Talk:Haplotype

To-do
This article is way too complicated to be understood by the general population

This is likely to be because the article as it stands is extremely poorly written and inaccurate. As a genetics statistician there are glaring inaccuracies. When I first came across it the base definition of a haplotype was that it may refer to one locus or a whole genome. This is just plainly wrong, and consulting any decent text book on genetics will demonstrate this (e.g. Bruce Weir's "Genetic Data Analysis II"; Pak Sham's "Statistics in Human Genetics"; Daniel Hartl's "Primer of Population Genetics"). I shall start working on re-writing this in a clear and succinct manner. Slack---line 14:31, 2 August 2007 (UTC)

Also I've noticed that in this and the article on linkage disequilibrium there are links to the proprietry software GoldenHelix. This may represent a conflict of interest. Besides there are plenty of free open-source software packages around that can calculate LD and haplotypes. Slack---line 14:31, 2 August 2007 (UTC)

I suggest the following ToDo list:


 * Clear definition of what a hapltoype is (Done).


 * Clear diagrams of how genotypes on chromosomes are related to haplotypes. (why is there a diagram of a metaphase chromosome in this article? Completely irrelevant and misleading Plijnzaad (talk) 16:22, 12 November 2015 (UTC) )
 * Clear example of how ambiguous phase leads to problems in determining an individuals haplotype from their genotype.


 * Discussion of [EM_algorithm] in estimating haplotype frequencies.


 * Discussion of Bayesian methods for estimating haplotype frequencies.


 * Brief discussion of the HapMap Project.


 * Haplotype associations in human genetics and disease mapping.


 * Detailed list of references on statistical aspects of resolving haplotypes.


 * Links to software used for estimating haplotypes (both EM and Bayesian).


 * Too much focus on the Y-chromosome. This is really a very small portion of the genome, and resolving haplotypes on the Y-chromosome is really quite easy, since males are homogametic and only carry one copy.

Slack---line 14:39, 2 August 2007 (UTC)

Microsatellites
Don't they use microsatellites more than SNPs nowadays to determine a patient's haplotype ? XApple 23:16, 17 October 2007 (UTC)

Extended haplotypes
The literature now refers frequently to extended haplotypes and yet I cannot find a cogent definition for when something is a haplotype and something else is an extended haplotype. Can anyone add this material and references supporting it to this page? RMJ 04:38, 18 October 2009 —Preceding unsigned comment added by Rmj03 (talk • contribs)

This article is pointless
It is unintelligible to a lay reader (and I suspect a non-lay reader)

There seems no point in having an article which doesn't help anyone. I would delete it if I knew how —Preceding unsigned comment added by 81.109.64.183 (talk) 00:24, 16 December 2010 (UTC)

definition of haplotype
The definition of haplotype is not an easy issue, as it depends on the context. There are various valid definitions, somewhat overlapping, but rarely comprehensive. Here is another definition:

'''Haplotypes can be defined as evolutionary conserved segments of DNA inherited together. It is at these regions that tag SNPs and LD effects are observed; such that genotyping one SNP in a locus can determine the effects of many others. ''' I found this definition in: Patnala R, Clements J, Batra J (2013) Candidate gene association studies: a comprehensive guide to useful in silico tools. BMC Genetics 14:39 http://www.biomedcentral.com/pubmed/23656885 — Preceding unsigned comment added by 137.224.252.10 (talk) 07:39, 17 May 2013 (UTC)

My suggestion
An intro diagram! A haplotype can be considered just part of a chromosome that is inherited together, right? So the intro is just a diagram of a stretch of DNA with a region highlighted in the center that represents a specific haplotype. You can show that there are SNPs both within and outside the region, etc. Alanraetz (talk) 19:55, 4 August 2013 (UTC) seconded Plijnzaad (talk) 16:20, 12 November 2015 (UTC)

Humans
I suggest drawing a line somewhere between the general "haplotype" and "human haplotype" to increase understanding that every being with DNA has haplotypes, not just people. Kortoso (talk) 21:12, 15 January 2016 (UTC)

External links modified
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 * Added archive https://web.archive.org/web/20071004231414/http://www.goldenhelix.com/SNP_Variation/HelixTree/haplotype_trend_regression.html to http://www.goldenhelix.com/SNP_Variation/HelixTree/haplotype_trend_regression.html
 * Added archive https://web.archive.org/web/20080827220132/http://pngu.mgh.harvard.edu/purcell/whap/ to http://pngu.mgh.harvard.edu/purcell/whap/

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External links modified
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I have just modified 4 external links on Haplotype. Please take a moment to review my edit. If you have any questions, or need the bot to ignore the links, or the page altogether, please visit this simple FaQ for additional information. I made the following changes:
 * Added archive https://web.archive.org/web/20080509091745/http://www.familytreedna.com/facts_genes.aspx to http://www.familytreedna.com/facts_genes.aspx
 * Added archive https://archive.is/20020918095630/http://cgi.uc.edu/cgi-bin/kzhang/haploBlockFinder.cgi/ to http://cgi.uc.edu/cgi-bin/kzhang/haploBlockFinder.cgi/
 * Added archive https://web.archive.org/web/20080517115912/http://www.stat.washington.edu/stephens/software.html to http://www.stat.washington.edu/stephens/software.html
 * Added archive https://web.archive.org/web/20080827220132/http://pngu.mgh.harvard.edu/purcell/whap/ to http://pngu.mgh.harvard.edu/purcell/whap/

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The introduction of this article doesn't make sense
All of the four supposed definitions decribe the very same thing. To some extent there could be a reduced meaning in which only single-nucleotide variants are considered, to the exclusion of structural variants, are considered, but it's more about simplifying the data than changing the meaning. --IP, 01:15, 19 December 2017 (UTC)
 * I agree. I also tried to read this a few years ago. But I gave up, wasn't able to understand. --Ettrig (talk) 08:39, 18 October 2020 (UTC)

What is an STR?
Subsection https://en.wikipedia.org/wiki/Haplotype#UEP_results_(SNP_results) contains the first occurrence of the acronym STR. Please improve readability by saying what this acronym stands for. If I knew, I'd fix it myself. — Preceding unsigned comment added by Page Notes (talk • contribs) 21:20, 31 October 2019 (UTC)
 * Perhaps added after your question, further in section is short tandem repeat. Shenme (talk) 00:46, 10 January 2022 (UTC)

Proposed merge of Gametic phase into Haplotype
Very short, cannot be expanded in a reasonable amount of time. Better put it as a subtopic of something larger. Artoria2e5 🌉 03:03, 19 January 2024 (UTC)
 * ✅ Klbrain (talk) 11:41, 19 February 2024 (UTC)