Understanding Third Party DNA Analysis Tools. Copyright 2014 James R. Lannin, Jr. aka Jimmy Chromosomes

Transcription

1 Understanding Third Party DNA Analysis Tools Copyright 2014 James R. Lannin, Jr. aka Jimmy Chromosomes

2 A Review of the Basics You have 46 chromosomes and they come to you in 23 pairs from your mother and father. For each numbered pair of "Autosomes" (1 through 22) you have one from your father and one from your mother. And you have a Y from your father and an X from your mother if you are male, or an X from your father and an X from your mother if you are female. (Your Mitochondrial DNA - mtdna - comes from outside the nucleus so it is not part of this discussion.) From Autosomal DNA Segment Analyzer (ADSA) Manual by Don Worth on DNA Gedcom

3 A Review of the Basics (p2) Thus, you actually have two chromosome 13s, and two chromosome 6s and so on. And, if you are female, you have two X chromosomes also. Most chromosome browsers plot only a single horizontal bar to depict segments that match on a chromosome - but a sequence of your DNA that matches someone else's (also known as a matching segment) can be on either chromosome of your or your match's pairs. This means two matching segments could occupy exactly the same location on a given chromosome but actually represent matches to two different common ancestors on opposite sides of your family - one in your mother's tree and one in your father's tree. From Autosomal DNA Segment Analyzer (ADSA) Manual by Don Worth on DNA Gedcom

4 A Review of the Basics (p3) Not all matching segments are representations of a legitimate DNA match. Because Family Tree DNA's autosomal DNA sequencing produces un-phased data (where the DNA values of your mother's and father's chromosomes at each genetic marker are not identified separately but are presented as a pair of letters in an arbitrary order at each SNP) it is possible for the equipment to find sequences of seemingly matching DNA when, in fact, matching markers are coming alternately and randomly from both chromosomes in the pair. From Autosomal DNA Segment Analyzer (ADSA) Manual by Don Worth on DNA Gedcom

5 Match? or No Match? Consider this example: From Autosomal DNA Segment Analyzer (ADSA) Manual by Don Worth on DNA Gedcom

6 Match? In the diagram above, let's imagine that the two chromosomes at the top are your chromosome 13 pair. And let's suppose the topmost one is from your father and the one just below it is from your mother. The "ladder rungs" that connect the strands of the double helix of one chromosome are pairs of molecules called "bases". A "rung" can be a Guanine molecule attached to a Cytosine molecule or an Adenine attached to a Thymine. Each "ladder rung" along a chromosome is called a "base pair" and is numbered from zero at the start of the chromosome to a number in the 100s of millions at the end of the chromosome, depending on the length of the particular chromosome. From Autosomal DNA Segment Analyzer (ADSA) Manual by Don Worth on DNA Gedcom

7 Or The vast majority of these base pairs (about 99%) are structured identically in all human beings. Only 1% of the base pair locations on a chromosome vary from one person to another. Base pairs that can differ between people are called SNPs (Single Nucleotide Polymorphisms - or "snips") and are what allows us to compare and contrast individuals' DNA. In the example above, when comparing your DNA to someone else's, the testing company compares either of the letters that appear at a given horizontal location along your two chromosomes with either of the letters that appear in the same location on the same chromosome pair of someone else's test results. From Autosomal DNA Segment Analyzer (ADSA) Manual by Don Worth on DNA Gedcom

8 No Match! For a match to be legitimate, all of the comparisons of a segment should come from the same chromosome of your pair and your predicted cousin's pair. However, you can see that, while this is the case for the last four SNPs in the example above, it is not the case for the first four. The comparison for the first half of the segment switches back and forth between chromosomes. The resulting "match" of the first four SNPs in this segment is not a match at all. Only the last half of this segment is a legitimate DNA match, and even then, your two chromosomes don't have tiny "Mom" and "Dad" labels on them, so the sequencer can't tell you which side of the family the match is on. From Autosomal DNA Segment Analyzer (ADSA) Manual by Don Worth on DNA Gedcom

9 Identity by State, Not Descent From Autosomal DNA Segment Analyzer (ADSA) Manual by Don Worth on DNA Gedcom

10 Definition of centimorgan (from ISOGG wiki) A centimorgan (abbreviated cm) is a unit of recombinant frequency which is used to measure genetic distance. It is often used to imply distance along a chromosome, and takes into account how often recombination occurs in a region. A region with few cms undergoes relatively less recombination. The number of base pairs to which it corresponds varies widely across the genome

11 Half-identical region A Half-identical region (HIR) is a region of two paired chromosomes where at least one of the two alleles from one person's pair of chromosomes matches at least one of the two alleles from another person's pair of chromosomes throughout the entire region. A half-identical region may be either identical by descent (IBD) or identical by state (IBS).

