Walter Steets Houston Genealogical Forum DNA Interest Group May 5, 2018

Transcription

1 GEDmatch: The Golden State Killer Tier 1 Tools Walter Steets Houston Genealogical Forum DNA Interest Group May 5,

2 Today s agenda Walter s Take on DNA Developments Growth in Number of DNA Testers DNA from Old Letters Non-genealogical Uses of Genetic Genealogical Data GEDmatch Review Analyze Your Data Tools - Free Tier 1 Tools Fee based GEDmatch Genesis DNAPainter 2

3 Currently about 17 million people have taken DNA tests. Over twice as many people have tested since the beginning of 2017 than had tested up to that time. At the beginning of this year, Blaine Bettinger predicted that over 20 million will have been tested by the end of the year. Now it looks that that number will be too low. Based on current rates, Alon Keinan of Cornell University predicts that over 100 million people will have tested their DNA by Growth in DNA Databases 3

4 DNA From Old Letters Living DNA, a UK-based genetic genealogy company, plans to offer testing of DNA samples from old letters or stamps by the end of 2018 at a cost of $1,000 - $ 2,500. Costs will probably come down as the number of people using the service increases. The Family Curator (Denise May Levenick) gives the following suggestions for preserving your old letters for eventual testing: Best chances with letters where the flap, seal, and stamp are intact. Great if letter opener has been used to open the envelope. Letters with least handling are good (e.g. in a bundle of envelops, letters in middle of pack are best). Store in acid-free paper folders in cool, moderate conditions. Avoid handling, heat, moisture, and freezing. 4

5 Non-genealogical Uses of Genealogical DNA Non-genealogical Uses of Genealogical DNA Short Summary of Golden State Killer case Informed Consent Privacy Practices at DNA Testing Organizations 5

6 Non-genealogical Uses of DNA What are Non-genealogical Uses of DNA? Search for Identities of Unknown Deceased Persons The DNA Doe Project, working with authorities from local governments, raises money to pay for extracting and analyzing DNA from unknown deceased persons. The DNA data files are then loaded into genetic genealogy websites and used for research by volunteer genealogists. The objective is to locate living relatives of the deceased. Search by Adoptees for Biological Parents Groups such as DNAAdoption.com and DNA Detectives facebook group focus on bringing together volunteers with genetic genealogy and searching experience, and those seeking their biological family. They relay heavily on genetic genealogy companies and websites. Criminal Investigations by Law Enforcement Example of Golden State Killer 6

7 Example of Adoptee Search and Criminal Investigation Finding Lisa (Boston Globe) 1986 A five-year old girl named Lisa is found abandoned by a man claiming to be her father in trailer park in Scotts Valley, Calif. She is adopted and grows up in Los Angeles Lisa begins a search for her biological parents with the help of a volunteer group called DNAAdoption and the San Bernardino County Sherriff s Crimes Against Children unit After an extremely complex DNA, genealogical, and police investigation, Lisa s mother is identified as a woman who had disappeared in New Hampshire in Late 2015 Later that year, police identify the man who had abandoned Lisa in the trailer park as a man who had died in prison in California in 2010 and who had likely murdered multiple people in New Hampshire including Lisa s mother and four people in the Bear Brook State Park case. Early 2017 Paul Holes, an investigator for the Contra Costa District Attorney, learns of the use of DNA in finding the New Hampshire killer. He had been looking for a new way to investigate the Golden State Killer case and thought this might be a the way. 7

8 Golden State Killer: The Crimes The Crimes (Washington Post) : East End Rapists commits 2 murders, 30 rapes, and numerous burglaries in Sacramento, CA area : Original Nightstalker commits 6 murders and many rapes and other crimes in Southern CA around Ventura county Both series of crimes widely terrorize people in the affected areas. 8

9 2001 Golden State Killer: The Investigation part 1 DNA evidence from the victims of both sets of crimes shows that the East End Rapist and the Original Nightstalker were the same man now called the Golden State Killer. He is thought to have committee over 12 Murders, 50 Rapes and 120 Burglaries. Early 2017 Paul Holes, the investigator from the Contra Costa County district attorney s office, and the FBI obtain a DNA sample which had been successfully preserved. Many other DNA samples from the case had deteriorated. April, 2017 Investigators find a match to their sample on Ysearch.org, an open website run by Family Tree DNA to allow comparison of Y DNA. tests Based mostly on the DNA match and a pedigree tree uploaded by the match s daughter, investigators are granted a warrant to obtain a sample of an Oregon s man DNA. The man voluntarily provides a sample which shows that he is not the Golden State Killer. (Los Angles Times) 9

