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https://www.readbyqxmd.com/read/28324958/ultrafast-oscillatory-flow-pcr-for-amplication-of-urine-short-tandem-repeats
#1
Haoyu Tang, Tao Dong
The short tandem repeats (STRs) in human urine which is the most sensitive body fluid can be serviced as biomarkers for the individual identification. PCR microchips are automated, sensitive and rapid. In this report, COMSOL with Finite Element Analysis (FEA) is employed to study the temperature distribution of the base layer to optimize the structure of the microfluidic chip. Meanwhile, the oscillatory PCR microdevice is preliminary tested by DNA samples extracted from urine with the FTA papers and CSF1PO, TPOX, TH01 Multiplex kits...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28315050/forensic-use-of-y-chromosome-dna-a-general-overview
#2
REVIEW
Manfred Kayser
The male-specific part of the human Y chromosome is widely used in forensic DNA analysis, particularly in cases where standard autosomal DNA profiling is not informative. A Y-chromosomal gene fragment is applied for inferring the biological sex of a crime scene trace donor. Haplotypes composed of Y-chromosomal short tandem repeat polymorphisms (Y-STRs) are used to characterise paternal lineages of unknown male trace donors, especially suitable when males and females have contributed to the same trace, such as in sexual assault cases...
March 17, 2017: Human Genetics
https://www.readbyqxmd.com/read/28303785/fast-gas-chromatography-with-tandem-mass-spectrometry-analysis-of-selected-persistent-organic-pollutants-and-organophosphorus-and-synthetic-pyrethroid-pesticides-in-indian-prawn-fenneropenaeus-indicus-in-compliance-with-the-eu-mrls
#3
Durvesh Sawant, Jitendra Kelkar, Pratap Rasam, Ajit Datar, Prashant Hase, Dheeraj Handique, Ankush Bhone, Sanket Chiplunkar, Manish Hate
A fast GC with tandem MS method was developed and validated for multiresidue determination of 95 chemical contaminants(24 synthetic pyrethroids, 17 organochlorines, 17 organophosphorus compounds, 18 polycyclic aromatic hydrocarbons, and 19 polychlorinated biphenyls) in Indian prawns (<i>Fenneropenaeus indicus</i>) as per the European Union maximum residual limit requirements. Chromatographic separation and MS determination were achieved within a short run time of 18 min, without compromising sensitivity and specificity...
March 16, 2017: Journal of AOAC International
https://www.readbyqxmd.com/read/28295384/noninvasive-fetal-genotyping-of-paternally-inherited-alleles-using-targeted-massively-parallel-sequencing-in-parentage-testing-cases
#4
Donggui Yang, Hao Liang, Yu Gao, Shaobin Lin, Zhiming He, Jun Gao, Hongyu Sun, Qing Li, Xiaoyan Ma, Xueling Ou
BACKGROUND: Researchers have sought to develop a noninvasive protocol for paternity analysis that uses fetal cell-free DNA (cfDNA) in maternal plasma. Massively parallel sequencing (MPS) is expected to overcome this challenge because it enables the analysis of millions of DNA molecules at a single-base resolution. STUDY DESIGN AND METHODS: Seven women were involved in prenatal paternity testing cases. Before conventional invasive procedures, cfDNA was isolated from maternal plasma...
March 10, 2017: Transfusion
https://www.readbyqxmd.com/read/28295144/androgen-receptor-polyglutamine-repeat-length-ar-cagn-modulates-the-effect-of-testosterone-on-androgen-associated-somatic-traits-in-filipino-young-adult-men
#5
Calen P Ryan, Alexander V Georgiev, Thomas W McDade, Lee T Gettler, Dan T A Eisenberg, Margarita Rzhetskaya, Sonny S Agustin, M Geoffrey Hayes, Christopher W Kuzawa
OBJECTIVES: The androgen receptor (AR) mediates expression of androgen-associated somatic traits such as muscle mass and strength. Within the human AR is a highly variable glutamine short-tandem repeat (AR-CAGn), and CAG repeat number has been inversely correlated to AR transcriptional activity in vitro. However, evidence for an attenuating effect of long AR-CAGn on androgen-associated somatic traits has been inconsistent in human populations. One possible explanation for this lack of consistency is that the effect of AR-CAGn on AR bioactivity in target tissues likely varies in relation to circulating androgen levels...
