Walter Steets Houston Genealogical Forum DNA Interest Group April 7, 2018

Transcription

1 Ancestry DNA and GEDmatch Walter Steets Houston Genealogical Forum DNA Interest Group April 7, 2018

2 Today s agenda Recent News about DNA Testing DNA Cautions: DNA Data Used for Forensic Purposes New Technology: DNA and Your Next Car GEDmatch Login Registering at GEDmatch Raw Data File Uploads Analyze Your Data Tools - Free Tier 1 Tools Fee based GEDmatch Genesis 2

3 DNA Data Used for Forensic Purposes GEDmatch Database Used by Authorities in a Washington State County to Identify an Unknown Deceased Person Agencies in Grays Harbor County, Washington had not been able to identify an apparent suicide which occurred in A group of volunteers at the DNA Doe project worked with county authorities to obtain a DNA sample for the person and load it into GEDmatch. GEDmatch presented some likely possibilities for his ancestry and provided some closed genetic matches which are being used to try to locate his extended family. Blaine Bettinger and other administrators of the Genetic Genealogy Tips & Techniques Facebook group posted the story with comments about the implications for genetic genealogy. Summary of Blaine Bettinger s Comments Bettinger believes that the Genetic Genealogy Tips & Techniques FB group should educate you, the genealogist using DNA, about all uses of DNA, including those not related to genealogy. For true informed consent, we must recognize that most of our test-takers know nothing about DNA. You as the family genealogist have an ethical obligation to help your potential test-takers be informed so they can give true informed consent. As a practical matter, It may only take a few negative news stories or litigations to cause many restrictions to be placed on DNA testing. There are things you can do to alleviate, but not completely erase, concerns (pseudonyms, new addresses, and so on).

4 LEXUS & 23ANDME: THE FUTURE OF CAR BUYING 4

5 Why Use GEDmatch Analyze Ancestry Segment Data Detailed data on DNA segments shared with your Matches may help identify your shared ancestors AncestryDNA reports total amount of DNA and number of DNA segments shared with your matches but no detailed information about each shared DNA segment GEDmatch provides reports and graphical displays including chromosome browsers about matches shared with Matches Analyze the DNA Your Matches Share with Each Other Ancestry and most other DNA testing companies provide data on DNA you share with your matches but no data on the DNA your Matches share with each other. Do Cross-company Matches Raw DNA files from Ancestry, FamilyTreeDNA, and MyHeritage may be loaded into either GEDmatch Classic and GEDmatch Genesis, the new version of GEDmatch currently completing development DNA files from 23andMe received before August, 2017 may be uploaded and compared in GEDmatch Classic Newer 23andMe data files must be loaded into GEDmatch Genesis GEDMatch Classic contains 1,000,000 DNA kits; Ancestry contains 7,000,000 5

6 DNA Data Transfer Process AncestryDNA.com GEDmatch.com Are Your Parents Related One-to-many matches Autosomal Matrix Comparison 2-D Chromosome Browser One-to-One Comparison DNAPainter.com Paint a New Match using data copied from GEDMatch Ancestry Raw Data File Copy GEDmatch One-to-One Data 6

7 Log Into GEDmatch 7

8 GEDmatch Registration GEDmatch registration is free One GEDmatch account can be used with DNA kits for multiple people Privacy and Security Considerations Optional Alias Use an alias, also called a nick name or a screen name, to avoid use of your real name. Address must be a real address but it can be one you create to use only for DNA contacts Use a free provider (e.g.dna23@gmail.com ) Use your internet provider (e.g.dna23@comcast.net) Password Always use a different, strong password for every online account. 8

9 GEDmatch Tools Selection Page Four Groups of Tools File Uploads Load DNA raw data files from most DNA testing companies Load GEDCOM files from genealogy websites and PC software (e.g. Ancestry) Analyze Your Data Free tools for analyzing DNA data Tier 1 Utilities Fee-based Tools - $10./month More advanced analysis Genesis Beta Accepts raw DNA data from companies previously not compatible with GEDmatch (e.g. newer 23AndMe) New algorithm with lower thresholds and better accuracy 9

