swifs fbu dna str training program v2.0 (02.16.2007) 24 pages
Post on 06-Apr-2018
218 Views
Preview:
TRANSCRIPT
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
1/24
Approvals
Unit Supervisor __________________________________________________
Section Chief __________________________________________________
Quality Manager ___________________________________________________________
Southwestern Institute of Forensic Sciences
Physical Evidence Section
STR Training Program
Version 2.0
Effective Date: 2/16/2007
Digitally signed by Timothy J. SliterDN: CN = Timothy J. Sliter, C = US
Reason: I am approving this documentDate: 2007.02.15 15:11:47 -06'00'
Digitally signed by Jim DempseyDN: CN = Jim Dempsey, C = USReason: I have reviewed this documentDate: 2007.02.15 15:30:41 -06'00'
Digitally signed by Stacy R. McDonald, Ph.D.DN: CN = Stacy R. McDonald, Ph.D., C = USReason: I am approving this documentDate: 2007.02.15 15:26:08 -06'00'
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
2/24
Page 2 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
Principle
The STR training program for DNA consists of three training modules:
Module 1. A knowledge module consisting of lectures and readings that provide a
foundation for understanding the theoretical and scientific basis of forensic DNA analysis.
Module 2. A technical module consisting of instruction and practice in the laboratory
procedures used by the Institute.
Module 3. A supervised casework module consisting of analysis, interpretation and reporting
of casework materials under the supervision of qualified DNA analysts.
Progress through the modules will be monitored by trainers and the technical manager. The
successful completion of each module must be demonstrated by competency testing.
Analysts must complete all three modules in order to be qualified as independent examiners.
Individuals functioning as technicians must complete Module 1 and Module 2.
Individuals with prior casework experience at other laboratories may be exempted from elements
of the training modules based on their previous training and experience. However, all
competency tests must be successfully completed.
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
3/24
Page 3 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
Module 1. Knowledge module.
Training goals: To understand the theoretical and scientific basis of forensic DNA testing
particularly as it applies to nuclear STR analysis.
Training Objectives: The trainee attends lectures and completes readings covering the followingtopics: 1) overview & history of STRs; 2) DNA extraction & quantitation; 3) the polymerase
chain reaction; 4) capillary electrophoresis; 5) parentage testing & Mutations; 6) statistics; 7) the
CODIS system; 8) special topics. A more detailed description of the topics covered in the
training is provided in Appendix 1. The reading list is provided in Appendix 2.
Assessment: Attendance at lectures and completion of readings and problem assignments will be
tracked on the training checklist.
Competency testing: At the completion of the training module, a knowledge-based competency
test will be administered. A list of sample competency test questions is provided in Appendix 1
as a guide to the trainees.
Module 2. Technical module.
Training goals: To master the Institutes technical procedures used in STR analysis.
Training objectives: The trainee will be instructed in the technical procedures and will perform
DNA extraction, quantitation, amplification, electrophoresis, data interpretation and allele calling
following the Institutes standard procedures on a minimum of 50 practice samples, including a
minimum of 10 semen/epithelial samples, 10 blood samples, 10 buccal swab samples, 10 mixed
bloods, 5 hairs, and 5 bone specimens.
Assessment: All documentation will be reviewed by a trainer for accuracy. Satisfactory
completion of the practice samples will be tracked on the training checklist.
Competency testing: At the completion of the training module, a technical competency test will
be administered. The results will be reviewed by a trainer for accuracy. Following successful
completion of the competency test, the trainee will be qualified to perform supervised casework
analysis.
Module 3. Supervised casework module.
Training goals: To perform casework analysis and report writing under the supervision of
qualified analysts.
Training objectives: Under the supervision and mentoring of a qualified analyst, the trainee will
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
4/24
Page 4 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
process casework evidence, perform interpretation and statistical analysis, and write reports. A
minimum of twenty (20) cases will be analyzed by the trainee. The supervising analyst will co-
sign the reports with the trainee. The trainer will keep a log of the supervised cases.
Assessment: Each report and its supporting documentation package will be reviewed by the
technical leader.
Competency testing: At the completion of the supervised casework module, the trainee will
conduct analysis on a mock case and will generate a report. The report and the supporting
documentation package will be reviewed by the trainer and technical leader. Additionally, one of
the supervised cases analyzed by the trainee will be used for a mock trial. Following successful
completion of the competency test, the trainee will be qualified to perform independent
casework.
