DNA Typing Methods Research Articles

Development of a forensic DNA research grade test material.

Advancements in forensic DNA typing technology and methods have increased sensitivity and, while beneficial, carry the weight of more challenging profile interpretation. In response, the forensic DNA community has often requested more complex reference materials to address commonly encountered measurement and interpretation issues such as complex DNA mixtures, DNA degradation, and PCR inhibition. The National Institute of Standards and Technology (NIST) released Research Grade Test Material 10235: Forensic DNA Typing Resource Samples to support the forensic DNA community. Components include three single source samples, two degraded samples, and three mixture samples. As part of the Research Grade Test Material (RGTM) process, automated methods for bottling, alternative sample tube types, and the addition of carrier RNA for stabilizing low-quantity samples were investigated. Both internal and external testing demonstrate the stability of the material over time at 4°C through qPCR testing. In the development of a data portal, users have been allowed to anonymously upload results and compare their data with NIST and others. This report describes the preparation and stability of this material.

Antibiotyping, RAPD- and ERIC-PCR fingerprinting of Klebsiella pneumoniae clinical isolates at a tertiary reference hospital in Denpasar, Bali, Indonesia.

Klebsiella pneumoniae is a healthcare-associated infections agent and could be an extended spectrum β-lactamase (ESBL) producer. Understanding the transmission of this bacterium in a hospital setting needs accurate typing methods. An antibiogram is used to detect the resistance pattern of the isolates. Random Amplified Polymorphic DNA (RAPD) and Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR are rapid, technically simple, and easy-to-interpret DNA typing methods. This study aimed to evaluate the use of antibiotyping, RAPD-, and ERIC-PCR to investigate the heterogeneity of K. pneumoniae isolated from clinical specimens. The antibiograms of 46 K. pneumoniae clinical isolates were determined by Vitek® 2 Compact. All isolates underwent RAPD-PCR using AP4 primer and ERIC-PCR using ERIC-2 primer. The dendrogram was generated using the GelJ software and analyzed to determine its similarity. The analysis of antibiogram and the molecular typing diversity index was calculated using the formula of the Simpson's diversity index. About 71.7% of the isolates were ESBL-producers, and more than 80% of isolates were susceptible to amikacin, ertapenem, and meropenem. The antibiotyping produced 32 diverse types with DI = 0.964. In addition, the RAPD-PCR produced 47 different types with DI = 1, while ERIC-PCR was 46 (DI=0.999). Antibiotyping, RAPD- and ERIC-PCR showed powerful discrimination power among the isolates, supported the diversity of K. pneumoniae isolates in current study. These combination could be promising tools for clonal relationship determination, including in tracking the transmission of the outbreak's agent in hospital setting.

Molecular typing of clinical and non-clinical <i>Escherichia coli</i> from Rivers State, Nigeria using amplification-based RAPD and ERIC-PCR typing methods

Due to the diverse nature of Escherichia coli, typing of these organisms is essential. This can provide key epidemiological information not just on the strains in circulation and their relationship, but also on the development and spread of drug resistant clones. Affordable PCR-based typing techniques have resulted in an increase in typing studies particularly in resource limited settings. But information from Nigeria on strain typing is limited. This study was therefore aimed at typing clinical and non-clinical strains of E. coli from Nigeria using the PCR based Random Amplification of Polymorphic DNA (RAPD) and Enterobacterial Repetitive Intergenic Consensus-PCR (ERIC-PCR) typing methods. 
 E. coli was isolated from clinical and non-clinical sources using Eosin Methylene Blue agar. Characteristic green metallic sheen colonies associated with E. coli were purified, identities determined using standard biochemical tests and confirmed using molecular methods. Susceptibility testing was carried out using the modified Kirby-Bauer disc diffusion test and RAPD and ERIC-PCR typing carried out on 48 confirmed E. coli isolates as previously described. ERIC-PCR typing resulted in the generation of 38 unique patterns with a 0.94 diversity. Nine of these were singletons comprised of only a single isolate, while the remaining 29 patterns were grouped to 10 clusters. RAPD gave similar results of 37 patterns, 9 singletons, 0.94 diversity and 13 clusters. For ERIC-PCR, all isolates with identical patterns were from the same source. RAPD, however, had identical patterns present in isolates from different sources. 
 Using the ERIC-PCR typing method, this study was able to identify non-clinical isolates as distinct from the clinical E. coli isolates as evidenced by 100% identical ERIC-PCR profiles of isolates from the same source and a lack of 100% relatedness in isolates from different sources.

