18

DYS464 and Male Infertility

Dr. Mark A. Jobling at the University of Leicester published a study in 2005 that examined DYS464, a Y-DNA marker commonly sequenced for genetic genealogical purposes.As it turns out, sequencing DYS464 can inadvertently detect an AZFc deletion.Deletion of AZFc (azoospermia factor c) causes spermatogenic failure and subsequently, male infertility.This marker is tested by at least 6 firms.

Dr. Jobling pointed out that a previous study had concluded that an AZFc deletion could be found in 1 in every 4000 males.In Dr. Jobling’s study there were 3 cases in 3255 males tested, which he states is “not significantly different from 1 in 4000.”A story in the New Scientist stated that “a study by Jobling’s team suggests that 1 in 1000 men has the deletion,” but I think that is an overstatement by the media. I haven’t seen anywhere that Dr. Jobling made such a statement – he was merely listing some of his data. Elsewhere, Ann Turner has suggested that at FTDNA, the number is around 1 in 8,000.Although the exact frequency has not yet been determined, it appears that it is rather low.

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2

The Measure of a Woman (or a Man)

My great-grandmother belongs to Haplogroup H, and I always feel a little bad for her.Not that I have anything against Haplgroup H’ers, but they got the short end of the stick.You see, currently all mtDNA sequences are compared to the Revised Cambridge Reference Sequence (rCRS), an mtDNA sequenced derived in the early 1980’s and recently updated.Since the source of most of the mtDNA for that sequence belonged to Haplogroup H, people who belong to Haplogroup H often have no deviations at all and their sequencing results tend to be a little boring.Imagine if your mtDNA testing company sends your results and they say: “You belong to Haplogroup H, and your deviations from the rCRS are as follows: 0.”You see, a little dull.

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2

The Qilakitsoq Mummies

A recent paper in the American Journal of Physical Anthropology examined mtDNA extracted from the hair and nails of eight Inuit mummies. These essentially freeze-dried mummies were discovered in 1972 in a natural tomb at Qilakitsoq in the Uummannaq Municipality of Greenland. Using C14 analysis, the mummies have been dated to approximately 1460.

The bodies were found in two separate positions about 1 meter apart. In Grave I, there were five bodies:

  1. I/1 = Male Infant #1 – about 6 months of age
  2. I/2 = Male Infant #2 – about 4 to 4.5 years of age
  3. I/3 = Female #1 – about 20-25 years of age
  4. I/4 = Female #2 – about 25-30 years of age
  5. I/5 = Female #3 – about 40-50 years of age

In Grave II, there were 3 bodies:

  1. I/6 = Female #4 – about 50 years of age
  2. I/7 = Female #5 – about 18-21 years of age
  3. I/8 = Female #6 – about 50 years of age

The researcher’s primary goals were to sequence the HVR1 region of each individual’s mtDNA, and then to compare the results to determine possible relatedness of the remains. All 8 individuals fell into Haplogroup A2, but belonged to three different maternal lineages which were mixed between the two grave sites:

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The Copernican Principle

I saw a recent article in the New York Times, “A Survival Imperative for Space Colonization” that grabbed my attention.I know it isn’t necessarily related to DNA, but I loved the article and the essence behind it, The Copernican Principle.

The Copernican Principle, is named after Nicolaus Copernicus, who stated that the Earth is not in a central, specially favored position.Although it might look like our galaxy is the center of the Universe, observers in all other galaxies would observe the same thing.This idea has been applied to the field of statistics.For example, if you are observing something and your location is not special, then you are observing the thing at a random point during its existence.That is, there is a 95% chance that you are seeing it in the middle 95% of its existence, and not during the beginning 2.5%, or the last 2.5%.That idea can be expressed using the following formula:

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11

Mitochondrial Eve and Y-chromosomal Adam

In the past decade, scientists have repeatedly referred to ‘Mitochondrial Eve‘, the (hypothesized) source of mtDNA for all humans alive today.  She is believed to have lived approximately 140,000 years ago in Africa.  There is also ‘Y-chromosomal Adam‘, the (hypothesized) source of every living man’s Y-DNA.  He is also believed to have lived in Africa, but more recently, between 60,000 and 90,000 years ago.  Thus, Mitochondrial Eve and Y-chromsomal Adam were not a couple – they were not the source of all human genetic material on the planet today.  Instead, the terms refer to the founders of all the mtDNA and Y-DNA respectively.

For a wonderful description of some of the genetic behind Mitochondrial Eve and Y-chromsomal Adam, go to “The Questionable Authority“, a blog which is part of Scienceblogs.  While you’re there, be sure to read the comments, where the discussion addresses the time disparity between the two DNA sources (140,000 years ago versus 60-90,000 years ago).

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A Map to The Genetic Genealogist

I think it is every blogger’s dream to have thousands of readers and rss subscribers waiting for your every post and checking the blog for new information first thing in the morning.Of course, there are very few blogs like that.People typically find new blogs through a variety of means, including links from other blogs, links from social networks or directories, and often through search portals.Here are the current top 15 searches that lead people to The Genetic Genealogist:

  • 23andme
  • genetic genealogist
  • amish genealogy database
  • genetic genealogy
  • anne wojcicki
  • craig venter
  • free matriclan & patriclan dna tests
  • wireless healthcare
  • robson encyclopedia
  • afro-brazilian roots bbc research
  • amish genetic mutations
  • blaine bettinger
  • reunio cohanim
  • mitomap
  • dna african american kittles

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21

Autosomal Genetic Testing

 

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Yesterday I posted a link to an article in the UK Guardian, “The genes that build America” in which the author attempted to summarize some of the recent controversial topics in genealogical research, including DNA testing.

For at least one of my readers, the article represented everything that is wrong with DNA testing, specifically the assignment of racial/ethnic percentages based on the results of autosomal testing.

In the past, I’ve tried to be as impartial as possible when discussing autosomal testing. As I’ve learned, however, being impartial can also be unfair and misleading. So, I’ve decided to get a little more personal and share my thoughts about autosomal testing.

In a single sentence, autosomal testing is simply too new and underdeveloped to be of much informative use for genealogists or the average public, at least in its current stage. This statement, I hope, will be completely incorrect in a few years as whole genome sequencing becomes affordable. Assigning percentages (as autosomal tests do) will only work when the entire genome can be sequenced and examined and analyzed. Short of whole genome sequencing (and maybe comprehensive SNP testing – as in millions of SNPs), I don’t believe that autosomal is worth the effort.

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