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Human Chromosome 22 Mapped

jamie posted more than 14 years ago | from the frame-thy-fearful-symmetry dept.

Science 208

tuck was the first of many to submit this important milestone in arguably the world's most important scientific endeavor. The Human Genome Project has completed mapping its first entire chromosome, number 22. Second-smallest of our 23 chromosomes, some of 22's genes can cause "heart defects, immune system disorders, cancers, schizophrenia and mental retardation." Portion of its DNA which is "junk" (encodes no protein): 42%. Read it at your favorite source: CNN, MSNBC, the Boston Globe, the Christian Science Monitor, the AP, or Reuters.

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Whos chromosome did they map? (2)

Anonymous Coward | more than 14 years ago | (#1488225)

I could be asking a stupid question here (blame it on my genes), but since everyone has different DNA, how do the scientists decide which genes are normal? I mean, if there is a hereditary disease that only a very few people get, you probably decide that the 'healthy' gene is the more normal gene. But what if the gene f.e. encodes eye-color, how do the scientists decide what gene to map? Or do they simply say that that and that gene encodes eye-color and leave it open what DNA sequence it has?

TIGR and HUGEP (2)

jw3 (99683) | more than 14 years ago | (#1488226)

Just one more afterthought. There is a basic difference in sequence strategy between the HGP and TIGR.

HGP does it by "clone by clone" strategy. That means, the chromosome is cut in smaller pieces, then again in even smaller pieces, the pieces get cloned (cloning in molecular biology means not the Dolly sheep: it means, a certain sequence is inserted into a epigenetic element called plasmid, which itself can propagate and thrive in bacteria), and then sequenced. This is cumbersome and requires a lot of manual work, but it provides unmatched quality of the sequencing.

TIGR adopted another strategy, the so-called shotgun method. In this strategy, you get a sequence, but you have not the slightest idea where from the genome does it come from. Only you when you have a lot of this sequences you can start assembling - using a lot of CPU, trying to match them one to another, like a puzzle, but trickier: a sequence often contains errors, especially at the end (you can only read a couple of hundreds bases, then the signals are to weak and not clear enough). This strategy requires considerably less highly trained man-power: just a lot of technicians and $$ for expensive sequencing machines (which were provided to TIGR by Perkin-Elmer). However, this method has a serious drawback: there are many sequences in the human genome, which are partly, or totally repeated. This repeat elements can be a royal pain in the sequencing project (been there, done that).

It is really a good thing that there are two sequencing project with two different strategies: the comparison between the two sequences could provide an enormous insight into a) quality of the sequencing b) human variablity. Venter from TIGR is definitely an enfant terrible, but I don't think he is one of those corporate Bad Guys (TM), rather one who was fed up with the slow pace of conventional scientific projects. On the other hand, HGP, representing "the slow pace", shows us also why a slow pace is needed sometimes.

Regards,

January

genes. (0)

Anonymous Coward | more than 14 years ago | (#1488227)

it has come to my attention that the gene for statuephillia has been sequenced on ch.22 this is a massive breakthrough for statuephiles and sexualists alike in order that we may begin to live in harmony together, at one with each other, the earth, and lovely smooth statues of young girls. may i use natalie portman as an example of the latter.

just as we are beginning to understand homosexuality in the sociological and genetic contexts, i pray to you all that you open your eyes a little to the wonderments of human nature, and the human genome itself.

thank you for your time.

H@AAD.com

Re:causing and associated with (1)

jw3 (99683) | more than 14 years ago | (#1488240)

Of course there are some cases when it is known exactly how a genetic disorder causes a certain type of illness - you all know of the Down syndrome, thalassomy, sickle cell anaemia - but there is *a lot* more.

Genetic Easter Eggs! (2)

ToastyKen (10169) | more than 14 years ago | (#1488241)


Imagine hiding easter eggs in junk DNA... Bend the frog's arm the right way and it croaks the genetic engineers' names....

The HGP is like the Periodic Table (4)

wowbagger (69688) | more than 14 years ago | (#1488242)

The analogy I like to use for the Human Genome Project is the development of the Periodic Table of elements.


Of itself, the periodic table didn't make any new chemicals. What it did was provide a framework to identify patterns that could be used to predict areas of research. For example, the discovery of helium: the table predicted the existance of the element, and allowed calculation of the spectral lines. The element was then identified in the sun, hence the name (helium, from helios, the sun).


Similiarly, the HGP of itself won't cure any diseases; rather it will allow the mapping of patterns. We'll be able to say, "This gene, which we know does this in wheat, is present in humans. Perhaps it does the same thing?".


Once we get one copy of the human genome sequenced, we'll still need to sequence many others, from [tall|short|skinny|fat|bald|hairy...] people, and start cross-referencing the results.


Think of it as a massive reverse engineering project on a program we only have uncommented object code for.


Unless the "junk" DNA are comments...

Re:23 Chromosomes (2)

rm-r (115254) | more than 14 years ago | (#1488243)

The pairs are not identical. Each gene on a cronosome refers to another on the second half of the pair. Some genes are dominant and others are recessive. If a gene is dominant than the behaviour to prescribes is used, recessive genes only surface when bothe genes across the pair are the same ie. brown eyes+brown eyes=brown eyes, brown eyes+blue eyes=brown eyes, blue eyes+blue eyes=blue eyes. It is the differance between the chronosomes in a pair that make us what we are. This also explains why males are more prone to some conditions- ie hymaphilia(sp?) A recessive gene on the X gene is not dominated on the Y chronosome as that gene simply is not there- where as females two of these genes to get it.

the correct term is (1)

Zugok (17194) | more than 14 years ago | (#1488244)

..introns. These are base pairs which don't get expressed, however they still are important in how exons are expressed.



There I've explained that in a sentence even a fool can undertand. Junk DNA my adenosine. Either sloppy journalism or else the researcher explaining this to the journalist was sloppy.

