Internet-of-DNA
The Internet of DNA globally
utilizes DNA data that is increasingly available for identifying and
potentially treating diseases. Scientists have been trying to share DNA
data for years, and companies today are beginning to make this a
reality.
Many scientists believe that
determining how to diagnose a patient and developing new medicine for a
cure will greatly enhance the Internet of DNA. However, there exists a
large concern regarding privacy; people do not like the notion of
sharing their DNA with the public, as it can identify an individual
just as easily as a fingerprint. Despite this matter, the Internet of
DNA gives researchers the opportunity to study genome data and make new
drug discoveries, which is now eligible for research and development
tax credits.
The Research & Development
Tax Credit
Enacted in 1981, the federal Research and
Development (R&D) Tax Credit allows a credit of up to 13% of
eligible spending for new and improved products and processes.
Qualified research must meet the following four criteria:
• New or improved products, processes, or software
• Technological in nature
• Elimination of Uncertainty
• Process of Experimentation
Eligible costs include employee
wages, cost of supplies, cost of testing, contract research expenses,
and costs associated with developing a patent. On December 18,
2015, President Obama signed the bill making the R&D Tax Credit
permanent. Beginning in 2016, the R&D credit can be used to offset
Alternative Minimum tax and startup businesses can utilize the credit
against payroll taxes.
What is the Internet of DNA
Advancements in genetics are increasing due to the
help of certain programs, such as 'the DNA Data to be Shared Worldwide
in Medical Research Project and the Human Genome Project'. One of
the many important practices of genetics is DNA sequencing. This is a
process which looks at the order of nucleotides in a string of DNA,
consisting of adenine, guanine, cytosine, and thymine.iv Analyzing the
DNA molecule sequence facilitates information about the patient to be
decoded.
Today, more than 200,000 people
have experienced the process of getting their genomes sequenced.
Researchers rely on artificial intelligence systems to analyze
data and detect certain structures in the information acquired.
Especially for a scientist studying DNA, modern technology is required
to identify the mutation in a patient’s DNA sequence. The
Internet of DNA will advance the future of medicine because it allows
researchers to search for individuals with the same illness. Patients’
genetic sequences can be studied, which has the potential to assist in
finding a treatment for specific diseases. Yet, to advance the
field of medicine, scientists need to review millions of genomes, if
not more, to find a cure. Researchers have to carefully study mutations
in genome sequences to see if there is a missing part of the DNA or
additional DNA combinations.
By using the Internet of DNA,
genomes no longer need to be saved on hard drives and delivered by
trucks from lab to lab. Researchers save time and money because there
is no need for long-term travel. After all, information can now be
accessed via the Internet. There have been recent developments in
technology to read DNA strands.
Improved Technology for DNA
Analysis
Pacific Biosciences created a machine called PacBio
RS II, intended for de novo assembly, targeted sequencing, base
modification detection, and isoform sequencing. De novo assembly
consists of large scale DNA reading that simplifies genome assembly.
Fewer readings are required, which leads to a lower cost and better
accuracy of information.
Targeted sequencing studies small
scale forms of DNA by examining certain areas of the genome. Base
modification detection looks at gene expression, host- pathogen
interaction, and DNA damage and repair. This machine utilizes the
Single Molecule Teal-Time (SMRT) DNA Sequencing System that provides
users with DNA sequencing of up to 40,000 base pairs, high accuracy,
and a broad range of DNA base modifications.
A company based in Seattle,
Washington called Stratos Genomics, Inc. created a unique machine that
is faster and more affordable compared to other technologies. Stratos
Genomics designed a form of technology that reads DNA sequences by
looking at single molecules. Their machine, called Sequencing by
Expansion technology (SBX), handles the process of nanopore sequencing
of expandable nucleotides. This utilizes a single molecule detection
process. The SBX consists of an Xpandomer, allowing for the
detection of specific base sequences. The company was recently awarded
$15 million from Roche Ventures and Fisk Ventures. This money will
assist in the next stages of development for SBX.
Internet of DNA Technology
Open Humans Network looks to make an expansion of
health data available for researchers to explore. The Personal Genome
Project uses this website to obtain full DNA sequences. Open Humans is
a network where people sign up to participate in one or more
studies. Before volunteers partake in the study, they agree that
the experimental results will be shared amongst other researchers. So
far, out of 4,100 volunteers, genomes were collected from 500.
MatchMaker Exchange is a system
that trades genetic data with hospitals. The system compares genomic
data from patients worldwide. This process gives researchers the chance
to develop more evidence by matching genes and comparing DNA from
individuals in different countries. Hospitals from Miami, Baltimore,
and Cambridge, UK have agreed to participate in using MatchMaker
Exchange.vii The program specifically links databases with genomic and
phenotypic information. These databases allow researchers to analyze
genes and help prove that certain genes are responsible for particular
illnesses.
MatchMaker Exchange has advanced
enough that the Tiers and API team are now working on connecting two
databases - PhenomeCentral and GeneMatcher. PhenomeCentral
contains clinical and genetic data from patients with undiagnosed rare
diseases. GeneMatcher’s database holds genes that are connected to
inherited disorders. it is also linked to another database known as
PhenoDB, which carries phenotype information.