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
5/24
Page 5 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
Appendix 1. Lecture/Reading topics
1. Overview & history of STRs
a. Categories of DNA polymorphisms (SNPs, RFLPs, STRs)
b. Microsatellites & genetic diseases
c. Structure and nomenclature of STRsd. Methods of STR analysis
e. Core forensic STRs
2. DNA extraction & quantitation
a. DNA extraction and clean-up methods
b. Differential extraction of semen stains
c. Special topics: teeth, bones, hairs
d. Quality control in DNA extraction
e. Hybridization methods of DNA quantitation
f. Real-time PCR methods of DNA quantitation
3. The polymerase chain reaction (PCR)
a. Biochemical principles of PCRb. Specificity, fidelity and optimization of PCR
c. Contamination and quality control in PCR
4. Capillary electrophoresis
a. Theory of capillary electrophoresis
b. Instrument components
c. Molecular seiving
d. Factors affecting sensitivity and resolution
e. Fluorescent dye detection and multicomponent analysis
f. Quality control in capillary electrophoresis
5. Parentage testing & mutations
a. Basic parentage testingb. Single parent parentage testing
c. Unknown remains
d. Germline mutations
e. Somatic mutations
f. Mechanism of tandem repeat mutation
6. Statistics
a. Hardy-Weinberg models
b. Databases
c. Populations and subpopulations
d. Random match probability
e. Likelihood ratios
f. Mixtures
g. Parentage calculations
h. Unknown remains calculations
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
6/24
Page 6 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
7. The CODIS system
a. Overview and history of the CODIS system
b. Indices
c. Profiles
d. System architecture
e. Data entryf. Profile searches
8. Special topics
a. Ancient/archival samples
b. Transfer/low copy number samples
c. Urine
d. Chimeras
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
7/24
Page 7 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
Appendix 2.
Readings
Core Readings (required)
1. Overview of STRs
a. JM Butler (2006) Genetics and genomics of core short tandem repeat loci used in
human identity testing. J. Foren. Sci. 51: 253-265.
b. Varsha (2006) DNA fingerprinting in the criminal justice system: An overview.
DNA Cell Biol. 25: 181-188.
c. L Carey & L Mitnik (2002) Trends in DNA forensic analysis. Electrophoresis 23:
1386-1397.
d. J Koreth et al. (1996) Microsatellites and PCR genomic analysis. J. Pathol. 178:
239-248.
e. DPA Kuhl & CT Caskey (1993) Trinucleotide repeats and genome variation. Cur.
Opin. Genet. Devel. 3: 404-407.f. A Edwards et al. (1991) DNA typing and genetic mapping with trimeric and
tetrameric tandem repeats. Am. J. Hum. Genet. 49: 746-756.
g. E Momhinweg et al. (1998) D3S1358: Sequence analysis and gene frequency in a
German population. Foren. Sci. Internat. 95: 173-178.
2. DNA extraction & quantitation
a. CT Comey et al. (1994) DNA extraction stategies for amplified fragment length
polymorphism analysis. J. Foren. Sci. 39: 1254-1269.
b. JM Butler (2005) Sample collection, DNA extraction, and DNA quantitation. Ch
3 inForensic DNA Typing, 2 Ed., Elsevier, pp 33-62.nd
c. V Castella et al. (2006) Forensic evaluation of the QIAshredder/QIAamp DNA
extraction procedure. Foren. Sci. Internat. 156: 70-73.d. JA Nicklas & E Buel (2003) Quantification of DNA in forensic samples. Anal.
Bioanal.. Chem. 376: 1160-1167.
e. PS Walsh et al. (1992) A rapid chemiluminescent method for quantitation of
human DNA. Nuc. Acids Res. 20: 5061-5065.
f. TP Whitehead et al. (1983) Enhanced luminescence procedure for sensitive
determination of peroxidase-labelled conjugates in immunoassay. Nature 305:
158-159.
g. G Tringali et al. (2004) Rapid and efficacious real-time quantitative PCR assay for
quantitation of human DNA in forensic samples. Foren. Sci. Internat. 146S: S177-
S181.