Differences of circular RNA expression profiles between monozygotic twins' blood, with the forensic application in bloodstain and saliva

Monozygotic twins (MZTs) possess identical genomic DNA sequences and are usually indistinguishable through routine forensic DNA typing methods, which can be relevant in criminal and paternity cases. Recently, novel epigenetic methods involving DNA methylation and microRNA analysis have been introduced to differentiate MZTs. In this study, we explore the potential of using epigenetic markers, specifically circular RNAs (circRNAs), a type of non-coding RNA (ncRNA), to identify MZTs, and investigate the unique expression patterns of circRNAs within pairs of MZTs, enabling effective differentiation. Epigenetics regulates gene expression at the post-transcriptional level and plays a crucial role in cell growth and aging. CircRNAs, a recently characterized subclass of ncRNA, have a distinct covalent loop structure without the typical 5′ cap or 3′ tail. They have been reported to modulate various cellular processes and play roles in embryogenesis and eukaryotic development. To achieve this, we conducted a comprehensive circRNA sequencing analysis (circRNA-seq) using total RNA extracted from the blood samples of five pairs of MZTs. We identified a total of 15,257 circRNAs in all MZTs using circRNA-seq. Among them, 3, 21, 338, and 2967 differentially expressed circRNAs (DEcircRNAs) were shared among five, four, three, and two pairs of MZTs, respectively. Subsequently, we validated twelve selected DEcircRNAs using real-time quantitative polymerase chain reaction (RT-qPCR) assays, which included hsa_circ_0004724, hsa_circ_0054196, hsa_circ_004964, hsa_circ_0000591, hsa_circ_0005077, hsa_circ_0054853, hsa_circ_0054716, hsa_circ_0002302, hsa_circ_0004482, hsa_circ_0001103, novel_circ_0030288 and novel_circ_0056831. Among them, hsa_circ_0005077 and hsa_circ_0004482 exhibited the best performance, showing differences in 7 out of 10 pairs of MZTs. These twelve differentially expressed circRNAs also demonstrated strong discriminative power when tested on saliva samples from 10 pairs of MZTs. Notably, hsa_circ_0004724 displayed differential expression in 8 out of 10 pairs of MZTs in their saliva. Additionally, we evaluated the detection sensitivity, longitudinal temporal stability, and suitability for aged bloodstains of these twelve DEcircRNAs in forensic scenarios. Our findings highlight the potential of circRNAs as molecular markers for distinguishing MZTs, emphasizing their suitability for forensic application.

Association of HLA class II DR/DQ alleles in children and adolescents with rheumatic heart disease from a tertiary care centre in North India

IntroductionRheumatic fever and RHD constitutes an important public health problem in India. The relatively low attack rate of RF, the high concordance rate for RF in monozygotic twins (19%) compared to dizygotic twins (2.5%), and the high familial incidence of RF suggest the involvement of host genetic factors in susceptibility to RF with consequential progression to RHD. ObjectiveTo study the association of HLA CLASS II DR/DQ alleles in children and adolescents with RHD from a tertiary care center in North India. Methods30 RHD patients and 30 age and sex-matched controls were included in our study and blood samples for HLA typing were processed through LAB Type™ reverse SSO DNA typing method. The assignment of the HLA typing was based on a comparison with already published HLA gene sequences. ResultsThe mean age of RHD patients and matched control groups were 12.97 ± 2.95 and 11.93 ± 3.23, respectively. In the cases and control group, males accounted for 63.3% and 50% of the patients respectively. A significant difference was found between the cases and controls for HLA DR∗ 15 (p-value 0.002), HLA DR∗ B4 (p-value 0.045), HLA DR∗ B5 (p-value 0.017), and HLA DQB1∗ 02 (p-value 0.005). ConclusionOur study suggests that HLA class II haplotypes may provide insight into the molecular mechanism of RHD and be a useful tool in predicting the clinical outcome in RF patients, thereby affording new means of intervention or vaccine design. Larger studies are needed to address this in our population.