12 Identical by Descent or Identical by State? An Identical by Descent (IBD) segment is a segment of DNA that is found to be identical (except for rare mutations or testing errors) in two people who are related to each other due to the fact that this segment was passed down to both of them from a common ancestor. An Identical by State (IBS) segment is a region of the genome where two people by coincidence share at least one matching base pair for the entire region. In such cases the segment does not come from a common ancestor.

13 ISOGG wiki statistics: Parent/child: cms 1st cousins: cms 1st cousins 1R: cms 2nd cousins: cms 2nd cousins 2R: cms 3rd cousins: 43-ca 150 cms 3rd cousins 1R: cms More distant cousins: 5-ca 50 cms image by Dimario, Wikimedia Commons

14 DNA Segments Shared With Matches End of 8 cm Segment 1 Start of 10 cm Segment 2 8 cm Segment 10 cm Segment Start of 8 cm Segment 1 End of 10 cm Segment 2 An 8 cm Segment match has a 50% chance of being Identical by Descent. A 10 cm Segment match has a 99% chance of being Identical by Descent. Table from John Walden and the International Society of Genetic Genealogy - ISOGG)

15 So Which atdna Matches Do I Compare With? Half of your 8 cm matches are Identical By Descent, half are Identical By State. Your 10 cm and above segment matches are almost certainly IBD. The larger the largest matching segment, the closer in generations is the MRCA. For the highest success rate, focus first on matches with 10 cm + segments in common.

16 Shared DNA Cheat Sheet by Kelly Wheaton KELLY (MOSIER) WHEATON Download the Shared DNA Cheat Sheet created by Kelly Wheaton from her link below.

17 DNA Segment Matching Tools Now that you ve received your atdna Test Results, what can you do with them? Find cousins! Discover your biogeographical origins! You Cousin 1 Cousin 2 Using 3 rd Party analytical tools is a great way to learn more about your matches (like which side of the family they re on) as well as ascertain which matches are IBD, IBS, or Undetermined

18 Me Cousin A Cousin B Sharing Matches with Matches TRIANGULATION

19 The Five Steps to Triangulation Collect many segments of your matches. Arrange them by chromosome and segment starting location number. Compare and group the overlapping segments. Assign Triangulated Groups to Paternal and Maternal sides of your family. Determine the MRCAs for each Triangulated Group and the Common Ancestor between you and the group.

20 Triangulation Steps to Common Ancestors CoAs & MRCAs Assign Triangulated Groups Compare and Group by Overlap, ICW Relationships Arrange Segments by Chromosome Collect Many DNA Segments of Your Matches

21 Why Does Triangulation Work? Two Scenarios for Mary to Have Two Matches on One Segment Scenario #1: Mary has matches on two halves of a chromosome pair. Chr. Mary John Sam Side M ACTGACTG ACTGACTG GAGAGAGA Mary s Maternal Ancestor P CGCGCGCG ATATATAT CGCGCGCG Mary s Paternal Ancestor Mary matches John & Sam, but they do not match each other. John & Sam are related to Mary on opposite sides of her family, John on the Maternal, Sam on the Paternal. Scenario #2: Mary has matches on only one half of a chromosome pair. Chr. Mary John Sam Side M ACTGACTG ACTGACTG ACTGACTG Mary s Maternal Ancestor P CGCGCGCG ATATATAT GAGAGAGA Mary s Paternal Ancestor Mary matches John & Sam, and John and Sam match both Mary and each other on the same segment. They are all three related on the same side of Mary s family, in this case, the Maternal side. They are a Triangulated Match.