3. The Polymerase Chain Reaction
a. YMD Lo () Introduction to the polymerase chain reaction. InMethods in
Molecular Medicine, Vol. 16: Clinical Applications of PCR, Humana Press, pp. 3-
10.
b. JM Butler (2005) The polymerase chain reaction (DNA amplification). Ch. 4 in
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
8/24
Page 8 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
Forensic DNA Typing, Elsevier, pp 63-83.
c. JS Chamberlain & JR Chamberlain (1994) Optimization of Multiplex PCRs. In
The Polymerase Chain Reaction, ed. KB Mullis et al., Birkhauser, pp. 38-46.
d. EPH Yap et al. (1994) False-positives and Contamination in PCR. In PCR
Technology: Current Innovations, ed. HG Griffen and AM Griffen, CRC Press,
pp. 249-258.e. AM Prince & L Andrus (1992) PCR: How to kill unwanted DNA. BioTech. 12:
358-360.
f. J Tamariz et al. (2006) The application of Ultraviolet Irradiation to exogenous
sources of DNA in plasticware and water for the amplification of low copy
number DNA. J. Forensic Sci. 51: 790-794.
g. M Delamoye et al. (2004) False homozygosities at various loci revealed by
discrepancies between commercial kits: implications for genetic databases.
Forensic Sci. Intern. 143: 47-52.
h. PS Walsh et al. (1996) Sequence analysis and characterization of stutter products
at the tetranucleotide repeat locus vWA. Nuc. Acids Res. 24: 2807-2812.
i. JJ Mulero et al. (2006) Characterization of the N+3 stutter product in thetrinucleotide repeat locus DYS392. J. Forensic Sci. 51: 1069-1073.
j. A Akane et al. (1994) Identification of the heme compound copurified with
deoxyribonucleic acid (DNA) from bloodstains, a major inhibitor of polymerase
chain reaction (PCR) amplification. J Forensic Sci 39: 362-372.
k. P Markoulatos et al. (2002) Multiplex polymerase chain reaction: a practical
approach. J Clin. Lab. Anal. 16: 47-51.
l. SS Tobe et al. (2007) Evaluation of six presumptive tests for blood, their
specificity, sensitivity, and effect on high molecular-weight DNA. J. Forensic Sci.
52: 102-109.
4. Capillary electrophoresis
a. KD Altria (1996) Fundamentals of capillary electrophoresis theory. InMethods inMolecular Biology Vol. 52: Capillary Electrophoresis, ed. K. Altria, Humana
Press, pp. 3-12.
b. K Lazaruk et al. (1998) Genotyping of forensic short tandem repeat (STR)
systems based on sizing precision in a capillary electrophoresis instrument.
Electrophoresis 19: 86-93.
c. JM Butler et al. (2004) Forensic DNA typing by capillary electrophoresis using
the ABI Prism 310 and 3100 genetic analyzers for STR analysis. Electrophoresis
25: 1397-1412.
d. JB Sgueglia et al. (2003) Precision studies using the ABI Prism 3100 genetic
analyzer for forensic DNA analysis. Anal. Bianal. Chem. 376: 1247-1254.
e. S Simeon et al. (2006) Discrepancies between forensic identification kits
explained by a laser power supply shutdown. Forensic Sci. Internat. 164: 72-74.
f. JR Gilder et al. (2007) Run-specific limits of detection and quantitation for STR-
based DNA testing. J. Forensic Sci. 52: 97-101.
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
9/24
Page 9 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
5. Parentage testing & mutations
a. PR Gunn et al. (1997) DNA analysis in disputed parentage: the occurrence of two
apparently false exclusions of paternity, both at short tandem repeat (STR) loci, in
the one child. Electrophoresis 18: 1650-1652.
b. L Gusmao et al. (2005) Mutation rates at Y chromosome specific microsatellites.
Hum. Mutat. 26: 520-528.c. L Henke & J Henke (2006) Supplemented data on mutation rates in 33 autosomal
short tandem repeat polymorphisms. J Forensic Sci. 51: 446-447.
d. B Brinkmann et al. (1998) Mutation rate in human microsatellites: influence of
the structure and length of the tandem repeat. Am. J. Hum. Genet. 62: 1408-1415.
e. RW Allen et al. (2000) DNA analysis in a paternity case involving a triploid fetus.
Transfusion 40: 240-244.
f. DS Negi et al. (2006) Multistep microsatellite mutation in the maternally
transmitted locus D13S317: a case of maternal allele mismatch in the child. Int. J.
