Demystifying DNA Demystifying DNA What is it? How do I get it? - - PowerPoint PPT Presentation

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Demystifying DNA Demystifying DNA What is it? How do I get it? - - PowerPoint PPT Presentation

Mar 14, 2023 364 likes •1.61k views

Demystifying DNA Demystifying DNA What is it? How do I get it? What is it? How do I get it? How do I get rid of it? How do I get rid of it? Alissa Bjerkhoel Litigation Coordinator, California Innocence Project Panel Attorney,

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Demystifying DNA –

What is it? How do I get it? How do I get rid of it?

Demystifying DNA –

What is it? How do I get it? How do I get rid of it?

Alissa Bjerkhoel Litigation Coordinator, California Innocence Project Panel Attorney, Appellate Defenders, Inc. Panel Attorney, Sixth District Appellate Program

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Disclaimer

I AM NOT A SCIENTIST

SCIENTIST NOT A SCIENTIST

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PRE‐DNA

Forensic “Sciences”

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Microscopic Hair Comparison

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Bullet Comparison

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Fingerprint Comparison

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Tool Mark Comparison

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Tire Tread Impression

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Bite Mark Comparison

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Shoe Print Evidence

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“With the exception of nuclear DNA analysis, however, no forensic method has been rigorously shown to have the capacity to consistently, and with a high degree of certainty, demonstrate a connection between evidence and a specific individual or source. “

2009 NAS Report

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DNA TESTING

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Common Sources

*Red blood cells do not contain DNA.

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Not So Common Sources

Trees and Plants Pets Bugs and Bacteria

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Chromosomes

  • 23 pairs of chromosomes
  • 46 total chromosomes
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Dense Packets of DNA Surrounded by Protein

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Molecular Structure

  • NUCLEOTIDES
  • 1. Base (A, C, G, T).
  • cytosine (C)
  • thymine (T)
  • adenine (A)
  • guanine (G)
  • 2. Five‐carbon sugar (D).
  • deoxyribose
  • 3. Phosphate group (P).
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Locus

  • The position or location of a particular piece of DNA is

commonly referred to as a locus (loci for more than one).

Locus

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Genetic Markers

  • Scientists examine the genetic locations (loci) where the

number of sequence repeats are the most variable amongst humans

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Alleles

  • Each locus (location of DNA on specific set of chromosomes) has two “alleles”
  • Alleles may be dominant or recessive
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Genetic Discrimination

  • Variable loci provide the capability of using DNA testing

for human identity.

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  • FLORIDA = 19,550,000
  • TAMPA = 352,957
  • MAIN STREET = 54
  • HOUSE LOCATED AT 123 = 6
  • LAST NAME ‐ SMITH = 4
  • FIRST NAME ‐ JOHN = 1
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PRE‐DNA TYPING

Two Main Steps:

  • 1. Extraction
  • 2. Quantification
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Isolation/Extraction

  • f DNA
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Extraction Techniques

  • Chemical and biological procedures are used to separate

DNA molecules from other material.

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Quantification

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  • Must quantify the amount of human DNA.
  • Need appropriate DNA levels for subsequent DNA

amplification & typing.

  • Optimal amounts result in higher quality data and easier

data interpretation

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Spectrofluorometers

  • DNA stained with a fluorescent dye.
  • The fluorescent intensity is measured with a

spectrofluorometer.

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DNA TYPING

(profiling/fingerprinting)

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RFLP

(Restriction Fragment Length Polymorphism)

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Alec Jeffreys ‐ 1985

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Jul 16, 2010 RFLP , Restriction Fragment Length Polymorphism Flash Lecture,DNA Fingerprinting https://www.youtube.com/watch?v=CfZkn7D6dro

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Analysis The size of the target DNA fragments are measured & compared (each fragment length is considered an allele).

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Colin Pitchfork

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  • What they mostly look like:
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  • Other problems with RFLP =
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PCR‐Based Testing Methods

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https://www.youtube.com/watch?v=2KoLnIwoZKU

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PCR Inhibition

  • PCR amplification can be affected by substances

known as “inhibitors.”