22 DNAGedcom.com View and Analyze your Segment Matches by Chromosome From 1-22 Plus X

23 DNA Gedcom HomePage

24 DNA Gedcom Registration Page

25 DNA Gedcom Login Page

26 Upload AncestryDNA Raw Data to DNA Gedcom

27 AncestryDNA Helper Tool by Jeff Snavely

28 Download Data From FTDNA to DNA Gedcom

29 Download Data From FTDNA to DNA Gedcom

30 Download Data From 23andMe to DNA Gedcom

31 Download Data From 23andMe to DNA Gedcom

32 Autosomal Tools Menu

33 Autosomal DNA Segment Analyzer (ADSA) - Version 2

34 What the ADSL Manual Covers

35 ADSL Links to Manual & Quick Start Guide

36 Links to Manual & Quick Start Guide ADSL Manual by Don Worth - ml.php ADSL Quick Start Guide - al.html.php

37 ADSA DNA Segment Analysis Page

38 Jworks Download Page (Juan Pizarro)

39 Kworks (Kitty Munson Cooper)

40 Sample X Chromosome Matches DNAGedcom Note: I used a minimum segment length of 2 cms and a minimum SNP count of 500. When asked what a good minimum comparison size for X Chromosome matches was, Roberta Estes of the DNA Explained blog said: Regarding what is a good match, it s both the cm length, generally over 7, and the total number of SNPS in that segment, generally over 500. Since males have only 1 X Chromosome, shorter segment lengths can be considered.

41 Created and Operated by John Olson and Curtis Rogers GEDMatch.com Tools for DNA & Genealogy Research

42 My GEDmatch Home Page

43 GEDmatch Statistics as of August 2014 The GEDmatch database contains data from are over 80,000 DNA kits. The Gedmatch genealogy database contains records of 25 million individuals. GEDmatch has over 50,000 registered users. Big Three DNA Testing Company Statistics as of August 2014 Dr. Maurice Gleeson at the International Genetic Genealogy Conference, Aug 2014

44 What is Gedmatch? GEDmatch is a website which accepts uploads of data from the three major testing companies. Steps to start using GEDmatch: Register and select a username and password. Upload your data following the clear instructions. Most of the tools are usable within an hour of upload. The One to Many comparison tool may take a day to be available, due to time required to process data.

45 What Can I Do at GEDmatch View your Admixture (ethno-ancestry composition). Compare your DNA results to others. Phase DNA results to one or more parents. Analyze your DNA. Compare or search GEDcoms

46 GEDmatch Data Analysis

47 Determining your deep ethnic ancestry. ADMIXTURE

48 Admixture Calculators Creations of Citizen Scientists Results are approximations; there is no guarantee of accuracy. The results can take a minute or more. Results have a link to creator s Project Page. Select the Admixture (heritage) option to view choices. For best results choose tests based on your predominant ethnic ancestry.

49 Select an Admixture Calculator Selecting the MDLP Project, then choosing the World-22 Admixture Proportions Calculator will give a good overview for a first-time user.

50 Magnus Ducatus Lituaniae Project - BGA analysis project for the territories of former Grand Duchy of Lithuania. Admin: Vadim Verenich Co-admin: Leon Kull MLDP PROJECT

51 MDLP World-22 Admixture Proportions

52 Admixture Graphing and Calculations by Dienekes Pontikos DODECAD

53 Meet the Ancestors!

54 Admixture Results by Chromosome

55 Dodecad V3 Admixture Proportions

56 Dodecad V3 Admixture Proportions Chromosome Painting

57 Davidski David Wesolowski Admixture Graphing EUROGENES PROJECT

58 Eurogenes K13 Admixture Proportions

59 Eurogenes K36 Admixture Proportions

60 Eurogenes Hunter Gatherer vs. Farmer Admixture Proportions

61 Eurogenes Jtest Admixture Proportions

62 Eurogenes EUtest Admixture Proportions

63 Feature Benefits of Admixture Options MDLP World 22 General Overall compares with 22 populations Worldwide. Dodecad - General Populations and Africa Eurogenes Best for Europeans, has some special extras (Jewish, hunter gatherer) HarappaWorld Best choice for South Asia Ethiohelix Best choice for African ancestry, use Africa+French with European mixture.

