The History of DNA Forensics

What is DNA?

DNA is the chemical substance which makes up our chromosomes and controls all inheritable traits (eye, hair and skin color)

DNA is different for every individual except identical twins

DNA is found in all cells with a nucleus (white blood cells, soft tissue cells, bone cells, hair root cells and spermatozoa)

Half of a individual’s DNA/chromosomes come from the father & the other half from the mother.

DNA Review:

DNA is a double-stranded molecule. The DNA strands are made of four

different building blocks. An individual’s DNA remains the

same throughout life. In specific regions on a DNA strand

each person has a unique sequence of DNA or genetic code.

Repeated DNA Sequences

VNTR’s--Tandemly repeated DNA sequences.

Interspersed Transposable Elements SINES LINES

Cutting Variable DNA Sections

Father: DNA is a long,long,long long molecule that is tightly wound.

Mother: DNA is a long,long molecule that is tightly wound.

Restriction Enzymes are proteins that cut DNA molecules at specific cut sites.

The History of Forensic DNA Analysis Resembles a War.

Laboratories Legal System (Prosecutors /

Defense Attorneys) Media Coverage

Conventional Blood Typing

Used for more than 50 years Utilized ABO blood typing groups Identified genetic variations in

blood proteins, tissue specific proteins and serum protein types

Major problem is that the conventional blood protein markers are not found in semen.

Development of DNA Analysis Techniques (1970’s)

RFLP (Restriction Fragment Length Polymorphism)

Southern Blot

Restriction Fragment Length Polymorphism

Restriction Enzymes (biological catalysts) cut DNA whenever they encounter a specific DNA sequence.

Gel electrophoresis separates the fragments of DNA according to their length.

Size Separation of DNA by Gel Electrophoresis

Total DNA Gel Electrophoresis

Restriction Enzymes

Southern Blot

A short segment of DNA that is complementary to a portion of the desired DNA fragments is labeled with a radioactive atom.

This probe binds to the fragment of interest on the gel electrophoresis.

Visualized using X-ray film.

A Schematic Representation of RFLP and Southern Blot of a Single-locus VNTR

History of DNA Analysis (1980’s)

In 1980 David Botstein and others used RFLP to construct a human gene map.

Used genetic variations as markers

Kary Mullis Invented PCR Methods (1984)

Polymerase Chain Reaction amplifies short specific regions of DNA

PCR is an in vitro technique that can yield millions of copies of desired DNA

Does not use radioactivity

PCR Amplifies DNA Exponentially

In 1984, Alec Jeffreys developed “DNA Fingerprinting.”

Was searching for disease markers Applied the technique to personal

identification Demonstrated that the DNA could

be retrieved from old dried blood stains

Applied the technique to high-profile forensic tests

A Typical DNA Profile

The Pitchfork Case (1986 & 1987) Jeffreys was consulted in the case of the

murder and rape of two British schoolgirls.

Suspect cleared from analysis of semen samples at the scene and blood samples from the suspect.

“Blooded” 4583 men Analysis of blood sample from Colin

Pitchfork provided a match.

Pennsylvania v Pestinikas (1986)

First PCR case done in the United States

Involved allegations of switching body parts at a funeral home

Commercial Development of Forensic DNA Testing in the United States:

Lifecodes Corporation—Founded in 1982 in Valhalla, NY as diagnostic company. Began performing forensic DNA testing in 1987

Cellmark—The US branch of Britain’s Imperial Chemical Industries opened in Germantown, MD in 1987. Performed the testing for the prosecutor in the Simpson case.

Trial of Accused Rapist Tommy Lee AndrewsNovember 3, 1987

First case in the U.S. to identify a criminal by DNA

Trial held in Orlando, Florida A scientist from Lifecodes and a

biologist from M.I.T. testified that semen left on the victim matched Andrew’s DNA (1 in 10 billion)

November 6, 1987 jury returned a guilty verdict.

The two major private companies raced each other to the courtroom.

In a shroud of secrecy and an environment of expediency they disregarded the usual methods of testing new scientific methods Publication and Peer Review Standardization Replication Evaluation of Performance

DNA analysis was considered an “infallible” prosecution tool.

“You can’t argue with science.” a juror in Queens

“[DNA evidence] is the single greatest advance in the search for truth since the advent of cross-examination.” Judge Joseph Harris of Albany, NY

DNA analysis was considered an “infallible” prosecution tool.