Legal Med. 120: 286-292.
g. P Hoff-Olsen et al. (1998) Variation in mutation rate and direction between
tetranucleotide STR loci in human colorectal carcinomas. Ann. Hum. Genet. 62:1-7.
h. AABB (2005) Annual Report Summary for Testing in 2004.
6. Statistics
a. N Rudin & K Inman (2002) Assessing the strength of the evidence. Ch. 8 inAn
Introduction to Forensic DNA Analysis, 2 Ed., CRC Press, pp. 139-156.nd
b. JM Butler (2005) STR population database analysis. Ch 20 inForensic DNA
Typing, 2 Ed., Elsevier, pp. 474-496.nd
c. JM Butler (2005) Profile frequency estimates, likelihood ratios, and source
attribution. Ch 21 inForensic DNA Typing, 2 Ed., Elsevier, pp. 497-517.nd
d. JM Butler (2005) Approaches to statistical analysis of mixtures and degraded
DNA. Ch 22 inForensic DNA Typing, 2 Ed., Elsevier, pp. 519-528.nd
e. JM Butler (2005) Kinship and parentage testing. Ch 23 inForensic DNA Typing,
2 Ed., Elsevier, pp. 529-537.nd
f. C Ladd et al. (2001) Interpretation of complex forensic DNA mixtures. Croatian
Med. J. 42: 244-246.
g. CS Tomsey et al. (2001) Case work guidelines and interpretation of short tandem
repeat complex mixture analysis. Croatian Med. J. 42: 276-280.
h. P Gill et al. (2006) DNA commission of the International Society of Forensic
Genetics: Recommendations on the interpretation of mixtures. Forensic Sci.
Internat. 160: 90-101.
7. The CODIS system
a. JM Butler (2005) Combined DNA index system (CODIS) and the use of DNA
databases. Ch 18 inForensic DNA Typing, 2 Ed., Elsevier, pp. 435-452.nd
8. Special Topics
a. DJ Johnson et al. (2007) Variation in Nuclear DNA concentrations during
urination. J.Forensic Sci. 52: 110-113.
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
10/24
Page 10 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
b. M Phipps & S Petricevic (In press) The tendency of individuals to transfer DNA
to handled items. Forensic Sci. Internat.
c. F-X Ricaut et al. (2005) STR-genotyping from human medieval tooth and bone
samples. Forensic Sci. Internat. 151: 31-35.
d. S Amory et al. (In press) STR typing of ancient DNA extracted from hair shafts of
Siberian mummies. Forensic Sci. Internat.e. RA de Weger et al. (2000) Monitoring of residual disease and guided donor
leucocyte infusion after allogeneic bone marrow transplantation by chimaerism
analysis with short tandem repeats. Brit. J. Haematol. 110: 647-653.
f. JC Giltay et al. (1998) Polymorphic detection of a parthenogenetic maternal and
double paternal contribution to a 46,XX/46,XY hermaphrodite. Am. J. Hum.
Genet. 62: 937-940.
g. M Klintschar et al. (2004) Persisting fetal microchimerism does not interfere with
forensic Y-chromosome typing. Forensic Sci. Internat. 139: 151-154.
h. R Kuhl-Burmeister et al. (2000) Equal distribution of congenital blood cell
chimerism in dizygotic triplets after in-vitro fertilization. Hum. Reprod. 15:
1200-1204.i. N Yu et al. (2002) Disputed maternity leading to identification of tetragametic
chimerism. N. Engl. J. Med. 346: 1545-1552.
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
11/24
Page 11 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
Appendix 3. Checklists
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
12/24
Page 12 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
STR Training
Lecture Checklist
Trainee: _________________________________________________________________
Lecture TopicCompletion
DateTrainerInitials
1. Overview and history of STRs
2. DNA extraction & quantitation
3. The polymerase chain reaction (PCR)
4. Capillary electrophoresis
5. Parentage testing & mutations
6.Statistics
7. The CODIS system
8. Special topics
Reviewed and Approved:
Technical Leader: ___________________________________ Date ___________________
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
13/24
Page 13 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
STR Training
Reading Checklist
Trainee: ___________________________________________________________________
Lecture TopicCompletion
DateTraineeInitials
1. Overview of STRs
JM Butler (2006) Genetics and genomics of core short
tandem repeat loci used in human identity testing. J.