Association Between HLA Polymorphisms and Sympathetic Ophthalmia in Han Chinese

ABSTRACT Purpose Sympathetic ophthalmia (SO) is considered as an autoimmune disease with unclear mechanisms. This study investigated the relationship between HLA polymorphisms and SO. Methods HLA typing was performed using the LABType reverse SSO DNA typing method. The allele and haplotype frequencies were assessed using the PyPop software. Statistical significance of genotype distributions between 116 patients and 84 healthy individuals (control) was determined using Fisher’s exact test or Pearson's chi-squared test. Results The SO group had a higher frequency of HLA-DRB1 * 04:05, HLA-DQB1 * 04:01, DRB1 * 04:05-DQB1 * 04:01 haplotype as compared to the control group (Pc < 0.001 for all). Conclusion This study revealed that DRB1 * 04:05 and DQB1 * 04:01 alleles, as well as DRB1 * 04:05-DQB1 * 04:01 haplotye could be potential risk factors for SO.

Additional predictions for forensic DNA phenotyping of externally visible characteristics using the ForenSeq and Imagen kits.

Multiplex DNA typing methods using massively parallel sequencing can be used to predict externally visible characteristics (EVCs) in forensic DNA phenotyping through the analysis of single-nucleotide polymorphisms. The focus of EVC determination has focused on hair color, eye color, and skin tone as well as visible biogeographical ancestry features. In this study, we researched off-label applications beyond what is currently marketed by the manufacturer of the Verogen ForenSeq kit primer set B and Imagen primer set E SNP loci. We investigated additional EVC predictions by examining published genome wide sequencing studies and reported allele-specific gene expression and predictive values. We have identified 15 SNPs included in the ForenSeq kit panel and Imagen kits that have additional EVC prediction capabilities beyond what is published in the Verogen manuals. The additional EVCs that can be predicted include hair graying, ephelides hyperpigmented spots, dermatoheliosis, facial pigmented spots, standing height, pattern balding, helix-rolling ear morphology, hair shape, hair thickness, facial morphology, eyebrow thickness, sarcoidosis, obesity, vitiligo, and tanning propensity. The loci can be used to augment and refine phenotype predictions with software such as MetaHuman for missing persons, cold case, and historic case investigations.

