Search Results for: admixture

Visualizing Recombination and Segment Loss

Blaine Bettinger 4 Comments

I posted a graphic online yesterday showing chromosome paintings for three generations, from a grandmother to her son to her grandson. I think these types of graphics are very interesting, but I shared this particular graphic because it – rather dramatically, I think – shows the loss of numerous African and Native American segments through just those three generations.

The grandmother has approximately 4% African DNA and 6% Native American DNA:

This 10% of non-European DNA, for example, quickly dwindles to almost non-existent in the grandchild, as shown in the images and tables below.

Since I’ve actually tested two of the grandmother’s grandchildren, below are results for both.

Grandchild #1:

Grandchild #2:

... Click to read more!

Recreating a Grandmother’s Genome – Part 1

Blaine Bettinger 22 Comments

My grandmother Jane died in 1984 when I was just 8 years old. I have some really great memories of her, faded with time but still filled with emotion. Bath times, spending time with her in the summer, newspaper hats, chrysanthemums.

However, in addition to those memories, she gave me a very unique genetic heritage. She was from a region of the world with a high degree of admixture, and thus it is from her that I obtained my Native American mtDNA, my Native American, African American, and Spanish autosomal DNA. It is an incredibly rich and fascinating genetic legacy.

In an attempt to learn more about my grandmother’s genetic heritage, I’m using GEDmatch’s new Lazarus tool to try to recreate as much of her genome as possible. Join me on the journey, and learn about this new tool. ... Click to read more!

Ancient Genomes at GEDmatch

Blaine Bettinger 3 Comments

A great resource from Jay Chandrakumar at Genetic Genealogy Tools (www.y-str.org) – SNPs extracted from sequenced ancient genomes and loaded into GEDmatch. Try out admixture tools with these GEDmatch profiles, but don’t expect many matches in One-to-Many!

Denisova – GEDMatch# F999903

Mezmaiskaya Neanderthal #1 – GEDMatch# F999909

Altai Neanderthal #2 – GEDMatch# F999902

Palaeo-Eskimo 2000 BC – GEDMatch# F999906

Clovis-Anzick – GEDMatch# F999912

For example, here’s the Palaeo-Eskimo 2000 BC (F999906) profile in MDLP K23b:

F999906 GEDmatch

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What Else Can I Do With My DNA Test Results?

Blaine Bettinger 130 Comments

DNAIn addition to the information you received from 23andMe, Family Tree DNA, or AncestryDNA about your ancestry, there is a wealth of additional information still within in your DNA.  Below (in alphabetical order) are some of the most popular and well-known tools for wringing every last bit of information out of your raw data, and maximizing the cost of your DNA test.  Please note that I have not used or verified all of these apps; always use caution when providing information to an unknown recipient.

Apps, Extensions, Programs, and Websites:

  • 23++ (http://23pp.david-web.co.uk/about/) (FREE) – An extension for the Google Chrome web browser that adds additional functionality to the 23andMe website. The extension especially adds a number of features to Relative Finder.
  • 529andYou (http://goo.gl/FQSiwW) (FREE) – An extension for the Google Chrome web browser that works with 23andMe’s Family Inheritance: Advanced tool (found under Ancestry Labs or, in the new beta website design, under My Results, Ancestry Tools) to collect information about DNA matches.  The information, which includes shared segment data, is stored in a local database on your computer.
  • David Pike’s Utilities (http://www.math.mun.ca/~dapike/FF23utils) (FREE) – A comprehesive suite of tools for analyzing raw data, including searching for Runs of Homozygosity (ROHs), searching for shared DNA in two files, and several advanced phasing tools.
  • DNAGedcom (http://www.dnagedcom.com) (FREE) – A suite of tools for 23andMe and Family Tree DNA customers.  Users can download their matches, shared segments, and other data into a handy spreadsheet for further analysis.
  • DNAMatch4iPad (http://www.dnamatch4ipad.com) ($) – A app for the iPad that is an “alternative to the use of conventional spreadsheets for the processing of autosomal DNA data.” Users download their match data from one of the testing companies in the form of a .CSV file and upload it to DNAMatch4iPad.
  • GEDmatch (http://gedmatch.com/) (FREE) – A powerful suite of tools for 23andMe, AncestryDNA, and Family Tree DNA raw data.  Users can compare their DNA to everyone else in the database or to a specific individual in the database, or perform numerous admixture analyses, phase their DNA, and much more.
  • Genes & Us (http://www.genesand.us)  (FREE) – A website for 23andMe users to “combine their genomes in order to better understand what disease risks most affect their family.”  For example, a mother and father can link their 23andMe accounts to the site and determine the possible combinations for their children’s DNA.  Appears to work with 23andMe’s new API offering.
  • Genetic Genealogy Tools (http://www.y-str.org) (FREE) – An impressive and ever-growing list of advanced tools for analyzing raw data, including an X-DNA Relationship Path Finder, Ancestral Cousin Marriages, Autosomal Segment Analyzer, a DNA Cleaner, a SNP Extractor, My-Health, and many more!  A terrific resource from Felix Jeyareuben Chandrakumar, an Australian software professional.
  • Genetic Genie (http://geneticgenie.org/) (FREE) – A tool that analyzes your 23andMe results to perform a methylation gene analysis (“Methylation Analysis”).  The site also provides a tool for a “Detox Profile” which looks for defects in the Cytochrome P450 detox enzymes.  The site uses the 23andme API, so users can link their 23andMe account to the service.
  • Genetrainer (https://www.genetrainer.com/) ($) – Users of 23andMe and Family Tree DNA can link their results to the Genetrainer service, which will then provide you with training plans and exercises personalized to the user.
  • HIR Search (http://hirs.snpology.com) (FREE) – Once your raw data is entered in the database, you can find HIRs (half-identical regions) that you share with others in the database.
  • Imputation Tools (http://mathgen.stats.ox.ac.uk/impute/impute_v2.html) and (http://faculty.washington.edu/browning/beagle/b4.html) (FREE) – Sometimes you find a SNP in the literature that isn’t tested by any of the big testing companies.  Imputation allows you to determine the most probable genotype for that SNP based on the surrounding SNPs and a database of known sequencing results (such as the 1000 Genomes data).  IMPUTE2, for example, is a computer program for phasing observed genotypes and imputing missing genotypes.  See more about IMPUTE2 here, including a link to a script to convert your 23andMe raw data to a useable form.  BEAGLE4 is similarly performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.  Learn how to use BEAGLE4 here.
  • Interpretome (http://esquilax.stanford.edu/) (FREE) – A collection of tools for analyzing 23andMe raw data using only a web browser (i.e., raw data is not uploaded).  The tools include an admixture analysis, health information, and a Neanderthal calculator.
  • Livewello (https://livewello.com) ($19.95) – Livewello generates health reports from Raw Data issued by labs including: 23andMe, AncestryDNA, Gene By Gene, National Geographic, BioCore, FamilyTreeDNA. For a 1- time fee of $19:95, users keep their accounts for life and get free App updates.
  • Minor Allele Program (http://www.ianlogan.co.uk/23andme/23andMe_index2.htm) (FREE) – A tool to identify rare SNPs in your 23andMe or Family Tree DNA raw data.  My own results are available here.
  • mtDNA Haplogroup Analysis (http://dna.jameslick.com/mthap/) (FREE) – A terrific tool for predicting your maternal haplogroup using a variety of formats, including 23andMe raw data.
  • NAT2PRED (http://nat2pred.rit.albany.edu) (FREE) – a tool for inferring human N-acetyltransferase-2 (NAT2) enzymatic phenotype from NAT2 genotype.  In other words, a tool for predicting the function of your NAT2 enzyme (either slow, rapid, or intermediate) based on your DNA.  The NAT2 enzyme is involved in activating and deactivating arylamine and hydrazine drugs and carcinogens, among other things.
  • Promethease (https://promethease.com/ondemand) ($5) – Analyze your 23andMe, Family Tree DNA, or AncestryDNA raw data and build a report based on SNPedia. Reports contain information about health and ancestry as well as several other new options.  A sample report is here.
  • Segment Mapper (http://kittymunson.com/dna/SegmentMapper.php) (FREE) – A tool to show specific DNA segments in a graphic chromosome-style chart.  This is a clever and powerful “mapping” tool.  Learn more about the tool here.
  • SNPTips (http://snptips.5amsolutions.com/) (FREE) – A Firefox browser extension that allows 23andMe customers to access their SNP genotype information without logging into their 23andMe account or leave the webpage they are browsing.  Users can simply hover their mouse cursor over a SNP RSID on a webpage and, if that was tested by 23andMe, the SNPTips extension will provide a popup with the user’s genotype and some relevant links.
  • SPA (http://genetics.cs.ucla.edu/spa/index.html) (FREE) – Spatial Ancestry analysis (SPA) is a method for predicting ancestry or where an individual is from using the individual’s DNA. 23andMe users can download the software and analyze their results with this admixture tool.

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Did I miss anything?  Do you have any suggestions or comments regarding the programs listed above? Feel free to let me know in the comments below! ... Click to read more!

AncestryDNA Launches New Ethnicity Estimate

Blaine Bettinger 22 Comments

AncestryDNAThere has been much discussion (see here and here for a few examples) of the so-called “Scandinavian Problem” with AncestryDNA‘s ethnicity estimate, in which certain populations appeared to be over-represented in the reference panel utilized by Ancestry.com.  I, for example, have no documented Scandinavian ancestry, but had 78% Scandinavian.  Many others experienced the same issue.

