DNA Doe Project · 2019-09-09 · •Sep 27, 2017 Joseph Chandler case uploaded to GEDmatch DNA DOE...
Transcript of DNA Doe Project · 2019-09-09 · •Sep 27, 2017 Joseph Chandler case uploaded to GEDmatch DNA DOE...
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DNA DOE Project Our First Two
Years of Success
Colleen Fitzpatrick, PhDMargaret Press, PhD
Co-FoundersDNA Doe Project
ISHI 3024 Sep 2019
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• Sep 27, 2017 Joseph Chandler case uploaded to GEDmatch
DNA DOE Project Chronology
• Feb 2017 First discussions
• Jul 10, 2017 First sample sent to lab for sequencing
• Oct 2017 Incorporated as 501(c)3
• Mar 6, 2017 Joseph Newton Chandler identified
• Mar 29, 2017 Buckskin Girl Identified
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DNA Doe Project StatsSept 2019
Shortest Solve Time 4 hrs
Avg Solve Time 60 days (no outliers)
Longest Solve Time 19 ½ mos
Volunteers ~ 70
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More DNA Doe Project StatsSep 2019
Bone extraction stage 6
Bioinformatics 7
Genealogical Research 17
Success Stories 16
DNA Processing 19
Total 68
Waiting shipment to lab 3
Only 1 slam dunk
~50% Success rate
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Active CasesPending CasesSuccess Stories
© 2019 Sarah Kladar
All
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Initial Challenge of Using Degraded DNA
• DNA was degraded – 88% No calls
Question: Would genetic genealogy tools work for degraded samples?
Joseph Newton Chandler III
• Nonuniform SNP Distribution
SNP Coordinate
Cal
l Rat
e
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Low confidence: Many matches
High confidence: Few matches
We found a happy medium
Initial Challenge - Degraded DNA
We still use a three- kit model
• Experimented with Confidence Levels
SNP Coordinate
Cal
l Rat
e
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• Degraded Our Own 23&Me data to match Chandler’s, compared matches before & after
Rank on GEDmatch Before
Ran
k o
n G
EDm
atch
Aft
er
Initial Challenge - Degraded DNA
Closest matches are the same rank
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Initial Challenge - Degraded DNA
➔ Initial 88% decreased to 55% no calls
➔More matches
➔ Solved the case
• Two 30x sequences ➔ One 60x sequence
30x
30x
60x
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Lessons Learned
• Single most important decision: Who will process the DNA sample?
- Your sample will be consumed
- Is it degraded or contaminated?
- Can the company handle compromised DNA?
• What is the quality/quantity of your DNA sample?
- With wrong type of processing the evidence will be lost forever
• Genealogy can always be redone
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~1 ng
ng DNA
SNP
Cal
l Rat
e
~70
%
~4 ng
~10
%~1
00
%
Lots
Whole Genome Sequencing
Both
Quantity vs Quality
> 1 ng70 % Call Rate
> 4 ng10 % Call Rate
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Advantages of WGS over Chip-Based Technology
• Unaffected by changes in DTC SNP testing platforms
• You have the whole genome on your hard drive
- No further degradation
- Sample will not be exhausted
• More robust when applied to degraded DNA
• Sequence can be reused to create multiple GEDmatch kits
• WGS includes mtDNA, Y-DNA, CODIS markers, SNPs
• Sequences can be combined to improve data
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What You Must Know about GEDmatch
• Terms of Service – Member default opt-out for law enforcement use
• Users must now opt-in to allow law enforcement to use their accounts
• Aggressive campaign to get users to opt-in
• August 2019 = 120,000 opt-ins = ~10%
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What You Must Know about FTDNA
• Terms of Service – Member default opt-in for law enforcement use
• Law enforcement required to complete submission form, identify themselves
• Only top 20 to 40 matches are shown
• Law enforcement upload costs $700
• If you have a close match, you receive reports, not access
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Three Main Challenges
• Condition of DNA
• Database composition
• Manpower limitations 70 Volunteers300 on waiting list
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- 99% no calls, improved with imputation
- Only 7.2% human DNA
DNA Challenges & Success Stories
- WGS successful with 4 ng
- Highest match 1C1R despite database restrictions
- 99% bacterial contamination
- Proprietary bioinformatics software
Heavy contamination
Mill Creek Shed Man
Degraded and contaminated DNA
Butler Co Jane Doe
Low input DNA
Orange Socks
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- Matches who do not know their parents
- Need extra time to solve a mystery to solve the mystery
- Father from another country
- Genetic networks, segment analysis, Y & mtDNA
Database Challenges & Success Stories
- Matches share multiple family lines
- Follow segments, find non-endogamous lines
Endogamy
Belle in the Well
High incidence of unknown parentage in database
Sheep Flat Jane Doe
Recent immigration
Lyle Stevik
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Another Database Challenge & Success Story
- Some ethnicities are under-represented
- Half of unsolved cases Native American/Hispanic women
- Solutions evolving, pushing tools
- New Jane Doe case solved in 10 days with only opt-ins
- Prompted outreach through our NA/Hispanic Task Force
GEDmatch opt-out default and FTDNA restrictions
To Be Announced
Ethnic composition of database
Special Mention
Kern Co Jane Doe
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• Estimated 15k Man-hours
Range of Difficulty
Buckskin Girl• Four clock hours
• ~ 20 Man-hours
• About 10 volunteers
• 19 1/2 Months
• ~ 30 Volunteers
• 1st cousin once removed
• Highly contaminated DNA
Mill Creek Shed Man
• African American ancestry
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Acknowledgements
Our generous donors
Dr. Gregory MagoonAerodyne Research
Justin LoeFull Genomes Corporation
GEDmatch FamilyTreeDNA
NCMEC
Bode Cellmark Forensics, Inc.
Dr. Weining TangGenologue
Fulgent Therapeutics, LLC
DNA Solutions Othram, Inc.HudsonAlpha Institutefor Biotechnology
Lucigen Corp.
UNTHSC
Our wonderful volunteers
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For Further Information
www.DNADoeProject.org
www.facebook.com/DNADoeProject
DNA Doe Project
Forensic Genealogy Online Training
Forensicgenealogytraining.org