March 14, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28292727/analysis-of-dna-from-post-blast-pipe-bomb-fragments-for-identification-and-determination-of-ancestry
#6
Esiri Tasker, Bobby LaRue, Charity Beherec, David Gangitano, Sheree Hughes-Stamm
Improvised explosive devices (IEDs) such as pipe bombs are weapons used to detrimentally affect people and communities. A readily accessible brand of exploding targets called Tannerite® has been identified as a potential material for abuse as an explosive in pipe bombs. The ability to recover and genotype DNA from such weapons may be vital in the effort to identify suspects associated with these devices. While it is possible to recover DNA from post-blast fragments using short tandem repeat markers (STRs), genotyping success can be negatively affected by low quantities of DNA, degradation, and/or PCR inhibitors...
March 1, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28288660/evidence-of-metachronous-development-of-ovarian-teratomas-a-case-report-of-bilateral-mature-cystic-teratomas-of-the-ovaries-and-systematic-literature-review
#7
Wen-Chung Wang, Yen-Chein Lai
BACKGROUND: Mature cystic teratomas are usually found in the ovaries. They are bilateral in 10 to 15% of cases and multiple cystic teratomas may be present in one ovary. The aim of this study is to clarify if development of mature cystic teratomas of the ovaries in a single host is metachronous or due to autoimplant or recurrence. CASE PRESENTATION: We report a woman with bilateral mature cystic teratomas of the ovaries. DNA profiles of these teratomas were investigated via short tandem repeat (STR) analysis and methylation statuses were determined via methylation sensitive multiplex ligation-dependent probe amplification methods...
March 14, 2017: Journal of Ovarian Research
https://www.readbyqxmd.com/read/28286611/the-relationship-between-str-pcr-chimerism-analysis-and-chronic-gvhd-following-hematopoietic-stem-cell-transplantation
#8
Seyed Asadollah Mousavi, Mina Javadimoghadam, Ardeshir Ghavamzadeh, Kamran Alimoghaddam, Azadeh Sayarifard, Seyed-Hamidollah Ghaffari, Bahram Chahardouli, Ali Basi
Background: The study attempts to assess the relationship between chimerism analysis using polymerase chain reaction of short tandem repeat (STR) and the incidence of chronic graft versus host disease (GvHD) as well as survival. Subjects and Methods: The retrospective cohort included all patients who received allo-HSCT during 2005-2013. Data collected by day +100 were reviewed in terms of the incidence of chronic GvHD and survival. Chimerism was evaluated for whole blood, T-cell and PMN cells on days 15, 30 and 60, respectively using polymerase chain reaction of short tandem repeat (STR)...
January 1, 2017: International Journal of Hematology-oncology and Stem Cell Research
https://www.readbyqxmd.com/read/28286147/evaluation-and-assessment-of-read-mapping-by-multiple-next-generation-sequencing-aligners-based-on-genome-wide-characteristics
#9
Subazini Thankaswamy-Kosalai, Partho Sen, Intawat Nookaew
Massive data produced due to the advent of next-generation sequencing (NGS) technology is widely used for biological researches and medical diagnosis. The crucial step in NGS analysis is read alignment or mapping which is computationally intensive and complex. The mapping bias tends to affect the downstream analysis, including detection of polymorphisms. In order to provide guidelines to the biologist for suitable selection of aligners; we have evaluated and benchmarked 5 different aligners (BWA, Bowtie2, NovoAlign, Smalt and Stampy) and their mapping bias based on characteristics of 5 microbial genomes...
March 9, 2017: Genomics
https://www.readbyqxmd.com/read/28284873/establishing-a-reference-dataset-for-the-authentication-of-spinal-muscular-atrophy-cell-lines-using-str-profiling-and-digital-pcr
#10
Deborah L Stabley, Jennifer Holbrook, Ashlee W Harris, Kathryn J Swoboda, Thomas O Crawford, Katia Sol-Church, Matthew E R Butchbach
Fibroblasts and lymphoblastoid cell lines (LCLs) derived from individuals with spinal muscular atrophy (SMA) have been and continue to be essential for translational SMA research. Authentication of cell lines helps ensure reproducibility and rigor in biomedical research. This quality control measure identifies mislabeling or cross-contamination of cell lines and prevents misinterpretation of data. Unfortunately, authentication of SMA cell lines used in various studies has not been possible because of a lack of a reference...
