Genotyping: Basics and Applications
Genotyping is the process of determining an individual's genetic structure by comparing and identifying their inheritance using a sequence of DNA and markers. In evolutionary biology, population biology, taxonomy, ecology, and genetics of organisms, genotyping is critical. DNA sequencing, polymerase chain reaction, restriction fragment length polymorphism (RFLP), random amplified polymorphic detection, amplified fragment length polymorphism (AFLP), DNA microarrays, and other methodologies can all be used.
Genotyping is the process of determining the genetic makeup of a person by sequencing small fragments of DNA and comparing it to that of other individuals using genetic markers. Genotyping can be used on a variety of organisms, such as humans. It can also be utilized to decide the genetic varieties of microorganisms such as viruses, fungi, and bacteria using reference characteristics. In molecular epidemiology and forensic microbiology, information acquired from genotyping is used to control pathogens, particularly microorganisms. In pedigree assessment, genotyping is crucial. Humans are genotyped to determine whether they are mothers or fathers. The dominant and recessive alleles of genes that determine particular traits will be revealed by genotype.
Genotyping Bioinformatic Analysis Content
Bioinformatic assessment for genotyping involves (Whole-genome sequencing data or whole-exome sequencing data) (1) data quality control, (2) mapping to a reference genome, and (3) SNP identification and annotation, (4) CNV identification and annotation, and (5) Indel identification.
Sequencing: Basics and Applications
The method of evaluating the appropriate order of the nucleotides in a provided fragment of DNA or RNA is known as sequencing. The genome contains almost all of the information needed for an organism's growth and improvement The progress of processes for evaluating the accurate nucleotide sequence of a provided fragment of DNA or RNA was aided by the accessibility of methods for producing and separating a few hundred nucleotides long nucleic acid fragments. Today, a variety of sequencing methods are accessible. These sequencing techniques, when combined with methods for creating genome libraries that comprise an organism's whole genome, make it easier to sequence that organism's entire genome and perform in-depth analyses of gene constructions, gene functions, gene sites, gene expressions, gene mapping, and gene regulatory areas.
Many viruses, bacteria, archaebacteria, yeast, and a variety of other microbes have had their genomes sequenced and mapped. The Human Genome Project enabled the sequencing and mapping of the entire human genome, with the first draft being published in 2003. It is a significant step forward in biological research Human genome sequences are now being utilized in the medical field to find genetic occurrences for rare diseases, screen newborns for disease risk, find genetic details of various cancers, create new therapeutics, and diagnostic tools, among other things.
Sequencing Bioinformatics Analysis Content
The raw sequence reads from a FASTQ or unaligned BAM (uBAM) file are integrated against the human reference genome in the bioinformatics pipeline for a standard DNA sequencing method. Sequence alignment is the next process, which involves allocating a genome positional framework to short reads in the reference genome and generating several metadata fields, such as alignment features (matches, mismatches, and gaps) in the Concise Idiosyncratic Gapped Alignment Report template. A Sequence Alignment Mapping (SAM/BAM) or CRAM file format is used to keep the aligned sequences and associated metadata. The BAM file is used by downstream algorithms to define a variety of genetic changes, such as single nucleotide variants, insertions and deletions (indels), and tumor mutation burden.
Difference Between Genotyping and Sequencing
| PARAMETERS |
GENOTYPING |
SEQUENCING |
| Definition |
Genotyping is the method of deciding an individual's genetic makeup and evaluating the group or taxonomy of that organism. |
The method of evaluating the exact order of nucleotides in a provided DNA or RNA fragment is known as sequencing. |
| Techniques |
RFLP, gene sequencing, PCR, DNA microarrays, AFLP, and other techniques are used. |
Sanger, Gilbert, Pyrosequencing, Next Generation Sequencing, Shotgun Sequencing, and other types of sequencing are available. |
| Major Concerns |
This is more concerned with whether genotype distinctions are causing phenotypic variations. |
This is more concerned with the nucleotide order and how it differs and shifts in other microbes. |
About CD Genomics Bioinformatics Analysis
The bioinformatics analysis department of CD Genomics provides novel solutions for data-driven innovation aimed at discovering the hidden potential in biological data, tapping new insights related to life science research, and predicting new prospects.
References
- Wallace JG, Mitchell SE. Genotyping‐by‐sequencing. Current protocols in plant biology. 2017, 2(1):64-77.
- Heffelfinger C, Fragoso CA, Moreno MA, et al. Flexible and scalable genotyping-by-sequencing strategies for population studies. BMC genomics. 2014, 15(1)
- Narum SR, Buerkle CA, Davey JW, et al. Genotyping-by-sequencing in ecological and conservation genomics. Molecular ecology. 2013, 22(11).
