haplotype interval effects
English translation: Complex explanation
| 08:06 Aug 27, 2006 |
| English language (monolingual) [PRO] Science - Genetics | |||||||
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|  Selected response from: Michael Barnett Local time: 05:08 | ||||||
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| 3 | Complex explanation |
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| 1 | further questions, not an answer |
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Answers
7 hrs confidence: 
Complex explanation Explanation: http://en.wikipedia.org/wiki/Haplotype I am not a geneticist, but my understanding from the literature is that there are two definitions of "haplotype". The definition that applies in the context of the "haplotype interval" is: a haplotype is a collection of "single nucleotide polymorphisms". That is, it a a part of a DNA sequence that contains coding that differs from the correspponding chromatid. The concept is explained well in the wikipedia citation above, except that I believe there is an error in the explanation - the part "Relation to Genotypes" uses the word "chromosome" where it should really say "chromatid". In any case, as I understand it, a haplotype interval, is the section of the chromatid that contains the haplotype. -------------------------------------------------- Note added at 7 hrs (2006-08-27 15:24:17 GMT) -------------------------------------------------- That's corresponding -------------------------------------------------- Note added at 7 hrs (2006-08-27 15:26:22 GMT) -------------------------------------------------- The explanation should say: That is, it a a part of a DNA sequence that contains coding that differs from the corresponding PART of the complementary chromatid. -------------------------------------------------- Note added at 7 hrs (2006-08-27 15:34:18 GMT) -------------------------------------------------- The measurement of the haplotype interval would involve counting the number of sequential nucleotides that define the haplotype. -------------------------------------------------- Note added at 14 hrs (2006-08-27 22:44:54 GMT) -------------------------------------------------- The following is in replay to the "further questions..." posed by the asker: The "effects of each interval on a trait" refers to the effect on the individual's specific characterisitc (the trait) contributed by the DNA sequence in that interval. (The DNA sequence is segmented into a collection of "intervals"). http://www.nature.com/ng/journal/v8/n4/abs/ng1294-365.html "The estimated effects of each haplotype..." : OK. The DNA strand is broken up into a series of segments (intervals). Although, each interval contains only one haplotype, a different haplotype may exist in the corresponding interval of the complimentary chromatid. -------------------------------------------------- Note added at 14 hrs (2006-08-27 22:49:41 GMT) -------------------------------------------------- Are "haplotype interval effects" and "haplotype effects within an interval" the same? Yes. Please note, I am not a geneticist. You might consult Proz.com user, Ms. Linda Battistuzzi, who translates in this field. |
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9 hrs confidence:
further questions, not an answer Explanation: I am the real Polish asker. Additional excerpts from the paper: "the effects of each interval on a trait" "the estimated effects of each haplotype for every interval in the genome" (more haplotypes in one interval?) "haplotype intervals with the larger estimated effects" Are "haplotype interval effects" and "haplotype effects within an interval" the same? -------------------------------------------------- Note added at 2 days32 mins (2006-08-29 08:38:40 GMT) -------------------------------------------------- Thanks a lot. Highly useful answers. |
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559 days confidence:
. Explanation: Hi, I am a geneticist working on pretty much the same thing (except in humans) and I don't think I've ever heard of a haplotype interval, though that doesn't necessarily mean there's no such thing. A haplotype is simply the combination of alleles (versions of a genetic variant) at a number of positions along a chromosome. The length of a haplotype is not biologically defined, but rather is defined by the number of genetic variants one has studied, although there is a pattern of stable haplotypes in the human population and these have fairly consistent lengths, and I guess a similar pattern could be expected in animal populations. Therefore, I think the authors of this paper have simply genotyped a large number of variants across the Cow genome, constructed stable haplotypes using the results, and described the size of those haplotypes using the term 'interval' instead of length. I think these intervals might also be what we call haplotype blocks in human genetics. That's my guess. Regarding 'haplotype effects', we can simply think of a haplotype as being a particular version of a piece of chromosome (i.e. in a given interval, a cow has two different versions of the chromosome, one from each of it's parents, and another cow might have two different versions). An interesting question might be, "Does one haplotype affect a trait like milk production?" If so, this would be a haplotype effect. I think the answer to your question, 'Are "haplotype interval effects" and "haplotype effects within an interval" the same?' is YES. Good luck, Gavin |
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