Bioinformatics




Bioinformatics










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Bioinformatics

by James G. Barr

Copyright 2022, Faulkner Information Services. All
Rights Reserved.

Docid: 00018033

Publication Date: 2208

Publication Type: TUTORIAL

Preview

Since the early 1950s when the first commercially-available digital
computers were introduced, government and industry leaders have been seeking
to leverage electronic data processing capabilities to discover the meaning
of data. While this process was applied initially to financial data, various forms of scientific and
engineering data were soon put to analysis, including biological data. The
result of these efforts spawned a new field of
investigation that was later dubbed bioinformatics. Quite simply, bioinformatics is the application of
computation tools and analysis to capture and interpret biological
data.

Report Contents:

Executive Summary

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Since the early 1950s when the first commercially-available digital computers
were introduced, government and industry leaders have been seeking to leverage
electronic data processing capabilities to discover the meaning of data. While
this process was applied initially to financial data, various forms of
scientific and engineering data were soon put to analysis, including biological
data. The result of these efforts spawned a new field of investigation that was
later dubbed bioinformatics.

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As defined by analyst Ardeshir Bayat, “bioinformatics is the application
of tools of computation and analysis to the capture and interpretation of
biological data.”1

Inter-disciplinary in nature, bioinformatics lies at the intersection of:

  • Biology
  • Computer science
  • Information science, and
  • Statistics

The National Human Genome Research Institute describes bioinformatics as
the “linguistics part of genetics.” Just as linguists look for patterns in
languages, the practitioners of bioinformatics look for patterns in DNA
and protein sequences.2

History of Bioinformatics

According to the Pacific Northwest National Laboratory (PNNL), “The
genesis of bioinformatics came in the early 1960s while researchers worked
to decipher the molecular sequences of proteins. If researchers know the
sequence of a protein, they can better identify the structure of the
protein and understand how it works in cellular processes. When a sequence
is known, it can also be connected to the gene that encodes it. Before the
advent of modern computers, protein sequences were assembled, analyzed,
and compared manually on sheets of paper taped side by side.

“The first large scale bioinformatics effort was the human genome
project, which ran from October 1990 through April 2003. In this project,
an international team of researchers sequenced and mapped all of the 3.1
billion protein base pairs in the genes that together make the human
genome. Even given the span of many lifetimes, humans could not have
manually sifted through this vast amount of data. Therefore, bioinformatics
did not make the human genome project faster; it made it possible.”3

Figure 1 depicts the final five years of human genome project
achievements.

Figure 1. Human Genome Project (1999-2003)

Figure 1. Human Genome Project (1999-2003)

Source: Wikimedia Commons

Bioinformatics and COVID-19

Not surprisingly, bioinformatics played a pivotal role in mitigating and
managing the COVID-19 pandemic, revealing, according to one study, the
following:

COVID-19 Cause – “After obtaining [the]
nucleic acid sequence, bioinformatics analysis demonstrated that COVID-19
was caused by the novel coronavirus SARS-CoV-2.”

Drug Development – “At present,
bioinformatics based on high-performance computing … will certainly be
used to accelerate the development of specific drugs.”

Vaccine Development – “[Many]
bioinformatics tools and algorithms have been used to develop safe
candidate vaccines for COVID-19.”4

As neatly summarized by the PNNL, “During the coronavirus pandemic,
researchers were able to sequence the virus’s genome, identify what was
likely to be causing the virus to enter cells, and develop a vaccine based
on the discovered genome within a matter of months. This would not have
been accomplished if researchers had manipulated handwritten codes to find
meaningful connections.”5

Market

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MarketsandMarkets predicts that the global bioinformatics market will
reach $21.8 billion by 2026, up from $10.7 billion in 2021, a compound
annual growth rate (CAGR) of 15.2 percent during the forecast period.6

Bioinformatics is attracting both private and public sector investment.

On the private side:

  • Hospitals and other healthcare facilities are viewing bioinformatics
    as a vehicle for improving patient care and lowering costs.
  • Pharmaceutical and other research establishments are embracing
    bioinformatics as an instrument for accelerating the creation and
    clinical examination of new drugs and drug variants.