10 Summer, 2017 Golden State Killer: The Investigation part 2 Contra County investigators convert their DNA sample into a format which can be read by GEDmatch. The closest matches in GEDmatch are 10 to 20 kits estimated to be about third cousins. This leads to a set of third great grandparents from the early 1800 s. The Contra Costa investigators develop the descendent trees for the third great grandparents and store their results on Ancestry.com. Census data, old newspaper reports, and a gravesite locator are used to find deceased relatives. More recent descendants are found using police databases and websites such as LexisNexis. April, 2018 Eventually investigators develop family trees for about 25 family groups with thousands of members. The trees are searched for men about the killer s age who could be linked to the crime locations. Two suspects are found. A DNA test on the relative of one suspect eliminates him as a possibility. Sacramento sheriff s deputies puts the second suspect under surveillance and picks up a discarded item containing his DNA. The DNA from the Golden State Killer matches that of the suspect who is arrested. 10

11 Informed Consent DNA Tests Genealogists frequently persuade other family members to have their DNA tested. The genealogy community has emphasized the need to obtain informed consent before obtaining or disseminating information or DNA data of others. The possible use of DNA for non-genealogical purposes including law enforcement now needs to be part of information provided to potential DNA testers. Family Information Almost all information in pedigree trees and DNA is intrinsically family information. Should genealogists need to obtain the informed consent of their extended family before posting any genealogical information? 11

12 Privacy Differences between DNA Testing Companies Allows Downloads of DNA Raw Data Files Allows Uploads of DNA Raw Data Files Chromosome Browser provides detailed data about Marches DNA Displays Information about Shared Matches Privacy Statement AncestryDNA Family Tree DNA MyHeritage GEDmatch Yes. Owner of DNA must agree to downloads. Yes Yes No No Yes Yes Yes No Yes Yes Yes Same as for Match Same as for Match Amount of DNA which Match shares with Shared Match Ancestry Privacy Policy Family Tree DNA Privacy Policy MyHeritage Privacy Policy All GEDmatch Privacy Policy 12

13 Ethical Distinctions Between Genealogical and Non -genealogical Use of Family Information Impact of Discovery of Search on Search Subject Genealogical Search Subjects of search are distant ancestors who have been deceased for many years. There are few if any concerns for privacy or the impact of discovery on the subject of the search. Non-genealogical Search Subjects are frequently living persons. Privacy issues and discovery may have major impact on life of subject of search e.g. subject of search is identified as biological parent in case of adoption search. Requests to Genealogist for Search Assistance Genealogical Search Genealogist expects to be asked for assistance from other genealogists in locating shared deceased ancestors and are usually pleased to do so. Non-genealogical Search Genealogist may not wish to disclose private information about living family members to adoptees. Genealogists may be willing to provide information to law enforcement for major crimes but more reluctant to implicate family members in less serious crimes or more speculative investigations. Consent to non-genealogical Use Genealogical Search Genealogists intend for their information to be used for genealogical search. Non-genealogical Search While genealogist may have legally consented to other uses of their information, its not what they intended. Could genealogical research material be subpoenaed or become the subject of a search warrant? 13

14 Genealogists Expectations of Use of Genealogical Data What are Expectations of Genealogists of the Use of DNA and Pedigree Information? That most information genealogists post on genealogy websites about their family pedigree becomes public That some or all of their DNA test data becomes public That their public DNA and pedigree information will be used by other genealogists to discover more about their shared ancestors. What are genealogists expectations about nongenealogical uses of their family s public genealogical information? 14

15 What s The Balance Privacy vs. Genealogical Research Should Things Change? Genealogists Post Less Information? Genetic Genealogy Companies and Websites Require More Formal Consent Before Uploading Family Information and DNA? Display Less DNA Information e.g. No Chromosome Browsers? Place More Restrictions on Access to Family and DNA Information Especially for Non- Genealogical Purposes? What about DNA from Deceased Persons? Government Place More Privacy Restrictions on Genetic Genealogy Companies? Make Law Enforcement Obtain a Court Approval to Access Information and DNA Data on Genealogy Websites? This Photo by Unknown Author is licensed under CC BY-NC-ND 15

16 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 16

17 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 17

18 Log Into GEDmatch 18

19 Updated GEDmatch Notices Webpage 19

20 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. 20

21 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 21

22 GEDmatch raw DNA upload utility 22

23 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 23

24 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 24

25 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. 25

26 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 26

27 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 27

28 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 29

29 Analyze Your Data: Autosomal Matrix Sharron s Maternal Matches 30

30 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 31

31 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 32

32 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. 33

33 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 35

34 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

35 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) 37

36 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 38

37 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 39

38 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 40

39 Tier 1: Triangulation Groups Graphic Bar Results Shows Triangulation Groups by Chromosone 41

40 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 42

41 GEDmatch Tool Set: Genesis Beta 43

42 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 44

43 Questions? 47