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Tuesday, February 14, 2012

Traits vs. Genes

If you get half your genes from your mum and the other half from your dad why don't you have half your mums feature's and half of your dad's?

There is something wonderful about this simple question, and all of genetics could be used to answer it. Three points seem to be worth making.

1) Dominance. If a specific trait is conferred by a dominant allele and both parents are heterozygous, then their child can lack a trait that they share.

2) Features are not genes. Some traits (features) are affected by many genes, and many genes affect multiple traits.

3) Many traits are complex. Geneticists distinguish between simple (Mendelian) traits and complex traits. Traits can show the following sorts of genetic complexity:
epistasis (where the effect of one gene depends on other genes)
incomplete penetrance (where a specific genotype doesn't always have the usual effect)
polygenic inheritance (where multiple genes affect the trait)
genetic heterogeneity (where different genes cause the same trait in different families or populations)
phenocopy (when traits that often have a genetic basis arise without a genetic basis)

Explaining all of this in detail would require a complete course in genetics!

Hybrid Sunfish

I did a post to my blog (here) about hybrid sunfish and wanted to ask the genetic experts for some clarification. As I understand it most sunfish can hybridize. The offspring are fertile but mostly male. What I don’t understand it why I seldom see hybrid sunfish in the wild. Is the success rate lower in producing hybrid offspring? Do fish tend to avoid mating with hybrids? Maybe this isn’t a question dealing with genetics as much as fish behavior. Perhaps you have some insights or could point me in the right direction.

I’m also curious what happens when hybrids do mate. Will some of the offspring revert back to “purer” sunfish? If two Bluegill/Sunfish hybrids mate what would the expected offspring be?

There is a lot known about hybrids in general, but I don't know anything about sunfish in particular. Comments from anyone who does are welcome (but you can't be anonymous).

Sunday, February 5, 2012

Software for large groups of IBD matches.

I received the following question, which I think is excellent.

Is there any software for plotting possible/probable relationships to MRCA [most recent common ancestor] for groups of 10-1,000 cousin matches suggested by various services, e.g. 23andMe, GEDmatch, FTDNA?

It seems to me that standard genealogical services are too rigid. Once you lay down a line of possible 3rd cousins and another for 4th cousins etc, linking them to various MRCAs who are perhaps 5 or 6 away becomes a bit of a nightmare.

The cousin matches referred to are typically based on shared segments longer than some threshold (typically 5 cM.) that appear to be identical by descent (IBD). In my case, 23andMe identifies 835 relatives but I know how I am related to only two (my mother and my sister).

I will contact scientists I know who work in this field to see if there is any software that is available to, and usable by, the general (informed, curious and sophisticated) public.

If you know of software that might be useful and want to see some of this data, I can send examples from 23andMe. It lists all IBD regions longer than the threshold that are shared with the user. Someone using this tool for genealogy will typically have such data for a small number of family members, and the information about most "cousins" is typically minimal. The person who posed this question can probably files to anyone who wants to see what they look like.

Saturday, February 12, 2011

Half-siblings vs. Full-siblings visualized

23andMe co-founder Linda Avey commented on a previous post ("Identifying half-siblings by genetic tests"), pointing out that 23andMe provides images that illustrate full-siblings and half-siblings. In fact, they will represent any relationship pictorially. If you have an account there, you can compare your genome to another, with regions of half-identity and full-identity marked differently.

half-sibling vs. full sibling graphic
This pair of images shows regions of half-identity (light blue), complete identity (black)and no identity (white). The comparison on the left shows two women who share a father but have different mothers. Since they both have their father's complete X chromosome, they are half-identical across this entire chromosome. The rest of the genome is an even mix of regions that are half identical and regions that show no identity. On the right, you see a 1:2:1 ratio of no identity, half-identity and full identity. The most telling difference between these comparisons is the complete lack of regions with full identity when half-siblings are compared. If you subscribe to 23andMe, you can make similar images between any pair of shared genomes using their family inheritance genome view tool, at

Andrea Badger, who sent me these specific images, also collected data on the fraction of the genome identical by descent when different types of relative are compared. She found that full siblings shared between 41% and 55% of their genomes (16 comparisons) while half siblings shared between 21.7 and 31.4% of their genomes (four comparisons). The expected fractions are 50% and 25%, but there is some spread.

This is why having lots of markers is important. When the whole genome is analyzed, the difference is clear. With a smaller number of markers, statistical fluctuations are more likely to confuse the issue. 23andMe now uses over 1 million markers. Family Tree DNA uses fewer markers and charges more, but they use plenty of markers (hundreds of thousands) and have a greater focus on genealogy. I am aware of other services that charge almost as much but test only a few markers (less than 100). If you are shopping for a test, you can find a lot of information at dna-forums.

Thanks, Andrea!

Saturday, August 7, 2010

Avoiding overlaps in chromosome image (karyotypes)

I have received a question about human cytogenetics (chromosome or karyotype analysis).