10 GEDmatch raw DNA upload utility 10

11 GEDmatch Raw DNA Upload Utility Creates GEDmatch kits GEDmatch kits are uploaded DNA raw data files Your address from your GEDmatch profile Name of DNA file owner real name Alias nick name or screen name for this kit Sex of DNA file owner Mitochondrial haplogroup optional Y haplogroup optional Are you authorized to upload this data? Choose File - Browse to the file on your computer containing the DNA raw data file Upload - Upload the file Upload may take several minutes 11

12 GEDmatch Tool Set: Analyze Your Data Order of Tool Use 1. Are your parents related? detects matching segments within your chromosomes. Unlikely but need to know. 2. One-to-many matches - Similar to Ancestry Matches a. Matrices Autosomal Matrix i. Identifies Shared Matches ii. limited to 5 matches in free version b. Chromosome Browsers 2D Chromosome Browser i. Identifies shared DNA segments c. Tag Groups Combine related matches into a Tag Group 3. Multiple Kit Analysis New Select Chromosome Browser, Matrices, and other tools by Tag Groups 4. People who match one or both of 2 kits i. Alternative to Matrix for identifying Shared Matches ii. Free version displays a large number of shared matches 5. One-to-one compare 12

13 Analyze Your Data: Are Your Parents Related? Effect of Closely Related Parents on Genetic Analysis May not be able to distinguish paternal from maternal cousins. Both chromosomes in a chromosome pair can have segments from the same ancestor. Genealogical paternal cousins can match maternal cousins if they share DNA segments from the ancestor common to the parents. Relationship estimates based on the total amount of shared DNA may be too close Shared DNA may include contributions from more than one ancestral line increasing the amount of shared DNA Are Your Parents Related Tool? Checks whether any of the pairs of chromosomes in your genome have matching segments. 13

14 Analyze Your Data: One-to-many Matches Displays DNA kits matching a base kit. Comparable to Matches in Ancestry. Kit Nbr Identifier for DNA Raw data sets loaded into GEDMatch. First letter indicates testing company List clicking L displays the One-to-many Matches for that Kit Nbr Select clicking allows matches to be selected for chromosome or matrix comparisons Autosomal and X-DNA Details clicking A or X displays one-to-one comparison between base kit and A row kit Total cm total shared cm Largest cm length of single largest shared segment Gen GEDmatche s estimate of the number of generations between MRCA and match Name name or alias of match 14

15 Analyze Your Data: Choosing Visualization Options After Selecting matches and clicking Submit in the One-to-many tool, the following screen will be displayed. Kits included shows the kit numbers of the kits selected on the One-to-many page Chromosome Browsers chooses the Chromosome Browser tools Matrices chooses the Matrix tools. On the screen below, Matrices have been clicked GEDcom Searches for matches within GEDComs. List/CSV used to download your matches or your matches with detailed segment data as Excel files Tag Groups combines the kits selected in One-to-many into a set called a Tag Group and then used in the Chromosome Browsers 15

16 Maternal Paternal Paternal Analyze Your Data: Autosomal Matrix Sharron s Matches Maternal Paternal Maternal Maternal Paternal Maternal Paternal Maternal Maternal Maternal Maternal Maternal Maternal Maternal Paternal Maternal Maternal 17

17 Analyze Your Data: Autosomal Matrix Sharron s Maternal Matches 18

18 The origin of IBD segments is shown using a pedigree chart of 12 individuals. Segments which are Identical by Descent (IBD): Example of 1 st Cousins Each box (male) and circle (female) represents a chromosome pair for the named person. For example, bars could be the chromosome pair for chromosome 1. Due to crossing over, offspring inherit recombinant chromosomes of their parents. The first cousins in the bottom row, Karen and Louis, share one IBD segment (borders marked by grey lines). Both have inherited this IBD segment from the same individual, namely their grandfather Carl (orange colored chromosome in the top row). Albert Bertha Carl Donna Edward Fiona Gregory Helen Ian Janice Karen Louis Adapted from Gklambauer, Wikimedia Commons 19