Foren. Sci. 51: 253-265.
Varsha (2006) DNA fingerprinting in the criminal justice
system: An overview. DNA Cell Biol. 25: 181-188.
L Carey & L Mitnik (2002) Trends in DNA forensicanalysis. Electrophoresis 23: 1386-1397.
J Koreth et al. (1996) Microsatellites and PCR genomic
analysis. J. Pathol. 178: 239-248.
DPA Kuhl & CT Caskey (1993) Trinucleotide repeats
and genome variation. Cur. Opin. Genet. Devel. 3: 404-
407.
A Edwards et al. (1991) DNA typing and genetic
mapping with trimeric and tetrameric tandem repeats.
Am. J. Hum. Genet. 49: 746-756.
E Momhinweg et al. (1998) D3S1358: Sequence analysis
and gene frequency in a German population. Foren. Sci.
Internat. 95: 173-178.
2. DNA extraction & quantitation methods
CT Comey et al. (1994) DNA extraction stategies for
amplified fragment length polymorphism analysis. J.
Foren. Sci. 39: 1254-1269.
JM Butler (2005) Sample collection, DNA extraction,and DNA quantitation. Ch 3 inForensic DNA Typing,
2 Ed., Elsevier, pp 33-62.nd
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
14/24
Page 14 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
V Castella et al. (2006) Forensic evaluation of the
QIAshredder/QIAamp DNA extraction procedure.
Foren. Sci. Internat. 156: 70-73.
JA Nicklas & E Buel (2003) Quantification of DNA in
forensic samples. Anal. Bioanal. Chem. 376: 1160-1167.
PS Walsh et al. (1992) A rapid chemiluminescent
method for quantitation of human DNA. Nuc. Acids Res.
20: 5061-5065.
TP Whitehead et al. (1983) Enhanced luminescence
procedure for sensitive determination of peroxidase-
labelled conjugates in immunoassay. Nature 305: 158-
159.
G Tringali et al. (2004) Rapid and efficacious real-time
quantitative PCR assay for quantitation of human DNAin forensic samples. Foren. Sci. Internat. 146S: S177-
S181.
3. The Polymerase Chain Reaction
YMD Lo (1998) Introduction to the polymerase chain
reaction. InMethods in Molecular Medicine, Vol. 16:
Clinical Applications of PCR, Humana Press, pp. 3-10.
JM Butler (2005) The polymerase chain reaction (DNA
amplification). Ch. 4 inForensic DNA Typing, Elsevier,
pp 63-83.
JS Chamberlain & JR Chamberlain (1994) Optimization
of Multiplex PCRs. In The Polymerase Chain Reaction,
ed. KB Mullis et al., Birkhauser, pp. 38-46.
EPH Yap et al. (1994) False-positives and
Contamination in PCR. In PCR Technology: Current
Innovations, ed. HG Griffen and AM Griffen, CRC
Press, pp. 249-258.
AM Prince & L Andrus (1992) PCR: How to kill
unwanted DNA. BioTech. 12: 358-360.
J Tamariz et al. (2006) The application of Ultraviolet
Irradiation to exogenous sources of DNA in plasticware
and water for the amplification of low copy number
DNA. J. Forensic Sci. 51: 790-794.
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
15/24
Page 15 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
M Delamoye et al. (2004) False homozygosities at
various loci revealed by discrepancies between
commercial kits: implications for genetic databases.
Forensic Sci. Intern. 143: 47-52.
PS Walsh et al. (1996) Sequence analysis andcharacterization of stutter products at the tetranucleotide
repeat locus vWA. Nuc. Acids Res. 24: 2807-2812.
JJ Mulero et al. (2006) Characterization of the N+3
stutter product in the trinucleotide repeat locus DYS392.
J. Forensic Sci. 51: 1069-1073.
A Akane et al. (1994) Identification of the heme
compound copurified with deoxyribonucleic acid (DNA)
from bloodstains, a major inhibitor of polymerase chain
reaction (PCR) amplification. J Forensic Sci 39: 362-
372.
P Markoulatos et al. (2002) Multiplex polymerase chain
reaction: a practical approach. J Clin. Lab. Anal. 16: 47-
51.