Re:23 Chromosomes (2)

3waygeek (58990) | more than 14 years ago | (#1488245)

It'll be interesting to see if male and female lifespans are equal in another 200 years or so, after sexual equality has been fully established.

According to Desmond Morris' The Human Sexes [discovery.com] , recently rerun on TLC, men's life expectancy was several years longer than women's for most of recorded history.

It has been only in this century that women's lifespans have caught up with, and exceeded, men's -- Morris attributes this to improvements in medical care, specifically the dramatic reduction in the number of women who die while giving birth.

Re:The HGP is like the Periodic Table (1)

Edwin Oostra (99197) | more than 14 years ago | (#1488246)

Interesting point, who is the John Doe, whose genes are being mapped ?

Re:causing and associated with (2)

jw3 (99683) | more than 14 years ago | (#1488247)

Of course there are some cases when it is known exactly how a genetic disorder causes a certain type of illness - you all know of the Down syndrome, thalassomy, sickle cell anaemia - but there is *a lot* more.

DAMNED!!! Why can't I send a cancel message? :-) I pressed the "Submit" button again! Grrr....

Back to the topic. There are cases, when finding one single disorder which causes one specific disease is easy. There are cases, when you can pin down a certain region - by tracing the genetic tree of the family, whose members have the disease. There are cases, where you are able to tell that - well, there *is* a genetic component of a certain disease. In some cases, you can tell two forms of the disease: a genetically inherited and a genetically independent form (e.g. the early-onset Alzheimers and the age-dependent Alzheimers disease).

There is yet one thing you have to keep in mind: there is no "gene causing disease X". It's rather: "a gene, whose malfunction or absence causes disease X". For example, a single nucleotide substitution can result in a non-active enzyme, or an enzyme with much slower activity. The whole metabolic pathway, to which this enzyme belongs, is hampered. In some cases a heterozygous organism will have another copy of the gene, which will do the job, or do the job at least in a part - and the disease shows fully in homozygous organisms.

Regards,

January

what is that? (1)

MeYatch (110355) | more than 14 years ago | (#1488248)

My friend says that this is not a real disease. She insists that it would have something to do with the neurons in your stomach and muscles and brain muscles. Doesn't exactly make much sense. I for one believe you, but maybe I am a worthless fool. Please clear this up for us.

Who's DNA is being used (1)

MarkH (8415) | more than 14 years ago | (#1488249)

Probably a stupid question this but who's DNA is being mapped here? Is it someone alive? Is it one or many individuals?

23 Chromosomes (1)

sirket (60694) | more than 14 years ago | (#1488252)

I thought human beings had 46 chromosomes?

Re:23 Chromosomes (2)

billybob (18401) | more than 14 years ago | (#1488254)

we have 23 PAIRS of chromosomes, for a total of 46. I think. someone tell me im not smoking phillipino crack rock here.

Re:23 Chromosomes (1)

vrza (103274) | more than 14 years ago | (#1488256)

You're right... Actually, I think there are 23 *pairs*, and each of them consists of two identical chromosomes.

Re:23 Chromosomes (2)

Imperator (17614) | more than 14 years ago | (#1488258)

IIRC, we have 21 pairs of autosomal chromosomes and 2 pairs of sex chromosomes (X is sex-linked, Y is sex-limited). Remember that meiosis leaves gametes with only one set of chromosomes, so you're guaranteed to inherit half your chromosomes from each of your parents.

(This is all an oversimplification, I'm sure.)

Junk DNA (3)

Lerc (71477) | more than 14 years ago | (#1488260)

Has any experimentation been done on creatures with differences in only their 'junk' DNA.

It just seems a bit iffy to say it's junk because it doesn't do something that we know other DNA does.

To reliably say it does nothing you would have to know how the whole system works, wouldn't you.

Re:23 Chromosomes (1)

Anonymous Coward | more than 14 years ago | (#1488262)

IIRC, we have 21 pairs of autosomal chromosomes and 2 pairs of sex chromosomes (X is sex-linked, Y is sex-limited). Remember that meiosis leaves gametes with only one set of chromosomes, so you're guaranteed to inherit half your chromosomes from each of your parents.

22 pairs of autosomes, 1 pair of sex chromosomes.
(XX is a pair, XY is a pair. Not two pairs per.)

Re:23 Chromosomes (0)

Anonymous Coward | more than 14 years ago | (#1488264)

Portion of its DNA which is "junk"

Well I guess the number of them doesn't matter since so much of it, just like tonsils (sp?) is unneeded waste anyhow.

Re:23 Chromosomes (1)

-brazil- (111867) | more than 14 years ago | (#1488266)

Not quite, the sex chromosomes form one pair. Females have 2 X chromosomes, while males have one X and one Y. So the sex of a child is determined by which one of the father's sex chromosomes is in the half-set of that particular sperm...

AFAIK, this is also the reason why males live shorter: the X chromosome is big and contains important information, so having 2 of them can be a life-saver, while the Y chromosome containy hardly any information beyond "this is a male".

Re:23 Chromosomes (1)

arielb (5604) | more than 14 years ago | (#1488268)

um tonsils guard against infections

You're not getting it (neither is CNN) (0)

Anonymous Coward | more than 14 years ago | (#1488269)

It is not the genes that cause the disease.
Its a mutation in on of these genes that cause the disease.
The way it is done is that you screen populations of diseased and nondiseased ppl. If a high percentage of diseased ppl have a cerain mutation in a certain gene you have association.
Next thing you mutate the gene in inbred mice. If the mutants die early of heart disease you have cause.
Its ok that CNN miss out on the facts but you should try to get a basic understanding on how things work before you post your thoughts on /.
Just basic Mendel(sp?)sonian studies have proved that homosexuality isn't caused by heritage.

Re:the correct term is (1)

Graham Clark (11925) | more than 14 years ago | (#1488270)


Introns are certainly one category of 'Junk', but there's much more. In general the term 'Low Information Density' would be preferre.