19 Analyze Your Data: Chromosome Browser Sharron s Maternal Matches Matches IDs 1, 2, 3, 4, 5, & 6 share a segment from a common ancestor who is not an ancestor of Match ID 7 - norapru8 20

20 Analyze Your Data: Chromosome Browser Sharron s Paternal Matches Norapru8 shared this segment from a common ancestor with Sharron s close relatives but not more distant ones. 21

21 Analyze Your Data: People who match both kits, or 1 or 2 kits Equivalent to Ancestry Shared Matches but displays more data Provides a list of all Shared Matches including Match kit number of match Shared total amount of shared DNA Largest length of longest DNA segment Gen GEDmatch s estimate of number of generations to MRCA 23

22 Analyze Your Data: Tag Groups Kits included in Tag Group kits were matches selected in the One-to-many tool For this set of kits, create a Tag Group with Description for example, family name or relationship Color choose a unique color for Tag Group Include First Kit indicate whether the first kit on the kit list, the base kit in the One-to-many selection, should be included in the group

23 GEDMatch One-to-One Comparison Tool Provides detailed information for each DNA segment shared between two kits Chr chromosome number Start Location starting location in megabase pairs (Mb) End Location end location in megabase pairs (Mb) Centimorgans amount of shared DNA in cm SNPs number of single nucleotide polymorphisms contained in segment This data may be copied and pasted into the DNAPainter chromosome browser. Comparing Kit M (Sharron ) and T (SD) 25

24 GEDmatch Tool Set: Tier 1 Utilities Order of Tool Use 1. One-to-many matches New Version! New version of the free One-to-many tool a. Matrices Autosomal Matrix i. Identifies Shared Matches ii. limited to 5 matches in free version b. Chromosome Browsers 2D Chromosome Browser i. Identifies shared DNA segments c. Tag Groups Combine related matches into a Tag Group 2. Triangulation Groups a. Graphic Tree results for each Triangulation Group b. Graphic Bar results for each chromosome 3. Triangulation a. List of triangulated segments, segments shared with base kit and two other kits. List may be cut and pasted into a spreadsheet 26

25 Tier 1: One-to-many Matches New Version! Displays DNA kits matching a base kit. Comparable to Matches in Ancestry. Select clicking allows matches to be selected for chromosome or matrix comparisons Kit identifier for DNA Raw data sets loaded into GEDMatch. Color identifies Tag Group First letter indicates testing company. Clicking on Kit displays one-to-one comparison between base kit and clicked kit Name and name or alias and address for match contact Autosomal and X-DNA Total cm total shared cm Largest length of largest shared segment. Clicking on Largest displays One-to-many tool Gen GEDmatch s estimate of the number of generations between MRCA and match 27

26 Tier 1: Triangulation Groups - Graphic Tree Results Tree representation of Triangulation Groups each box shows Kit number and name of member of Triangulation Group Chromosome number and length of shared DNA Left-most chart shows position of shared segment on genome 28

27 Tier 1: Triangulation Groups Graphic Bar Results Shows Triangulation Groups by Chromosone 29

28 Tier 1: Triangulation Shows Triangulated Segments - all segment matches where the segment is shared between the base kit and two other kits. Several thousand matching segments may be displayed. Most triangulated segments are less than 20 cm so single segment matches are probably 4 th cousin or greater. Hovering over the Kit number with the mouse cursor displays the name and address of the shared match 30

29 GEDmatch Tool Set: Genesis Beta 31

30 GEDmatch Tools Selection Page - Review Four Groups of Tools File Uploads Load DNA raw data files from most DNA testing companies Load GEDCOM files from genealogy websites and PC software (e.g. Ancestry) Analyze Your Data Free tools for analyzing DNA data Tier 1 Utilities Fee-based Tools - $10./month More advanced analysis Genesis Beta Accepts raw DNA data from companies previously not compatible with GEDmatch (e.g. newer 23AndMe) New algorithm with lower thresholds and better accuracy 32

31 Questions? 35