USING OF GENETIC-POPULATION STUDIES RESULTS FOR ASSESSMENT OF SELECTION WORK IN DAIRY CATTLE POPULATIONS

The article presents the results of complex research that continues previous work aimed at determining the polymorphism of the CSN2, PRL, LEP, and TNF-α loci and analyzing the productivity of dairy cattle with different genotypes for these loci. The goal of the work is to analyze the selection work with populations of dairy cows based on the results of typing individuals for allelic variants of the CSN2, PRL, LEP, and TNF-α loci, which are associated with economically valuable traits but are not directly evaluated by traditional phenotype-based methods. To analyze the data, the observed (Ho) and expected (He) heterozygosity and Wright's fixation index (Fis) were used. Individual animal typing was performed using AS-PCR (CSN2), SSCP (TNF-α), and PCR-RFLP (PRL, LEP) methods. The studies revealed an excess of heterozygous individuals for the CSN2 and TNF-α loci and a significant predominance of homozygous individuals for the LEP locus in the population of Ukrainian Black-and-White dairy cows. For the prolactin (PRL) and leptin (LEP) genes, a deviation from genetic equilibrium was shown due to the increase in the number of homozygous individuals. In the population of Ukrainian Red-and-White dairy cows, a high level of inbreeding (39%) was found for the PRL locus, which was reflected in a deviation from the genetic equilibrium state (χ2 = 13.50). In the case of the beta-casein and leptin loci, the situation is opposite, with a marked excess of heterozygous individuals (-0.24 and -0.18, respectively), but no deviations from the equilibrium state were observed in the population (χ2 values of 2.06 and 2.42, respectively). For both populations, there were no significant changes in the ratio of different alleles and genotypes for several loci investigated, and the impossibility of fixing desired alleles using traditional breeding methods was demonstrated. Based on a comparative analysis of different types of DNA markers and typing methods (AS-PCR, SSCP, and PCR-RFLP), the sensitivity of the Ho, He, and Fis parameters to the number of alleles at the locus was established, which should be taken into account when conducting genetic-population studies. Keywords: polymorphism, population, cows, allele, genotype, homozygosity, variability, fixation.

Reverse complement-PCR, an innovative and effective method for multiplexing forensically relevant single nucleotide polymorphismmarker systems.

DNA analyses from challenging samples such as touch evidence, hairsand skeletal remains push the limits of the current forensic DNA typing technologies. Reverse complement PCR (RC-PCR) is a novel, single-step PCR target enrichment method adapted to amplify degraded DNA. The sample preparation process involves a limited number of steps, decreasing the labor required for library preparation and reducing the possibility of contamination due to less sample manipulation. These features of the RC-PCR make the technology a unique application to successfully target single nucleotide polymorphisms(SNPs) in fragmented and low copy number DNA and yield results from samples in which no or limited data are obtained with standard DNA typing methods. The developed RC-PCR short amplicon 85 SNP-plex panel is a substantial improvement overthe previously reported 27-plex RC-PCR multiplex that will provide higher discrimination power for challenging DNA sample analyses.

Application of Two Sex Markers by Nested PCR for Gender Determination

Sex determination is one of the basic components in victim identification. There are many available methods,namely forensic anthropology method and conventional DNA typing method. In this study, nested PCRtechnique was employed in sex typing of burnt teeth through amelogenin (AMEL) and sex-determiningregion Y (SRY) markers. In this study, 17 teeth samples were burnt at temperatures that ranged from 100°Cto 500°C for 2 min - 10 min. The whole tooth was used for DNA extraction by phenol-chloroform method.Accurate sex determination was achieved in 13 samples by both AMEL and SRY markers. The SRY markerachieved higher sensitivity as compared to AMEL marker. The sensitivity of both markers was improvedconsequent to nested PCR. Factors such as degraded DNA materials and the presence of tooth caries greatlyaffect sex typing results. Results showed that nested PCR proved to be a good method to amplify highlydegraded DNA material as it greatly increased the DNA copy, and thus increased the possibility of sextyping.

Current Methods for Body Fluid Identification Related to Sexual Crime: Focusing on Saliva, Semen, and Vaginal Fluid.

Although, DNA typing plays a decisive role in the identification of persons from blood and body fluid stains in criminal investigations, clarifying the origin of extracted DNA has also been considered an essential task in proving a criminal act. This review introduces the importance of developing precise methods for body fluid identification. Body fluid identification has long relied on enzymatic methods as a presumptive assay and histological or serological methods as a confirmatory assay. However, because the latest DNA typing methods can rapidly obtain results from very small and even old, poorly preserved samples, the development of a novel corresponding body fluid identification method is required. In particular, an immunochromatographic method has been introduced to identify saliva and semen from sexual crimes. In addition, for vaginal fluid identification, attempts have been made in the past decade to introduce a method relying on body fluid-specific mRNA expression levels. At present, the development of molecular biological methods involving microRNA, DNA methylation, and resident bacterial DNA is ongoing. Therefore, in criminal investigations, body fluid identification is an essential task for correctly applying the results of DNA typing, although further research and development are required.

Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing

Massively parallel sequencing (MPS) has rapidly become a promising method for forensic DNA typing, due to its ability to detect a large number of markers and samples simultaneously in a single reaction, and sequence information can be obtained directly. In the present study, two kinds of forensic genetic markers, short tandem repeat (STR) and identity-informative single nucleotide polymorphism (iiSNP) were analyzed simultaneously using ForenSeq DNA Signature Prep Kit, a commercially available kit on MPS platform. A total of 152 DNA markers, including 27 autosomal STR (A-STR) loci, 24 Y chromosomal STR (Y-STR) loci, 7 X chromosomal STR (X-STR) loci and 94 iiSNP loci were genotyped for 107 Tibetan individuals (53 males and 54 females). Compared with length-based STR typing methods, 112 more A-STR alleles, 41 more Y-STR alleles, and 24 more X-STR alleles were observed at 17 A-STRs, 9 Y-STRs, and 5 X-STRs using sequence-based approaches. Thirty-nine novel sequence variations were observed at 20 STR loci. When the flanking regions were also analyzed in addition to target SNPs at the 94 iiSNPs, 38 more alleles were identified. Our study provided an adequate genotype and frequencies data of the two types of genetic markers for forensic practice. Moreover, we also proved that this panel is highly polymorphic and informative in Tibetan population, and should be efficient in forensic kinship testing and personal identification cases.

Specific amino acid patterns define split specificities of HLA-B15 antigens enabling conversion from DNA-based typing to serological equivalents

The HLA-B15 typing by serological approaches defined the serological subgroups (or splits) B62, B63, B75, B76, B77 and B70 (B71 and B72). The scarcity of sera with specific anti-HLA antibodies makes the serological typing method difficult to discriminate a high variety of HLA antigens, especially between the B15 antigen subgroups. Advancements in DNA-based technologies have led to a switch from serological typing to high-resolution DNA typing methods. DNA sequencing techniques assign B15 specificity to all alleles in the HLA-B*15 allele group, without distinction of the serological split equivalents. However, the presence of antibodies in the patient defined as split B15 antigens urges the identification of HLA-B*15 allele subtypes of the donor, since the presence of donor-specific antibodies is an important contraindication for organ transplantation. Although the HLA dictionary comprises information regarding the serological subtypes of HLA alleles, there are currently 394 B15 antigens out of 516 in the IPD-IMGT/HLA database (3.38.0) without any assigned serological subtype. In this regard, we aimed to identify specific amino acid patterns for each B*15 serological split, in order to facilitate the assignment of B*15 alleles to serological equivalents after high-resolution molecular typing. As a result, serological specificities of 372/394 not yet assigned alleles could be predicted based on amino acid motifs. Furthermore, two new serological types were identified and added, B62-Bw4 and B71-Bw4.

Large-scale identification of human bone remains via SNP microarray analysis with reference SNP database

Single nucleotide polymorphisms (SNPs) are valuable markers complementary to conventional forensic short tandem repeat (STR) markers in genetic typing, with potential advantages in challenging forensic casework. With the advent of high-throughput technologies, such as microarrays and massively parallel sequencing, the use of SNP typing has now expanded to large-scale forensic applications. Herein, a forensic case is presented to demonstrate the usefulness of SNP typing in identifying large-scale human bone remains with reference database construction. A total of 402 bone remains were recovered from an island in the Jeju Province of Korea where a massive disaster occurred in 1948. The first phase of the identification process was accomplished via conventional DNA typing methods including autosomal and Y-chromosomal STR typing, and mitochondrial DNA sequencing, which resulted in the identification of 74 of 402 remains. The second phase of the identification involved the remaining 327 unidentified remains using SNP typing as a supplementary tool based on Affymetrix resequencing array. The SNP markers of 782 family members were also analyzed and a reference database was constructed for comparison. An additional 51 bone remains were identified in the second phase. SNP data obtained from the supplementary genotyping yielded additional genetic information as well as contributed to kinship testing to determine the second degrees of relationship. In addition SNPs are useful in discriminating ambiguous relationship when only STR data are available. A software program developed for SNP typing system enabled efficient kinship analysis for large-scale forensic identification. The results and the casework are described and discussed.