I don't quite get it, _who's_ DNA are they using (2)

joshv (13017) | more than 14 years ago | (#1488271)

I have never seen this answered to my satisfaction. Are they using a particular individual's DNA, multiple DNA samples from many individuals, or does it matter?

The Nature article said that individual human DNA differs from person to person by about 1 base pair in 1000.

If this is true, it seems like having one individual's sequence might be useful, but it is not going to tell you all that much about the variance from person to person. You'll get a general idea of what's going on, but it seems like you would have to sequence quite a few more individuals before you could really say how genetic changes effect a gene's expression.

-josh

Re:Amazing timing... (1)

Graham Clark (11925) | more than 14 years ago | (#1488272)

The timing is actually entirely coincidental. We've been working on this for several years, and I've been involved in problem-solving in the closing stages. There's no way we'd have been able to time the finishing to match, and there's no way we (or Nature) would have been willing to delay it to that purpose.

I'd agree that it's happy timing, though.


Well, as you ask: (1)

Graham Clark (11925) | more than 14 years ago | (#1488273)

The Sanger Centre's hoping to be able to announce the completion of Chromosome 20 sometime next year, and I understand that the GSC in St. Louis is hoping to do the same for Chromosome 7. Both have stats pages up, if you're interested. The Sanger's is at http://www.sanger.ac.uk/HGP/stats.shtml

Re:Support the HGP (1)

kermyt (99494) | more than 14 years ago | (#1488274)

The HGP is a joint venture funded by biotechnical outfits. These companies that map this information do so because for the first six months they have patent rights on processes they discover from (or in) this information. These companies only care about "the good of mankind" _after_ the patent window has expired.

-- The constitution may not be perfect, But it's better than what we got.

Re:what is that? (2)

legoboy (39651) | more than 14 years ago | (#1488275)

Your friend is right. Rather than the word 'diseases', I should have probably used 'afflictions'.

Myoneurogastrointestinal encephalomyopathy.. Shall we break it down, perhaps?

Myo - muscle
neuro - nerves
gastro - stomach
intestinal - speaks for itself
encephalo - brain
pathy - feeling/suffering. So far as I can tell, this means that due to something between the muscles and nerves in the gastrointestinal region, the brain is feeling a plot of pain. Fun, neh?

------

Re:Amazing timing... (1)

Gurlia (110988) | more than 14 years ago | (#1488276)

Hmm, if this DNA-patenting thing gets through, the next thing after the Open Source movement might be the Open DNA movement, where a certain RMS II will fight to regain lost rights of the public to access their DNA... and he will start to license DNA sequences under the DPL (DNA public license) to prohibit corporate entities from taking freely-accessible DNA and making it "proprietary".

(Disclaimer: if your sense of humor doesn't match mine, please don't take this as flamebait... somebody help me, I've been infected by the GPL virus and I can't stop Open Sourcing every topic that comes up on /.!!! :-O )

Boy... This takes me back to... (1)

jtseng (4054) | more than 14 years ago | (#1488277)

When I was just a wee undergrad taking cell physiology (I think it was my senior year at UMD)... Anyways I think the theory is that introns are indeed a necessary part of the DNA. Since they don't seem to code for anything in particular, mutations can occur in these areas and nothing will happen to the cell/multicellular organism. The greater number/size of introns may result in a lesser chance of damaging exons.


So the theory goes.

Re:Who's DNA is being used (1)

Graham Clark (11925) | more than 14 years ago | (#1488278)

There are various libraries of samples being used, some derived from one person and others from panels of several to many individuals, suitably anonymous and from a wide range of decents.

Actually, it probably won't make much odds as there's little differewnce between people at that level. The point is, though, to do a Human Genome Project rather than a White European Male Genome Project.

Re:causing and associated with (2)

orcrist (16312) | more than 14 years ago | (#1488289)

but I strongly doubt there would be gene that's ONLY function is disease... what sense would that make?

Why should it make sense? Assuming you don't suscribe to Creationism, there's no reason to assume a reason behind any particular genetic coding, any more than you should assume the function of gravity is to make your milk spill. Rather than 'function', which tends to sound like a design with a purpose, think 'effect' or 'result'. So, the effect of foo genes or gene-sequences is bar desease. A mutation has 4 possible results:

1. It helps a creature and/or its offspring thrive and reproduce.
2. It hinders a creature and/or its offspring from thriving or reproducing.
3. It has advantages/disadvantages which don't (yet) affect the reproduction chances.
4. It has no effect at all (or yet).

That's it. No point system other than:
1. You have children.
2. They inherit some of your genes and some of your partner's genes, and perhaps some of the genes mutate.
3. Repeat.

People tend to think that their's some grand design behind everything that is. I'll leave the resolution of this question to the Philosophers and Theologians, but I think we can agree that if there is one, it's not something we're capable of recognising...

Chris

Re:23 Chromosomes (1)

thomasd (3336) | more than 14 years ago | (#1488290)

Interesting you should mention it... but that's another case of a previously-thought-to-be-useless tissue turned out to play a part in the immune system.

'course, they only found this out after mine was gone.

Junk DNA? (2)

substrate (2628) | more than 14 years ago | (#1488291)

I know next to nothing about DNA but the term junk DNA seems... wrong. First of all contrast the articles in the 6 or so URLs listed. Only one referred to them as junk DNA, this sounds more like the reporters lack of understanding or bias than something the scientist said.

Second, consider a gene as an information exchange mechanism. Most forms of information exchange include some amount of material that isn't essential to the message but can't really be classified as junk either. It may be redundancy, it may be for error detection or correction or it may be for clarification.

Run an estimate of the actual needed text in the average paragraph written or spoken in English. The percentage that is 100% essential is pretty astonishinly small. It's a bit higher for a text but a bit lower for a novel. Mathematical proofs are pretty concentrated information but consider what happens if a little bit of information is transmitted wrong, say a sign is reversed. It's difficult to recover from it.

Likewise I think a 100% essential gene would be very difficult. Any random genetic damage would have impact. Gene replication would have to be absolutely exact and so on.

