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The YHRD Database

One of the steps in analyzing the results of a Y-DNA test is to search through Y-DNA databases to look for potential matches. These matches, depending on how well they match, might be relatives, either close or distant (in recent genealogical terms – we’re all distantly related, of course).

One of those databases is YHRD (Y-STR haplotype reference database). The project has two main goals:

  1. The generation of reliable Y-STR haplotype frequency estimates for minimal and extended Y-STR haplotypes to be used in the quantitative assessment of matches in forensic and genealogical casework, and;
  2. The assessment of male population stratification among world-wide populations as far as reflected by Y-STR haplotype frequency distributions

According to the YHRD website:

“To this end, a growing number of diagnostic and research laboratories have joined in a collaborative effort to collect population data and to create a sufficiently large reference database. All institutions contributing in this project, participated in an obligate quality control exercise.
“This database is interactive and allows the user the search for Y-STR haplotypes in various formats and within specified metapopulations. Related information i.e. STR characteristics, mutations, population genetic analyses etc. is documented.”

The YHRD database is contantly being updated, and on August 10th, Release 22 was added:

“Release 22 is out with 52,655 haplotypes in 464 populations. 50,867 haplotypes of these are completely typed for 9 (Minimal haplotype) and 23,981 for 11 loci (Extended or SWGDAM haplotype). Twenty populations were added or updated today: two Amerindian tribal populations from the Formosa province in Argentina (Pilaga, Toba), one from Venezuela (Caracas), two from provinces in Colombia (Boyaca, Cundinamarca), three from Siberian nomad populations (Western and Central Evens, Iengra Evenks), one from Belarus (Pinsk), three from Ukraine (Kiev, Lviv, Lugansk), three populations from Capetown in South Africa, three from Ravenna, Rimini and Val Marecchia in Italy, one from Hungary, one from Peru and one from Oran in Algeria. We would like to thank the following colleagues for submissions and updates: Daniel Corach and his group (Buenos Aires, Argentina), Brigitte Pakendorf and her group (Leipzig, Germany), Neal Leat and his group (Capetown, South Africa), Susi Pelotti and her group (Bologna, Italy), Pamzsav Horolma and her group (Budapest, Hungary), Ignacio Briceno Balcazar and his group (Bogota, Colombia), Lisbeth Borjas and Tatiana Pardo (Venezuela), Sergey Kravchenko and his group (Kiev, Ukraine), Gian Carlo Iannacone and his group (Lima, Peru) and Carlo Robino and his group in Torino, Italy. Please refer to the section YHRD contributors to get more information.”

HT: … Click to read more!

RootsTelevision & Megan Smolenyak at the FGS Conference

For all you lucky people that live in or near Indiana, note the following, from DearMYRTLE:

Roots Television at FGS
Roots Television would like to invite you to join us at exhibit booths 318 and 320 at the Federation of Genealogical Societies (FGS) 2007 Conference from August 15-18!

Come meet Megan Smolenyak Smolenyak, Dick Eastman and a special surprise guest (on opening day) in Fort Wayne, Indiana at the Grand Wayne Convention Center, 120 West Jefferson Blvd. Throughout the conference, we’ll feature the latest and greatest programs from the Roots Television website. Visit us to be among the first to learn about our Societies & Libraries contest ($1,000 prize to the winning organization!) and to watch Dick Eastman and our surprise guest conduct interviews (or maybe even be interviewed yourself!). Be sure to come by to share in the excitement!

And while you’re there, don’t miss … Click to read more!

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Gene Genie #13: Into the Future

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Welcome to edition #13 of the Gene Genie. There were many interesting and exciting submissions for this issue, so I hope you do a little exploring and learn something new about genes, personal genetics, and personalized medicine.

Splicing Genes. Let’s start off with something fun. I don’t know if we’ll ever try to splice our genes with those from famous or successful people, but here’s at least one conversation that might result!

With new genetic discoveries being announced every day, how does one keep up-to-date? Well, luckily we have a few helpful suggestions from our fellow bloggers. Scienceroll gives us 7 Tips: How to be up-to-date in genetics/genomics? And Clinical Cases and Images – Blog adds to the discussion with 6 Tips on Staying Up-to-Date in Genetics (and Any Specialty).
Genetically Naked? Berci at Scienceroll wrote a wonderful overview of the Personal Genome Project and gathers together many of the recent discussions about the Project. Reading the post, we are reminded of what a … Click to read more!

