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:
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;
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.”
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!
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.Letâ€™s start off with something fun.I donâ€™t know if weâ€™ll ever try to splice our genes with those from famous or successful people, but hereâ€™s at least one conversation that might result!
“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.”
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 authorâ€™s of the study I highlighted yesterday stated: â€œThe first reported ancient Y SNP data was typed from a Native American sample of an extinct tribe (Kuch et al. 2007).â€I thought Iâ€™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 Cabotâ€™s arrival in 1497.Although estimates vary widely, they may have been as few as 500 to 1000 individuals.The Beothuk avoided Europeans, and eventually disease and conflict led to their extinction in the 1820s.
In the past, scientists have primarily examined the mtDNA of ancient DNA.After all, mtDNA is much more prevalent (100â€™s to 1000â€™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.Using a well-established set of anti-contamination procedures, DNA was extracted and five SNPs were typed for each individual (when possible): M119, M95, M122, M7, and M134.According to YCC nomenclature, those SNPs delineate the O1, O2a, O3*, O3d, and O3e haplogroups.The scientists found that:
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.Â He poses a number of interesting and thought-provoking questions about the topic.Â Make sure you read the comments that others have left.Â Hsien at EyeonDNA wrote so much that she made her answers a full-length post.
The subject is traveling all over the blogosphere.Â The Rocketfish Manifesto addresses personal genome sequencing with a little bit of humor.Â And John Hawks’ Anthropology Weblog has a lengthy post with some new insights.Â There is a lot of great reading material available if you’re interested in the Personal Genome Project.
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:
â€œSomeone 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.â€
Just a quick reminder that the 12th issue of Gene Genie will be hosted here on The Genetic Genealogist on August 12th! If you have a gene- or genetic-related post, submit it via the carnival site, or directly to me.