February 6, 2017: Neuromuscular Disorders: NMD
https://www.readbyqxmd.com/read/28273507/flanking-region-variation-of-forenseq%C3%A2-dna-signature-prep-kit-str-and-snp-loci-in-yavapai-native-americans
#11
Frank R Wendt, Jonathan L King, Nicole M M Novroski, Jennifer D Churchill, Jillian Ng, Robert F Oldt, Kelly L McCulloh, Jessica A Weise, David Glenn Smith, Sreetharan Kanthaswamy, Bruce Budowle
Massively parallel sequencing (MPS) offers advantages over current capillary electrophoresis-based analysis of short tandem repeat (STR) loci for human identification testing. In particular STR repeat motif sequence information can be obtained, thereby increasing the discrimination power of some loci. While sequence variation within the repeat region is observed relatively frequently in some of the commonly used STRs, there is an additional degree of variation found in the flanking regions adjacent to the repeat motif...
February 27, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28264849/genetic-diversity-and-in-vitro-antifungal-susceptibility-of-200-clinical-and-environmental-aspergillus-flavus-isolates
#12
Mojtaba Taghizadeh-Armaki, Mohammad Taghi Hedayati, Saham Ansari, Saeed Mahdavi Omran, Sasan Saber, Haleh Rafati, Jan Zoll, Henrich A van der Lee, Willem J G Melchers, Paul E Verweij, Seyedmojtaba Seyedmousavi
Aspergillus flavus has been frequently reported as the leading cause of invasive aspergillosis in certain tropical and sub-tropical countries.Two hundred A. flavus strains originating from clinical and environmental sources and collected between 2008 and 2015 were phylogenetically identified at the species level by analyzing partial β-tubulin and calmodulin genes. In vitro antifungal susceptibility testing was performed against antifungals using the EUCAST (European Committee on Antimicrobial Susceptibility Testing) broth microdilution method...
March 6, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28258706/preimplantation-genetic-haplotyping-for-six-chinese-pedigrees-with-thalassemia-using-a-single-nucleotide-polymorphism-microarray
#13
Xu Liu, Yanwen Xu, Jishan Sun, Zheng Zhang, Jing Wang, Chenhui Ding, S Lilly Zheng, Jianfeng Xu, Canquan Zhou
OBJECTIVE: To demonstrate the accuracy and feasibility of using single nucleotide polymorphism (SNP) array-based preimplantation genetic haplotyping (PGH) in Chinese population, as the currently short tandem repeat (STR) method is labor-intensive and time-consuming. METHOD: Six pedigrees with thalassemia who underwent preimplantation genetic diagnosis (PGD) in the First Affiliated Hospital of Sun Yat-sen University in China were included in this study. In vitro fertilization (IVF) cycles and embryo biopsies were performed in clinics...
March 4, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/28258488/flexplex27-highly-multiplexed-rapid-dna-identification-for-law-enforcement-kinship-and-military-applications
#14
Ranjana Grover, Hua Jiang, Rosemary S Turingan, Julie L French, Eugene Tan, Richard F Selden
Rapid DNA identification is the use of a rugged, field-deployable system to generate short tandem repeat (STR) profiles in law enforcement, military, immigration, and homeland security applications. A performance verification study was conducted on the ANDE Rapid DNA identification system using FlexPlex27, a highly multiplexed, 27 locus assay that generates data for the expanded CODIS core loci and all additional STR loci required for international databasing. The assay contains 23 autosomal loci (D1S1656, D2S1338, D2S441, D3S1358, D5S81, D6S1043, D7S820, D8S1179, D10S1248, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, D22S1045, FGA, CSF1PO, Penta E, TH01, vWA, TPOX, and SE33), three Y-chromosomal loci (DYS391, DYS576, and DYS570), and Amelogenin...
March 3, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28253571/-application-study-of-droplet-digital-pcr-to-detect-maternal-cell-contamination-in-prenatal-diagnosis
#15
J Geng, C Liu, X C Zhou, J Ma, L Du, J Lu, W N Zhou, T T Hu, L J Lyu, A H Yin
Objective: To develop a new method based on droplet digital PCR (DD-PCR) for detection and quantification of maternal cell contamination in prenatal diagnosis. Methods: Invasive prenatal samples from 40 couples of β(IVS-Ⅱ-654)/β(N) thalassemia gene carriers who accepted prenatal diagnosis in Affiliated Women and Children's Hospital of Guangzhou Medical University from October 2015 to December 2016 were analyzed retrospectively. Specific primers and probes were designed. The concentration gradient were 50%, 25%, 12...