“In rape cases, when the semen has been matched with the defendant’s and the chance that it came from another person is 33 billion to 1, you don’t need a jury.” Robert Brower, defense attorney.

New York v Castro

First successful defense against DNA analysis

Jose Castro, janitor in a nearby building, was accused of the stabbing deaths of Vilma Ponce and her two-year old daughter, Natasha.

New York v Castro

Lifecodes Corporation reported that the blood found on Castro’s watch matched that of Vilma Ponce with a frequency of 1:189,200,000 in the Hispanic population.

Defense mounted the first successful attempt to have DNA evidence excluded.

New York v Castro

Two defense and two prosecution witnesses agreed that Lifecodes had failed to use generally accepted scientific techniques. Their data was poor and they did not follow procedures for interpreting the data

Castro later confessed and pled guilty to the murders.

The FBI and The Royal Canadian Mounted Police Set Up DNA Laboratories

1987 FBI with NIH began collaborative research to establish DNA identification techniques

In late 1988 FBI set up their own laboratory at their Pennsylvania Avenue headquarters

RCMP also set up their own DNA laboratory.

FBI Worked With Pioneers in the Field

They used four different DNA probes GeneLex Dr. Raymond White of Howard Hughes

Medical Center Lifecodes Cellmark

DNA probes and primers are the

key patented biomolecules used to identify the individual genetic variability.

The FBI and RCMP brought standardization to the indusdry. Established detailed laboratory

protocols Performed validation studies Cut through the competitive nature

that clouded the environment of the testing methods and tools

Defense Strategy

In 1989, National Association of Criminal Defense Lawyers (NACDL) set up a DNA Task Force.

Headed by Barry Scheck, a professor at Benjamin N. Cardozo Law School and Peter Neufeld, a private attorney in Manhattan

Defense Strategy

Tried to reopen all the convictions involving evidence processed by Lifecodes

Escalated the conflict surrounding DNA testing

Launched a public relations campaign critical of DNA typing

In 1990 Scheck and Neufeld Prepare for United States vs Yee.

Three members of Hell’s Angels motorcycle gang of Cleveland Ohio were accused of killing David Hartlaub thinking he was a member of a rival gang

The victim was shot 14 times with a MAC 10 machine gun.

Blood Evidence on the Scene

Most was determined to be that of the victim

Some belonged to one of the defendants

Theory—a ricocheting bullet had hit one of the suspects.

Prosecution Expert Witnesses

Thomas Caskey, Baylor College of Medicine

Kenneth Kidd, Yale geneticist Bruce Budowle, FBI DNA scientist

Defense Expert Witnesses

Richard Lewontin, geneticist from Harvard

Daniel Hartl, geneticist at Washington University

Eric Lander, mathematician and geneticist at M.I.T.

Defense Argued:

FBI’s published articles on matching criteria were “ambiguous” and “inconsistent.”

Prosecution Countered:

In spite of disputes over match criteria, the multi-probe match produced a highly likelihood that the specimens came from two different people.

United States vs Yee

DNA matches were admitted as evidence at the trial and at the appeal.

The documents from the FBI would later find their way into the courtroom.

The National Academy of Science’s National Research Council (NCR) Report

A federal study intended to be the definitive study on the problems of forensic DNA

The most contended issue--How to calculate statistical probability The frequencies of sub-groups could

differ widely from that in the larger population

NCR Report—DNA Technology in Forensic Science (1992) Criticized:

Ceiling principle No population geneticists or

staticians on the panel Inconsistencies Did not address paternity cases or

PCR

NCR Report—DNA Technology in Forensic Science

The report was to be the final word in clarifying the role of DNA forensics.

This document is often cited by defense lawyers in arguing of the exclusion of DNA evidence.

The Media and DNA Forensics

First the Media proclaimed that the “new technology was a miracle.”

It recorded it’s “glowing victories.” Followed by giving opponents to

DNA analysis a venue for airing objections and charges (many of which were unfounded and unchallenged)

The Media and DNA Forensics

The Washington Post headline read, “Panel Backs DNA Tests as Crime Evidence.”

Nature Published Articles Exploring Forensic DNA

Alec Jeffreys announced his methods in Nature.

