JS_196e__Introduction_to_STR_part_1_of_2_upload

JS_196e__Introduction_to_STR_part_1_of_2_upload - JS 196e-...

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JS 196e- Introduction to STRs I. Pre class activities a. Quiz b. Review Assignments and Schedules II. Learning Objectives (C5 )    Short Tandem Repeats  1. Biology of STRs 2. Fluorescence and Detection formats 3. Stutter 4. Statistics and Interpretation
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Announcements and Assignments Read Butler C5,6&7/ InmanC6-C7 Read posted article by Moxon and Wills – Microsatellites: Agents of Evolution 1999. Sci Amer. 280: 94 – Posted on my website Read - Butler, J.M. (2006) Genetics and genomics of core STR loci used in human identity testing. J. Forensic Sci. 51(2): 253-265: Posted on my website Visit- Web Link- www.cstl.nist.gov/biotech/strbase Additional optional readings Budowle et al. 2001. JFS 46:453-489 (CODIS STR Pop) Walsh et al. 1996 NAR. 24:2807-2812, Levinson et al. 1987. Mol Biol Evol. 4:203-221, Brinkmann. 1998 Am J Hum Genet 62:1408, Henke et al. Am J Hum Genet 64:1473. Next time- Run Gels 130-245 and Bruce Wiley 300
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Short Tandem Repeats: a subgroup of tandem repeats (Kuhl and Caskey 1993. Curr. Opin. in Genet. Dev. 3:404) Head to tail arrangements of sequence units ( 4bp), Common in genomes (thousands distributed) Polymorphic: vary in length by no. of and/or by content of repeats. Stably inherited on a human time scale (for most) Well studied b/c others are implicated in Human Diseases and therefore the subject of clinical studies.
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  STR Polymorphisms    occur by variation in       1)  The number of repeats  GAAT GAAT GAAT 5' 3' GAAT GAAT GAAT GAAT GAAT 5' 3' and/or      2) The content of the repeats  GAAT GAAT GAAT GAT GAAT 5' 3' *
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Short Tandem Repeats (STRs) the repeat region is variable between samples while the flanking regions where PCR primers bind are constant AATG 7 repeats 8 repeats AATG AATG Homozygote = both alleles are the same length Heterozygote = alleles differ and can be resolved from one another Primer positions define PCR product size Fluorescent dye label
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D18S51 18q21.3 AGAA L18333 13 7-27 43 Locus Name Chromosomal Location Repeat Motif ISFH format GenBank Accession Allele in GenBank Allele Range Number of Alleles Seen CSF1PO 5q33.3-34 TAGA X14720 12 6-16 15 FGA 4q28 CTTT M64982 21 15-51.2 69 TH01 11p15.5 TCAT D00269 9 3-14 20 TPOX 2p23-pter GAAT M68651 11 6-13 10 VWA 12p12-pter [TCTG][TCTA] M25858 18 10-24 28 D3S1358 3p [TCTG][TCTA] Not available -- 9-20 20 D5S818 5q21-31 AGAT G08446 11 7-16 10 D7S820 7q11.21-22 GATA G08616 12 6-15 22 D8S1179 8 [TCTA][TCTG] G08710 12 8-19 13 D13S317 13q22-31
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JS_196e__Introduction_to_STR_part_1_of_2_upload - JS 196e-...

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