I am doing a project in detecting the numerical abnormalities in chromosomes. Is it possible to get the microscopic chromosome images without any overlaps? ... mail me your suggestions.
I'm mailing you a sample image. The chromosomes in this image are overlapped and have crossovers. Is it possible to have the microscopic image without this type of crossovers. When I try to count the number of chromosomes the chromosomes that have crossovers and overlaps are counted as one. And my research concept is not mainly on this overlaps. So I'm trying for images without overlaps and crossovers. My concept is based on classification of the chromosomes so I need good well spread image

I have no training in cytogenetics per se, so I invite replies from those with such training (either academic human cytogeneticists or clinical laboratory specialists in cytogenetics (CLSp(CG)). As usual, answers should be provided in the form of comments from identified people with relevant expertise.

It seems to me that there are two questions here. One concerns the technical issue of whether it is possible to routinely obtain spreads without overlapping chromosomes. The other is whether there are already standard methods for dealing with this problem in the image analysis.

Sunday, July 4, 2010

Identifying half-siblings by genetic tests

I have received four related questions from different people. They all concern the issue of half-siblings, and the utility of genetic tests for establishing such a relationship.

1) Is it absolutely possible to tell if two females have the same father? These supposedly half sisters do not share the same mother. The father in question is deceased. Will our DNA reveal, certainly, that we share the same father? How do we find a reliable U.S. company to do this for us?

Information from a company like 23andme will provide you with enough markers to be completely sure. I'm not entirely sure how their interface works, so I can't tell you how easy the interpretation will be, but there will be enough data for you to be sure, and you will be able to get help with the interpretation. The reason is that two women who share a father will have an entire X chromosome in common. That is extremely unlikely to occur otherwise.

2) My sister donated a kidney to me. We were told that we matched 5 out of 6 genetic markers. From that information, is it possible to make an "educated guess" as to whether we are more likely to be full or half sisters? We believed we were half-sisters but some interesting coincidences lead me to believe that we may be full-sisters.

The six markers used for this test are not conclusive. As you know, even half-siblings can be a perfect match. A conclusive test would require many markers. Fortunately, companies like 23andme and Navigenetics provide information about many markers (about 450,000), and those tests could tell you definitively. If you are full siblings, then there will be parts of the genome (about one-fourth of the total) where you are identical for long stretches. That would be extremely unlikely if you are only half siblings. However, a small number of markers (less than 200 or so) would make it harder to make a definitive distinction between being half siblings and being full siblings. Six is definitely too few.

3) I wonder if you could help me. In trying to find my biological father, I came up with what could be two half siblings. The parents in both cases are deceased. I have been given a price of $500 for the three of us to test by saliva. Do you think without any parents, this could prove half siblings or would it be a waste of money?

You will share one of your two alleles with a half-sibling at about half of the sites in your genome. So, the answer is that with enough markers (thousands) the answer will be absolutely clear. The source of DNA (saliva, cheek swab, blood) does not matter much. 23andme will do about 450,000 markers for $400 (per person) and give you lots of additional information. The technology is pretty standard so other firms are probably OK. Just make sure that there are many markers (more than 100,000) and that you get access to the data (not just their interpretation of the data). Once you get your results you'll want to look for large regions of the genome where you and the putative half-sibling share markers. Of course, your putative half-siblings will have to agree to this analysis.

4) I heard that a recent study proved that men don't have half children but any children by the same man are full brothers and sisters irregardless of all different birth mothers. Is there a genetic truth to this?

Two children with the same father and different mothers are referred to as half-siblings. What you are referring to is almost certainly a legal or cultural distinction, not the sort of thing that can be proved by a study.

As usual, I invite additional answers in the form of comments. We are looking for answers from people with some expertise, and you will be asked to log in so that we know who you are (no anonymous answers).

Sunday, January 10, 2010

A beginner's guide to genetics

Could you please recommend me a few sites on the internet, blogs, or books that's sort of like a beginner's guide to genetics? I would like to learn more about genetics, but I don't exactly know where to begin. One of the books I've read is great, it's called "Genes and DNA" by Charlotte K. Omoto and Paul F. Lurquin. I'm looking for something like that. But most of the other books at the library that I find seem too complicated, and I believe I should begin with the basic stuff first.

Unfortunately, I am not extremely familiar with books of this sort. I provide a link to the reviews of "A Beginner's Guide to Genetics and its Applications." Amazon recommends "Genetics for Dummies" and "Abraham Lincoln's DNA and Other Adventures in Genetics" as similar books. The latter sounds like an interesting read. I also try to recommend informative sites via my Gene Info web site.

I'm posting the question here in the hope that a reader will have suggestions. Although it would be nice to hear from non-experts, I will stick to the policy that while questions can be anonymous, comments (answers) are moderated, and I will only approves comments from people who identify themselves.