SS Tobe et al. (2007) Evaluation of six presumptive tests
for blood, their specificity, sensitivity, and effect on high
molecular-weight DNA. J. Forensic Sci. 52: 102-109.
4. Capillary electrophoresis
KD Altria (1996) Fundamentals of capillaryelectrophoresis theory. InMethods in Molecular Biology
Vol. 52: Capillary Electrophoresis, ed. K. Altria,
Humana Press, pp. 3-12.
K Lazaruk et al. (1998) Genotyping of forensic short
tandem repeat (STR) systems based on sizing precision
in a capillary electrophoresis instrument. Electrophoresis
19: 86-93.
JM Butler et al. (2004) Forensic DNA typing by capillary
electrophoresis using the ABI Prism 310 and 3100
genetic analyzers for STR analysis. Electrophoresis 25:
1397-1412.
JB Sgueglia et al. (2003) Precision studies using the ABI
Prism 3100 genetic analyzer for forensic DNA analysis.
Anal. Bioanal. Chem. 376: 1247-1254.
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
16/24
Page 16 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
S Simeon et al. (2006) Discrepancies between forensic
identification kits explained by a laser power supply
shutdown. Forensic Sci. Internat. 164: 72-74.
JR Gilder et al. (2007) Run-specific limits of detection
and quantitation for STR-based DNA testing. J. ForensicSci. 52: 97-101.
5. Parentage testing & Mutations
PR Gunn et al. (1997) DNA analysis in disputed
parentage: the occurrence of two apparently false
exclusions of paternity, both at short tandem repeat
(STR) loci, in the one child. Electrophoresis 18: 1650-
1652.
L Gusmao et al. (2005) Mutation rates at Y chromosome
specific microsatellites. Hum. Mutat. 26: 520-528.
L Henke & J Henke (2006) Supplemented data on
mutation rates in 33 autosomal short tandem repeat
polymorphisms. J Forensic Sci. 51: 446-447.
B Brinkmann et al. (1998) Mutation rate in human
microsatellites: influence of the structure and length of
the tandem repeat. Am. J. Hum. Genet. 62: 1408-1415.
RW Allen et al. (2000) DNA analysis in a paternity case
involving a triploid fetus. Transfusion 40: 240-244.
DS Negi et al. (2006) Multistep microsatellite mutation
in the maternally transmitted locus D13S317: a case of
maternal allele mismatch in the child. Int. J. Legal Med.
120: 286-292.
P Hoff-Olsen et al. (1998) Variation in mutation rate and
direction between tetranucleotide STR loci in human
colorectal carcinomas. Ann. Hum. Genet. 62: 1-7.
AABB (2005) Annual Report Summary for Testing in
2004.
6. Statistics
N Rudin & K Inman (2002) Assessing the strength of the
evidence. Ch. 8 inAn Introduction to Forensic DNA
Analysis, 2 Ed., CRC Press, pp. 139-156.nd
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
17/24
Page 17 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
JM Butler (2005) STR population database analysis. Ch
20 inForensic DNA Typing, 2 Ed., Elsevier, pp. 474-nd
496.
JM Butler (2005) Profile frequency estimates, likelihood
ratios, and source attribution. Ch 21 inForensic DNATyping, 2 Ed., Elsevier, pp. 497-517.nd
JM Butler (2005) Approaches to statistical analysis of
mixtures and degraded DNA. Ch 22 inForensic DNA
Typing, 2 Ed., Elsevier, pp. 519-528.nd
JM Butler (2005) Kinship and parentage testing. Ch 23
inForensic DNA Typing, 2 Ed., Elsevier, pp. 529-537.nd
C Ladd et al. (2001) Interpretation of complex forensic
DNA mixtures. Croatian Med. J. 42: 244-246.
CS Tomsey et al. (2001) Case work guidelines and
interpretation of short tandem repeat complex mixture
analysis. Croatian Med. J. 42: 276-280.
P Gill et al. (2006) DNA commission of the International
Society of Forensic Genetics: Recommendations on the
interpretation of mixtures. Forensic Sci. Internat. 160:
90-101.
7. The CODIS system
JM Butler (2005) Combined DNA index system(CODIS) and the use of DNA databases. Ch 18 in
Forensic DNA Typing, 2 Ed., Elsevier, pp. 435-452.nd
8. Special Topics
DJ Johnson et al. (2007) Variation in Nuclear DNA
concentrations during urination. J.Forensic Sci. 52: 110-
113.