64 GEDmatch Data Comparisons

65 One to Many Matches

66 One to One Comparison

67 X One to One Comparison

68 GEDmatch Miscellaneous Utilities

69 Phasing

70 People Who Match One or Both of Two Kits Input Screen

71 People Who Match One or Both of Two Kits

72 Predict Eye Color

73 Are Your Parents Related?

74 Are Your Parents Related?

75 Are Jim s Parents Related? NO!

76 3-D Chromosome Browser Input

77 3-D Chromosome Browser

78 3-D Chromosome Browser

79 3-D Chromosome Browser

80 Archaic DNA Matches

81 DNA File Diagnostic Utility

82 GEDmatch Kit Numbers GEDmatch assigns a letter prefix to your testing company s kit number: A****** for AncestryDNA F****** for FamilyTreeDNA M****** for 23andMe Forgetting to include the initial letter of the GEDmatch kit number is one of the biggest reasons for GEDmatch tools not to work.

83 Rebecca Walker Attended University of Alaska Anchorage Lives in Kansas City, Missouri Beckins LLC Genome Mate Desktop Software A Tool for Managing DNA Comparisons

84 Genome Mate

85 Tracking & Organizing Your Matches Until now, Genetic Genealogists needed to be competent, if not expert, in the use of spreadsheet software like Excel, if they wanted to track and organize their DNA matches to find MRCAs and CoAs. Setting up and organizing the columns, rows and cells can be confusing for some. Now, there is a desktop computer program which does all of the hard stuff for you. It is:

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87 What is Genome Mate? Genome Mate is a desktop tool used to organize in one place the data collected while researching DNA comparisons. Besides data storage it has many features to aid in identifying common ancestors. Genome Mate is like a dashboard, a central control system for your Genetic Genealogy Investigations. Works with FamilyTreeDNA, AncestryDNA, DNAGedcom, GEDmatch and 23andMe,. Download at:

88 What is Genome Mate? Genome Mate can be downloaded for free, but it s author, Rebecca Walker, asks that if you like it and use it, please make a donation. If you use Genome Mate, you ll agree that she deserves it! To make best use of Genome Mate, you should have already uploaded your data to DNA Gedcom and GEDmatch. Instructions for downloading data into Genome Mate are easy to follow if you read them carefully. Download Genome Mate at: Clear instruction for using Genome Mate can be found on Rebecca s blog at

89 Features Multiple Profiles for multiple kits Import of 23andMe, FTDNA and GedMatch data Chromosome Mapping of Common Ancestors In Common With (ICW) Groups Import of Gedcom data for each Profile Surname Matching and Searching Display of Overlapping Segments X-List of X Chromosome Donors All of your data is stored locally on your computer. A server is used to initially download the application and to install updates as they become available.

90 Main Page The main screen displays DNA comparisons sorted by chromosome and segment start/end points. These can be filtered by several means so that just the data of interest is displayed. Data is displayed both graphically and in table format. Research notes can be added and are maintained in a database on your computer. The application supports multiple profiles so there can be a profile for each relative tested. When the most recent common ancestors (MRCA) are found for a DNA segment, these can be added to the chromosome map. One of the most useful functions is the the ability to look at all the matches which overlap a DNA segment across all sources (23andMe, GedMatch, FTDNA) since not everyone subscribes to all three.

91 Links to More Information App Overview Getting Started with 23andMe Data Getting Started with FTDNA Data Getting Started with GedMatch Data Getting Started with Ancestry Data You Tube Videos Getting Started With Genome Mate Genome Mate Demo ICW on Genome Mate

92 Import Data Screen

93 Table View

94 Graph View

95 Triangulated Matches on Graph Page

96 Match Details Page

97 Segment View

98 User Options Screen

99 Setup Form Letter Screen

100 Sample Initial Sent to a Match Redacted

101 Neanderthal Denisovan Bronze Age Neolithic Farmers Paleolithic Hunter-Gatherers Genetic Genealogy Tools and Other Things Felix Jeyareuben Chandrakumar Works at Hewlett-Packard Australia Pty. Limited Attended University of South Australia Lives in Adelaide

