Genomics


DNA molecules are made of two twisting, paired stands. Each strand is made of four chemical units, called nucleotides bases. The bases are adenine (A), thymine (T), guanine (G) and cytosine (C). A always pairs with a T, and C with a G.

gene is the basic physical and functional unit of heredity. Genes, which are made up of DNA, act as instructions to make molecules called proteins. In humans, genes vary in size from a few hundred DNA bases to more than 2 million bases.

3 billion of these base pairs, which reside in the 23 pairs of chromosomes within the nucleus of our cells. Each chromosome contains hundreds to thousands of genes, which carry the instructions for making proteins. Each 30,000 genes in human genome make an average of 3 proteins.

  • 60 base pairs per minute x 60 minutes x 8 hours/day x 365 days/year = 10,512,000 bps/yr
  • 3,000,000,000 bps/10,512,000 bps = 285 years to type the whole 3 billion bps in human genome.
  • Genetics research is the study of heredity or inherited traits (such as eye color) and alterations in specific genes that may impact the individual potential for a given health condition.
  • Genomics research is the study of a complex set of genes (either inherited or arising from alterations that occur after birth), identifying not only their sequences but how they are expressed and interact to affect how a condition develops.

Everything started with the Human genome project (HGP). The Human genome project was completed in 2001. HGP took over 13 years of international formal cooperation (US, UK, Japan, France, Germany, China, etc.) to identify all the approximately 20,500 genes in human DNA. The cost of the project was about $ 2.7 billion dollars. The identity of the volunteers whom DNA was sequenced is intentionally not known. In addition, HGP determined the sequences of the 3 billion chemical base pairs that make up human DNA.

Genomics Sequencing

Genomics plays a role in 9 of the 10 leading causes of death, including:

  •   Heart disease
  •   Cancer
  •   Stroke
  •   Diabetes
  •   Alzheimer’s disease

Next Generation sequencing is extremely compute intensive, it produces data that are extremely large. This causes huge problems in analysis of data.

High Throughput means: sequencing millions of gene sequences at the same time instead of one gene sequence at a time.

Mi sequencer does small genome work and on the other side of the scale you have the Hi Sequencer X series which does the whole human genome and sequences it in less than 3 days with 2 Terabyte of data output per person.

  • DNA sequencing leading found a lot HER2 (Biomarker) proteins in the cerebrospinal fluid. This led to a successful treatment of the brain cancer with Herceptin medication

Some researchers are calling this “personalized medicine”.

  • 2nd relapse, 2nd stem cell transplant, some sides affects, Sequencing his genes and looking for the mutation that causes Acute Myeloid Leukemia (AML). They found FLT3 gene that was expressed higher than normal. They used a drug-gene interaction database and found Sutent to be helpful. The patient was an oncologist researching on leukemia.
  • The BC’s POG (personallized onco-genomics) helped to find at tumour with a rare protein malfunction and the patient was treated with commonly available blood pressure medication. One month later the patient was cancer free.
  • For Diabetes, there have been many studies for risks associated with hereditary genes but no treatment has been found, yet. The research is in progress to find a viable treatment.

Children’s Mercy Hospital in Kansas City working with Cerner

  • For acutely ill kids (genetic disease)
  • It is a research not a routine test yet.

kids who were never diagnosed are referred for genome sequencing of their mother’s, father’s and themselves

  • 50-hour Utlra-rapid whole genome sequencing
  • They changed the 15 hours in alignment to 1.5 hours
  • Variant Detection from 3 hours to 0.5 hour
  • Ultra-rapid procedure is now takes 25-hours to complete.

CentOS (abbreviated from Community Enterprise Operating System) is a Linux distribution that attempts to provide a free, enterprise-class, community-supported computing platform

  • Variants: variation of genes related to the genetic condition
  • Isilon: it is a big data storage system
  • Oracle: provides the grid engine for computing in distributed environment

There are over 427 companies around the world that are involved in the genomics industry. The market value expected to hit 19 billion dollars.

MarketsandMarkets is a US based Market research company. It is world’s No. 2 firm in terms of annually published premium market research reports. Serving 1700 global fortune enterprises with more than 1200 premium studies in a year, M&M is catering to multitude of clients across 8 different industrial verticals.  The sequencers are producer more data than computer advances can keep up with.

The human genome is the basis for developing a variety of products to improve the identification, treatment and prevention of ill health.

  1. Identification of disease genes can have applications in clinical diagnostics and predictive testing. For example, the polymerase chain reaction (PCR) technique, a highly sensitive and accurate genome-based diagnostic method that multiplies the DNA of a pathogen making it easier to detect, can be simplified for use in poor countries to diagnose infectious diseases, such as leishmaniasis and dengue fever, more rapidly, accurately and at less cost.
  2. New treatment can be developed by identifying new drug targets or tailoring drugs to specific genetic characteristics of individuals. Eg differential drug absorption can influence dosing levels and side effects.
  3. In developed preventive measures, genomics can, for example, help identify multiple vaccine targets, useful in developing vaccines for organisms with a complex multi-host life cycle, such as the malaria parasite.

An important and unusual aspect of the Human Genome Project was the call by the scientists involved to devote a portion of the funds to exploring the ethical, legal, and social implications of release of information on the human genome sequence. Foremost in the scientists’ minds was the knowledge that each individual’s genome sequence holds the key to his or her disease susceptibility. A component of human behavior is also very likely to be genetically controlled. It is not difficult to imagine potential misuse of this information by such entities as insurance companies, the military, or law enforcement agencies.

An example of perceived misuse of genetic information was when a major railroad company decided to perform DNA tests on its employees in order to identify susceptibility to carpal tunnel syndrome. The Equal Employment Opportunity Commission filed a lawsuit to block the DNA testing, claiming that it would provide the basis for genetic discrimination.

Potential for ‘genomic divide’ between rich and poor:

  •  Of US$70 billion/year health research, 10% devoted to health problems of 90% of world’s population
  •  Of 1,223 new drugs from 1975-1996, only 13 treated tropical disease
  • ‘Genomic divide’ will lead to health and economic inequalities, leading to political and social unrest
  • Vital that secure strategies to ensure benefits of genomics are universal
  • Potential for a ‘genomic divide’ between rich and poor nations

There has been a lot of discussion in the news media about the future of genomics. It is not always easy to separate the hype from realistic projections. Nevertheless, certain trends are clear. The first is the downward trajectory of sequencing costs. Just as computing costs have decreased in a predictable way for more than 20 years, the price of sequencing, as shown in the graph of this slide, is decreasing in a linear fashion over time. This decline in costs is a major reason for the dramatic increase in the number of sequenced base pairs deposited in GenBank. Note that the scale of the graph is logarithmic. If the trend in sequencing costs continues, it is imaginable that the cost of sequencing an entire human genome could drop to around $1,000. This affordability opens the possibility that individuals will have their genomes sequenced in order to determine their susceptibility to diseases, for example. Even with only a modest reduction in sequencing costs, there is every likelihood that the genomes of a whole host of organisms will be fully sequenced. This achievement will greatly facilitate the field of comparative genomics.

  • In medicine, we are likely to see a move in approach from curative to preventive
  • Medicine will become more personal
  • Gene therapy will cure diseases
  • Improvements in global food production and the development of draught resistant or pest resistant crops,
  • The development of ecologically friendly alternatives to petroleum
  • The creation of new ways to manage the impact of climate change
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