Alternatives to amelogenin markers for sex determination in humans and their forensic relevance.

Forensic DNA typing and subsequent molecular methods of sex determination in humans have been proven to be an imperious tool to criminal justice system. In current practice, most of the short tandem repeat (STR) based commercial kits contain amelogenin as the sexing marker. Amelogenin gene which contributes to the tooth enamel formation is present on both X and Y chromosome with a variation in base pair size. However, huge discrepancies have been observed with amelogenin based sex determination mostly due to X and Y deletion in the population and mutation in primer binding sites. Some ethnicities such as those in Indian population are affected badly with inappropriate sex determination by amelogenin marker due to the presence of high frequency of Y deletion in the population. Presence of PCR inhibitors, degradation in the DNA samples and presence of mixed DNA also contribute to the discrepancy in results obtained by amelogenin analysis. To overcome this problem, many alternative markers/techniques such as STS, SRY, TSPY, DXYS156, SNPs, DYZ1 and Next generation sequencing have been discussed in much detail with their respective pros and cons. In this regard, inclusion of one or more alternative markers along with amelogenin will decrease the anomalies in sex determination observed while using the amelogenin marker alone in forensic sample analysis.

Somatic Mutations and Loss of Heterozygosity of HLA Genes Are Frequently Occurred and Tightly Associated with Poor Prognosis in Adult T Cell Leukemia-Lymphoma

