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short tandem repeats

Mehrdad Zeinalian, Morteza Hashemzadeh-Chaleshtori, Rasoul Salehi, Mohammad Hassan Emami
Microsatellite instability (MSI) is a molecular hallmark for some colorectal cancers (CRCs) in which short tandem repeats are prone to mutations along with DNA sequences. It is due to DNA-mismatch-repair system deficiency because of a germline/somatic mutation in mismatch-repair (MMR) genes. The germline mutations lead to Lynch syndrome (LS) while epigenetic gene silencing results in sporadic CRC tumors. We discuss in our paper the most important clinical aspects of MSI testing in CRCs. We reviewed the most reliable relevant studies and clinical trials according to their high-quality methods, particularly within two recent decades...
2018: Advanced Biomedical Research
Nathan Scudder, Dennis McNevin, Sally F Kelty, Simon J Walsh, James Robertson
Use of DNA in forensic science will be significantly influenced by new technology in coming years. Massively parallel sequencing and forensic genomics will hasten the broadening of forensic DNA analysis beyond short tandem repeats for identity towards a wider array of genetic markers, in applications as diverse as predictive phenotyping, ancestry assignment, and full mitochondrial genome analysis. With these new applications come a range of legal and policy implications, as forensic science touches on areas as diverse as 'big data', privacy and protected health information...
March 2018: Science & Justice: Journal of the Forensic Science Society
Jian Zhang, Zhenghui Li, Xiaoting Mo, Wenhua Ma, Hantao Zhang, Ziqing Lin, Jian Ye
There is currently no large population data-based data set in Kashgar Prefecture Uyghur. The allele frequencies of 18 autosomal short tandem repeat (STR) loci included in the DNATyper™ 19 kit were evaluated in 2600 Uyghur individuals living in Kashgar Prefecture, Northwest China. The values of combined power of discrimination (CPD) and combined probability of exclusion (CPE) of all 18 autosomal STR loci were 0.99999999999999999998235 and 0.99999998670, respectively. Phylogenetic analyses revealed that the Uyghur population has a closer relationship with the Xinjiang-Kazakh, Inner Mongolia-Mongolian, and other three Uyghur populations...
March 10, 2018: International Journal of Legal Medicine
Rebecca S Just, Jodi A Irwin
Some of the expected advantages of next generation sequencing (NGS) for short tandem repeat (STR) typing include enhanced mixture detection and genotype resolution via sequence variation among non-homologous alleles of the same length. However, at the same time that NGS methods for forensic DNA typing have advanced in recent years, many caseworking laboratories have implemented or are transitioning to probabilistic genotyping to assist the interpretation of complex autosomal STR typing results. Current probabilistic software programs are designed for length-based data, and were not intended to accommodate sequence strings as the product input...
February 21, 2018: Forensic Science International. Genetics
Nikhil Bose, Katie Carlberg, George Sensabaugh, Henry Erlich, Cassandra Calloway
DNA from biological forensic samples can be highly fragmented and present in limited quantity. When DNA is highly fragmented, conventional PCR based Short Tandem Repeat (STR) analysis may fail as primer binding sites may not be present on a single template molecule. Single Nucleotide Polymorphisms (SNPs) can serve as an alternative type of genetic marker for analysis of degraded samples because the targeted variation is a single base. However, conventional PCR based SNP analysis methods still require intact primer binding sites for target amplification...
February 4, 2018: Forensic Science International. Genetics
Ruiyang Tao, Jiashuo Zhang, Yingnan Bian, Rixia Dong, Xiling Liu, Chao Jin, Ruxin Zhu, Suhua Zhang, Chengtao Li
Due to the unique inheritance pattern, X-chromosomal short tandem repeats (X-STRs) have several advantages in complex kinship cases, such as deficiency cases or grandparent-grandchild and half-sisters testing. In our study, 541 unrelated individuals gathered from Mongolian and Eastern Chinese Han populations were successfully genotyped using the Investigator Argus X-12 kit. We calculated allele/haplotype frequencies and other forensic parameters of the two populations and further explored their genetic distance with already published Chinese populations and six global populations...
March 9, 2018: Scientific Reports
Jesica Carina Guzmán-Alberto, Gabriela Martínez-Cortes, Héctor Rangel-Villalobos
Atypical situations arise during the constant resolution of paternity cases, which constitute challenges requiring additional genetic systems and non-standard methods. We report a paternity case presenting three alleged father (AF)-child incompatibilities for the markers TPOX, D2S441, and the indel locus B02 (11/11 vs 8/8; 14/14 vs 10/10; 2/2 vs1/1, respectively). Considering the presence of mutations/null alleles, the residual paternity indexes (PI) obtained with 23 autosomal short tandem repeats (STRs) and 38 indels suggest that the AF is the father (PI = 1...
