Question: Difference Between Genotyping And Resequencing
3
gravatar for Mutated_Dater
9.5 years ago by
Mutated_Dater290
Mutated_Dater290 wrote:

Greetings

I am a computer scientist who needs to learn some biology. I'm finding this tough as many of the terms seem to refer to the very similar things which I don't have enough knowledge to resolve.

What is the difference between DNA resequencing and genotyping? I have read about the use of DNA chips to resequence and individual's DNA to find out where their DNA differs from the reference genome. But i have also heard the term genotyping used to find out the genotype of an individual and hence see how their DNA sequences differs from the refernce genome.

DNA resequencing and genotyping seem like the same thing to me. The best I can think of is that DNA resequencing is one method to genotype something and there were other methods before chips came along. I can see from wikipedia that there are many different methods of genotyping

BlockquoteGenotyping is the process of elucidating the genotype of an individual with a biological assay. Also known as a genotypic assay, techniques include PCR, DNA fragment analysis, allele specific oligonucleotide (ASO) probes, DNA sequencing, and nucleic acid hybridization to DNA microarrays or beads. Several common genotyping techniques include restriction fragment length polymorphism (RFLP), terminal restriction fragment length polymorphism (t-RFLP),[2] amplified fragment length polymorphism (AFLP),[3] and multiplex ligation-dependent probe amplification (MLPA).[4]

Are all of these tehcniques used with equal prevalence is one of them industry standard or the preferred one? I don't really want to get confused by reading about a whole load of tehniques that are soon to be obsolete.

thanks for your time

genotyping • 18k views
ADD COMMENTlink written 9.5 years ago by Mutated_Dater290
5
gravatar for Pierre Lindenbaum
9.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

Genotyping is about the simple mutations in your DNA: there a large number of known varitations in the genomes (also known as SNP, rs, Indels, microsatellites, STS...). You'll find some of them in this database http://www.ncbi.nlm.nih.gov/projects/SNP

for example, rs25 is a common mutation , a 'A' or a 'G' in the Human chr7 at position 11584142. When you're genotyping an individual, you're just looking at a few known mutations.

DNA resequencing: involves a complete sequencing of the genome/segment of DNA. It can be fast thanks to the next generation sequencing technologies and first sequenced genome which helps in mapping the new sequences.

ADD COMMENTlink written 9.5 years ago by Pierre Lindenbaum129k

needless to say that when you do resequencing you are trying to detect all previous variation types on the resequenced region.

ADD REPLYlink written 9.5 years ago by Jorge Amigo11k
5
gravatar for Biomed
9.5 years ago by
Biomed4.7k
Bethesda, MD, USA
Biomed4.7k wrote:

Humans are diploid organisms. This means the chromosomes are in pairs (i.e there are two chromosome 1's etc.etc) Each chromosome has one allele and both chromosomal alleles form the genotype of the individual at that spot in the genome. So when you use a technology to determine what that individual's alleles are at a given position in the genome (often done for a single nucleotide at a time) you determine the genotype, or you are genotyping. Most of the time genotyping will look for a predetermined allele and will report that allele to be present or absent.

When you resequence you do not look for a sparce set of predetermined alleles but you are simply sequencing the whole or parts of a samples genome to see what the whole targeted regions all alleles/genotypes are. This gives you more resolution and has an advantage of determining not foreseen changes.

Genotyping is generally a cheaper and more accessible technology. If you have a specific project in mind I can discuss advantages and disadvantages on a specific case.

ADD COMMENTlink written 9.5 years ago by Biomed4.7k
1

What is the point of resequencing? The fact it has a name implies it is something other than 'determining the sequence again' which would just be sequencing

ADD REPLYlink written 9.5 years ago by Mutated_Dater290

For some species we have a 'reference' sequence, which is actually an abstraction, representing a sort of 'average' sequence for several individuals. But it is an abstraction. In reality, the sequences of individuals all differ slightly. As a rule of thumb, the sequences of any two humans differ at about 1 base in 1000. These slight differences can have profound biological effects. For some biological studies the 'reference' sequence tells you all you want to know. For other studies the individual or group variation is important, so you 'resequence' individuals.

ADD REPLYlink written 9.5 years ago by Charles E. Grant220

So are you inferring "reference genome thus => resequencing" or that you sequence first and then select a subset and "resequenced", but with a higher depth? Basically, is a reference genome necessary to say you are doing resequencing?

ADD REPLYlink written 2.1 years ago by beausoleilmo320
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