As I stated, I don't know anything about genes or DNA, but from an information theory standpoint calling 'unused' DNA junk seems wrong.

I would like to learn more about genes though, can anybody recommend a good progression of texts on the subject? Something to take somebody from absolute layman to at least having a general idea of the subject?

Re:TIGR and HUGEP (1)

Graham Clark (11925) | more than 14 years ago | (#1488292)

Several of the HGP institutions are involved in the SNP project, which uses a similar chromosome-specific-shotgun strategy to that used by Celera, with the data to be placed in the public domain. This is largely funded by pharmaceutical companies, with the aim of finding single-base differences between individuals that might be relevant to disease and its treatment.

I was actually at a seminar about it at lunchtime. It seems to be going nicely.

Re:Whos chromosome did they map? (0)

Anonymous Coward | more than 14 years ago | (#1488293)

FWIW, I have very pale blue/grey eyes.

On a very sunny day, there's hardly anything (short of wearing sunglasses) that I wouldn't do for darker eyes. Let's go brown all the way.

Re:Support the HGP (1)

jtseng (4054) | more than 14 years ago | (#1488294)

Someone correct me if I'm wrong... Are the results of the HGP going to be designated as common public property so everyone can profit from it? Just wondering.

Re:Junk DNA (2)

DanaL (66515) | more than 14 years ago | (#1488295)

One theory put forward by Richard Dawkins is that the 'junk' DNA is sort of like a parasite, it got attached to our DNA long, long ago and is just sort of hitching a ride along with the 'non-junk' DNA's reproductive cycle.

Dana

Re:Junk DNA (2)

Gurlia (110988) | more than 14 years ago | (#1488296)

If you can remove the sequences completely and still have a healthy animal develop, chances are it was indeed junk. This is not surprising, mutations can cause anything, including the inclusion of unused DNA.

Um... I wouldn't be so quick to believe that something is "junk" just because we human beings can find no reason for its existence, or just because according to one of our profound, sublime theories "junk" is to be expected and therefore anything unknown to us can be safely labelled "junk". Take the example of our appendix. Many believed (and perhaps many still believe) that the appendix was useless. Which is why they called it the appendix in the first place. However, this is wrong. The appendix does serve a function in our body. For many years before this was known, however, people even thought of removing their appendix just to avoid the possibility of getting appendicitis (shudder). I hope we don't do this with our DNA... you might be able to survive without your appendix's function, but screwing up your DNA could permanently damage your offspring. No kidding!

Re:causing and associated with (1)

thefallen (16891) | more than 14 years ago | (#1488297)

Let me be more clear. I agree with your points, but my "make sense" was more like "is propable enough to appear and stay": If there's gene that's there just to make me die, isn't it more propable it will disappear than otherwise? Sure, if it's sickness that comes after I've reproduced, it won't be all like that... but, because people DO live after having spent their age of being able to reproduce, it might imply that old persons would be usable to community. Thus, I don't see why there's still gene that kills us in our gene pool.

Gene history (1)

Steeltoe (98226) | more than 14 years ago | (#1488298)

This is not my idea and I have no specific details for supporting it. But from what I have heard speculated at different places, the "junk-regions" of the DNA could house a chemical history of previous generations for each individual. Don't take my word for it though, it's just a thought to the mind-provoking 'junk DNA'.

- Steeltoe

Re:the correct term is (1)

cave76 (25851) | more than 14 years ago | (#1488309)

The "junk" DNA also contains strucural (telomeres, etc) and regulatory elements (promoters, response elements, etc). The term of "junk" DNA has been around for a while in the scientific community, not just in journalism, left over from earlier days of this type of research. Mike

Re:23 Chromosomes (1)

K.V. I (115691) | more than 14 years ago | (#1488310)

Don't know about the leangth of life(though it is true for a few specific diseases-show me a woman with hemophilia) but as i recall, the two items recorded on the Y chromosome are the This is Male, and the ears do have hair in them.

Re:Open Source Human (1)

Lars Arvestad (5049) | more than 14 years ago | (#1488311)

Yeah, I don't really like the idea of open-sourcing the genome. There is always the risk of a fork of the code base, and before you know it, we are two different species! Wouldn't you hate not being able to mix genes with everyone? Eh, I mean, like, 50% of everyone.

Lars

--

Re:Introns ?= junk DNA (2)

jcorradi (120184) | more than 14 years ago | (#1488312)

Actually, introns != junk DNA . Introns are intervening sequences within genes that are spliced out before the RNA is translated into protein. Introns often contain regions important for regulation of gene expression and serve as a way to generate more diversity in gene products (by the production of alternatively spliced RNA transcripts). Junk DNA refers to regions of DNA between genes with function (if any) unknown. Just want to keep the discussions accurate.

Re:23 Chromosomes (0)

Anonymous Coward | more than 14 years ago | (#1488313)

What did they call those nifty charts we had to use to figure that out in High/Jr. High school?

Ex:

|X |y
--+--+--
X |XX|Xy
--+--+--
y |Xy|yy

Re:23 Chromosomes (0)

Anonymous Coward | more than 14 years ago | (#1488314)

What did they call those nifty charts we had to use to figure that out in High/Jr. High school? Ex: ....|X |y --+--+-- X.|XX|Xy --+--+-- y..|Xy|yy

Re:I don't quite get it, _who's_ DNA are they usin (0)

Anonymous Coward | more than 14 years ago | (#1488315)

They have collected samples from almost all ethnic groups in the world (not all know this though). Most of it was from volunteers and from donations to medical science. But more than one group of less technologicaly advanced people had blood samples taken and used with out thier consent of knowledge of what it was going to be used for.

Re:23 Chromosomes (0)

Anonymous Coward | more than 14 years ago | (#1488316)

What did they call those nifty charts we had to use to figure that out in High/Jr. High school?
(forgot to use plain text)

Ex:

....|X |y
--+--+--
X.|XX|Xy
--+--+--
y..|Xy|yy

Re:I don't quite get it, _who's_ DNA are they usin (2)

Lars Arvestad (5049) | more than 14 years ago | (#1488317)

They are doing the MDMI (multiple data many individuals) approach. What they get is basically an average genome. And certainly a good map of the genome.

