Approvals Unit Supervisor

__________________________________________________
Digitally signed by Timothy J. Sliter DN: CN = Timothy J. Sliter, C = US Reason: I am approving this document Date: 2007.02.15 15:11:47 -06'00' __________________________________________________
Digitally signed by Jim Dempsey DN: CN = Jim Dempsey, C = US Reason: I have reviewed this document Date: 2007.02.15 15:30:41 -06'00' ___________________________________________________________

Digitally signed by Stacy R. McDonald, Ph.D. DN: CN = Stacy R. McDonald, Ph.D., C = US Reason: I am approving this document Date: 2007.02.15 15:26:08 -06'00'

Section Chief

Quality Manager

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Southwestern Institute of Forensic Sciences Physical Evidence Section STR Training Program Version 2.0 Effective Date: 2/16/2007

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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 following topics: 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 Page 3 of 24

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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 cosign 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 STRs d. Methods of STR analysis e. Core forensic STRs 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 The polymerase chain reaction (PCR) a. Biochemical principles of PCR b. Specificity, fidelity and optimization of PCR c. Contamination and quality control in PCR 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 Parentage testing & mutations a. Basic parentage testing b. Single parent parentage testing c. Unknown remains d. Germline mutations e. Somatic mutations f. Mechanism of tandem repeat mutation 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.

8.

The CODIS system a. Overview and history of the CODIS system b. Indices c. Profiles d. System architecture e. Data entry f. Profile searches 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. 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 in Forensic DNA Typing, 2nd Ed., Elsevier, pp 33-62. 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: S177S181. The Polymerase Chain Reaction a. YMD Lo () Introduction to the polymerase chain reaction. In Methods in Molecular Medicine, Vol. 16: Clinical Applications of PCR, Humana Press, pp. 310. b. JM Butler (2005) The polymerase chain reaction (DNA amplification). Ch. 4 in

2.

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4.

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 the trinucleotide 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. Capillary electrophoresis a. KD Altria (1996) Fundamentals of capillary electrophoresis theory. In Methods in Molecular 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 STRbased DNA testing. J. Forensic Sci. 52: 97-101.

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5.

6.

7.

8.

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. Statistics a. N Rudin & K Inman (2002) Assessing the strength of the evidence. Ch. 8 in An Introduction to Forensic DNA Analysis, 2nd Ed., CRC Press, pp. 139-156. b. JM Butler (2005) STR population database analysis. Ch 20 in Forensic DNA Typing, 2nd Ed., Elsevier, pp. 474-496. c. JM Butler (2005) Profile frequency estimates, likelihood ratios, and source attribution. Ch 21 in Forensic DNA Typing, 2nd Ed., Elsevier, pp. 497-517. d. JM Butler (2005) Approaches to statistical analysis of mixtures and degraded DNA. Ch 22 in Forensic DNA Typing, 2nd Ed., Elsevier, pp. 519-528. e. JM Butler (2005) Kinship and parentage testing. Ch 23 in Forensic DNA Typing, 2nd Ed., Elsevier, pp. 529-537. 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. The CODIS system a. JM Butler (2005) Combined DNA index system (CODIS) and the use of DNA databases. Ch 18 in Forensic DNA Typing, 2nd Ed., Elsevier, pp. 435-452. 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. c. d. e.

f.

g. h.

i.

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. 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 allogeneic bone 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.

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Appendix 3. Checklists

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STR Training Lecture Checklist Trainee: _________________________________________________________________ Completion Date Trainer Initials

Lecture Topic 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 ___________________

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STR Training Reading Checklist Trainee: ___________________________________________________________________ Completion Date Trainee Initials

Lecture Topic 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 forensic analysis. 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: 404407. 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 in Forensic DNA Typing, 2nd Ed., Elsevier, pp 33-62.