“DNA fingerprinting dispute laid to rest” Budowle and Lander Oct. 27, 1994

“Lander and Budowle declare that

after 400 technical papers, 100 scientific conferences, three sets of DNA analysis guidelines, 150 court cases, and an exhaustive three-year study by the National Research Council—’The DNA fingerprinting wars are over.’”

1994

National Research Council reconvened to try to rectify the deficiencies of their first report.

The trial of the century convened: “Dollars v DNA” or California v OJ Simpson.

Summary

Forensic DNA testing was developed rapidly by short-sighted commercial interests

Standards were not developed as quickly as necessary

Prosecution oversold DNA evidence Expert witnesses had a vested

interest in fueling the controversy.

Summary

Sensational and inaccurate media coverage spread misinformation about DNA.

The judicial system is sometimes indifferent to choices that could expedite justice.

The Media and DNA Forensics

The DNA Technology in Forensic Science report strongly endorsed the continued use of DNA typing in the courts.

The New York Times front page article headline read “U.S. Panel Seeking Restriction on Use of DNA in Courts.”

Where is Forensic DNA Analysis Today?

Forensic labs have implemented a process of peer review, self-regulation and accreditation

DNA analysis has freed over 156 convicts. The Innocence Project at Yeshiva University is run by Barry Sheck and Peter Neufeld.

Where is Forensic DNA Analysis Today?

Paternity testing. Historical case of Thomas Jefferson

as the likely father of children of slave, Sally Hemmings.

Resolved questions surrounding the disputed descendent of the Czar Nicholas II

Terms to Know

ABO Blood Typing RFLP Southern Blot PCR Kary Mullis Alec Jeffreys DNA

Fingerprinting

DNA typing DNA profiling Probe Primer

Resources

DNA in the Courtroom; Coleman & Swenson, GeneLex Press 1994.

DNA Technology in Forensic Science; Committee on DNA Technology in Forensic Science—National Research Council; National Academy Press 1992

Ch 13 - DNA

• Nucleotides and DNA.

• Double helix.

• Base pairing and double helix.

• Sequence of bases in DNA and synthesis of proteins.

• DNA replication and its significance to forensic science.

• Recombinant DNA technology.

• DNA strands that code for protein synthesis Vs. strands that contain repeated sequence of bases.

• Restriction Fragment Length Polymorphism (RFLP).

• RFLP technique and interpretation of DNA band patterns.

• Polymerase Chain Reaction (PCR).

• RFLP Vs. PCR.

• Short Tandem Repeat (STR).

• Nuclear Vs. Mitochondrial DNA.

• DNA computerized data base in criminal investigation.

• Preservation of blood stains for DNA analysis.

http://www.biology.washington.edu/fingerprint/dnaintro.html

http://www.biology.arizona.edu/human_bio/problem_sets/DNA_forensics_1/DNA_forensics.html

http://whyfiles.org/014forensic/genetic_foren.html

http://whyfiles.org/014forensic/genetic_foren2.html

http://www.fbi.gov/hq/lab/handbook/examsdna.htm

http://arbl.cvmbs.colostate.edu/hbooks/genetics/medgen/dnatesting/dnatest_tech.html

• DNA: abbreviation for deoxyribonucleic acid- the molecules carrying the body’s genetic information. DNA is double-stranded in the shape of a double helix

• Chromosome: a rodlike structure in the cell nucleus, along witch the genes are located. It is composed of DNA surrounded by other material, mainly proteins

• Polymer: a substance composed of a large number of atoms. These atoms are usually arranged in repeating units, or monomers

• Nucleotide: the unit of DNA consisting of one of four bases-adenine, guanine, cystine, or thymine-attached to a phosphate sugar group

• Proteins: polymers of amino acids that play basic roles in the structures and functions of living things

• Amino acids: the building blocks of proteins. There are 20 common amino acids. Amino acids are linked together to form a protein. They types of amino acids and the order in which they’re linked determine the character of each protein

• Human Genome: the total DNA context found within the nucleus of a cell. In humans, it is composed of approximately 3 billion base pairs of genetic information

• Replication: the synthesis of new DNA form existing DNA

• Polymerase Chain Reaction (PCR): a technique for replicating or copying a portion of a DNA strand outside a living cell. This technique leads to millions of copies of the DNA strand