102 Felix s Popular Tools

103 BAM Analysis Kit

104 Genetic Genealogy Kit

105 Genetic Genealogy Kit Ethnic Origins

106 Genetic Genealogy Kit Mito-Map

107 Genetic Genealogy Kit Mito-Map Details

108 Genetic Genealogy Kit Mitochondrial Phylogeny

109 Genetic Genealogy Kit New Kit Screen

110 Genetic Genealogy Kit Matching Kits

111 Genetic Genealogy Kit Phased Segment Visualizer

112 Genetic Genealogy Kit Phasing Utility

113 Genetic Genealogy Kit ISOGG Y-Tree

114 ISOGG Y-Tree AddOn for Google Chrome

115 SNP Map A program to view SNP data, and see how the data compares to other populations and regions of the world.

116 What is SNP Map? The purpose of SNP Map is to help you explore your autosomal genome data from 23andMe or FamilyTreeDNA. In particular, it's meant to help identify segments of your chromosomes that show ancestry, either recent or ancient, that show similarities with different regions of the world, and the populations within those regions.

117 What Does SNP Map Compare? One thing you'll discover, is that genetically, people all over the globe are quite similar. At some positions on the chromosome, people can have alternate alleles for that position. Some of these are the SNP locations that the DNA services test. Although any allele can occur in people from any part of the globe, studies have shown that the frequencies of the alleles are often different among people from different parts of the world.

118 What Does SNP Map Help You Do? For most SNPs the frequency differences are small - too small to be very useful for identifying the region or population from which a person might have ancestry. But there are some SNPs that have sizable frequency differences. These difference usually vary over distance, so that the difference is small between adjacent populations, or even adjacent regions, but significant between distant regions. Finding these SNPs and displaying information about them is what SNP Map helps you do.

119 SPA Special Ancestry Analysis Predict Ancestry or Geographic Origin Produces 2 and 3 Dimensional Mapping

120 SPA Overview

121 SPA Download Page

122 Geographic Population Structure Prediction A new journey into your ancestry!

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124 Kitty Munson Cooper s DNA Utilities Tools for DNA Analysis

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128 Make a graphic chromosome map from a CSV of overlapping segments KITTY COOPER S SEGMENT MAPPER

129 Kitty Cooper s Segment Mapper Input Screeen

130 Kitty Cooper s Segment Mapper Sample Output

131 Sometimes you might like to see a detailed picture of all the largest overlapping DNA segments on one chromosome. KITTY COOPER S ONE CHROMOSOME MAPPER

132 Kitty Cooper s One Chromosome Map Input Screen

133 Kitty Cooper s One Chromosome Map Sample Output

134 For Once You ve Found a Few Common Ancestors KITTY COOPER S ANCESTOR CHROMOSOME MAPPER

135 Kitty s Chromosome Mapper - Input Screen

136 Kitty Cooper s Ancestor Chromosome Mapper Sample Screenshot

137 Sample Output Kitty Cooper s Chromosome Mapper Sample Output from Jim Bartlett

138 Anders Pålsen, a Norwegian Genetic Genealogy Blogger FENNOSCANDIA BIOGRAPHIC PROJECT

139 Fennoscandia Biographic Project Home Page

140 Anders Pålsen does Nordic DNA Analysis All grandparents born in Norway, Sweden or Finland? your 23andme/FamilyFinder/deCODEme genotype file zipped to NEW! Estonians, Lithuanians, Latvians, Germans, Nederlands, Belgians, Luxenbourg, Austrians, Checkz, Slovaks, Balkans, Danes, Poles, Icelanders and Russians also welcome! ANALYSIS STATUS: FILE PREPARATIONS!

141 When All is Said and Done SOME CLOSING THOUGHTS

142 DNA Test Analysis Timeline Get Autosomal Test Results Upload to GedMatch and/or DNAGedcom Contact and Collaborate Study Your 10 cm+ Matches Triangulate ICW Matches This is a simple timeline to illustrate the recommended process to move from DNA testing to finding genetic cousins and enlisting them in a collaborative effort to develop the genealogical links between matches. Additional benefits can include a better understanding of our deep ancestral heritage.

143 The End Presentation Copyright 2014 James R. Lannin, Jr. aka Jimmy Chromosomes