Browsing by Subject "INDELs"
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Item A Novel Multiplex Assay for an Ancestry-Informative Marker (AIM) Panel of INDELs(2016-05-01) Sturm, Sarah A.; Bobby L. LaRue; Bruce Budowle; Raghu R. KrishnamoorthyThe current standard for forensic laboratories in criminal casework is to use Short Tandem Repeat (STR) markers to develop an evidentiary profile. Commercially available STR amplification kits yield amplicons 100 to 500 base pairs (bp) in length. Commonly, forensic DNA samples are highly degraded to approximately 180-200 bps in length, resulting in incomplete STR profiles. Therefore, markers that can be generated with smaller amplicons may be better suited for degraded DNA samples. Additionally, there are cases where no STR match was obtained through a DNA database search and thus no investigative lead is obtained. The bioancestry of a sample donor could aid law enforcement in such cases. A class of markers that could provide investigative value from degraded DNA samples is Ancestry-Informative Marker (AIM) Insertion/Deletions (INDELs). INDELs are polymorphisms that can be amplified from degraded samples due to their smaller amplicon size. AIMs have the ability provide bioancestry information. This project tested the hypothesis that a multiplex PCR-based assay of INDELs can be developed, and subsequently be analyzed by capillary electrophoresis for population identity testing applications. The use of this assay would require no additional tools or machinery than what already is in standard forensic laboratories. To test this hypothesis, a previously developed panel of AIM-INDEL markers was used to develop this multiplex assay.Item Multiplex of INDELs for Human Identification Markers(2016-05-01) Sage, Kelly A.; Bobby L. LaRue; Patricia A. Gwirtz; Kunlin JinForensic scientists commonly use short tandem repeat (STR) loci when comparing an evidentiary profile to that of a reference profile. In commercially available STR kits, the amplified products tend to range from 100- 500 base pairs (bp) in length. For genomic DNA of degraded biological samples, the fragments are usually 180-200bps or less. Therefore, degraded biological samples may not produce a full STR profile. Another viable option has been proposed to enable successful typing of some degraded DNA samples. Insertion/ deletion (INDEL) polymorphisms are intergenic regions of the genome in which amplified products can be smaller in length than most STRs. Using highly discriminating markers is desirable to distinguish individuals. A multiplex panel of human identification (HID) INDEL markers that can individualize people would be beneficial. This project tested the hypothesis that INDELs, which can be used to identify individuals with high discriminatory power, can be developed as a multiplex PCR approach. To test this hypothesis, primers were designed and multiplexed together to amplify specific INDELs that have been previously identified to be suitable for human identity testing purposes.Item Selection of an Ancestry-Informative Marker (AIM) Panel of INDELs(2015-05-01) Thompson, Lindsey M.; LaRue, Bobby L.; Hodge, Lisa M.; Oglesby, MichaelShort Tandem Repeat (STR) loci are commonly used for forensic identification purposes. Most commercially available STR kits yield amplified fragments with lengths between 100 and 600 base pairs (bp). However, the genomic DNA of forensic samples can be highly degraded, yielding incomplete STR profiles. Small insertion/deletion polymorphisms (INDELs) in the intergenic regions of the genome, are viable options for typing degraded samples. Furthermore, when there are no suspects for comparison, ancestry-informative markers (AIMs) are useful for developing investigative leads. This project tested the hypothesis that using publicly available genome data, a panel of AIM-INDELs can be selected for the purposes of distinguishing the Caucasian, East Asian and African population groups. To test this hypothesis, the data from the 1000 Genomes Project were mined to select a panel of AIMs that can be used for the purposes of providing ancestry information as an investigative lead to law enforcement.