Biomedical subjects

Erin K Hanson

Publications and source records attributed to Erin K Hanson.

4 recordsLinked to original sources

PubMed2006

Testing and evaluation of 43 "noncore" Y chromosome markers for forensic casework applications.

A developmental validation study was performed on three Y-STR multiplex systems, Multiplex III (MPIII), Multiplex IV (MPIV), and Multiplex V (MPV), to ascertain their potential applicability to forensic casework. MPIII contains eight Y-STRs, including DYS426, DYS435, DYS436, DYS441, DYS442, DYS446, DYS462, and Y-GATA-A10, and one InDel, YAP (DYS287). MPIV contains 21 Y-STR loci, including DYS443, DYS444, DYS445, DYS447, DYS448, DYS449, DYS452, DYS453, DYS454, DYS455, DYS456, DYS458, DYS463, DYS464, DYS468, DYS484, DYS522, DYS527, DYS531 DYS557, and DYS588. MPV contains 13 Y-STR loci, including DYS459, DYS476, DYS488, DYS513, DYS549, DYS561, DYS570, DYS575, DYS576, DYS590, DYS594, DYS598, and DYS607. Full genetic profiles were consistently obtained for all three multiplexes with 25-50 pg of male DNA. No significant amplification was observed with 1 mug of female DNA. Each multiplex permitted the determination of the number of male donors in male:male DNA admixtures. Species specificity studies demonstrated some cross-reactivity with some primate samples. Environmentally compromised blood samples produced full or partial profiles after exposure to various conditions for up to 1 year. Full profiles were recovered from simulated casework specimens including cigarette butts and postcoital cervicovaginal swabs. Population data were collected to determine individual loci gene diversity and multiplex discriminatory capacity.

Animals↗

PubMed2005

Comprehensive annotated STR physical map of the human Y chromosome: Forensic implications.

A plethora of Y-STR markers from diverse sources have been deposited in public databases and represent potential candidates for incorporation into the next generation of Y-STR multiplexes for forensic use. Here, based upon all of the Y-STR loci that have been deposited in the human genome database (>400), we have sequentially positioned each one along the Y chromosome using the most current human genome sequencing data (NCBI Build 35). The information derived from this work defines the number and relative position of all potentially forensically relevant Y-STR loci, their location within the physical linkage map of the Y chromosome and their relationship to structural genes. We conclude that there exists at present at least 417 separate Y-STR markers available for potential forensic use, although many of these will be found to be unsuitable for other reasons. However, from this data, we were able to identify 28 pairs of duplicated loci that were given separate DYS designations and four pairs of loci with overlapping flanking regions. Removing one locus from each set of duplicates reduced the number of potentially useful loci from 417 to 389. The derived information should be useful for workers who are designing novel Y-STR multiplexes to ensure the presence of non-synonymous loci and, if so desired, to avoid loci that lie within structural genes. It may also be useful for forensic casework practitioners (or molecular anthropologists) to aid in distinguishing between chromosomal rearrangements (such as duplications and deletions) and bona fide DNA admixtures or null alleles caused by primer binding site mutations. We illustrate the practical usefulness of the chromosomal positioning data in the design of eight multiplex systems using 94 Y-STR loci.

Chromosome Mapping↗

PubMed2005

Whole genome amplification strategy for forensic genetic analysis using single or few cell equivalents of genomic DNA.

Evidentiary items sometimes contain an insufficient quantity of DNA for routine forensic genetic analysis. These so-called low copy number DNA samples (< 100 pg of genomic DNA) often fall below the sensitivity limitations of routine DNA analysis methods. Theoretically, one way of making such intractable samples amenable to analysis would be to increase the number of starting genomes available for subsequent STR (short tandem repeat) analysis by a whole genome amplification strategy (WGA). Although numerous studies employing WGA have focused primarily on clinical applications, few in-depth studies have been conducted to evaluate the potential usefulness of these methods in forensic casework. After an initial evaluation of existing methods, a modified WGA strategy was developed that appears to have utility for low copy number forensic casework specimens. The method employs a slight, but important, modification of the "improved primer extension preamplification PCR" method (I-PEP-PCR), which we term mIPEP (modified-I-PEP-PCR). Complete autosomal STR and Y-STR (Y chromosome short tandem repeat) profiles were routinely obtained with 5 pg of template DNA, which is equivalent to 1-2 diploid cells. Remarkably, partial Y- and autosomal STR profiles were obtained from mIPEP-treated DNA recovered from bloodstains exposed to the outside environment for 1 year whereas non-mIPEP-treated samples did not produce profiles. STR profiles were obtained from contact DNA from single dermal ridge fingerprints when the DNA was subjected to prior mIPEP amplification but not when the mIPEP step was omitted.

Blood Stains↗

PubMed2004

A highly discriminating 21 locus Y-STR "megaplex" system designed to augment the minimal haplotype loci for forensic casework.

In order to increase significantly the discriminatory potential of Y-STR systems available to the forensic community, we have developed and validated a 21-locus Y-STR multiplex system. Since the system was designed specifically to augment the European Y chromosome typing community's "minimal haplotype" Y-STR set (MHL) for forensic casework, it contains a novel constellation of markers not contained therein. The system, which we refer to as Multiplex IV (MPIV), permits the co-amplification of DYS 443, DYS 444, DYS 445, DYS 447, DYS 448, DYS 449, DYS 452, DYS 453, DYS 454, DYS 455, DYS 456, DYS 458, DYS 463, DYS 464, DYS 468, DYS 484, DYS 522, DYS 527, DYS 531, DYS 557, and DYS 588. Although the multiplex contains 21 Y-STR loci, of which one is bi-local and one is tetra-local, there are actually 25 sites exhibiting allelic variation, and this has prompted us to use the descriptor "megaplex" to describe the system. This report describes a number of performance checks that were employed to characterize the system including sensitivity, specificity, discriminatory capacity, and nonprobative casework studies. Although 1 ng of male DNA was found to be the optimal amount of input template, a complete 21-locus profile was obtained with as little as 50 pg of male DNA (i.e., approximately 8 to 9 diploid cells). The specificity of the system was demonstrated by the lack of significant female DNA derived artifacts when tested using either 300 ng of female DNA alone or an admixture of male/female DNA in which the female component was present in a 100-fold excess. The ability of the system to determine the number of male donors was demonstrated by testing different admixtures of DNA at different ratios from two male donors. Cervicovaginal samples taken up to 48 h post coitus yielded a complete 21-locus Y-STR profile of the semen donor, thus confirming the potential utility of the system for forensic casework. Preliminary estimates of the gene diversity (h) of the individual loci for the Caucasian and African-American population indicated that 15 of the 21 loci possessed an h of > or = 0.5 in at least one population. Multi-locus haplotype analysis revealed that the 21-plex system could augment the use of the minimal haplotype loci and increase significantly the discriminatory capacity of Y-STR analysis.

Chromosomes, Human, Y↗