MatchMaker Exchange is seeking to
develop different algorithms to improve the system and make it easier
to search. The company wants to create algorithms that rank how closely
a phenotype matches with one another and how similar genes are. Once
these algorithms are developed, the MatchMaker Exchange process will
become more efficient in assisting researchers to further understand
data results.
23andMe Inc. collects DNA samples
and has recently partnered with Pfizer Inc., one of the largest
pharmaceutical companies in the world. 23andMe sells $99 tests to
consumers who want to find out more about their genetic histories.
After working with Pfizer, the companies decided to let researchers
have access to DNA samples. The samples were provided by buyers from
23andMe Inc., who agreed to let their information be used in
experiments.
23andMe is looking to make
similar deals with 10 other drug makers and biotechnology companies.
Meanwhile, Pfizer is seeking to enroll 5,000 patients to research the
genetics associated with lupus. What makes 23andMe appealing to so many
companies is that it collects additional information about a person’s
life with the consent of the individual. Now, scientists can also
analyze individual characteristics and how they are associated with
that person's health.
Global Alliance for Genomics and
Health consists of computer programmers and geneticists who work to
build innovative projects. Their end goal is to accelerate the creation
of possible genomic medicine. One project involved a search engine that
sifts through DNA sequences from thousands of human genomes.
Global Alliance was created
because scientists were anxious about the privacy restrictions in
transferring DNA. Researchers wanted the ability to share genomes in
order to advance their own work in the health field. They wanted to
create this alliance because at that time, the cost of examining
genomes decreased by almost $8,000. This created more opportunities to
study DNA.vii
Technology
for DNA Privacy
Global Alliance produced a tool
called Beacon that allows owners to choose what information from their
records is open for search by the public. This method of searching
genomes allows scientists to find information and still keep
individual's privacy intact.vii
Twenty databases are currently
used with Beacon, which provides access to an abundance of genomes. The
system only generates results to yes or no questions, but the questions
can range from being broad to being very detailed. One of the biggest
issues with examining DNA is that patients worry about their privacy,
but Beacon has found an alternative way to resolve this concern.
Cloud-Based Technology
Many companies are now developing cloud-based
software to support the Internet of DNA. Just some of these efforts are
discussed below.
Google
Google created Google Genomics,
which is a cloud computing software that gives users access to an
individual’s genetic profiles. From the cloud, genome data can be
shared, and virtual experiments can be done easily. This is primarily
possible because of the simple access to a large repository of data.
The National Cancer Institute
stated they would pay $19 million to store copies of 2.6 petabytes of
DNA data in Google’s cloud. Google Genomics will assist in
efforts to discover how DNA impacts certain illnesses. Scientists are
optimistic that such endeavors will prove beneficial in illness
detection.
Apple
Apple is looking to use an
application called ResearchKit to collect information about symptoms,
DNA samples, and other topics. Scientists would have access to this
vast amount of information through a computing cloud. Apple’s goal is
for people to have the opportunity to choose whether or not to share
their DNA information with other individuals, including
scientists. The experiments would look at 100 or fewer genes per
person, which would not cost more than a few hundred dollars per test.
If Apple’s goal is accomplished, then studying DNA will also be easier
for scientists because of the mass amount of information made available
via the cloud.
DNAnexus
and Tute Genomics
These companies partnered with
each other to create a method for scientists to look at a DNA sequence
and analyze it in one process. DNAnexus uses a cloud-based system
which manages collected genomic data. Tute Genomics focuses on the
analysis of genomes and creates files of a genomic profile for
scientists. Both companies work well to create an environment that
stores information and analyzes it in one simple procedure. Users save
time and money from using this integrated platform instead of multiple
machines.
The Application of DNA to
Diseases
Brain mapping is a way to learn about how the brain
functions and how certain diseases are linked to it. There is
also a strong correlation to mutations in DNA strands and certain
diseases. Studying DNA and how the brain works can help close the gap
in research to discover a cure for illnesses such as Alzheimer's and
autism.
Alzheimer’s disease usually
occurs in older people. It has a significant impact on a person’s life,
especially in the loss of memory and eventually thinking, language, and
behavioral skills. Studies indicate that people with Alzheimer's
have millions of extra pairs of DNA in their brains. Scientists
have yet to figure out the cause of extra pairs of DNA in people with
Alzheimer’s and why it causes the disease to develop in the first
place. This is an effort that can be advanced with the Internet of DNA.
Autism impacts a child’s brain
for the rest of his life, which is why early detection is crucial. It
is best to attempt reducing symptoms associated with the disease early
on. Stanley Nelson is a geneticist from the University of
California-Los Angeles who believes that analyzing genetic samples of
individuals with autism will contribute to finding out how the illness
develops in the first place. As of now, researchers use a
database called Autism Genetic Resource Exchange to analyze DNA
samples. The database contains and utilizes samples from approximately
10,000 participants.
Conclusion
In the future, individuals will need to share their
DNA data with scientists in order to further the medicinal field.
Without large scale studying of genomes, it is more challenging for
researchers to discern the causes of varying diseases.
If companies can find a way to
protect individuals' private information while sharing genomes, then
using the Internet of DNA can provide limitless, valuable findings.
Development of new technology to share DNA data can create many more
possibilities for scientists and researchers. R&D tax credits are
available to companies that create new technology and are involved with
innovation of modern processes in the health field.