• Restriction Enzymes: chemicals that act as scissors to cut DNA molecules at specific locations

• Restriction Fragment Length Polymorphisms (RFLP): different fragment lengths of base pairs that result from cutting a DNA molecules with restriction enzymes

• Hybridization: the process of joining two complementary strands of DNA together to form a double-stranded molecule

• Short Tandem Repeats (STRs): regions of a DNA molecule that contain short segments consisting of three to seven repeating base pairs

• Multiplexing: a technique that simultaneously detects more than one DNA marker in a single analysis

• Amelogenin gene: a genetic locus found useful for determining gender

• Mitochondria: small structures located outside the nucleus of a cell. These structures are responsible for supplying energy to the cell. Maternally inherited DNA is found in each mitochondria

• Sequencing: a procedure used to determine the order of the base pairs that comprise DNA

• Substrate control: an unstained object adjacent to an area upon which biological material had been deposited

• Buccal cells: cells derived from the inner cheek lining

Ch. 13 - Forensic DNA

The Cell

• The smallest unit of life• The nucleus is the

“brain” of the cell– contains all the genetic

info the cell needs to exist & to reproduce

• In most types of cells, genetic information is organized into structures called chromosomes

Chromosomes

• In most types of cells, genetic information is organized into structures called chromosomes– usually X shaped

• Y chromosome in males

– 23 pairs in humans• one from mother & one

from father

Genes

• Each chromosome contains hundreds to thousands information blocks called genes

• Each gene is the blueprint for a specific type of protein in the body– only identical twins will have

all the genes identical

Chromosomes

• Each chromosome is a single polymeric molecule called DNA– if fully extended the

molecule would be about 1.7 meters long

– unwrapping all the DNA in all your cells

• cover the distance from earth to moon 6,000 times

Structure of DNA

Nucleotides

• DNA is a polymer built from monomers called nucleotides

• Each nucleotide is consists of– deoxyribose

• pentose sugar

– phosphoric acid

– a nitrogenous base

The phosphate The sugar

Nitrogenous Bases

• The Purines– Adenine (A)

– Guanine (G)

Nitrogenous Bases

• The Pyrimidines– Cytosine (C)

– Thymine (T)

The DNA Backbone

• The monomers are linked together by phosphodiester bridges (bonds)– links the 3’ carbon in

the ribose of one nucleotide to the 5’ carbon in the ribose of the adjacent nucleotide

The DNA Double Helix

• DNA is normally a double stranded macromolecule

• Two polynucleotide chains are held together by H-bonding– A always pairs with T

– C always pairs with G

5’ T-T-G-A-C-T-A-T-C-C-A-G-A-T-C 3’

3’ A-A-C-T-G-A-T-A-G-G-T-C-T-A-G 5’

In a double helix the strands go in opposite directions

Functions of DNA

• Two Functions– To transmit information from one generation of

cells to the next – To provide the information for the synthesis of

components (proteins) necessary for cellular function

DNA Fingerprinting

• The basic structure of everyone’s DNA is the same– the difference between people is the ordering of the

base pairs

• Every person can be distinguished by the sequence of their base pairs– millions of base pairs make this impractical

– a shorter method uses repeating patterns that are present in DNA

VNTR’s

• DNA strands contain information which directs an organism’s development– exons

• Also contain stretches which appear to provide no relevant genetic information– introns

– repeated sequences of base pairs• Variable Number Tandem Repeats (VNTRs)

• can contain anywhere from 20 to 200 base pairs

VNTRs

• All humans have some VNTRs

• VNTRs come from the genetic information donated by parents– can have VNTRs from mother, father or a

combination– will not have a VNTR that is from neither

parent

D1 = biological daughter of both parentsD2 = child of mother & former husbandS1 = couple’s biological sonS2 = adopted son

VNTR Analysis

• Usually an individual will inherit a different variant of the repeated sequence from each parent

VNTR Analysis

• PCR primers bracket the locus

• PCR reaction forms a nucleotide chain from the template

VNTR Analysis

• The length of the amplified DNA & its position after electrophoresis will depend on the number or repeated bases in the sequence

Analysis used 3 different VNTR loci for each suspect giving6 bands

Although some individuals have several bands in common, the overall pattern is distinctive for each

Suspects A & C can be eliminatedB remains a suspect