The AncestryDNA team were well aware of the issues, and have been working on an update to their ethnicity algorithm, reference panel, and user interface.  Indeed, at “The First DNA Day at the Southern California Genealogy Society Jamboree” in June of this year, Ken Chahine (Senior Vice President and General Manager, DNA) gave a presentation in which he announced that the ethnicity calculations at AncestryDNA were undergoing a complete overhaul and a major update would be provided to all customers later this year. ... Click to read more!

GEDmatch.com Adds Phasing Tool

Blaine Bettinger 5 Comments

Today (or perhaps yesterday?) popular DIY genomics website GEDmatch.com released a new tool for phasing DNA data.  Listed under a link entitled “Generate phased data file,” the tool allows users of the GEDmatch.com site to phase their chromosomes if they have their parent’s raw data.

(A similar tool was previously created by David Pike at http://www.math.mun.ca/~dapike/FF23utils/; with David’s tool, users receive their results directly and do not need to upload their DNA test results; accordingly, users have a variety of options depending on their privacy tolerance).

What the Heck is “Phasing”?

Currently, SNP chip testing performed by 23andMe or Family Tree DNA is unable to attribute a test result to either one of your parents.  For example, if your results for SNP rs00000 are “AG,” the test alone cannot determine whether the “A” came from your mother or father. ... Click to read more!

Genetic Genealogy and Personal Genomics in the Classroom – Part I

Blaine Bettinger 2 Comments

Today begins the first in a series of articles about the use of genetic genealogy and personal genomics in the classroom, ranging from high school to college-level.

Many scientists and health care experts believe that genetics will be a vital component to several facets of our lives in the future, especially in the field of medicine.  Indeed, some consider the study of genetics to be one of the most promising solutions to many of the health dilemmas facing society today, including advancing our understanding of interactions between genetics and the environment.  Accordingly, today’s students should have at least a basic grasp of genetics, and science educators must find innovative ways to share those concepts with their students.

A Need for Genetics Education ... Click to read more!

WDYTYA Reveals More Information About Ancestry.com’s New Autosomal DNA Testing

Blaine Bettinger 8 Comments

[Update (2/24/12): Some genealogy forums are reporting that callers to Ancestry.com are being told that the autosomal DNA test will publicly launch in approximately 1 month (late March or early April).]

Tonight’s episode of Who Do You Think You Are? featured African-American actor Blair Underwood. For those not familiar with Who Do You Think You Are, the 1-hour program examines the genealogy of a celebrity, typically focusing on one or two of their most interesting families.

DNA Testing

This episode was of particular interest to me because it featured Ancestry.com’s new autosomal DNA testing service, which I’ve written about before (see “Ancestry.com’s Autosomal DNA Product – An Update”). While there wasn’t too much new information about the DNA product in this episode, it was an interesting sneak peek at the service. ... Click to read more!

A Review of Family Tree DNA’s Family Finder – Part II

Blaine Bettinger 8 Comments

Last week I wrote about the results of my Family Finder autosomal DNA test by Family Tree DNA (see “A Review of Family Tree DNA’s Family Finder – Part I“).  The Family Finder test uses a whole-genome SNP scan to find stretches of DNA shared by two individuals, thus identifying your genetic cousins (and will soon include the Population Finder analysis of admixture percentages).  I currently have over 33 genetic cousins in Family Finder, and I’m working with them to identify our common ancestor(s).

The Affymetrix microarray chip used by FTDNA includes over 500,000 pairs of SNPs located on the X chromosome and the autosomes (no Y chromosome SNPs).  Via SNPedia:

FamilyTreeDNA uses an Affymetrix Axiom CEU microarray chip with 3,269 SNPs removed (563,800 SNPs reported) for autosomal and X (but not Y or mitochondrial) ancestry testing for $289. Other sources have cited 548011 snps. This platform tests 1871 of the 12442 snps in SNPedia. ... Click to read more!

Using Genome-Wide SNP Scans to Explore Your Genetic Heritage

Blaine Bettinger 6 Comments

Mary Carmichael, a science editor for Newsweek, is in the midst of a week-long dilemma.  This Friday, after reading a series of articles written by members of the DTC genetic testing community, she will decide whether she should purchase a genome-wide SNP analysis.  Although the decision might be a simple one for some, in light of the recent critique of DTC genetic testing in the media, in the literature, and by the government, it is certainly understandable that Mary is looking for further insight into her decision.

Today, Mary is asking “What Can I Learn From At-Home DNA Tests?” and has gathered answers to her question from a wide variety of writers and scientists, including myself.  Since the Newsweek site only has space for a brief introduction to each topic, this post is meant to be a more in-depth answer what Mary could learn about her ancestry from a DTC test. ... Click to read more!