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Argus BioSciences Now Testing Y-DNA

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Argus BioSciences is now testing Y-DNA:

“The Y-chromosome test looks at 96 key single nucleotide polymorphisms (SNPs) to determine your paternal haplogroup. Your report includes a phylogenetic tree of global Y-chromosome haplogroups. The SNP assays are carried out in collaboration with Marligen Biosciences, a leader in the development of cutting edge multiplex assays.”

“These kits employ a two tiered strategy that efficiently detects 96 polymorphic markers in multiplexed PCR and detection reactions. Samples are first analyzed with a screening multiplex (A-R) that determines the major haplotype group of each sample. Subsequently, samples are analyzed with one of the haplogroup-specific multiplexes (AB, CD, E, FGHI, J, KLMN, O1, O2, PQ, R1 or R2) to determine the precise haplotype of each sample.”

I reviewed Argus BioSciences back in March. Congratulations on their new … Click to read more!

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Beothuk DNA in Newfoundland


Yesterday I wrote about a study that used SNPs to haplotype the Y chromosomes of ancient DNA obtained from skeletons found along the Yangtze River in China. The ability to extract and use SNP data from ancient Y-DNA is a relatively new scientific development. Indeed, the author’s of the study I highlighted yesterday stated: “The first reported ancient Y SNP data was typed from a Native American sample of an extinct tribe (Kuch et al. 2007).” I thought I’d briefly mention this earlier study as well since it contains a lot of interesting information.
The Beothuk were a Native American group that lived on Newfoundland at the time of John Cabot’s arrival in 1497. Although estimates vary widely, they may have been as few as … Click to read more!

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Y Chromosomes of Prehistoric People Along the Yangtze River

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In the past, scientists have primarily examined the mtDNA of ancient DNA. After all, mtDNA is much more prevalent (100’s to 1000’s of copies per cell) than nuclear DNA (just 1 copy per cell) and thus it is easier to find samples that are not degraded by time. New amplification techniques as well as improved anti-contamination procedures have made it possible for Y chromosomal DNA to be
In a new study (epub ahead of print – which means that it is available online before it is published in Human Genetics), researchers examined the remains of male skeletons that were buried in the loessal soil in Maqiao, Xindili, Wucheng, Daxi, and Taosi, areas along the Yangtze River. Interestingly, these skeletons were buried without chests or coffins. … Click to read more!

The Celebrity Genome Debate Rages On

Jason Bobe over at The Personal Genome has a great post this week called “False Alarm: The Celebrity Meme” about the use of ‘famous’ scientists in early genome sequencing.  He poses a number of interesting and thought-provoking questions about the topic.  Make sure you read the comments that others have left.  Hsien at EyeonDNA wrote so much that she made her answers a full-length post.

The subject is traveling all over the blogosphere.  The Rocketfish Manifesto addresses personal genome sequencing with a little bit of humor.  And John Hawks’ Anthropology Weblog has a lengthy post with some new insights.  There is a lot of great reading material available if you’re interested in the Personal Genome … Click to read more!

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Ethical and Legal Issues Surrounding Large-Scale Genomic Databases


I recently came across a review article by Henry T. Greely, a Professor of Law, Professor (by courtesy) of Genetics, and Director of the Center for Law and Bioethics at Stanford. The article is entitled “The Uneasy Ethical and Legal Underpinnings of Large-Scale Genomic Biobanks (pdf)” and was recently published in the Annual Review of Genomics and Human Genetics.
According to Mr. Greely, the identity of participants in large-scale genomic biobanks cannot effectively protected. A biobank is defined as a database of genotypic and phenotypic data. Using genetic information, physical information, or a combination of the two, people can identify an individual in such a large database:

“Someone really interested could get a DNA sample from me – from a licked stamp, a drinking glass, or some tissue – and have it genotyped for a few hundred dollars, but few will have to go to the genomic data; the phenotypic and demographic data will often be sufficient.”

“Eliminating name, mailing address, and social security number does not eliminate identifiers; it just eliminates the easiest identifiers, making the search somewhat more difficult and expensive.”

Unfortunately, it is impossible to remove all the data one could use to identify biobank … Click to read more!