The next step is to hunt for SNP:s, which stands for Single Nuceleotide Polymorphisms. And the race has already started. Both companies and universities are hunting for them. They are expected to be useful for things like identifying inheritedable deseases.

Lars

--

Re:causing and associated with (1)

jw3 (99683) | more than 14 years ago | (#1488320)

Sickle cell anaemia seems to be sustained by natural selection, because people with this disease are immune to malaria.

Although the malfunctioning genes were quickly eliminated during human evolution (now it changed, because people with even grave diseases can still live or even reproduce), there are some DNA sequences which are more prone to errors during replication than others, due to the DNA chemistry and nature of eukaryotic replication mechanisms. Of course, theoretically such "weak spots" could be eliminated by natural selection - but in most cases probably the enhancements in the repair mechanisms would cost more then a sporadic mutation. Don't forget that natural selection does not act on organisms, but on genes.

Regards,

January

Re:23 Chromosomes (0)

Anonymous Coward | more than 14 years ago | (#1488322)


What did they call those nifty charts we had to use to figure that out in High/Jr. High school?


They're called Punnett Squares

Re:42% junk? Life, the Universe, and Everything? (2)

Graham Clark (11925) | more than 14 years ago | (#1488339)

What exactly does "mapped" mean?

In general it means that the location has been established relative to known markers. In this case, though, the chromosome has been sequenced : the areas have had their composition established base-by-base.

Does that mean they know what all the bases are in the average human?

Roughly, yes. The sequence is a mosaic derived from several people.

Does this imply any knowledge of the pattern of such variations?

Not in itself, no, although other work is continuing to establish this.

Does it imply any knowledge of the function of the encoded proteins?

Again, not in itself. Many of the identified genes have been studied already. Others have similarities to genes already known, either from humans or other creatures. Some have been inferred from features of the sequence itself and are of totally unknown function.

A biology class I took said that human DNA was 96% junk (not protein encoding).

Was this biology class wrong?

No. The vast majority doesn't code for protein, and most of this has no known function. Closely related species have widely differing amounts of this, so (together with other reasons) the current hypothesis is that it doesn't do much that's useful for the organism. Some of it is composed of "selfish" elements such as transposons : it might be the case that in a looser sense a lot of it is.

I Decoded the Junk DNA...OH NO (4)

MagusOceanus (61084) | more than 14 years ago | (#1488340)

I extracted the Junk DNA and respliced it so that it would stand without the DNA that is neccessary to humans, inserted it in a cell and watched it grow. 5 hours later to my horror it took a flat retangular shape, black lines appeared on a white surface. They connected to form letters in clear English which read...

"Mr _________ , You have been selected as a final entry for the Publisher's Clearinghouse largest drawing, enclosed is a Check worth $30,000,000 if you have the winning number!!! Please open and send your entry form within the next 24 hours, and get a GUARANTEED prize."

I tried the Junk DNA of other chromosomes and got ads for term life insurance, timeshares, and then the Junk DNA materialized in front of me into a pushy Amway distributer!!!! The horror!!! Cellular SPAM!!! AGHHHHHHHH

It depends how you define 'junk' (0)

Anonymous Coward | more than 14 years ago | (#1488341)

It hasn't just been mapped, it has been fully sequenced (with a few small gaps). According to the original article, only about 3% of the sequenced DNA is actually 'exonic' (i.e. stuff that ends up as 'spliced mNA', the final step before 'translation' into protein). The 42% figure presumably comes from "the 41.9% of the sequence that represents tandem and interspersed repeat sequences" (not exactly 42, so no need to consult the Hitch Hiker's guide!). But there are various other kinds of noncoding DNA too, including some sequences that are known to be required for expression and regulation of the genes (promoters, enhancers, etc.), untranslated sections of exons, introns (sequences which are 'transcribed' from the DNA into RNA, but are spliced out before the RNA is translated into protein), and intergenic regions. Apart from the protein coding sequences and regulatory elements, most of the rest (including the introns) is of uknown function, and usually classified as 'junk'. It's interesting that some organisms (including Fugu, the 'Puffer Fish'), have 'compressed' genomes containing a much lower proportion of 'junk' (presumably because God remembered to strip the comments from his source code :-)

For information on diversity in human genomic sequences see:

http://www.stanford.edu/group/morrinst/hgdp/faq. html

One sentence from the original article that is worth quoting to Slashdot readers -

"Making the sequence of human chromosome 22 freely available to the community early in the data collection phase has benefited studies of disease-related and other genes associated with this human chromosome"

which sounds a lot like 'Release early, release often' to me. At least this part of the genome is now Open Source.

I wonder... (1)

veldrane (70385) | more than 14 years ago | (#1488342)

How many people had the word, "Gattaca" pop in their minds when they saw the mention of finding the human gene that could lead to heart problems?

-Vel

Re:I don't quite get it, _who's_ DNA are they usin (0)

Anonymous Coward | more than 14 years ago | (#1488343)

You don't have to do the complete sequence of many people in order to find out how the DNA varies from person to person. Once you know the rough sequence of a length of DNA, you can read the exact sequence of that length from any sample of DNA. Think of DNA as content-addressable memory: you can't access it randomly, or even sequentially, but if you know the sequence of a couple of small lengths, each a dozen or so bases long, and seperated by a few hundred bases, it's easy to read the few hundred bases between them. To find out what a length of DNA from any person looks like, find the same piece of the Canonical DNA sequence you just downloaded from the HGP, use it to design the two short primers (and make sure that they're unique over the whole genome), yank out the bit of interest from DNA sample and sequence. There are projects going on currently to do just this sort of thing on large scale. They are only possible because we already have a large fraction of the Canonical sequence.

