SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages

8/2/2019 SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages

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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.


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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.



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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



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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.



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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



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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



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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.


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



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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.


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.



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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.



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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.



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Appendix 3. Checklists



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STR Training

Lecture Checklist

Trainee: _________________________________________________________________

Lecture TopicCompletion

DateTrainerInitials

1. Overview and history of STRs


3. The polymerase chain reaction (PCR)



6.Statistics

7. The CODIS system

8. Special topics

Reviewed and Approved:

Technical Leader: ___________________________________ Date ___________________



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STR Training

Reading Checklist

Trainee: ___________________________________________________________________


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



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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.



15/24


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.


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.



16/24


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



17/24


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.



18/24


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.


Technical Leader: ____________________________________ Date ___________________



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STR Training

Practice Sample Checklist

Trainee: ___________________________________________________________________


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)


Technical Leader: ____________________________________ Date ___________________



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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.


Technical Leader: __________________________________ Date ___________________



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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 ___________________



22/24


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.



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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?



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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.

Documents

SWIFS FBU DNA STR Training Program v2.0 (02.16.2007) 24 Pages