61

This is a great biological question! It asks a lot about how empirical science is done in the field of modern biology. I'm glad we encourage such questions from curious people who want to learn more. Your genome has a sequence that is unique to you, gifted to you by your parents and by small changes from random chance. Your genome is pretty close to what ...


13

Here I will assume we are talking about eukaryotic sequence specific transcription factors (ssTFs) and try to answer your first and part of the second question. There is in any case not definitive answer yet. An estimate of ssTFs genes in humans is given in the 2009 Nature Reviews Genetics paper by Vaquerizas, JM et al, A census of human transcription ...


13

The main reason is because the genetic differences between individuals of the same species are tiny. For the vast majority of studies, they can simply be ignored. Differences between individuals are usually (not always, but mostly) differences in SNP genotypes. These are single nucleotide differences which, while they can have phenotypic effect, don't ...


13

In a genome that is 3 billion base pairs, a difference of 0.5% works out to a difference of 15 million bases. When a single base change can change the amino acid sequence of a protein, that can add up to a huge amount of diversity, which is what we see over the nearly 8 billion humans on the planet, and the 99.5% sameness is why we are linked together so ...


11

No, your approach will not work, you are taking a very simplistic view of an extremely complex system. Some of the problems you are ignoring are: Genes (eukaryotic genes anyway) are spliced to produce mRNA, a process that removes introns and leaves only the exons. If you just translate the entire chromosome file you will get noise. Splicing also changes ...


11

This Nature paper from 2004, by Jane Grimwood et al. goes at least a long way towards giving an answer to the question of the OP. In short: there were inordinately many duplications, especially during an event 30-40 million years ago, as well as during a much more recent event. These duplications are, uncharacteristically, predominantly intra-chromosomal ...


9

This question cannot be answered as simply as you put it, but it's not too much to elaborate on. The order of the base pairs will be drastically different, but the same proteins and amino acids will be coded for in genes, just at different points along the DNA. For example, you may find the same sequence to code for a protein in a mouse as in a human, but ...


9

If a DNA letter is one of A,T,C and G, and there are 3 billion base pairs, why don't we say that there are 6 billion letters in the genome? It is a convention, and stating the actual number of bases would not add any information, but would actually lead to more confusion. It's like saying I have six pairs of socks vs. I have twelve socks. It ...


9

Important notes: I am not going into the ethical aspects of editing/removing CCR5 in human embryos, neither will I discuss potential effects of introducing that mutation into the human population. Both of these are very important issues, but out of the scope for this answer. As of now I'm not aware of any reliable sources of what was actually done in ...


8

These are sequencing gels (in the cases here even radioactive ones) - they are run a lot longer than ordinary agarose gels and they are made from polyacrylamide. Im my experience, the most likely cause for skewing of lanes (not only bands) are samples, which still contain too much salts from the PCR reactions. This can also happen to only a few bands as seen ...


7

The question makes it clear that the poster is aware of the different ways of estimating human genetic variation, and he is also no doubt aware of the fact that Wikipedia is written by “people like you” who may not be experts in the field or have updated an old entry based on limited data. Let me address what appears to be the cause of confusion in this ...


6

Alleles are variations of a same locus that codes for a protein (gene). These alleles can come in different forms, one of which is SNP. For example, sickle cell anemia arises from an allele of the beta-globin gene which has had a change from A to T. Meanwhile, for the ABO gene that determines your blood group, the O allele has a missing nucleotide (G) that ...


5

A single run of sequencing won't cover the entire genome, in most cases. That's why they do multiple rounds in order to increase horizontal (covering more regions of genome) and vertical (a.k.a depth; more reads per locus so that you can be more confident) coverage. Edit by dd3: In the cases where "a new gene is discovered", i.e. genome reannotation, it is ...


5

Why do you think it was "fixed?" Here's a nice review of the history of human cytogenetics, which included not only the original image from 1956 but points out a report which comments on the standardization of chromosome number. The autosomes were indeed numbered by length, and the sex chromosomes are traditionally put at the end as they are "numbered" 23 ...