Introduction: Adult T cell leukemia-lymphoma (ATL) is clinically divided into aggressive (acute and lymphoma) and indolent (chronic and smoldering) subtypes. Recent studies revealed that ATL has a wide variety of gene alternations (Nat Genet. 2015; 47:1304, Nature. 2016; 534:402). Consistent with the notion that human leukocyte antigen (HLA) play a critical role for immune response, reduced expression of HLA has been shown to associate with poor prognosis in various types of malignancies (Oncogene. 2008; 27:5869). However, it is extremely difficult to assess the impact of somatic mutations of HLA genes in cancer cells because of its highly polymorphic nature. Taking advantage of computational tools using whole-exome sequencing data, somatic mutations of HLA class I genes were previously reported in about 3% of various types of cancers (Nat Biotechnol. 2015; 33:1152). To date, HLA typing has been performed through partial sequencing data of polymorphic exons, resulting in the loss of critical information on the entire region of HLA genes. In this context, using a next generation sequence (NGS)-based HLA DNA typing method, we analyzed the entire region of HLA genes in ATL cells and its impact on clinical outcomes. Methods: The present study was approved by the Investigational Review Board of University of the Ryukyus and Tokai University. Peripheral blood mononuclear cells collected from 25 ATL patients (Pts) (20 with acute type and 5 with chronic type) were analyzed. Cell adhesion molecular 1 (CADM1)-positive ATL cells and CADM1-negative non-ATL cells were separated by a magnetic-activated cell-sorting protocol, and genomic DNAs in each fraction were distinctively extracted. The PCR products of the eight HLA loci (HLA-A, -B, -C, -DRB1, -DQA1, -DQB1, -DPA1 and -DPB1) were obtained using the previously designed long ranged PCR primers (Tissue Antigens. 2012; 80:305) that cover the entire HLA gene sequences from the enhancer-promoter region to the 3'UTR region. The full-length level HLA genotypes were determined by mapping of sequence reads obtained by the Ion Torrent system to HLA allele reference sequences in the international ImMunoGeneTics project (IMGT)-HLA database. Somatic mutations and loss of heterozygosity (LOH) generated in ATL cells were identified by detail comparison of sequence data between the ATL and non-ATL cells. Survival curves were estimated using the Kaplan-Meier method and compared by the log-rank test. Results: We found a total of 20 somatic mutations in ATL cells among 9 Pts, including 15 single nucleotide variations (SNVs) and 5 insertions/deletions (indels) (Table 1). Of the 15 SNVs, 3 were nonsense mutations in exon 2/3 of HLA-A/B, 7 were nonsynonymous mutations in exon 1/4/5 of HLA-A/B/C, and 2 were mutations at splice sites in intron 2 of HLA-B/C. The mutations of splice sites in intron 2 and all the 5 indels caused frameshift generating premature stop codons. In contrast to the exons, there were only 3 mutations found in introns. Of 8 Pts harboring LOH, two Pts showed LOH in HLA-A gene, 4 Pts in HLA-A, -C, and -B genes, one Pt in HLA-DRB1, -DQA1, -DQB1, -DPA1 and -DPB1 genes, and one Pt in all the HLA-genes from HLA-A to HLA-DPB1. All the somatic mutations altering the structure of the HLA proteins (St-mt) and/or LOH were found in Pts with acute type ATL, while no St-mt or LOH were detected in Pts with chronic type ATL. Pts with St-mt/LOH (n = 9) significantly worsened in 3 years overall survival rate as compared to that in Pts without St-mt/LOH (n = 16) (11 % vs. 32 %, P = 0.016) (Fig. 1A). Among Pts with acute type ATL, Pts with St-mutations/LOH (n = 9) also showed a trend to worsen in the survival rate as compared to those in Pts without St-mutation /LOH (n = 11) (11 % vs. 30 %, P=0.064) (Fig. 1B). Conclusion: NGS-based HLA gene analyses at full-length level revealed that St-mt/LOH were frequently occurred predominantly in HLA class I loci in tumor cells from Pts with aggressive ATL. Importantly, St-mt/LOH in HLA genes were associated with aggressive phenotypes and poor prognosis, suggesting the possibility that ATL cells would develop immune escape mechanisms through a variety of acquired abnormalities in HLA gene. Since allogeneic stem cell transplantation is an essential therapeutic option for aggressive ATL, comprehensive knowledges on HLA gene abnormalities provide considerable advantage to optimize therapeutic modalities. Disclosures Fukushima: Daiichi-Sankyo: Research Funding.

Looking for the pinpoint: Optimizing identification, recovery and DNA extraction of micro traces in forensic casework

Many challenges are encountered in the analysis of micro traces such as touch DNA or telogen hair samples. Although DNA typing methods have become immensely more sensitive over the last years, recovery of the minute amounts of biological material in micro traces requires further enhancement. For example felony cases, where an offender oftentimes only contributes minor amounts of touch DNA, separation of victim and offender DNA poses difficulties. Whereas complete sampling of evidence generates admixed profiles, single particle collection is labor- and time-intensive. Besides optimization of identification and collection of bio particles during this study, a novel sampling strategy for enhanced DNA yield as well as success rate but simultaneous avoidance of mixture creation is proposed for tapings in forensic casework. Improvement of another crucial step in micro trace analysis, DNA extraction, involved evaluation of efficiency and DNA recovery of different extraction methods, namely magnetic bead based Maxwell extraction, Chelex, Casework Direct Kit and Investigator Casework GO! kit. Direct lysis approaches seemed to be most suitable for low template traces. Recently developed commercial kits even allow the presence of inhibitors. Improvement of embraced aspects successfully facilitates processing of micro traces in terms of time and labor.

