M2 Flashcards
FIGG is adjacent to Forensic DNA Analysis, and needs to
fit in w/forensic needs, standards, etc.
FIGG uses forensic evidence that is the
custody of the LE agency/Forensic lab
Forensic Labs are better suited to make decisions about:
- Sample quality and quantity
- Whole sample consumption
- Maintaining chain of custody
- Choosing sequencing method
*Maintaining ownership of work products (genetic data/trees/records) - STR Profile Comparisons
FIGG Workflow Checklist
- Violent Crime or UHR & meets Policy, laws, and Terms of Service
- STR Profile Developed
- Uploaded to CODIS/National Database
- No Hits
- FDS performed (if permitted by law)
- Authorization to perform FIGG
- Is there Sufficient DNA extract remaining from original extraction
or - Return to original evidence item & generate new DNA extract
DNA Quality & Quantity Evaluation
- What is the DNA quantity & quality?
*When was the extract last quantitated? - Does the extract need to rehydrated?
- What is the volume of extract remaining?
- Where is the DNA extract?
- Is whole sample consumption allowed?
3 SNP Technology Methods
- SNP Microarray
- Whole Genome Sequencing
- Target Kit - Kintelligence
SNP Microarray
EVALUATES
~600,000 SNPs
AMOUNT of DNA NEEDED
~200 ng (but has shown to work with ~1ng)
COST
Cheapest $500-$700
EFFECTIVNESS
Not good with DEGRADED DNA
Whole Genome Sequencing (WGS)
EVALUATES
Whole
AMOUNT of DNA NEEDED
50ng-50pg
COST
Most Expensive $1,500-$8,000
EFFECTIVENESS
Recommended for DEGRADED DNA
Target Kit - Kintelligence
by Verogen
EVALUATES
~10,230 SNPs
AMOUNT of DNA NEEDED
1ng
COST
Mid-Range $1,000-$1,500
EFFECTIVENESS
Future In-House (Crime Lab) Capability
Questions to Consider about SNP Technology Methods
- What is the best method for the sample?
– Quality & Quantity of DNA - Is this the last drop of DNA in the case?
–Whole Sample Consumption - authorized?
– Recommendation – WAIT! - Cost of Sequencing Method?
– Funding Sources - Outsourcing: Risks & Benefits
Next Generation Sequencing (NGS)
- Not a “new” science
- Well established/studied
- The APPLICATION of the method is NEW
SNP Microarray most common Chip
Lumina Global Screening Array
SNP Microarray instrument
I-Scan
* Most public labs do not have
SNP Microarray
High imputation accuracy at minor allele frequencies of
> 1% across ALL 26 1000 Genomes Project Reference Sample
Whole Genome Sequencing (WGS)
instrument
NovaSeq 6000
Whole Genome Sequencing (WGS)
“sequencing coverage” or “sequencing depth” = the number of
unique sequencing reads that align to a region in a reference genome or de novo assembly
Whole Genome Sequencing (WGS)
A 30x human genome means that the reads align
to any given region of the reference about 30 times, on average.
** scans back and forth 30 times
Whole Genome Sequencing (WGS)
The higher the sequencing depth, the more times the
genome read, resulting in a more accurate and reliable information.
Targeted SNP Kits - Verogen Forenseq Kintelligence Kit involves
- Extended Kinship
- 10,230 SNPs - Forensically curated
– eliminate Health SNPs - Eliminates medically sensitive SNPs
- Specifically designed for FIGG
- GEDmatch PRO integration
- Illumina’s MiSeq FGx Sequencing System
– In-house > 150 public forensic labs in the US
– Good for Chain of Custody
Targeted SNP Kits - Verogen Forenseq Kintelligence Kit Works with
Compromised samples
– Microbial DNA
– Other contaminants
Targeted SNP Kits - Verogen Forenseq Kintelligence Kit Input is
Low Input
* Recommended = 1 ng
* 50 pg - 5 ng
– 250 pg - 5 ng = 100% call rate
– 50 pg and 100 pg = 99.9% call rate
High Average Coverage - 1500x
Autosomes
- There are 22 pairs of chromosomes
– NOT SEX hormones - Passed on from BOTH parents
Meiosis
- How your atDNA gets passed down
** a type of cell division that reduces the number of chromosomes in the parent cell by half and produces four gamete cells. This process is required to produce egg and sperm cells
Recombination
is a process by which pieces of DNA are broken and recombined to produce new combinations of alleles. This recombination process creates genetic diversity at the level of genes that reflects differences in the DNA sequences of different organisms.
Genetic Tree
Is made up of only ancestors who you received DNA from
Genealogy Tree
very ancestor in history that had a child who had a child who had a child that ultimately led to you
Testing Considerations
- A person from the OLDEST generation in a family will have MORE of an ancestor’s DNA than someone from a YOUNGER generation
- Once you get past SECOND COUSINS, there is a chance that they WON’t share any DNA
Identical By Descent (IBD)
a matching segment of DNA shared by two or more people that has been inherited from a common ancestor without any intervening recombination.
*The segments are considered to match if all the alleles on a paternal or maternal chromosome are identical (barring rare mutations and genotyping errors) and if the minimum threshold conditions set by the testing company have been met.
Identical By Chance (IBC)
a segment where an accident of recombination means that a segment matches, but this is not a genuine match.
Centimorgans (cM)
unit of recombinant frequency which is used to measure genetic distance
a unit measure for the frequency of genetic recombination
*Used to measure the amount of DNA SHARED w/a match
- Some centimorgans have more SNPs than others
Centimorgans (cM)
To be considered a match,
a threshold of a certain number of matching SNPs per centimorgan must be met
Segments
is the location on a chromosome where the SHARED DNA is located
- More and longer segments usually means a closer match, and vice versa
Autosomal Relationship Probability
Just because a relationship is the highest probability DOES NOT mean that is the ACTUAL relationship
Relationship Estimate Calculations
- Every site has their own algorithm for determining the most likely relationship based on the amount of shared cMs
- Crowd-sourced data allowed for the creation of the SharedcM Project
- MyHeritage has a tool called cM Explainer that considers a matches age
- dna-sci.com has a tool that considers the number of segments
Biogeographical Ancestry
AKA Admixture or Ethnicity Estimate
- Assigning DNA to a geographic area
Biogeographical Ancestry Determined
- Companies create panels of reference populations
- Reference populations have ancestry from the area they are a reference for
- DNA is compared to DNA of reference population
Biogeographical Ancestry Limitations
- We assume that the DNA of those who still live in the area is the same DNA as those who used to live there
- Every database has different reference populations
- The estimate will only be as good as the reference population used
- As reference populations are updated, estimates will change
- Broader categories (ex. continent) are more likely to be accurate than narrow ones
- Issues imposing modern day borders on DNA (DNA comes from people, not places)
GEDmatch Admixture Projects:
MDLP (Magnus Ducatus Lituniae Project)
Although GEDmatch says this project has a global focus, the creator describes it as a project for the territories of former GRAND DUCHY & LITHUANIA
GEDmatch Admixture Projects:
Eurogenes
European focus
GEDmatch Admixture Projects:
Dodecad
Eurasian focus (European, Asian, or North African)
GEDmatch Admixture Projects:
HarrapaWorld
This project focuses on Southeast Asia DNA
GEDmatch Admixture Projects:
puntDNAL
ancient DNA groups
GEDmatch Admixture Projects:
EthioHelix
African, East African, & Ethiopian
GEDmatch Admixture Projects:
GedrosiaDNA
Eurasian (Europe & Asia) & Sub-Saharan African