5

Here is what the data says. UK government must have had some scientific evidence when it settled on a 10 variable-length sections of genome for their database, SGM+. In one such variable sections, some people have 10 repeats of CTTT, others have 11, others have 12 etc. The largest of those fragments, at its maximum length, are about 350 base pairs. The US ...


5

First of all, the reference genome strand specificity is referred to as sense (positive strand) or antisense (negative strand). Now let's consider to sequencing data or FASTQ files. When we align reads, a resulting SAM or BAM file has a column specifying strand information, we usually see a + or - strand. For more background on the strand names here's a ...


5

It is as safe as to publish your fingerprints. Right now, there is little that anyone can do with your genetic information but in the future, this will change. One of the feared consequences it concerns what companies may do with that information. Can it be used against you? In some cases, it may. For example, if you have a predisposition for a genetic ...


4

When designing PCR primers we typically use a minimum length of 20 bases, because the probability of a sequence of N bases appearing by random is $\frac{1}{4^N}$, and $\frac{1}{4^{20}}$ is about 9x$10^{-13}$, or about 1 in a trillion. Since the human genome is a little over 3 billion bases long, a 20 base sequence should appear only once. However, most of an ...


4

Back-of-the-envelope calculation The definition of the centimorgan is that it is the length of DNA in a chromosome corresponding to a 1% chance of crossover occurring. In human chromosomes 1 cM = approx. 1Mbp. Your value for the length of DNA in the genome = 3.3 Gbp = 3300 MBp Ignoring complications like the Poisson distribution: 1 cM corresponds to ...


4

The long and short of it is that genetic variation is actually not very predictive in comparison to "environmental" effects such as lifestyle. Only a quarter of the variation in lifespan between twins is attributable to inherited factors (including genetics and epigenetics) [1] - the rest is environmental, from lifestyle to air quality. Most genetic ...


4

Even though individual humans only have around 2-5% Neanderthal genome, it's not the same 2-5% across people. In total, at least 20%, and perhaps as much as 40% of the Neanderthal genome could be recovered from modern human populations: We identified Neandertal lineages that persist in the DNA of modern humans, in whole-genome sequences from 379 European ...


4

SNP is not a specific data type but rather a biological phenomenon. The abbreviation "Single Nucleotide Polymorphism" only means there is a variability (between individuals) in a single letter in a specific position in DNA sequence. It depends on the speaker how they decide to describe the variability; wether they choose to focus on the possible ...


3

The GOLD database (Genomes Online DB) contains data on the sequencing status, and also some stats (number of chromosomes, genome size) -- but this extra data is not available for all species.


3

If you want an actual number, well, it depends (of course). First off, what is your definition of loci? That term is broad, and can be construed to mean everything from large, megabase-length genes to every individual base. That being said, it turns out there are some serious runs of homozygosity (ROH, meaning long regions of the genome that are ...


3

There are several lists on Wikipedia, for example for plants, bacteria and eucaryotes.


3

Sequences that don't appear in a genome are called "nullomers". That article claims that there are no 10bp sequences that don't appear in the human genome, and 80 11bp sequences that don't, citing this paper.


3

The devil is in the details, and therefore we cannot just state that we have understood X% of the DNA. We know e.g. that 2% of the human DNA encode proteins. And for a good number of proteins we know what they do. So you might know that a particular codon AGT encodes a serine residue in a protein, which could have a catalytic activity. Or it has a structural ...


3

You may consider consulting the H2DB database. The database is quite new, so the number of heritability estimates is not very high at the moment (currently 225 estimates for human, 838 estimates in total), but it's a start. The database is described in a paper by Kaminuma et al.(2)


3

First, you need to know which genome sequence does the SNP file refer to. They must have mentioned the reference sequence that they used. As others mentioned the case of CT is heterozygosity. If you just want to mark the changes then discard the residue that is already present in the reference genome and use the other allele. However, you want to keep a ...


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