What’s going on behind the Scenes of Genetic Testing?
This is a description of the full genomics pipeline from sequencing data to final data related to diseases.
How do people recognize genes related to certain diseases? How did people learn from sequencing to find data about a person’s condition, his predisposition to various problems? Or just how the whole pipeline works, connecting raw data and knowledge used in real life.
This article will sort out the basics of any genetic testing to find SNP and further stages of typical research.
How to conduct a genetic study step by step?
1. How is genetic data collected?
Data on the sequences of biological polymers (for example DNA) are contained in almost every human cell or even in its biological traces. By collecting saliva, hair or any biological fluids, it is possible to find the cherished unique prints of a living organism in them.
This is how the first stage of genetic research takes place. This is a physical data fence.
2. Sequencing step
The next step is to find the DNA chain from the sample taken. It sounds simple, but this step hides a specific purification of the sample, DNA extraction, purification of the DNA itself, sampling of the desired fragment of the biopolymer and only after the sequencing steps.
You may be wondering what sequencing is, and what your data has to do with it, but first you need to figure out what it is. Sequencing is the process of reading composite monoblocks of the entire polymer (for example, the determination of nucleotides in DNA), at the output of which DNA sequences (reads) are obtained.
The first type of sequencing was invented by Sanger. Sanger sequencing, also known as the “chain break method”, is a method for determining the nucleotide sequence of DNA. With the subsequent development of technology, this method has been transformed into pyrosequencing, chain growth sequencing, and much more.
3. From FastQ to SNPs
After DNA sequencing, a file is formed in a certain format — fastq. This format contains the name of the reading, the DNA sequence itself and the quality of this reading. However, these data do not provide much useful information, since these data do not speak about genes, transcriptional regulation, or other basic things. Therefore, to obtain this information, you need a file of another sample, often it is a VCF file.
VCF files contain an indication of the replacement of a certain nucleotide in a certain place, and just these data indicate the diversity in genes, the presence of disease markers and much more. Getting this VCF file containing information about the SNP (single nucleotide polymorphisms) is a key task of bioinformatics, which is backed by a large number of various applications, pipelines and much more. I will write a separate article about a specific task “From FastQ to SNPs”, because it really deserves more attention.
4. Human choose
The last stage of interpreting the results of the study applies, of course, to people. Clinical bioinformatics, using databases of various genomic information, compare the found polymorphisms and draw final conclusions. This is where the last decisive stage takes place, on the basis of which conclusions are drawn on the entire clinical trial.
Where is it in our life?
In fact, these genetic tests are still expensive operations and not everyone can afford such a study. On the other hand, every year the price tag for ordinary classical genetic testing falls, and both for a genome-wide study (that is, a study of the entire DNA) and for a study of a sample of genes. In general, this kind of activity is becoming more and more and it is useful to know and understand what is happening behind the scenes with your most intimate data.
Summary
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