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Early Testing Kits

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DQa1 Kits

  • First PCR‐based DNA test kit.
  • Relatively low power of discrimination.
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PM‐DQa1 kits

(PolyMarker)

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PM‐DQa1 kits

(PolyMarker)

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Short Tandem Repeat (STR)

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What is an “STR”?

Short segments of our DNA that are next to each other (tandem) and repeat over and over again.

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Benefits of More Markers

  • Over time, DNA breaks

down (degrades)

  • Larger fragments of DNA

break down first, smaller later (harder to rip a small piece of paper than a large one)

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Post‐Amplification Testing

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  • Amplified product is then subjected to capillary

electrophoresis for separation.

  • Alleles are separated by size using a gel or capillary

method.

  • The machine produces an electropherogram report.
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In two‐minute form . . .

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Comparing Reports

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YSTR

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Y‐STR

  • Detects alleles at different areas on the male chromosome.
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Y‐STR

  • Good for cases where lots of female DNA.
  • Passed down from father to son
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mtDNA

(mitochondrial testing)

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About

  • mtDNA is the DNA located inside the mitochondria

within cells.

  • mtDNA is organized as a circular, covalently closed,

double‐stranded DNA.

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  • mtDNA is inherited solely from the mother.
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Nucleotide Position Cambridge Reference Sequence (CRS) Differing Sequences from CRS

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Pros

  • Ability to obtain DNA profiles from evidence that is not

suitable for nuclear DNA analysis.

  • Helpful in associating maternally related individuals.
  • Lowest power of discrimination. Any maternally

related individuals will share the same mtDNA profile.

  • Longest processing time of any DNA test.
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How to Get DNA Testing:

PENAL CODE SECTION 1405

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1405 Requirements

(1) CONDITION: Evidence is available and in a condition that would permit DNA testing. (2) CHAIN OF CUSTODY: Evidence to be tested has been subject to a chain of custody. (3) IDENTITY AN ISSUE: Identity of the perpetrator of the crime was, or should have been, a significant issue in the case. (4) MATERIAL: Evidence sought to be tested is material to the issue of the convicted person’s identity as the perpetrator. (5) REASONABLE PROBABILITY: Results would raise a reasonable probability that, in light of all the evidence, the convicted person’s verdict or sentence would have been more favorable. (6) PRIOR TESTING: Evidence was not tested previously or was tested previously, but the requested DNA test would provide results that are reasonably more discriminating and probative of the identity

  • f the perpetrator or accomplice or have a reasonable probability of contradicting prior test results.

(7) METHOD: Testing requested employs a method generally accepted within the relevant scientific community. (8) DELAY: Motion is not made solely for the purpose of delay.

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Uriah Courtney

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TESTING AT TRIAL (2005) – San Diego Sheriff’s Department

  • Amylase was detected in the crotch of the underwear
  • DNA analysis performed
  • Debris observed on toothpicks
  • DNA analysis performed
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THE CONVICTION

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CONCESSION & JOINT STIPULATION

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POST‐CONVICTION DNA TESTING

CALIFORNIA INNOCENCE PROJECT

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RESULTS

  • Fingernail scrapings ‐ Victim
  • Vaginal swabs ‐ Victim
  • Underwear – 1 allele
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STR RESULTS FROM THE SHIRT

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ISOLATING THE PERPETRATOR PROFILE

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CALIFORNIA INNOCENCE PROJECT

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  • THE HIT
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16 years later

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Ronald Cotton – Served 10 years

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Richard Jones – Served 17 years

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Michael McAlister – Served 29 years

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How to Get CODIS Upload:

PENAL CODE SECTION 1405.1

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DNA Identification Act (1994)

  • Allowed the FBI to establish NDIS for law

enforcement

  • Allowed disclosure of data to criminal justice

agencies for law enforcement identification purposes

  • Did not authorize defendants to request crime

scene evidence be run through CODIS or allow disclosure of data to them

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NDIS SDIS‐CA SDIS ‐TX SDIS‐FL