On the public side, “Many countries are investing in their national
population sequencing programs to understand the link between genetics and
diseases. Government organizations are sequencing the genomes of millions
of citizens to advance research and help develop better ways to diagnose
and treat cancer, rare diseases, and other conditions. These large
sequencing projects are expected to drive the requirement of
bioinformatics products and services.”7

One factor which may inhibit the growth of bioinformatics is the
potential for personal privacy violations, particularly if genome and
other forms of analysis run afoul of statutory safeguards such as the US
Health Insurance Portability and Accountability Act (HIPAA) or the
European Union (EU) General Data Protection Regulation (GDPR).

Prominent players in the bioinformatics market include:

  • Thermo Fisher Scientific (US)
  • Eurofins Scientific (Luxembourg)
  • QIAGEN (Netherlands)
  • Agilent Technologies (US)
  • Illumina (US)8

Application

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According to Fios Genomics, a leading provider of bioinformatics services,
"The field of bioinformatics has advanced considerably" over the past
half-century, in an effort to keep pace with progress in molecular biology and
computer science. “The rise of the Internet in the 1990s coupled with the creation of
next-generation sequencing (NGS) technologies in the 2000s created a boom
in the availability of biological data to [be] analyzed. In turn, this led
to the swift production of new bioinformatics tools.”

Today, bioinformatics is used to analyze data sets containing:

  • Genome sequence data
  • Gene variation data
  • Gene expression data
  • Single-cell data
  • Proteomics data
  • Metabolomics data
  • Epigenetics data

Importantly, such analysis can aid in therapeutic research, including the
examination of study data related to cancer, heart disease, and other
serious or life-threatening conditions. Beyond medicine, bioinformatics
can also advance agricultural and environmental research.9

Bioinformatics has found application in a wide range of sectors and
interests, including:

  • Alternative energy (biofuels)
  • Antibiotic resistance
  • Bio-weapon development
  • Climate change
  • Crop improvement
  • Drug discovery
  • Evolutionary studies
  • Forensic science
  • Preventive medicine
  • Stem cell therapy
  • Veterinary science
  • Waste clean-up10

Drug Repurposing

One of the most exciting bioinformatics use cases involves drug
“repurposing” – also known as drug repositioning, reprofiling, or
retasking. The basic idea is to take existing medications – which often
required years of effort and millions of dollars to develop and test – and
repurpose them to treat diseases or conditions for which they were not
originally designed.11

While generally applicable to all areas of medicine, drug repurposing may
be a “game changer” for cancer patients. Researchers report that “Despite
the advances in oncology research, cancers are still associated with the
most unmet medical needs. Drug repurposing has emerged as a useful
approach for the search for effective and durable cancer treatment. It may
also represent a promising strategy to facilitate precision cancer
treatment and to overcome drug resistance. The repurposing of non-cancer
drugs for precision oncology effectively extends the inventory of
actionable molecular targets and thus increases the number of patients who
may benefit from precision cancer treatment.”12

Future

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As we look to 2023 and beyond, bioinformatics will continue to mature as
“improvements in high throughput computing expand the amount and
complexity of data that researchers can examine.”13

Elaborating on these improvements, Telefonica observes that “Big Data
development has been one of the great driving forces for the improvement
of research work in recent years. Other important contributions regarding
innovation within the framework of connectivity and digitization have been
Artificial Intelligence and Machine Learning, supported by the 5G network,
as they offer new perspectives for tackling an increasing number of
biomedical problems, thanks to the creation of algorithms and mathematical
models that extract maximum knowledge from data.

“[There] is already an initiative called the International Cancer Genome
Consortium … which studies genetic, transcriptomic and epigenetic
changes in more than 50 different types of tumors. This project has
identified almost 4 million genetic mutations in participating patients,
which could prove invaluable in the fight against cancer in the years to
come.”14

Special Use Cases

While the scope of bioinformatics is both large and diverse – dictated by
near-continuous developments in both biology and computing – the coming decade
will likely feature a number of special use cases:

Pandemic Prevention – Many virologists
and epidemiologists are warning about the potential for another pandemic.
Bioinformatics will help focus a concerted government effort to prevent
another COVID-style outbreak by improving “zoonotic disease surveillance,”
or the ongoing observation of diseases transmitted between humans and
animals.