Side Note.... (1)

jyak (112533) | more than 14 years ago | (#1488344)

I read an very interesting book in college last year called the Biotech Century [amazon.com] about gene technology. I don't know much on the subject but this brought alot to my attention.

I highly recommend this book if interested in knowing of what has been developed and patented and topics like the such in genetics: engineering and technology.

Re:causing and associated with (1)

Communomancer (8024) | more than 14 years ago | (#1488346)

"Is it just me or is there not a big difference between causation and association? Seems to me along the line of correlation vs. causation."

I'd go ahead and say that association vs. causation is exactly the same thing as correlation vs. causation. However, while a causitive relationship implies a correlative relationship, the reverse is not true. Two phenomena can have a high correlation between them, but not have a one be directly causing the other. They might both, for instance, be caused by an unknown third variable.

Anyway, this has been hashed and rehashed forever...statisticians and behavioral scientists have had this indoctrinated in them forever. Sometimes the media screws it up, however, when they go and "report" the results.

Re:Open Source Human (3)

jquiroga (94119) | more than 14 years ago | (#1488347)

Of course, that would be awful, but what about the installation process? Everyone would want to improve it.

Currently, parents are forced to accept all the default values, and many are clamoring to get at least an installation menu, to be able to choose hair color, IQ and IP address :-)

Re:Junk DNA (1)

Spunk (83964) | more than 14 years ago | (#1488348)

The appendix does serve a function in our body.

Seriously? I thought that was still a mystery.
Would you be so kind as to enlighten those of us who are biologically not in-the-know?

Re:Junk DNA (2)

mwillis (21215) | more than 14 years ago | (#1488350)

I don't know about this statement:

If it were truly junk, any mutation that discarded it should be advantageous since it would take less resources to replicate the mutated version than the "junky" version.

You are assuming that of course mutation is an efficient process, like a hedge trimmer going in and snipping and improving just what needs to be done.

What color is the inside of my linen closet painted? It doesn't matter, and it won't make a difference to the resale value of my house.

We're evolved machinery. Now that we can see the source code, we know that it's not very well written, and has lots of sections that ramble or go nowhere. It's natural to resist facts that challenge our species' well developed sense of being the pinnacle of design. Look at how people dumped on Darwin during and after his lifetime!

Instead, we should be impressed that we work so well, despite how we're written.




More info on chromosome 22 (3)

lovebyte (81275) | more than 14 years ago | (#1488359)

The Sanger centre [sanger.ac.uk] has more info on chromosome 22 [sanger.ac.uk] .

Congratulations to all who participated in its sequencing. We look forward to the first draft of the human genome by spring 2000.

Here's an scientific link. (1)

Gab (9164) | more than 14 years ago | (#1488360)

Chromosome 22 [sanger.ac.uk]

Gab

Re:23 Chromosomes (1)

DAVEO (61670) | more than 14 years ago | (#1488361)

how about the apendix?

Re:23 Chromosomes (0)

Anonymous Coward | more than 14 years ago | (#1488363)

..and get infected easily as well.

how bout them appendix's too?

Amazing timing... (1)

fantomas (94850) | more than 14 years ago | (#1488365)

Amazing that this should happen while the WTO meets in Seattle and discusses extending patent laws to cover ownership of genetic material.

( ...Global agreements being discussed by WTO trade ministers in Seattle this week include the Trade Related Aspects of Intellectual Property (TRIPS) that allows private ownership of commercially valuable knowledge such as software, agricultural innovations, and pharmaceuticals. WTO members are currently reviewing clauses of the TRIPS agreement related to the patenting of plants, animals, genetically engineered organisms and other forms of life. ...)

Misc. DNA topics (1)

Elvii (428) | more than 14 years ago | (#1488366)

I forget what it's called, but what if those fragments of DNA are "leftovers"? Wonder if some of that 42 percent junk dna is something like that, and has no proteins as it doesn't do anything *anymore*?

Disclaimer: IANAGR (I Am Not A Genetic Researcher)

Also, I must admit I don't trust mankind in general... I hope this knowledge of ourselves doesn't get misused/abused. I know any advance is a double-edged sword, I just hope this sword is handled with wisdom to do the right thing with it.

David


bash: ispell: command not found

What does that mean? (5)

jw3 (99683) | more than 14 years ago | (#1488369)

In a recent /. discussion [slashdot.org] we argued about the Human Genome Project v. TIGR [tigr.org] . As you see, the HUGEP is doing quite well. The raw data from the sequencing project should be available next year.

Will this finish a task? No, it is just a beginning - having the sequence, the real work starts: searching ORFs (Open Reading Frames - sequences which could possibly be genes), running database searches, and slowly passing to the most exciting fields of modern molecular biology - from genomics to transcriptomics and proteomics. Transcriptomics is looking for genes, which actually got expressed, and proteomics - similarly, looking for expressed proteins. Making transcription / translation (translation is the process in which proteins get synthetized) profiles can lead us to 1) function of proteins (e.g. protein X. is expressed under this and this conditions, so it must take part in this and this metabolic response) 2) regulation - DNA is a single strand, but various enzymes are present in various copy numbers under various conditions.

Those are enormous projects. A lot of work has to be done before the raw sequence will actually be of any use; nethertheless, it is a milestone of molecular biology and will be a fine achievement for the end of our century.

Another project will be to determine the variability of human genome: screening for different gene allels, mutations etc. This will be one of the most important goals in human genomics in the next few years.

Whats on the catch... erm, chromosome 22? 22 is 33,400,000 bases long (Mycoplasma pneumoniae, one of the smallest bacteriums, has about 816,394 bases). It contains several already known genes responsible for various genetic disorders, and possibly a gene responsible for certain types of schizophrenia.

By the way, a much better source of information is the Nature science update [nature.com] page - the original scientific publication has been published today in Nature [nature.com] .

Regards,

January

How well are other chromosomes progressing? (1)

thefallen (16891) | more than 14 years ago | (#1488371)

I wouldn't start systematical study from 1. chromosome so I presume it was the one they knew most of, how's study for others doing?