M Phipps & S Petricevic (In press) The tendency of
individuals to transfer DNA to handled items. Forensic
Sci. Internat.
F-X Ricaut et al. (2005) STR-genotyping from human
medieval tooth and bone samples. Forensic Sci. Internat.
151: 31-35.
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
18/24
Page 18 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
S Amory et al. (In press) STR typing of ancient DNA
extracted from hair shafts of Siberian mummies.
Forensic Sci. Internat.
RA de Weger et al. (2000) Monitoring of residual disease
and guided donor leucocyte infusion after allogeneicbone marrow transplantation by chimaerism analysis
with short tandem repeats. Brit. J. Haematol. 110: 647-
653.
JC Giltay et al. (1998) Polymorphic detection of a
parthenogenetic maternal and double paternal
contribution to a 46,XX/46,XY hermaphrodite. Am. J.
Hum. Genet. 62: 937-940.
M Klintschar et al. (2004) Persisting fetal
microchimerism does not interfere with forensic Y-
chromosome typing. Forensic Sci. Internat. 139: 151-
154.
R Kuhl-Burmeister et al. (2000) Equal distribution of
congenital blood cell chimerism in dizygotic triplets after
in-vitro fertilization. Hum. Reprod. 15: 1200-1204.
N Yu et al. (2002) Disputed maternity leading to
identification of tetragametic chimerism. N. Engl. J.
Med. 346: 1545-1552.
Reviewed and Approved:
Technical Leader: ____________________________________ Date ___________________
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
19/24
Page 19 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
STR Training
Practice Sample Checklist
Trainee: ___________________________________________________________________
Lecture TopicCompletion
DateTrainerInitials
1. Blood stains (minimum 10)
2. Buccal swabs (minimum 10)
3. Semen/epithelial cell stains (minimum 10)
4. Mixed bloods (minimum 10)
5. Hair roots (minimum 5)
6. Bone (minimum 5)
Reviewed and Approved:
Technical Leader: ____________________________________ Date ___________________
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
20/24
Page 20 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
STR Training
Supervised Casework Log
Trainee: _________________________________________________________________
Case Number Report Date CosignerInitials
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
Reviewed and Approved:
Technical Leader: __________________________________ Date ___________________
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
21/24
Page 21 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
STR Training
Competency Tests
Trainee: ___________________________________________________________________
Lecture Topic CompletionDate
TrainerInitials
1. Knowledge-based test (Module 1)
2. Technical test (Module 2)
3. Mock case (Module 3)
4. Mock trial (Module 3)
Reviewed and approved:
Technical Leader: ___________________________________ Date ___________________
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
22/24
Page 22 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
Appendix 4. Sample Competency Test Questions
1. List the steps in the organic extraction of DNA from a liquid blood sample. Briefly
explain the purpose of each step.
2. List the steps in the QIAamp extraction of DNA from a liquid blood sample. Briefly
explain the purpose of each step.3. Why is a hair shaft a poor choice of material for nuclear DNA?
4. As a general rule, all of the tissues of an individual will show the same STR profile.
Describe three exceptions to this general rule.
5. List the steps in the organic extraction of DNA from a vaginal swab. Briefly explain the
purpose of each step.
6. Explain the purpose of Proteinase K in the organic differential extraction method.
7. Explain the purpose of dithiothreitol in the organic differential extraction method.
8. Explain the purpose of EDTA in organic Stain Extraction Buffer.
9. Explain the purpose ofphenol in the organic extraction method.
10. Explain the purpose of chloroform in the organic extraction method.
11. Explain the purpose of autoclaving and irradiating reagents and supplies used in DNAextraction.
12. Explain the purpose ofthe Microcon YM100 device in the organic extraction method.
13. Whyis it important to vortexwell during the PCIA step of the organic extraction
method?
14. In the organic extraction method, why are stains solubilizingat 56 C?o
15. List four elements of the organic stain extraction process that are taken to reduce the
possibility of transfer contamination.
16. Approximately how much DNA is in 1 uL of human blood?
17. What characteristics of the D17Z1 locus make it useful in quantitating human DNA
(Quantiblot procedure)?
18. In the QuantiBlot procedure; what are the functions of Spotting Solution?
19. In the QuantiBlot procedure, what is the function of SDS in the prehybridization
solution?