*Exchange and control of this system is strictly limited to law enforcement

LDIS –Los Angeles LDIS –Fort Worth LDIS –Orlando

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  • 14,047,860 offender profiles
  • 3,796,117 arrestee profiles
  • 985,797 forensic unknowns
  • CODIS has produced over 491,537 hits

assisting in more than 481,098 investigations

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1405.1 Requirements (1) PUTATIVE PERPETRATOR: DNA profile is attributable to the putative perpetrator of the crime. (2) PROFILE REQUIREMENTS: Profile meets requirements for permanent inclusion. (3) NOTICE: Defense provides written notice to CA CODIS administrator, DOJ, and AG.

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Problems with “TOUCH DNA”

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Contamination – Lukis Anderson

  • 26 year old homeless man (Anderson) with a long rap sheet
  • 66 year old murder victim
  • DNA under fingernails was Anderson’s
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Probabilistic Genotyping

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Number of Assumed Contributors can Greatly Impact Results

Number of Assumed Contributor Statistic 2 contributors Exclusion 3 contributors 16 billion x more likely

NSW Forensic & Analytical Science Service, Sydney (Zane Kerr, ISHI 2015)

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Different Runs of the Same Sample Produce Different Results

Run Statistic 1st run 12 million x more likely 2nd run 17 times more likely

Augenstein, Forensic Magazine, October 2017, Reporting on presentation at ISHI 2017

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Different PG Software Produced Different Results

PG Software Statistic TrueAllele Inconclusive STRMix 10 million x more likely 10k x more likely 100 x more likely

State v. Hillary

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Courts Are Not Requiring Disclosure of Source Code…

The prosecution has no obligation to turn over STRMix’s source code because it is in the possession of a third party and there is no indication the software did not operate appropriately. – People v. Superior Court (Dominguez), 4th Dist., Div. 1 The source code is a protected trade secret of the creator and owner of the software and his company; Chubbs has not demonstrated how TrueAllele’s source code is necessary to his ability to test the reliability of its results. – People v. Superior Court (Chubbs), 2nd District, Div. 4,

  • non. pub.
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…But keeping evidence

  • ut on other grounds

“[B]ecause the sum of the parts simply does not add up to a reliable whole, the DNA analysis/likelihood ratio resulting from the use of the STRMix probabilistic genotyping software must be excluded” ‐ United States v. Gissanter “Because Bullet was only validated to analyze complex mixtures of up to four contributors, and because [the analyst] did not reliably conclude that only four people contributed DNA to this mixture, this evidence is not reliable” ‐ United States v. Williams But See: STRmix is generally accepted by the relevant scientific community and that evidence produced using STRMix is admissible ‐ People v. Juan Manuel Venegas, Superior Court of Shasta County

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Statistics

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Allele Frequency is Determined by Referencing Documented Population Databases

https://strbase.nist.gov//population/PopSurvey.htm#ReferenceListing).

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Statistics are Subject to Kelly analysis

Statistical calculations are subject to a Kelly analysis to determine whether the methodology used was generally accepted in the scientific community, and whether correct scientific procedures were followed in calculating the probability. ‐ People v. Venegas (1998) 18 Cal.4th 47, 84.

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Multiple Ways of Interpreting DNA Mixtures

  • Combined Probability of Inclusion (CPI)
  • Combined Probability of Exclusion (CPE)
  • Random Match Probability (RMP)
  • Random Man Not Excluded (RMNE)
  • Likelihood Ratio (LR)
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John Butler, Introduction to Interpretation: Statistical Approaches and Assumptions (2012)

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Changing Model/ Terminology

  • In 2011, SDPD modified their interpretation guidelines

– More samples will not be interpretable due to complexity/low level

  • In 2015, SDPD changed from CPI to LR
  • In 2018, SDPD started using STRMix
  • In 2019, SDPD adopted different language for conveying

results – “The SDPD will no longer use the term inconclusive to describe a likelihood ratio value between 0.01 and 100. Likelihood ratio values between 0.5 and 2 will now be reported as uninformative.”

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Consult Your Own Experts/ Get Your Own Testing