Biodiversity Prospecting – Spurred by
government and industry, bioinformatics will be employed to accelerate
“the search for plant and animal species from which medicinal drugs,
biochemicals, and other commercially valuable material can be obtained.”15

Climate Repair – Bioinformatics will be
utilized in an effort to cultivate microbes capable of regulating climate
change.16

Medical Sensing – An emerging
bioinformatics tool, medical sensors will be widely deployed within their
human hosts to measure specific biological, chemical, or physical
processes. Promising a revolution in healthcare, sensor data will:

    • Provide early warning indicators of diseases, injuries, or other
      physical or mental maladies.
    • Permit people to discriminate between normal “aches and pains” and
      serious conditions.
    • Give physicians actionable intelligence on the state of their
      patients’ health, facilitating the process of differential diagnosis.
    • Allow the medical community to invest in equipment and personnel
      according to disease patterns and prognostications.
    • Enable epidemiologists to detect and trace disease outbreaks and
      progressions.
    • Extend the average individual’s lifespan and improve his or her
      quality of life.
    • Reduce government spend on healthcare as the public policy emphasis
      shifts from disease treatment to prevention.

Remote Medicine – Bioinformatic
technologies will help facilitate the continuing trend toward remote
medicine, including:

    • Remote patient monitoring
    • Remote medical diagnosis
    • Remote medical treatment (including robotic surgery)

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References

1 Ardeshir Bayat. “Bioinformatics.” The BMJ, Volume 324. April
27, 2002:1018.

2 “Bioinformatics.” National Human Genome Research Institute.
July 25, 2022.

3 “Bioinformatics.” Pacific Northwest National Laboratory.
2022.

4 Lifei Ma, Huiyang Li, Jinping Lan, Xiuqing Hao, Huiying Liu,
Xiaoman Wang, and Yong Huang. “Comprehensive Analyses of Bioinformatics
Applications in the Fight Against COVID-19 Pandemic.” Elsevier Ltd.
November 2, 2021.

5 “Bioinformatics.” Pacific Northwest National Laboratory.
2022.

6 “Bioinformatics Market by Product & Service (Knowledge
Management Tools, Data Analysis Platforms, Structural Analysis, Functional
Analysis, Services), Applications (Genomics, Proteomics), & Sector
(Medical, Animal, Agricultural) – Global Forecast to 2026.”
MarketsandMarkets. July 2021.

7 Ibid.

8 Ibid.

9 “What Is Bioinformatics – Overview and Examples.” Fios
Genomics. 2022.

10 “Application of Bioinformatics.” Leverage Edu. July 22,
2022.

11 Pan Zheng, Shudong Wang, Xun Wang, and Xiangxiang Zeng.
“Editorial: Artificial Intelligence in Bioinformatics and Drug
Repurposing: Methods and Applications.” Frontiers Media S.A. 2022.

12 Kenneth K W To and William C S Cho. “Drug Repurposing for
Cancer Therapy in the Era of Precision Medicine.” National Library of
Medicine | Bentham Science Publishers. February 14, 2022.

13 “Bioinformatics.” Pacific Northwest National Laboratory.
2022.

14 “Big Data, Artificial Intelligence and Bioinformatics:
Three Tools That Save Lives.” Telefonica S.A. November 15, 2021.

15 Oxford Languages.

16 Quirin Schiermeier, Tosin Thompson, and Jeff Tollefson.
“COP26: Meet the Scientists Behind the Crucial Climate Summit.” Springer
Nature Limited. November 16, 2021.

About the Author

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James G. Barr is a leading business continuity analyst
and business writer with more than 40 years’ IT experience. A member of
“Who’s Who in Finance and Industry,” Mr. Barr has designed, developed, and
deployed business continuity plans for a number of Fortune 500 firms. He
is the author of several books, including How to Succeed in Business
BY Really Trying, a member of Faulkner’s Advisory Panel, and a
senior editor for Faulkner’s Security Management Practices.
Mr. Barr can be reached via e-mail at jgbarr@faulkner.com.

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