March 6, 2018: International Journal of Legal Medicine
Shao-Kang Mo, Zi-Lin Ren, Ya-Ran Yang, Ya-Cheng Liu, Jing-Jing Zhang, Hui-Juan Wu, Zhen Li, Xiao-Chen Bo, Sheng-Qi Wang, Jiang-Wei Yan, Ming Ni
Kinship testing based on genetic markers, as forensic short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), has valuable practical applications. Paternity and first-degree relationship can be accurately identified by current commonly-used forensic STRs and reported SNP markers. However, second-degree and more distant relationships remain challenging. Although ∼105 -106 SNPs can be used to estimate relatedness of higher degrees, genome-wide genotyping and analysis may be impractical for forensic use...
March 2, 2018: Forensic Science International. Genetics
Nicholas R Ladwig, J Kenneth Schoolmeester, Laura Weil, Jocelyn S Chapman, Charles Zaloudek, Sarah E Umetsu
Inflammatory myofibroblastic tumor (IMT) is a neoplasm of intermediate malignant potential that only rarely involves the gynecologic tract. Several cases of IMT arising in various locations including the lung, bladder, trachea, and breast in association with pregnancy have been reported in the literature, and 3 cases involving the placenta have been previously described. We report 2 cases of IMT identified in association with pregnancy; the first was an intrauterine mass delivered entirely separate from the placenta and fetus, and the second was an incidental mass identified within the placental parenchyma following delivery...
March 2, 2018: American Journal of Surgical Pathology
Elena A Salina, Mikhail A Nesterov, Zeev Frenkel, Antonina A Kiseleva, Ekaterina M Timonova, Federica Magni, Jan Vrána, Jan Šafář, Hana Šimková, Jaroslav Doležel, Abraham Korol, Ekaterina M Sergeeva
BACKGROUND: The IWGSC strategy for construction of the reference sequence of the bread wheat genome is based on first obtaining physical maps of the individual chromosomes. Our aim is to develop and use the physical map for analysis of the organization of the short arm of wheat chromosome 5B (5BS) which bears a number of agronomically important genes, including genes conferring resistance to fungal diseases. RESULTS: A physical map of the 5BS arm (290 Mbp) was constructed using restriction fingerprinting and LTC software for contig assembly of 43,776 BAC clones...
February 9, 2018: BMC Genomics
José R Sandoval, Daniela R Lacerda, Marilza S Jota, Ronald Elward, Oscar Acosta, Donaldo Pinedo, Pierina Danos, Cinthia Cuellar, Susana Revollo, Fabricio R Santos, Ricardo Fujita
This study focuses on the descendants of the royal Inka family. The Inkas ruled Tawantinsuyu, the largest pre-Columbian empire in South America, which extended from southern Colombia to central Chile. The origin of the royal Inkas is currently unknown. While the mummies of the Inka rulers could have been informative, most were destroyed by Spaniards and the few remaining disappeared without a trace. Moreover, no genetic studies have been conducted on present-day descendants of the Inka rulers. In the present study, we analysed uniparental DNA markers in 18 individuals predominantly from the districts of San Sebastian and San Jerónimo in Cusco (Peru), who belong to 12 families of putative patrilineal descent of Inka rulers, according to documented registries...
March 3, 2018: Molecular Genetics and Genomics: MGG
Chenglong Yu, Bernhard T Baune, Ma-Li Wong, Julio Licinio
BACKGROUND: Major depressive disorder (MDD) is a leading contributor to global disease burden. Recent studies have shown that genetic factors play significant roles in the susceptibility to this condition; however, the underlying genetic basis currently remains largely unknown. Short tandem repeat (STR) has been proposed as an explanatory factor in the "missing heritability" of complex diseases or traits. METHODS: We investigated STR variations from 15 MDD patients and 10 ethnically matched healthy controls based on their deep whole-genome sequencing (WGS) data...
February 24, 2018: Journal of Affective Disorders
Jun Li, Yaoyao Zhang, Kunjie Hu, Yaqi Zhao, Ruirui Lin, Yan Li, Zhuoran Huang, Xu Zhang, Xuexia Geng, Jianhua Ding
In this study, complete mitogenomes of P. increta and M. stellatarum (Lepidoptera: Sphingidae) were sequenced and compared with other Sphingidae species. The mitogenomes containing 37 genes and a AT rich region are circular molecules with 15,252 and 15,290 base pairs in length respectively. Except cox1 all 13 protein-coding genes (PCGs) are initiated by ATN codons. Most of PCGs terminate with TAA except nad5 and cox1 in P. increta and nad5 and cox2 in M. stellatarum. Ile and Leu2 are the most frequently used codon families in both species and codons CGC, CCG, TCG and ACG are absent in P...
February 28, 2018: International Journal of Biological Macromolecules
Atif Adnan, Xiaoni Zhan, Kadirya Kasim, Allah Rakha, Xing Jia Xin
Forensic statistical parameters based on allelic frequencies of commonly used short tandem repeats were estimated for the Han population of Jiangsu province from P.R. China. The 6-dye GlobalFiler™ PCR amplification kit incorporates 21 autosomal STRs, providing reliable DNA typing results with enhanced the power of discrimination. Here, we analyzed the GlobalFiler™ STR loci in 516 unrelated individuals from Jiangsu Han population. A total of 256 alleles were observed ranging between 5 and 35.2 repeat units, and SE33 showed the greatest power of discrimination (34 alleles) in Jiangsu Han population...
