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How to Track down Bad Genes in Your Genome?


How many genes do we have? Scientists estimated that there are probably 20,000 to 25,000 genes, which are essentially the molecular remote controls to our body's functionality. You should understand them properly in the grand scheme of your health, said Dr. Agus[1].

Many genes get translated into proteins, and these proteins make the stuff of our bodies. One protein makes hair; another makes cartilage; others make muscle. Besides those protein-coding genes, some genes are switches which turn other genes on and off. And, still other genes (i..e, body-plan genes) that give those switches orders. Together, in a complex cascade of timing and intensity, they combine to produce the amazing diversity of life on this planet. To learn more about the human genome, read [3].


In this article, we will look at two ways of tracking your genetic makeup, which may offer clues to your risk for certain ailments:

  • Family Health Tree[15]
  • Genetic Testing

Genetically Inherited Diseases


DNA has a vital quality—it doesn't stay the same. When a baby is conceived, the fertilized egg receives half its DNA from the mother and half from the father, creating wholly new combinations. It's why we look a bit like our parents, but also different. Another way that DNA can change is mutation.


Mutations can happen as our DNA copies itself when our cells divide and our bodies develop. Sometimes, one of the DNA's chemical letters is replaced with another letter, sometimes letters are missing entirely. This can cause minute changes that no one is even aware of. But when mutations occur in the cells we pass down to our children, they can cause big changes, like rare genetic disorder named microcephaly.


Children with microcephaly are born with brains that can be a half the normal size. The reason is that a gene helps direct brain growth become defective. In his research, Dr. Chris Walsh[4] has found that some 21 different mutations are responsible for microcephaly. These mutations stop the brain cells from dividing at a very early stage of development.

Family Health Tree

In 2010, one study by the Cleveland Clinic concluded that learning about your family tree is the best tool to predict genetic cancer risks[5]. Family history is one of the most underused but extremely powerful tools to understanding your health. Patterns of familial illness can predict someone's brewing health risks.


Good family health trees are rare—a government survey estimated less than a third of families have one, and time-crunched doctors seldom push their patients to remedy that. To fill that gap, the US surgeon general operates a free website[6] that will help you to create a family health history and share it electronically with relatives and your doctor.


In your effort to create a family health tree, you should follow up either parent's side of the family.[15]  For example, the threat of breast or ovarian cancer can lurk on either side of the family. Because genes seldom render our destiny, a family health tree should also reflect shared environmental or lifestyle factors that can further affect an inherited risk.

Genetic Testing

A single-nucleotide polymorphism (SNP, pronounced snip; plural snips) is a DNA sequence variation occurring when a single nucleotide — A, T, C or G — in the genome (or other shared sequence) differs between members of a biological species or paired chromosomes in a human.


SNPs occur every one hundred to three hundred bases along the 3-billion-base genome. They are thought to provide the genetic markers for our response to disease. These DNA differences do not cause the disease, but they are a marker of the relative risk of a disease. For example, the degree of genetic risk you inherit is related, in part, to how many risk markers you have residing at each SNP—none, one, or two.


Since the completion of the Human Genome Project, hundreds of studies have been published that describe the associations between SNPs and hundreds of specific diseases, traits, and conditions[7]. These studies have opened the door for the personal genomics industry by providing a platform by which DNA, obtained through a simple saliva sample, can reveal your individual genetic map.

Is DNA Sequencing a Diagnostic Test?

Before getting too excited about personal genomics, we need to understand that genetic testing is not a diagnostic test.[18]  For instance, it won't tell you if you have lupus[14] or cancer.  As Adam Siepel of Cold Spring Harbor Laboratory said:[16]


“Everyone in this area knows there are huge pitfalls. The idea of using today’s genome-sequencing technology to let people make medical decisions is really terrifying.

The process is too error-prone to be ready for medical prime time. “You’d have to be sure you’ve ironed all these things out. And we’re nowhere near ironing them all out.”



The troubles with genome sequencing can be summarized as follows:
  • Mutated DNA Samples
    • Scientists collect the DNA from millions of cells (i.e., blood or saliva). While those cells all originated from a single fertilized egg with a single genome, they picked up mutations as they divided. 
  • Technical noise
    •  Chemical reactions during DNA sequencing can go awry. Some sequencing methods involve attaching glowing molecules to bases, for example, and sometimes the molecules fall off “You’ve lost the flashlight,” said Christopher Mason.
    • To squelch technological noise, DNA sequencing companies have built in their own error correction. 
  • Computational noise
    • Computer programs may map some fragments of DNA to the wrong part of the genome. 
      • “You can take the same genome and add it up and get a different answer (i.e. total SNPs in your genome),” Mark Gerstein said.
      • If you sequence the same person’s genome twice, using the same sequencing machine and the same software, the results will not be identical. “95% is about as good as it gets,” Mason said.

In summary, Genetic testing only shows your genetic predisposition to common conditions, so that prevention measures may be taken or early diagnosis may be made. Even though DNA sequencing may only give you a general list of your "ingredients" without telling you exactly how those ingredients mix and interact in your body, it does provide an important foundation to know more about your overall health. Knowing your genetic map, it also offers the potential for a personalized care using gene therapy[9,10] in the future.



Tracking or Not?


Should we find out our own genetic makeup or not? This has always remained controversial[8]. However, let's conclude this article by echoing what Douglas L. Brutlag has said in [12]:


To be sure, the ability to diagnose inherited disease without the ability to cure or treat it leads to numerous social and ethical problems. For example, insurance companies have been free to increase rates for those in high-risk groups. When insurance companies define high-risk groups on the basis of Inheritance, they are in effect holding individuals responsible for their genetic makeup. The social stigma associated with certain genetic differences can also, like more visible phenotypes, lead to discrimination. The most frustrating effects of genetic diagnosis would occur with diseases that have a clearly debilitating or fatal effect but for which there is no hope of a cure or therapy. That is why it is important not only to know the sequence of the human genome but also to understand it well enough to devise cures and rational, inexpensive therapies.

References

  1. The End of Illness by David B. Agus, MD
  2. What Darwin Never Knew
  3. Understanding the Human Genome
  4. Christopher A. Walsh Laboratory — Research on Developmental Disorders of the Brain
  5. Cleveland Clinic research shows family health history valuable in predicting disease
  6. My Family Health Portrait
  7. Locating SNPs in a Gene or in Genes
  8. Would you want to know the genetic road map of your child?
  9. A Step Closer to Personalized Medicine: Improving Gene Therapy to Treat a Devastating Genetic Disease
  10. Gene therapy for breast cancer. --Review of clinical gene therapy trials for breast cancer and MDR1 gene therapy trial in Cancer Institute Hospital.
  11. How to Build Your Family Tree on the Web
  12. Understanding the Human Genome by Douglas L. Brutlag, Ph.D.
  13. Can Personalized Healthcare Survive Obamacare's Medicine Assembly Line?
  14. Lupus: An Unpredictable Auto-Immune Disease
  15. Know Your Family Tree, Boost Your Family’s Health (Cleveland Clinic) 
  16. Carl Zimmer's Game of Genomes (Season 3)
  17. Outside Variants Wired into Epigenetic Circuits That Can Boost Disease Risk
    • Outside variants can come into close proximity with disease genes when DNA strands twist and fold. 
    • They suggest a new level of gene regulation and may help explain how identical single-nucleotide polymorphisms (SNPs) can lead to different clinical outcomes.
  18. Before you send your spit to 23andMe, what you need to know

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