Re:Junk DNA (1)

Todd Stewart (63317) | more than 14 years ago | (#1488373)

I don't think the researchers are calling it useless. I think this phrase was just sloppy journalism or sloppy phrasing by the scientist interviewed.

A better technical term would of been "extra stuff" not junk.

Re:23 Chromosomes (0)

Anonymous Coward | more than 14 years ago | (#1488378)

Actually the major reason men have shorter lives is..... testosterone(sp?) Among it's wonderful qualities are the fact that it is a minor immune suppresant and has a lot of the side effects that other steriods have. It boils down to the fact that estrogen is just better for you

but I am not a doctor, just a hobby biologist

Re:causing and associated with (1)

thefallen (16891) | more than 14 years ago | (#1488379)

Mmm resistant to malaria... well there's the good side I was looking for. Also, does this mean that most of mankind was prone to malaria back then? We don't see lots of malaria here north... Heh yeah, I've understood it's common misunderstanding of evolution, also, that people think it makes what's "good": it does what's propable, which leads into kludges like this.

Pauly Shore's (2)

cje (33931) | more than 14 years ago | (#1488380)

Are they using a particular individual's DNA .. ?

After we finish mapping some DNA we can go munch on some grindage, buuuuuuuuudy! :-)

Re:The HGP is like the Periodic Table (0)

Anonymous Coward | more than 14 years ago | (#1488381)

It's a secret. But just between you and me, it's Elvis Presley.

Re:Who's DNA is being used (0)

Anonymous Coward | more than 14 years ago | (#1488382)

If these samples are from many individuals, will the sequence from one gene make sense in the context of differing adjacent genes from other individuals even if they are all decent people?

Actually... (2)

Millennium (2451) | more than 14 years ago | (#1488383)

I heard somewhere that the sequence "GATTACA" actually appears at least once in every single human gene (this being why they chose it for the movie title). Furthermore, it's the only sequence that does that.

I'm no genetic researcher, and neither is the person who told me this, but I suppose it's possible.

"Junk" DNA? (2)

Millennium (2451) | more than 14 years ago | (#1488384)

I'd be careful calling it that. Someone proposed the idea that it's mutation fodder (that is, a safe place for mutations to occur). That's a possibility.

But there've also been posts talking about a lot of redundancy and such. It's possible that all this "junk" DNA still has uses that we haven't seen yet. I guess we won't know until we've mapped out the whole thing.

Who knows... maybe someday we'll all have something like a mini-RAID coded into our DNA.

Great, but on the other hand... (1)

meckardt (113120) | more than 14 years ago | (#1488386)

Undoubtedly, the mapping of the human genome will revolutionize medicine during the 21st century. But it opens at least one can of worms... Will individuals have rights to their genetic map? Like any information, if this gets out, could this information be used against a person.

Say, if you carry the gene predisposing you to some form of cancer, could an insurance co. deny you coverage for that condition? Could an employer not hire (or fire you) because you have a genetic tendency toward alcoholism? Could police or the FBI tag you as being a potential criminal because of some combination of traits in your genes?

Stuff like this worries me sometimes.

Mike Eckardt [geocities.com] meckardt@yahoo.spam.com

Re:causing and associated with (0)

Anonymous Coward | more than 14 years ago | (#1488389)

The thing about cycle cell anemia is that it has advantages for people with one normal and one cycle cell gene. Oh and it is less common in people who's ancestors come from locations without malaria. And based on mitochondrial DNA the human race has been traced to one female proto-human. All evidance puts this individual in Africa (most evidance) or in Asia (less evidance)

Re:Support the HGP (1)

proj_2501 (78149) | more than 14 years ago | (#1488391)

Whoever patents the X chromosome will make bank. No reproduction without a license.
--
"I was a fool to think I could dream as a normal man."

Re:More info on chromosome 22 (0)

Anonymous Coward | more than 14 years ago | (#1488398)

The Sanger Centre's website is at www.sanger.ac.uk [sanger.ac.uk] .

Microsoft Bloat == Genetic Propensity (0)

TheHornedOne (50252) | more than 14 years ago | (#1488399)

Now it all becomes clear..

42% of our this chromosome is "bloatware". Poor Microsoft engineers can't be helped.. they've been battling this urge to include stuff in their code that does nothing and just takes up space. Kinda like salmon feeling the urge to return home to spawn.

Well, this should take care of some of the lawsuits against them.. "This bloatware, it's not our fault! Quit picking on us! We're products of our GENETIC HERITAGE and we can't be blamed for it! Help, help, we're being oppressed!"

Open Source Human (3)

jquiroga (94119) | more than 14 years ago | (#1488400)

Soon we will be Open Source. I fear that the temptation to develop and try patches will be irresistible to many.

Re:How well are other chromosomes progressing? (1)

thefallen (16891) | more than 14 years ago | (#1488401)

Oops, doubletypo, "would start from 1." or "wouldn't start from 22.", pick which one you like.

causing and associated with (3)

xnixnix (31045) | more than 14 years ago | (#1488402)

From the CNN article:
More than 30 human disorders are already associated with changes to
genes of chromosome 22. These include a form of leukemia, disorders
of fetal development and the nervous system, and schizophrenia.

From the introduction:
some of 22's genes can cause "heart defects, immune system disorders, cancers, schizophrenia
and mental retardation."

Is it just me or is there not a big difference between causation and association? Seems to me along the line of correlation vs. causation. Anyway, I believe that scientists have still
a long way to go before they find the genes that cause certain disorders. And then they will still have to prove that these genes are in no way responsible for any other functions in the human body to safely alter them. Seeing all the good possible uses for medicine it still gives me the creeps how through the use of genetics and monocausal argumentation a new "scientifically backed" racism could emerge again. Now don't scream technophobe but how would you all react once the genes allegedly causing things like alcoholism, homosexuality, autism, criminalism, lazyness or whatever unwanted psychic or physical trait you can think off where identified? Have we got our ethics ready to handle this or will it be "what can be done will be done"? On whom will we test genetic engineering for a better race? The inhabitants of prisons, mental institutions, military institutions or just unwanted embryos? Will we allow babys to live with these disorders? Will we allow people to work without mandatory testing of genetic normality?
History has shown that scientists have often produced technology that was later misused by the
willing. Hopefully this time they think more before they hand this Pandoras box to the masses.

