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A predictive model for vertebrate bone identification from collagen using proteomic mass spectrometry

Yang, Heyi; Butler, Erin R; Monier, Samantha A; Teubl, Jennifer; Fenyö, David; Ueberheide, Beatrix; Siegel, Donald
Proteogenomics is an increasingly common method for species identification as it allows for rapid and inexpensive interrogation of an unknown organism's proteome-even when the proteome is partially degraded. The proteomic method typically uses tandem mass spectrometry to survey all peptides detectable in a sample that frequently contains hundreds or thousands of proteins. Species identification is based on detection of a small numbers of species-specific peptides. Genetic analysis of proteins by mass spectrometry, however, is a developing field, and the bone proteome, typically consisting of only two proteins, pushes the limits of this technology. Nearly 20% of highly confident spectra from modern human bone samples identify non-human species when searched against a vertebrate database-as would be necessary with a fragment of unknown bone. These non-human peptides are often the result of current limitations in mass spectrometry or algorithm interpretation errors. Consequently, it is difficult to know if a "species-specific" peptide used to identify a sample is actually present in that sample. Here we evaluate the causes of peptide sequence errors and propose an unbiased, probabilistic approach to determine the likelihood that a species is correctly identified from bone without relying on species-specific peptides.
PMCID:8149876
PMID: 34035355
ISSN: 2045-2322
CID: 4887812

Evaluation of ForenSeqâ„¢ Signature Prep Kit B on predicting eye and hair coloration as well as biogeographical ancestry by using Universal Analysis Software (UAS) and available web-tools

Sharma, Vishakha; Jani, Krupa; Khosla, Pavan; Butler, Erin; Siegel, Donald; Wurmbach, Elisa
This study examined 266 individuals from various populations including African American, East Asian, South Asian, European, and mixed populations to evaluate the ForenSeqâ„¢ Signature Prep Kit Primer Mix B. Focus was placed on phenotypic and biogeographical ancestry predictions by Illumina's Universal Analysis Software (UAS). These outcomes were compared to those obtained through web-tools developed at the Erasmus Medical Center (EMC) and available from the Forensic Resource/Reference on Genetics-knowledge base (FROG-kb), as well as to eye color predictions by the 8-plex system. Due to drop-outs, predictions for eye and hair color by UAS failed for various samples in each run. By including reads below thresholds, predictions could be obtained for all samples through the web-tools. Eye and hair color predictions for African Americans, East Asians, and South Asians showed no errors. Difficulties however, were noted in intermediate (neither blue nor brown) eye color predictions. These were mitigated by the 8-plex system through exclusion of one eye color (e.g. "not brown"). Additionally, notable discrepancies were observed in hair color predictions, where some black/dark-brown haired individuals were predicted to have blond hair. Overall, ancestry predictions were more accurate by FROG-kb compared to UAS, which did not predict South Asian ancestry, particularly Indian individuals.
PMID: 30767247
ISSN: 1522-2683
CID: 3685302

Systematic assessment of the performance of illumina's MiSeq FGxâ„¢ forensic genomics system

Almalki, Nouran; Chow, Hoi Yan; Sharma, Vishakha; Hart, Katie; Siegel, Donald; Wurmbach, Elisa
This study assesses the performance of Illumina's MiSeq FGx System for forensic genomics by systematically analyzing single source samples, evaluating concordance, sensitivity and repeatability, as well as describing the quality of the reported outcomes. DNA from 16 individuals (9 males/7 females) in nine separate runs showed consistent STR profiles at DNA input ≥400 pg, and two full profiles were obtained with 50 pg DNA input. However, this study revealed that the outcome of a single sample does not merely depend on its DNA input but is also influenced by the total amount of DNA loaded onto the flow cell from all samples. Stutter and sequence or amplification errors can make the identification of true alleles difficult, particularly for heterozygous loci that show allele imbalance. Sequencing of 16 individuals' STRs revealed genetic variations at 14 loci at frequencies suggesting improvement of mixture deconvolution. The STR loci D1S1656 and DXS10103 were most susceptible to drop outs, and D22S1045 and DYS385a-b showed heterozygote imbalance.  Most stutters were typed at TH01 and DYS385a-b, while amplification or sequencing errors were observed mostly at D7S820 and D19S433. Overall, Illumina's MiSeq FGx System produced reliable and repeatable results.  aSTRs showed fewer drop outs than the Y- and X-STRs.
PMID: 27943350
ISSN: 1522-2683
CID: 3095252

