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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.