Biol 4902 B Assignment 1 Total (48): Name: Student Number: Part I. Case Synopsis Jenny and her boyfriend Dave arrive back at their apartment after a night out and notice their front door is slightly ajar. Their dog is barking loudly and they hear a sound coming from the kitchen. Dave goes to the kitchen and observes an intruder with a baseball bat going through the cupboards. Dave grabs a kitchen knife and attacks the intruder and cuts the intruder’s hand. The intruder spits on Dave, hits him with the baseball bat and runs out of the kitchen. As he runs out the front door he pushes Jenny in the chest and drops the baseball bat. When the police arrive, Dave tells them the intruder was a male with brown hair. Dave mentions the spitting incident and the police collect his shirt. They observe that Dave’s arm is bruised and bleeding. They notice a pair of underwear and a bra on the living room floor with what appears to be some white staining and collect them as Jenny says she didn’t leave them there. The police collect Jenny’s shirt since the intruder pushed her. One investigator notices red staining on the kitchen floor and takes a swab of it. Swabs are also taken of the blade of the kitchen knife Dave says he used to stabs the intruder and the handle of the baseball bat that was left at the scene. In addition, swabs of the cupboard knobs that the intruder was seen going through are taken. Finally, a reference (comparison) sample was collected from Dave. Exhibits collected Item NumberItem Description1Swab of potential blood from kitchen floor2Dave’s shirt3Jenny’s shirt4Underwear with white staining from living room floor5Bra with white staining from living room floor6Swab from kitchen knife blade7Swab from baseball bat handle8Swab from cupboard knob9Cheek swab (comparison sample) from Dave Part I Questions (4) The forensic scientist performing the case assessment did not accept item 8 for DNA analysis. Explain the rationale. Why is a reference sample from Dave required? Why is a reference sample from Jenny not needed? Part II. Body Fluid Results Items 1 to 7 were submitted for body fluid testing. Summary of body fluid results ItemHCKMPhadAPP30Micro1PosPosn.t.n.t.n.t.n.t.2n.t.n.t.Posn.t.n.t.n.t.3NegPosn.t.n.t.n.t.n.t.4n.t.n.t.n.t.PosPosNeg5n.t.n.t.n.t.PosPosPos6PosPosn.t.n.t.n.t.n.t.7???????????? HC – Hemochromogen KM – Kastle-Meyer Phad – Phadebas AP – Acid Phosphatase Micro – Microscopic examination for semen pos -> positive result neg -> negative result n.t. -> not tested Part II Questions (12) There was a dog at the scene. However, the ABAcard Hematrace test was not used on item 1. Explain why this test wasn’t used for this item and not generally used for most crime scenes. Would item 2 be submitted as a differential extraction? Explain. Provide two different explanations for how the underwear (item 4) was AP and P30 positive while the microscope examination was negative. What body fluid tests, if any, would you request for item 7? Part III. Extraction and Quantification Five of the evidence items were submitted for DNA extraction (no differential extractions regardless of your answer above). The extracted samples were quantified using the Quantifiler Trio kit that was discussed in class which has four targets. The results are presented below. Summary of quantification results ItemSmall Autosomal target concentration (ng/μl)Large Autosomal target concentration (ng/μl)Y target concentration (ng/μl)IPC (CT value)14.550.32722.214.171.1247510.48.56.8276?4.50.13670.0730.0150.04227 Part III Questions (16) Based on the quantification results, do items 1 or 2 give any indication that they might be degraded? Explain. Based on the quantification results, do any of the samples appear to be inhibited? Explain. For item 5, you are allowed to request one amplification. Would you select an autosomal STR or a Y-STR amplification? Explain. Referring to the quantification results for item 7 above, describe how you would set up a 1.2 ng Y-STR amplification reaction. You have 50 µl of the DNA sample and your lab uses 10 µl of template DNA in a 20 µl PCR reaction Note: The minimum volume available to pipet is 1 µl. Use the data from the standard curve below to create a graph with the equation of the standard curve. Provide a copy of the graph and show the equation of the curve. Based on this equation, calculate the concentration of the small autosomal target for item 6 with a CT value of 23. Standard Curve Small Autosomal Concentration (ng/μl)CT value3021.19324.220.327.480.0330.530.00333.48 Part IV. Capillary Electrophoresis Results The DNA profile electropherogram for item 6 is provided. A suspect was arrested and his DNA profile was generated (see results in table below). Part IV Questions (18) For the DNA profile from item 6, list ALL minus one repeat stutter peaks (locus name and the allele of the stutter peak) for the loci in the green and red channels. Use a stutter threshold of 10%. *Ignore Yindel, Amelogenin and DYS391 in green channel* Are the peaks in the orange channel considered alleles? Explain. What is the purpose of the orange channel? Assuming two contributors, interpret the genotypes of the major contributor at each of the loci and fill in the table below. *Ignore Yindel and DYS391 (both in green dye channel and have been marked XX)* DNA Profile Results LocusMajor Contributor – Item 6SuspectAmelogeninXYD8S117913,15D21S1130,30D18S5117,17D22S104515,15D5S81810,11D13S31711,12D7S8209,10SE3318,19 Assuming two contributors, and after accounting for any stutter peaks, what is the ratio of the major and minor contributors at SE33? Explain why the ratio of the major and minor contributors isn’t identical at all loci. Can the suspect be excluded as the source of the major DNA profile from item 6? Explain.
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