 2014]
- Metal Slug 3 OST#23 Bioinformatics - Video - June 27th, 2014 [June 27th, 2014]