Qualitative and quantitative assessment of Illumina's forensic STR and SNP kits on MiSeq FGxâ„¢

Sharma, Vishakha; Chow, Hoi Yan; Siegel, Donald; Wurmbach, Elisa
Massively parallel sequencing (MPS) is a powerful tool transforming DNA analysis in multiple fields ranging from medicine, to environmental science, to evolutionary biology. In forensic applications, MPS offers the ability to significantly increase the discriminatory power of human identification as well as aid in mixture deconvolution. However, before the benefits of any new technology can be employed, a thorough evaluation of its quality, consistency, sensitivity, and specificity must be rigorously evaluated in order to gain a detailed understanding of the technique including sources of error, error rates, and other restrictions/limitations. This extensive study assessed the performance of Illumina's MiSeq FGx MPS system and ForenSeqâ„¢ kit in nine experimental runs including 314 reaction samples. In-depth data analysis evaluated the consequences of different assay conditions on test results. Variables included: sample numbers per run, targets per run, DNA input per sample, and replications. Results are presented as heat maps revealing patterns for each locus. Data analysis focused on read numbers (allele coverage), drop-outs, drop-ins, and sequence analysis. The study revealed that loci with high read numbers performed better and resulted in fewer drop-outs and well balanced heterozygous alleles. Several loci were prone to drop-outs which led to falsely typed homozygotes and therefore to genotype errors. Sequence analysis of allele drop-in typically revealed a single nucleotide change (deletion, insertion, or substitution). Analyses of sequences, no template controls, and spurious alleles suggest no contamination during library preparation, pooling, and sequencing, but indicate that sequencing or PCR errors may have occurred due to DNA polymerase infidelities. Finally, we found utilizing Illumina's FGx System at recommended conditions does not guarantee 100% outcomes for all samples tested, including the positive control, and required manual editing due to low read numbers and/or allele drop-in. These findings are important for progressing towards implementation of MPS in forensic DNA testing.
PMCID:5679668
PMID: 29121662
ISSN: 1932-6203
CID: 3065002

Body fluid identification by mass spectrometry

Yang, Heyi; Zhou, Bo; Deng, Haiteng; Prinz, Mechthild; Siegel, Donald
Standard methods for body fluid identification typically rely on detection of the functional proteins specific to or enriched in them, such as hemoglobin in blood, alkaline phosphatase and PSA in semen, or alpha-amylase in saliva. While these markers can be relatively specific, the multiple methods used to identify them frequently rely on nonspecific chemical, enzymatic, or antibody reactions that usually require the structural integrity of the markers and are not confirmatory because other proteins or substances can also give positive test results. Recent advances in proteomics and mass spectrometry offer the ability to simultaneously detect multiple body fluid protein markers in a single, confirmatory test. Here, multiple markers for blood, saliva, and semen are identified by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS). Data demonstrate the ability to detect these body fluids at nanoliter to subnanoliter levels and to distinguish mixtures. Protein stability of mock samples assayed after 16 months showed no diminution of signal. Because multiple peptides from multiple protein markers are detected and effectively sequenced by MALDI MS/MS, the assay is confirmatory. As mass spectrometry detects whatever peptides are present in a sample, no a priori knowledge of an unknown stain is necessary to perform the test.
PMID: 23525663
ISSN: 0937-9827
CID: 508892

Targeted Delivery of Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand to Keratinocytes with a Pemphigus mAb