20. In the QuantiBlot procedure, what is the probe, and what is the probe label.
21. In the.QuantiBlot procedure, the blue color is caused by what enzyme?
22. What are the characteristics of Proteinase K that make it useful in DNA extraction
methods?
23. In the organic stain extraction protocol, how is Proteinase K inactivated/removed? Why
is Proteinase K inactivation/removal important?
24. What is a DNA polymerase?
25. What properties of Taq DNA polymerase make it useful in PCR?26. What properties of AmpliTaq Gold make it useful in PCR?
27. What is the purpose of Bovine Serum Albumin in PCR amplification?
28. What is multiplex PCR?
29. What is the purpose of primers in PCR.
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
23/24
Page 23 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
30. List the chemical components of a typical PCR reaction, and briefly explain the purpose
of each component.
31. Describe the positive and negative controls used in PCR amplification.
32. What is the size range of amplification products produced by the Profiler Plus kit?
33. What is the size range of amplification products produced by the Cofiler kit?
34. Describe the artifacts that would be expected if excess DNA template were amplifiedusing the Profiler Plus kit.
35. What is the purpose of the Amplification Blank in PCR? List the components of the
Amplification Blank.
36. What is the purpose of the Positive Control in PCR?
37. What is hot-start PCR? What are the advantages of hot-start PCR?
38. Describe the precautions used during PCR set-up to prevent contamination of PCR
reactions.
39. How does AmpliTaq Gold differ from AmpliTaq.
40. What are some substances encountered in forensic applications can inhibit the activity of
Taq DNA polymerase?
41. Why is the amount of template DNA important in setting up a PCR reaction?42. Why is the concentration of primers important in setting up a PCR reaction?
243. Why is MgCl included in the PCR reaction?
44. Why is a polymer used in gene fragment analysis using capillary electrophoresis?
45. What is the function of the heating plate in capillary gel electrophoresis?
46. Briefly describe three injection techniques used in capillary electrophoresis. Which
technique is used in this lab?
47. What size standard is used in STR typing as performed in this lab?
48. What is ROX-500? How is it used in STR typing?
49. What is an allelic ladder and how is it used?
50. How is the allelic ladder used in STR typing?
51. Describe the controls used in a 310 run: What is conditioning?52. Why is an allelic ladder sample run multiple times during a 310 run?
53. What is allele drop-out?
54. What is a stutter peak? What is the typical size range of a stutter peak?
55. What are stochastic effects?
56. What parameters of a 310 run will influence the rate of fragment migration through the
capillary, and why?
57. What is the purpose of the 310 matrix?
58. What is multicomponent analysis? What is its relevance to STR typing?
59. What component of the PCR amplification mix carries the label used in 310 analysis?
60. What fluorescent dyes are used in STR analysis in this lab?
61. What chromosome is D3S1358 located on?
62. Describe two types of DNA polymorphisms of importance in forensic DNA analysis.
What is an STR?
63. What uses are made of STRs outside of forensics?
This is an uncontroll ed copy of a control led document.
-
8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages
24/24
Page 24 of 24STR Training Prog ram, Version 2.0 (eff. 2/16/2007)
64. Explain the terms excitation and emission as they pertain to STR analysis. What would
be the indications of a bad matrix file?
65. List the components of a 310 sample, and briefly describe the purpose of each
component.
66. What is the standard injection time for a 310 run?
67. What parameters of a 310 run will affect peak resolution? Why does each 310 samplecontain ROX-500?
68. Why is each 310 run begun with two consecutive runs of an allelic ladder sample?
69. Describe two artifacts that might be observed in an electropherogram that would be
eliminated by rerunning the same 310 sample.
70. Describe two artifacts that might be observed in an electropherogram that would require
reamplification of the sample?
71. What problems might lead to a leak detection error at the beginning of a 310 run?
72. Explain the relationship of the Hardy-Weinberg law to forensic DNA analysis.
73. For the Hardy-Weinberg law to be true, what characteristics must be true for a
population?
74. Explain the meaning of the theta correction factor used in forensic DNA statistics.75. What are the three statistics standardly reported for a parentage test.
76. Under what conditions would a likelihood ratio calculation be performed for a DNA
mixture?
77. Explain the difference between drop-out and a null mutation.
78. Explain the difference between a somatic mutation and a germline mutation.
top related