Scientists from the University of Utah have traced a mutation in the adenomatous polyposis coli (APC) gene to a Mr. and Mrs. George Fry, who arrived in the New World aboard the William & Mary around 1630.
The mutation, c.426_427delAT, is believed to increase the carrier’s chances of developing colon cancer from 2 in 3 by age 80, a significant increase from the normal of 1 in 24. The study is available here for FREE – thank you open access – and is entitled “American Founder Mutation for Attenuated Familial Adenomatous Polyposis.”
Scientists traced two branches (from two of the Fry’s four children) of the family back to the Fry family, one in Upstate New York and one in Utah. The family in Utah, with more than 5,000 people, has been the focus of scientific study for over 14 years because of their unfortunately high risk of colon cancer. In fact, members of the Utah branch constitute 0.15% of all colon cancer in the state of Utah!
As of the end of November, the Personal Genome Project has a newly-designed and user-friendly website. Compare the OLD site and the NEW site – what an improvement! Misha Angrist, aka genomeboy.com and one of the “First 10″ aptly called the site “PGP 2.0″.
The new site is extremely well organized and contains information about the project and about participating in the project, if one is so inclined. Since this project will contain so much personal information about each individual that joins, participants will go through an extensive consent process that will include education, physician assistance, and even an online assessment to gauge the participant’s grasp of genetics and the risks of participation, among other things. I know that the team is working feverishly behind the scenes to gather as much information as possible to create an extensive consent protocol.
PLoS Genetics has a new paper (PLoS Genet 3(11): e185. doi:10.1371/journal.pgen.0030185) that examines autosomal microsatellite markers (repeating units of base pairs) from Native American DNA:
“We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberiansâ€”signals of the southward dispersal of human populations from the northwestern tip of the Americas”
Forty advanced placement science students at Soldan International High School in St. Louis have submitted their DNA for testing with the National Geographic Society’s Genographic project. An article in the St. Louis-Post Dispatch highlights some of the statements made by the students and faculty:
“Many times students don’t see the relevance of what they’re learning,” said Assistant Principal Alice Manus, the Soldan project coordinator. “What they’re learning here will have all sorts of relevance because, really, we’re looking into their lives.”
One student, named John, had more reason to be excited about this test than most – his father died when he was only 13. “I never knew him that well,” said the Soldan sophomore. “Maybe this will tell me more about who he was and where he came from.”
Update: Ugo Perego is not affiliated withh the website mentioned in the last two sentences.
Did Joseph Smith father children with any of his plural wives? The Deseret News has a lengthy article about recent efforts by a geneticist to answer the long-debated question about the founder of the Latter Day Saint movement.
Ugo Perego, the director of operations at the Sorenson Molecular Genealogy Foundation, has used genetic genealogy in an attempt to identify or rule out potential descendants of Smith. In 2005, Perego showed that three males were not descendants of Smith, and new testing has shown that two more alleged descendants of Smith are not his true descendants.
In order to rule out descendants, it was first necessary to characterize the Y-DNA thought to belong to Joseph Smith. According to the article:
Genome Technology Online mentioned the new partnership between DNAPrint Genomics, Inc. and BioServe, a company that offers â€œthe Global RepositoryÂ®, a growing library of over 600,000 human DNA, tissue and serum samples linked to detailed clinical and demographic data from 140,000 consented and anonymized patients from four continents.â€
As part of the partnership, DNAPrint will analyze the 600,000 human samples in the Global Repository using the ANCESTRYbyDNA test.According to Richard Gabriel, the CEO and President of DNAPrint Genomics:
“By removing the question of ancestry from a clinical sample researchers can more readily evaluate which medicines will produce side effects within certain ethnic groups, and which medicines will work for the widest spectrum of a population.”
I’ve spoken before about the enormous effect that affordable SNP and whole-genome sequencing will have on genetic genealogy. In that previous article, I mentioned a study using SNP analysis to identify a person’s ancestry based on autosomal DNA (all the nuclear non-sex DNA). Another study, released today in PLoS Genetics, used SNP chips to identify SNP markers that are characteristic of a certain ancestral origins. According to the authors:
“We have developed a novel algorithm to identify a subset of SNP markers that capture major axes of genetic variation in a genotypic dataset without use of any prior information about individual ancestry or membership in a population.”
To accomplish this, the researchers:
“…studied here 274 individuals from 12 populations (20 Mbuti, 20 Mende, 22 Burunge, 42 African Americans, 42 Caucasians, 20 Spanish, 11 Mala, 20 East Asians, 20 South Altaians, 20 Nahua, 20 Quechua, and 19 Puerto Ricans). Three of these populations are admixed (Caucasians, African Americans, and Puerto Ricans). All individuals were typed using the 10K Affymetrix array.”
Itâ€™s always been my belief that personal genetics (inexpensive whole-genome analysis) will bring about some exciting changes in the field of genetic genealogy.One of the biggest areas of change will undoubtedly be in the area of autosomal genetic testing.(Remember that autosomal testing examines nuclear DNA, which is DNA other than mtDNA, Y-DNA, or X chromsomes).
A new study takes one of the first steps in the genetic genealogy revolution by examining SNP variations in four self-identified American populations â€“ European, Latino/Hispanic, Asian, and African American (see reference below).â€œThese population labels were used, despite the controversy surrounding the correspondence between notions of race and population structure inferred from explicit genetic data, because they are the labels used by NIH, FDA, and many, if not most, biomedical researchers.â€The researchers sequenced the exons and flanking regions of 3,873 genes from 76 unrelated individuals.
A study in the September Journal of Field Archaeology analyzes mtDNA that was isolated from Native American aprons and from quids – chewed plant material.Â From an article in science:
“The quids and aprons belonged to a vanished tribe that archaeologists call the Western Basketmakers. Between about 500 B.C.E. and 500 C.E., they lived in caves and rock shelters in what is now southern Utah and northern Arizona.”
“They pulled mitochondrial DNA from 48 quids and from 18 aprons that had been stained with what was likely menstrual blood. Then they scanned the DNA for various molecular markers called haplogroups, which appear in different frequencies in different parts of the world.”
The researchers discovered that 14% of the samples belonged to Haplogroup A.Â They also point out that museum and university collections have many sources of Native American DNA (such as quids, textiles, and cigarettes).
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.