I want to see this on the news. (1)

legoboy (39651) | more than 14 years ago | (#1488403)

And do you know why I want to see this on the news?

It is because I would really like to see reporters try to get their mouths around diseases such as Myoneurogastrointestinal encephalomyopathy and Lysosomal alpha -N-acetylgalactosaminidase deficiency.

They aren't that hard, but still... I want to see it.

------

Hmm. (1)

psichan (94135) | more than 14 years ago | (#1488404)

Now we can use this new information for the good of humanity!

Just think. Now you can hack your friends genetic information and make them cancerous! (nmnot really) But seriously, this could help prevent alot of problems later in life and stuff.

Faulty headline (0)

Anonymous Coward | more than 14 years ago | (#1488405)

Saying that a chromosome is "mapped" means that you know the location of some identifiers on the chromosome. Thats a far thing from sequencing something. Also not putting up the link to sanger proves someone has not been checking their facts. Bad journalism!

Re:Junk DNA (1)

cyoon (99971) | more than 14 years ago | (#1488406)

DNA commonly has a lot of information in it which has no apparent purpose. Lots of repeated information, sometimes long chains of the same segment over and over and over again. The theories behind its existence is speculative and no one really knows for sure. Some say that it's for redundancy checking, increasing mobility, or increasing survivability. I'm actually surprised that the amount of "junk" DNA is that low ... I thought it would be higher than that.

Introns ?= junk DNA (2)

LL (20038) | more than 14 years ago | (#1488407)

It is still an open question what role the junk DNA, technically called introns [uq.edu.au] plays in organism development. Unlike the simple unicelluar critters (prokaryotes) such as bateria, all higher level organisms (eukaryotes) have these long non-coding sequences [sciam.com] which have been retained across evolutionary generations despite the extra energy/space required. The whole area is akin to the physists search for all the various subatomic particles after the cracking of the atom. We can see the bits and pieces, we can assemble the various sequences, but there's no unifying standard model of how or why. With Nobel prizes and new killer apps in the air, it is not surprising that universities and institutes are throwing money into the research.

The 19th centure might have been the dominance of physics and engineering but there's a lot of speculation and anticipation (especially by the empty hands of the biologists and zoologists) that the next century will be their turn at the gravy train :-). Fun times ahead.

LL

42% junk? Life, the Universe, and Everything? (1)

orz (88387) | more than 14 years ago | (#1488426)

What exactly does "mapped" mean? Does that mean they know what all the bases are in the average human? My understanding was than many bases varied a lot between individuals and ethnicities and what-not. Does this imply any knowledge of the pattern of such variations? Does it imply any knowledge of the function of the encoded proteins?

A biology class I took said that human DNA was 96% junk (not protein encoding).

Was this biology class wrong?

Is there an enormous devation in percentage of junk from chromosone to chromosone?

Or did a Douglas Adams fan do some subtle hack on the results?

Re:causing and associated with (1)

thefallen (16891) | more than 14 years ago | (#1488427)

I'm not genetic engineer or such, but I strongly doubt there would be gene that's ONLY function is disease... what sense would that make? Besides, isn't gene just mark to enable code that's sleeping somewhere? Or is it the code? I dunno. But still doesn't make sense to have all bad gene, one that does effect which is bad sometimes but good sometimes or something that's bad _now_, but not that.

Re:Junk DNA (1)

Anonymous Coward | more than 14 years ago | (#1488428)

There's no such thing as "junk" DNA. If it were truly junk, any mutation that discarded it should be advantageous since it would take less resources to replicate the mutated version than the "junky" version. DNA isn't just about coding proteins! See http://anime.jyu.fi/~saren/Docs/JunkDNA.html for more information on why "junk" DNA isn't junk.

Re:Junk DNA (1)

Helge Hafting (14882) | more than 14 years ago | (#1488429)

Has any experimentation been done on creatures with differences in only their 'junk' DNA.
There have been quite a few experiments on mice.

It just seems a bit iffy to say it's junk because it doesn't do something that we know other DNA does.
If you can remove the sequences completely and still have a healthy animal develop, chances are it was indeed junk. This is not surprising, mutations can cause anything, including the inclusion of unused DNA.

Re:How well are other chromosomes progressing? (1)

Anonymous Coward | more than 14 years ago | (#1488430)

We started with 22 because it's the smallest autosome. We'll finish the others in another 16 months or so.

Re:23 Chromosomes (0)

Anonymous Coward | more than 14 years ago | (#1488431)

AFAIK, this is also the reason why males live shorter: the X chromosome is big and contains
important information, so having 2 of them can be a life-saver, while the Y chromosome containy
hardly any information beyond "this is a male".


This has absolutely *nothing* to do with why males live shorter lives. It's thought that males' shorter lifespans are not genetic, and are due to lifestyle choices / greater stress induced by their more demanding role in our male-dominated society.

It'll be interesting to see if male and female lifespans are equal in another 200 years or so, after sexual equality has been fully established.

Support the HGP (3)

cyoon (99971) | more than 14 years ago | (#1488432)

/.ers should be trying to support the HGP as much as they can. Yeah, we joke about how it's all Open Source and all, but there's a very real possibility that chromosomes can be patented. Many organisms have already been patented (famous example: microbe that eats oil spills). Many human derivative cells have been patented and are under license right now. Companies are right now in a race against the HGP to map chromosomes and then patent them! I wish I had URL's available, but if you go to Google [google.com] and type in "human genome project patent" [google.com] you'll find a lot of sources where patenting DNA sequences is discussed.

Bottom line: human chromosomes may be patented. Fight it.

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