Hello everybody. My name is Alexander Sokolov, and I am an expert in quantum cryptography. I want to tell you how to make a DNA sequencer, a device for decoding deoxyribonucleic acid (DNA), at home. The market price for such a device is about $50,000 dollars.
Figure 01: The “heart” of my device for reading DNA
Let me provide you a brief introduction about genetics. In 2003, a sensational declaration was made – scientists had finally decrypted the human genome. This is known as the Human Genome Project, and completion of this great international project that would allow for reading DNA was for about $3 billion dollars. The human genome is built from DNA, which is the source code (or building plan) of an organism. DNA is a double helix consisting of 4 kinds of nucleotides (Adenine, Guanine, Cytosine, and Thymine), which are repeated in the human genome about 3 billion times. As all the information on your computer is encrypted in bits, the instruction for assembling all the proteins of the human body is encrypted in the nucleotides. If we know what order the nucleotides are located in a DNA sequence, we could theoretically collect all the necessary proteins and obtain a model of a person. In fact, scientists did not decode DNA. Scientists just translated the chemical sequence into a set of zeros and ones on the computer. At the moment, we only understand the function of 5% of the genome; we can only venture to guess about the other 95%.
The cost of the first human DNA sequencing was about $100 million dollars. Over time, this figure has decreased significantly, and is now about $1000 dollars. The customer pays, the customer’s DNA is sequenced, and the laboratory gives the customer a hard drive with about 3 GB of information containing that individual’s genome in digital format.
Today, there are three main sequencers on the market. The most utilized product, HiSeq, is developed by Illumina, and provides the cheapest form of genome sequencing – fluorescent method. This method involves a laser being shined at DNA, and the newly added fluorescent-labeled nucleotides glow in response. The sequencing process requires several days, and during this time, the genomes of several people are processed. The device itself costs about $1 million dollars, and since the technology has been outdated for about 3 years (newer, cheaper, and faster sequencers have appeared), it would cost about $1000 dollars per day to pay it off.
The second device on the market by popularity literally appeared a couple of years ago. The product is called Nanopore, which is developed by Oxford Nanopore Technologies, and is based on technology that involves DNA being sequenced through a nanopore. The DNA is drawn up through the protein and electrical signals are read from it. The Nanopore is the cheapest device on the market, and is positioned as a one-time home sequencer that costs about $1000 dollars.
The third device is known as a Personal Genome Mahine (PGM), a semiconductor sequencer, that costs about $50,000 dollars. The process of sequencing the genome takes about several hours.
Figure 02: Personal Genome Mahine (PGM)
PGM was my choice and I needed it for my home laboratory, but I did not have $50,000 dollars. I therefore had to make a sequencer myself.
Before continuing, let me briefly talk about how a semiconductor sequencer works. The entire DNA chain is divided into fragments of about 300-400 nucleotides in length. These fragments are called reads, which are attached to small spheres and copied many times. Copying is necessary because this amplifies the signal from each specific read. This results in a single bundle of identical DNA fragments that "hang" onto each sphere. A set of different spheres is called a DNA library.
The heart of PGM is a disposable chip – a matrix. This matrix is similar to the matrix in a camera, but instead of having pixels reacting to light, there are pH transistors that react to changes...Read more »