February 25, 2017: Zhonghua Fu Chan Ke za Zhi
https://www.readbyqxmd.com/read/28249201/genome-wide-screening-for-highly-discriminative-snps-for-personal-identification-and-their-assessment-in-world-populations
#16
Liming Li, Yi Wang, Shuping Yang, Mingying Xia, Yajun Yang, Jiucun Wang, Daru Lu, Xingwei Pan, Teng Ma, Pei Jiang, Ge Yu, Ziqin Zhao, Yuan Ping, Huaigu Zhou, Xueying Zhao, Hui Sun, Bing Liu, Dongtao Jia, Chengtao Li, Rile Hu, Hongzhou Lu, Xiaoyang Liu, Wenqing Chen, Qin Mi, Fuzhong Xue, Yongdong Su, Li Jin, Shilin Li
The applications of DNA profiling aim to identify perpetrators, missing family members and disaster victims in forensic investigations. Single nucleotide polymorphisms (SNPs) based forensic applications are emerging rapidly with a potential to replace short tandem repeats (STRs) based panels which are now being used widely, and there is a need for a well-designed SNP panel to meet such challenge for this transition. Here we present a panel of 175 SNP markers (referred to as Fudan ID Panel or FID), selected from ∼3...
February 16, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28246934/forensic-characteristics-and-phylogenetic-analyses-of-the-chinese-yi-population-via-19-x-chromosomal-str-loci
#17
GuangLin He, Ye Li, Xing Zou, Ping Li, PengYu Chen, Feng Song, Tianzhen Gao, Miao Liao, Jing Yan, Jin Wu
The demographic characteristics and genetic polymorphism data of 56 Chinese nationalities or 31 administrative divisions in Chinese mainland have repeatedly been the genetic research hotspots. While most genetic studies focused on some particular Chinese populations based on autosomal or Y-chromosomal genetic markers, the forensic characteristics and phylogenetic analyses of the seventh largest Chinese population (Yi ethnicity) on the X-chromosomal genetic markers are scarce. Here, allele frequencies and forensic statistical parameters for 19 X-chromosomal short tandem repeat loci (DXS7424-DXS101, DXS6789-DXS6809, DXS7423-DXS10134, DXS10103-HPRTB-DXS10101, DXS10159-DXS10162-DXS10164, DXS10148-DXS10135-DXS8378, and DXS7132-DXS10079-DXS10074-DXS10075) of 331 Chinese Yi individuals were obtained...
February 28, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28243773/how-many-single-nucleotide-polymorphisms-snps-are-needed-to-replace-short-tandem-repeats-strs-in-forensic-applications
#18
Hyo-Jung Lee, Jae Won Lee, Su Jin Jeong, Mira Park
Short tandem repeats (STRs) are the most commonly used forms of genetic information in forensic identification. In recent times, advances in the information on single nucleotide polymorphisms (SNPs) have raised the possibility that these markers could replace the forensically established STRs. In this work, we conducted comparative simulation studies that allowed us to estimate the number of SNPs needed if these markers were used instead of STRs in criminal cases and paternity investigations.
February 27, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28243771/analysis-of-four-novel-x-chromosomal-short-tandem-repeats-within-71%C3%A2-kb-of-the-xp22-3-region
#19
Takeki Nishi, Kenji Fukui, Kimiharu Iwadate
DNA testing using X-chromosomal short tandem repeat (X-STR) polymorphisms has been used in maternity/paternity and complex kinship cases. Analyses of repeat sequences, surveys on racial statistics, and development of practical applications for DNA testing continue to be reported. In this study, we identified four novel tetranucleotide STR loci located in the X chromosome, which is the basis of X-STR research. These four tetranucleotide STRs were located within 71 kb of the chromosome Xp22.3 region. Using sequence analysis of the structure of repeat sequences, we identified simple repeat sequences of TAAA, CTTT, TATC, and GATA with rare insertions...
February 27, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28242557/sensitive-dip-str-markers-for-the-analysis-of-unbalanced-mixtures-from-touch-dna-samples
#20
Fabio Oldoni, Vincent Castella, Frederic Grosjean, Diana Hall
Casework samples collected for forensic DNA analysis can produce genomic mixtures in which the DNA of the alleged offender is masked by high quantities of DNA coming from the victim. DIP-STRs are novel genetic markers specifically developed to enable the target analysis of a DNA of interest in the presence of exceeding quantities of a second DNA (up to 1000-fold). The genotyping system, which is based on allele-specific amplifications of haplotypes formed by a deletion/insertion polymorphism (DIP) and a short tandem repeat (STR), combines the capacity of targeting the DNA of an individual with a strong identification power...
February 14, 2017: Forensic Science International. Genetics
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