March 2, 2018: International Journal of Legal Medicine
Eigil Kjeldsen, Christine J F Nielsen, Amit Roy, Cinzia Tesauro, Ann-Katrine Jakobsen, Magnus Stougaard, Birgitta R Knudsen
Acquisition of resistance to topoisomerase I (TOP1)-targeting camptothecin (CPT) derivatives is a major clinical problem. Little is known about the underlying chromosomal and genomic mechanisms. We characterized the CPT-K5 cell line expressing mutant CPT-resistant TOP1 and its parental T-cell derived acute lymphoblastic leukemia CPT-sensitive RPMI-8402 cell line by karyotyping and molecular genetic methods, including subtractive oligo-based array comparative genomic hybridization (soaCGH) analysis. Karyotyping revealed that CPT-K5 cells had acquired additional structural aberrations and a reduced modal chromosomal number compared to RPMI-8402...
March 2018: Cancer Genomics & Proteomics
Le Wang, Man Chen, Bo Wu, Yi-Cheng Liu, Guang-Feng Zhang, Li Jiang, Xiu-Lan Xu, Xing-Chun Zhao, An-Quan Ji, Jian Ye
Next-generation sequencing (NGS) has been used to genotype forensic short tandem repeat (STR) markers for individual identification and kinship analysis. STR data from several NGS platforms have been published, but forensic application trials using the Ion S5™ XL system have not been reported. In this work, we report sensitivity, reproducibility, mixture, simulated degradation, and casework sample data on the Ion Chef™ and S5™ XL systems using an early access 25-plex panel. Sensitivity experiments showed that over 97% of the alleles were detectable with down to 62 pg input of genomic DNA...
March 1, 2018: Journal of Forensic Sciences
Jing Zhou, Jianxin Tan, Dingyuan Ma, Jingjing Zhang, Jian Cheng, Chunyu Luo, Gang Liu, Yuguo Wang, Zhengfeng Xu
Merosin-deficient CMD type 1A (MDC1A), caused by mutations of laminin subunit alpha 2 (LAMA2), is a predominant subtype of congenital muscular dystrophy (CMD). Herein, we described a Chinese patient with MDC1A who was admitted to hospital 17 days after birth because of marasmus and feeding difficulties. Mutations were identified by targeted capture and next generation sequencing (NGS) and further confirmed by Sanger sequencing. Paternity was confirmed by short tandem repeat analysis. Physical examination showed malnutrition, poor suck and appendicular hypotonia...
2018: Frontiers in Genetics
Lathem Wojno, Caitlyn Minutella, Donald Moylan, Arla Bush, Kirk Wojno
OBJECTIVES: To determine if tissue contamination in histologic specimens can significantly affect the results of prognostic molecular markers that are routinely used as confirmatory tests to safely assign appropriate candidates to prostate cancer active surveillance protocols. MATERIALS AND METHODS: This study evaluates 2,134 cases from a single, large urology practice that were successfully tested for DNA specimen provenance verification using short tandem repeat analysis for the presence of a significant level of contaminating DNA...
February 21, 2018: Urology
Tomoki Yoshikawa, Hikaru Fujii, Akiko Okutani, Miho Shibamura, Natsumi Omura, Kazutaka Egawa, Hirofumi Kato, Takuya Inagaki, Shizuko Harada, Souichi Yamada, Shigeru Morikawa, Masayuki Saijo
LC16m8 (m8), a highly attenuated vaccinia virus (VAC) strain, was developed as a smallpox vaccine, and its safety and immunogenicity have been confirmed. Here, we aimed to develop a system that recovers infectious m8 from a bacterial artificial chromosome (BAC) that retains the full-length viral genomic DNA (m8-BAC system). The infectious virus was successfully recovered from a VAC-BAC plasmid, named pLC16m8-BAC. Furthermore, the bacterial replicon-free virus was generated by intramolecular homologous recombination and was successfully recovered from a modified VAC-BAC plasmid, named pLC16m8...
2018: PloS One
T N Patel, M Chakraborty, P Bhattacharya
CONTEXT: Tumor progresses through a series of genetic alterations that involve proto-oncogenes and tumor suppressor genes - the gatekeeper, caretakers, and landscaper genes. Microsatellites are short tandem repeat sequences, present over the span of human genome and are known to be variable at multiple loci due to errors in DNA Mismatch Repair machinery. AIM: The present study was aimed to evaluate the association between Microsatellite Instability (MSI) and evolution of Chronic Myeloid Leukemia (CML) - genetically a rare event but profound in this pilot study...
April 2017: Indian Journal of Cancer
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