Kouno, Michiyoshi; Lin, Chenyan; Schechter, Norman M; Siegel, Don; Yang, Xiaoping; Seykora, John T; Stanley, John R
We determined the feasibility of using an anti-desmoglein (Dsg) mAb, Px44, to deliver a biologically active protein to keratinocytes. Recombinantly produced Px44-green fluorescent protein (GFP) injected into mice and skin organ culture delivered GFP to the cell surface of keratinocytes. We replaced GFP with tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) to produce Px44-TRAIL. We chose TRAIL as a biological model because it inhibits activated lymphocytes and causes apoptosis of hyperproliferative keratinocytes, features of various skin diseases. Px44-TRAIL formed a trimer, the biologically active form of TRAIL. Standard assays of TRAIL activity showed that Px44-TRAIL caused apoptosis of Jurkat cells and inhibited IFN-gamma production by activated CD4+ T cells. Enzyme-linked immunoassay with Px44-TRAIL showed delivery of TRAIL to Dsg. Immunofluorescence with Px44-TRAIL incubated on skin sections and cultured keratinocytes or injected into mouse skin, human organ culture, or human xenografts detected TRAIL on keratinocytes. Px44-TRAIL caused apoptosis of the hyperproliferative, but not differentiating, cultured keratinocytes through binding to Dsg3. Foldon, a small trimerization domain, cloned into Px44-TRAIL maintained its stability and biological activity at 37 degrees C for at least 48 hours. These data suggest that such targeted therapy is feasible and may be useful for hyperproliferative and inflamed skin diseases.Journal of Investigative Dermatology advance online publication, 4 April 2013; doi:10.1038/jid.2013.85.
PMCID:3681880
PMID: 23439393
ISSN: 0022-202x
CID: 403512

Proteomic analysis of menstrual blood

Yang, Heyi; Zhou, Bo; Prinz, Mechthild; Siegel, Donald
Menstruation is the expulsion of the endometrial lining of the uterus following a nearly month long preparation for embryo implantation and pregnancy. Increasingly, the health of the endometrium is being recognized as a critical factor in female fertility, and proteomes and transcriptomes from endometrial biopsies at different stages of the menstrual cycle have been studied for both diagnostic and therapeutic purposes (1 Kao, L. C., et al. 2003 Endocrinology 144, 2870-2881; Strowitzki, Tet al. 2006 Hum. Reprod. Update 12, 617-630; DeSouza, L., et al. 2005 Proteomics 5, 270-281). Disorders of the uterus ranging from benign to malignant tumors, as well as endometriosis, can cause abnormal menstrual bleeding and are frequently diagnosed through endometrial biopsy (Strowitzki, Tet al. 2006 Hum. Reprod. Update 12, 617-630; Ferenczy, A. 2003 Maturitas 45, 1-14). Yet the proteome of menstrual blood, an easily available noninvasive source of endometrial tissue, has yet to be examined for possible causes or diagnoses of infertility or endometrial pathology. This study employed five different methods to define the menstrual blood proteome. A total of 1061 proteins were identified, 361 were found by at least two methods and 678 were identified by at least two peptides. When the menstrual blood proteome was compared with those of circulating blood (1774 proteins) and vaginal fluid (823 proteins), 385 proteins were found unique to menstrual blood. Gene ontology analysis and evaluation of these specific menstrual blood proteins identified pathways consistent with the processes of the normal endometrial cycle. Several of the proteins unique to menstrual blood suggest that extramedullary uterine hematopoiesis or parenchymal hemoglobin synthesis may be occurring in late endometrial tissue. The establishment of a normal menstrual blood proteome is necessary for the evaluation of its usefulness as a diagnostic tool for infertility and uterine pathologies. Identification of unique menstrual blood proteins should aid the forensic community in distinguishing menstrual blood from circulating blood.
PMCID:3494145
PMID: 22822186
ISSN: 1535-9476
CID: 508922

Cardiac Channelopathies Linked to Sudden Infant Death Syndrome/Sudden Unexplained Death Syndrome

Wang, Dawei; Siegel, Donald; Tang, Yingying; Prinz, Mechthild; Sampson, Barbara
ORIGINAL:0008448
ISSN: n/a
CID: 508872