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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 peroxidaselabelled conjugates in immunoassay. Nature 305: 158159. 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: S177S181. 3. The Polymerase Chain Reaction

YMD Lo (1998) Introduction to the polymerase chain reaction. In Methods 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 in Forensic 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.
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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 and characterization 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: 362372. P Markoulatos et al. (2002) Multiplex polymerase chain reaction: a practical approach. J Clin. Lab. Anal. 16: 4751.

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 capillary electrophoresis theory. In Methods 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.

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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.
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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. Forensic Sci. 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: 16501652. 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.

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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 in An Introduction to Forensic DNA Analysis, 2nd Ed., CRC Press, pp. 139-156. Page 16 of 24

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JM Butler (2005) STR population database analysis. Ch 20 in Forensic DNA Typing, 2nd Ed., Elsevier, pp. 474496. JM Butler (2005) Profile frequency estimates, likelihood ratios, and source attribution. Ch 21 in Forensic DNA Typing, 2nd Ed., Elsevier, pp. 497-517. JM Butler (2005) Approaches to statistical analysis of mixtures and degraded DNA. Ch 22 in Forensic DNA Typing, 2nd Ed., Elsevier, pp. 519-528. JM Butler (2005) Kinship and parentage testing. Ch 23 in Forensic DNA Typing, 2nd Ed., Elsevier, pp. 529-537. 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, 2nd Ed., Elsevier, pp. 435-452. 8. Special Topics

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DJ Johnson et al. (2007) Variation in Nuclear DNA concentrations during urination. J.Forensic Sci. 52: 110113. 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.

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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 allogeneic bone marrow transplantation by chimaerism analysis with short tandem repeats. Brit. J. Haematol. 110: 647653. 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 Ychromosome typing. Forensic Sci. Internat. 139: 151154.

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 ___________________

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STR Training Practice Sample Checklist Trainee: ___________________________________________________________________ Completion Date Trainer Initials

Lecture Topic 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 ___________________

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STR Training Supervised Casework Log Trainee: _________________________________________________________________ Case Number 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 ___________________
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Report Date

CosignerInitials

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STR Training Competency Tests Trainee: ___________________________________________________________________ Lecture Topic 1. Knowledge-based test (Module 1) 2. Technical test (Module 2) 3. Mock case (Module 3) 4. Mock trial (Module 3) Completion Date Trainer Initials

Reviewed and approved:

Technical Leader: ___________________________________ Date ___________________

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Appendix 4. Sample Competency Test Questions 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25. 26. 27. 28. 29. List the steps in the organic extraction of DNA from a liquid blood sample. Briefly explain the purpose of each step. List the steps in the QIAamp extraction of DNA from a liquid blood sample. Briefly explain the purpose of each step. Why is a hair shaft a poor choice of material for nuclear DNA? As a general rule, all of the tissues of an individual will show the same STR profile. Describe three exceptions to this general rule. List the steps in the organic extraction of DNA from a vaginal swab. Briefly explain the purpose of each step. Explain the purpose of Proteinase K in the organic differential extraction method. Explain the purpose of dithiothreitol in the organic differential extraction method. Explain the purpose of EDTA in organic Stain Extraction Buffer. Explain the purpose of phenol in the organic extraction method. Explain the purpose of chloroform in the organic extraction method. Explain the purpose of autoclaving and irradiating reagents and supplies used in DNA extraction. Explain the purpose of the Microcon YM100 device in the organic extraction method. Why is it important to vortex well during the PCIA step of the organic extraction method? In the organic extraction method, why are stains solubilizingat 56oC? List four elements of the organic stain extraction process that are taken to reduce the possibility of transfer contamination. Approximately how much DNA is in 1 uL of human blood? What characteristics of the D17Z1 locus make it useful in quantitating human DNA (Quantiblot procedure)? In the QuantiBlot procedure; what are the functions of Spotting Solution? In the QuantiBlot procedure, what is the function of SDS in the prehybridization solution? In the QuantiBlot procedure, what is the probe, and what is the probe label. In the.QuantiBlot procedure, the blue color is caused by what enzyme? What are the characteristics of Proteinase K that make it useful in DNA extraction methods? In the organic stain extraction protocol, how is Proteinase K inactivated/removed? Why is Proteinase K inactivation/removal important? What is a DNA polymerase? What properties of Taq DNA polymerase make it useful in PCR? What properties of AmpliTaq Gold make it useful in PCR? What is the purpose of Bovine Serum Albumin in PCR amplification? What is multiplex PCR? What is the purpose of primers in PCR.