Differences of microRNA expression profiles between monozygotic twins’ blood samples

Monozygotic (MZ) twins are widely regarded as genetically identical, and traditional DNA typing methods are insufficient in identifying MZ twins. So the discrimination of MZ twins become a forensic problem. MicroRNAs (miRNAs) are a class of small, endogenous, non-protein-coding RNA molecules of approximately 22 nucleotides in length, and exist extensively in a variety of eukaryotic cells. MiRNAs regulate gene expression and play fundamental roles in multiple biological processes, including cell differentiation, proliferation and apoptosis as well as aging and disease processes. The goal of this study is to explore the differential expression of miRNAs within MZ twin pairs, and aimed to find new biomarkers for distinguishing MZ twins. Thus, the miRNA expression profiles of seven pairs of healthy MZ twins of different sex and age were analyzed by miRNA microarray. A total of 545 miRNAs were found to be differentially expressed in these MZ twin pairs, and 2, 5, 22, 53 and 132 differentially expressed miRNAs were shared across six, five, four, three and two pairs of MZ twins respectively. These findings had been confirmed by real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assays on select miRNAs, including miR-151a-3p, miR-3653-3p, miR-142-3p, miR-4325, miR-16-5p, let-7i-5p, miR-222-3p, miR-550b-3p, miR-4791 and miR-27a-3p. The results demonstrated that there are differences in the expression of miRNAs within MZ twin pairs, suggesting a role of miRNAs in identifying MZ twins.

Application of next generation sequencing for species identification in meat and poultry products: A DNA metabarcoding approach

Species substitution is one of the forms of food fraud for economic gain. The vast majority of existing DNA typing methods are targeted methods that developed for the determination of the specific species in food products. However, these methods are inappropriate for the analysis of unknown food products or a blend of more than one species. This study aimed to investigate the ability of high-throughput DNA metabarcoding to identify mammalian and avian species in mixed products. Next-generation sequencing of a short segment of the 16S ribosomal RNA (16S rRNA) mitochondrial gene was performed. Duplicate samples and two different databases produced very similar results. Although the relative abundance of reads obtained from each species could not make a quantitative assessment of the original species composition, this method still has the potential to determination of high and low contents of animal species in mixed products. Subsequently, we performed a market survey to identify animal species in 27 meat and poultry products sold in China using the developed DNA metabarcoding approach. The results indicated the presence of mislabeling of processed meat and poultry products.

Prevalence and Mechanisms of Carbapenem Resistance Among Acinetobacter baumannii Clinical Isolates in Egypt.

The increasing number of carbapenem-resistant Acinetobacter baumannii clinical isolates is a major concern, which restricts therapeutic options for treatment of serious infections caused by this emerging pathogen. The aim of this work is to assess the antimicrobial resistance profile and identify the molecular mechanisms involved in carbapenem resistance in A. baumannii isolated from different clinical sources in Mansoura University Hospitals, Egypt. Antimicrobial susceptibility testing has shown that resistance to carbapenem has dramatically increased (98%) with concomitant elevated levels of resistance to quinolones, trimethoprim/sulfamethoxazole, and aminoglycosides. Polymyxin B and colistin are considered the last resort. Random amplified polymorphic DNA (RAPD) typing method revealed great diversity among A. baumannii isolates. Coexistence of diverse intrinsic and acquired carbapenem-hydrolyzing β-lactamases has been detected in the tested isolates: Ambler class A: blaKPC (56%) and blaGES (48%), and Ambler class B: blaNDM (30%), blaSIM (28%), blaVIM (20%), and blaIMP (10%). Most isolates (94%) carried blaOXA-23-like and blaOXA-51-like simultaneously. blaOXA-23-like was preceded by ISAba1 providing a potent promoter activity for its expression. Sequencing analysis revealed that ISAba1 has been also inserted in carbapenem resistance-associated outer membrane protein (OMP) (carO) gene in three isolates, two of which were clonal based on RAPD typing, leading to interruption of its expression as confirmed by SDS-PAGE analysis of OMP fractions. Carbapenem resistance genes are widely distributed among A. baumannii clinical isolates from different clinical sources. Therefore, enhanced infection control measures, effective barriers, and rational use of antimicrobials should be enforced in hospitals for minimizing the widespread resistance to carbapenems and all other antibiotics.