M2 Flashcards
(44 cards)
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.