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30. 31. 32. 33. 34. 35. 36. 37. 38. 39. 40. 41. 42. 43. 44. 45. 46. 47. 48. 49. 50. 51. 52. 53. 54. 55. 56. 57. 58. 59. 60. 61. 62. 63.

List the chemical components of a typical PCR reaction, and briefly explain the purpose of each component. Describe the positive and negative controls used in PCR amplification. What is the size range of amplification products produced by the Profiler Plus kit? What is the size range of amplification products produced by the Cofiler kit? Describe the artifacts that would be expected if excess DNA template were amplified using the Profiler Plus kit. What is the purpose of the Amplification Blank in PCR? List the components of the Amplification Blank. What is the purpose of the Positive Control in PCR? What is hot-start PCR? What are the advantages of hot-start PCR? Describe the precautions used during PCR set-up to prevent contamination of PCR reactions. How does AmpliTaq Gold differ from AmpliTaq. What are some substances encountered in forensic applications can inhibit the activity of Taq DNA polymerase? Why is the amount of template DNA important in setting up a PCR reaction? Why is the concentration of primers important in setting up a PCR reaction? Why is MgCl2 included in the PCR reaction? Why is a polymer used in gene fragment analysis using capillary electrophoresis? What is the function of the heating plate in capillary gel electrophoresis? Briefly describe three injection techniques used in capillary electrophoresis. Which technique is used in this lab? What size standard is used in STR typing as performed in this lab? What is ROX-500? How is it used in STR typing? What is an allelic ladder and how is it used? How is the allelic ladder used in STR typing? Describe the controls used in a 310 run: What is conditioning? Why is an allelic ladder sample run multiple times during a 310 run? What is allele drop-out? What is a stutter peak? What is the typical size range of a stutter peak? What are stochastic effects? What parameters of a 310 run will influence the rate of fragment migration through the capillary, and why? What is the purpose of the 310 matrix? What is multicomponent analysis? What is its relevance to STR typing? What component of the PCR amplification mix carries the label used in 310 analysis? What fluorescent dyes are used in STR analysis in this lab? What chromosome is D3S1358 located on? Describe two types of DNA polymorphisms of importance in forensic DNA analysis. What is an STR? What uses are made of STRs outside of forensics?

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STR Training Program, Version 2.0 (eff. 2/16/2007)

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64. 65. 66. 67. 68. 69. 70. 71. 72. 73. 74. 75. 76. 77. 78.

Explain the terms excitation and emission as they pertain to STR analysis. What would be the indications of a bad matrix file? List the components of a 310 sample, and briefly describe the purpose of each component. What is the standard injection time for a 310 run? What parameters of a 310 run will affect peak resolution? Why does each 310 sample contain ROX-500? Why is each 310 run begun with two consecutive runs of an allelic ladder sample? Describe two artifacts that might be observed in an electropherogram that would be eliminated by rerunning the same 310 sample. Describe two artifacts that might be observed in an electropherogram that would require reamplification of the sample? What problems might lead to a leak detection error at the beginning of a 310 run? Explain the relationship of the Hardy-Weinberg law to forensic DNA analysis. For the Hardy-Weinberg law to be true, what characteristics must be true for a population? Explain the meaning of the theta correction factor used in forensic DNA statistics. What are the three statistics standardly reported for a parentage test. Under what conditions would a likelihood ratio calculation be performed for a DNA mixture? Explain the difference between drop-out and a null mutation. Explain the difference between a somatic mutation and a germline mutation.

Not a Controlled Document

STR Training Program, Version 2.0 (eff. 2/16/2007)

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This is an uncontrolled copy of a controlled document.