scholarly journals Investigation of Mosaicism Detected in STR Typing

2021 ◽  
Vol 45 (4) ◽  
pp. 150-155
Author(s):  
Haeun You ◽  
Sang Won Lee ◽  
Soong Deok Lee ◽  
Sohee Cho
Keyword(s):  
Tandem Repeats ◽  
Chromosomal Abnormalities ◽  
Chromosome Analysis ◽  
Normal Male ◽  
Str Typing ◽  
Discrimination Power ◽  
Str Analysis ◽  
Hair Samples ◽  
High Discrimination ◽  
Repeated Analysis

Short tandem repeats (STRs) are the most popular markers for human identification in forensics. These markers can be easily analyzed through a multiplex polymerase chain reaction and electrophoresis and provide high discrimination power. However, in STR analysis, several atypical phenomena can be observed such as allelic dropouts, drop-ins, or imbalance, which may be due to DNA polymerase slippage or DNA degradation effects. The observed atypical STR profiles can also provide information for mixed DNA samples or chromosomal abnormalities. In this study, we report a case of mosaicism detected in routine casework of paternity testing. Hair samples from a phenotypically normal male were tested, and the result presented a typical STR profile of a female for the amelogenin gene (XX). Through chromosome analysis using peripheral blood, it was found that 45,X/46,XY mosaicism resulted in the discrepancy between the genotype and the phenotype. In addition, the amount of Y chromosome detected was particularly low in hair compared to that in blood. This study shows that mosaicism can make interpretation difficult during STR analysis and suggests that sample types and repeated analysis should be considered even for routine STR testing.

scholarly journals Development of Candida auris microsatellite typing and its application on a global collection of isolates

2019 ◽  
Author(s):  
Theun de Groot ◽  
Ynze Puts ◽  
Indira Berrio ◽  
Anuradha Chowdhary ◽  
Jacques F. Meis
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tandem Repeats ◽  
Cost Effective ◽  
Whole Genome ◽  
Candida Auris ◽  
Str Typing ◽  
Pathogenic Yeast ◽  
Str Analysis ◽  
Microsatellite Typing

AbstractCandida auris is a pathogenic yeast that causes invasive infections with high mortality. Infections most often occur in intensive care units of healthcare facilities. It is crucial to trace the source and prevent further spread of C. auris during an outbreak setting, therefore, genotyping of C. auris is required. To enable fast and cost-effective genotyping, we developed a microsatellite typing assay for C. auris.Short tandem repeats (STRs) in C. auris were identified, and a novel STR typing assay for C. auris was developed using 4 panels of three multiplex PCRs. Having shown that the microsatellite typing assay was highly reproducible and specific, a robust set of 444 C. auris isolates was investigated to identify genotypic diversity. In concordance with whole-genome sequencing (WGS) analysis we identified five major different C. auris clusters, namely, South-America, South-Asia, Africa, East-Asia and Iran. Overall, a total of 40 distinct genotypes were identified, with the largest variety in the East Asian clade. Comparison with WGS demonstrated that isolates with <20 SNPs are mostly not differentiated by STR analysis, while isolates with 30 or more SNPs usually have differences in one or more STR markers.Altogether, a highly reproducible and specific microsatellite typing assay for C. auris was developed, which distinguishes the five different C. auris clades in identical fashion to WGS, while most isolates differing >20 SNPs, as determined via WGS, are also separated. This new C. auris specific genotyping technique is a rapid, reliable, cost-effective alternative to WGS analysis to speedily investigate outbreaks.ImportanceCandida auris is an emerging fungal pathogen now recognized as a threat to public health. The pathogen has spread worldwide and mainly causes hospital associated outbreaks. To track and trace outbreaks and to relate them to new introductions from elsewhere, whole genome sequencing and amplified fragment length polymorphism (AFLP) have been used for molecular typing. While the former is costly and only available in few centers, AFLP is a complicated technique and standardization is not possible. We describe a novel simple microsatellite genotyping technique based on small tandem repeats in the C. auris genome. Further we show that this microsatellite based genotyping technique has been proven comparable to WGS. Overall, this work provides a novel, rapid, reliable and cost-effective method of molecular outbreaks investigations of C. auris.

Fingerprint of PGI Mantova Cucumis melo by ICP-MS and Chemometric Analysis

2020 ◽  
Vol 17 (1) ◽  
pp. 94-104
Author(s):  
Antonio F. Mottese ◽  
Maria R. Fede ◽  
Francesco Caridi ◽  
Giuseppe Sabatino ◽  
Giuseppe Marcianò ◽  
...  
Keyword(s):  
Cucumis Melo ◽  
Principal Component ◽  
Inorganic Elements ◽  
Discrimination Power ◽  
Icp Ms ◽  
High Discrimination ◽  
Strong Relation ◽  
Trace Element Contents ◽  
Safe Food

Background and Objectives: In this work, yellow and green varieties of Cucumis melo fruits belonging to different cultivars were studied. In detail, three Sicilian cultivars of winter melons tutelated by TAP (Traditional agro-alimentary products) labels were considered, whereas asun protected the Calabrian winter melon was studied too. With the aim to compare the selective uptakes of inorganic elements among winter and summer fruits, the “PGI Melone Mantovano” was investigated. The purpose of this work was to apply the obtained results i) to guarantee the quality and healthiness of fruits, ii) to producers defend, iii) to help the customers in safe food purchase. Method: All samples were analyzed by ICP-MS and the obtained results, subsequently, were subjected to Cluster analysis (CA), Principal component analysis (PCA) and Canonical discriminant analysis (CDA). Results: CA results were generally in agreement with samples origin, whereas the PCA elaboration has confirmed the presence of a strong relation between fruit origins and trace element contents. In particular, two principal components justified the 57.32% of the total variance (PC1= 40.95%, PC2= 16.37%). Finally, the CDA approach has provided several functions with high discrimination power, confirmed by the correct classification of all samples (100%). Conclusions: CA, PCA and CDA could represent an integrated to label to discriminate the origin of agri-food products and, thus, protect and guarantee their healthiness.

scholarly journals Assessment of QIAGEN™ Investigator® 24plex GO! kit workflow for autosomal STR profiling of forensic reference samples

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Hashom Mohd Hakim ◽  
Hussein Omar Khan ◽  
Siti Afifah Ismail ◽  
Nurul Hazirah Mat Lazim ◽  
Japareng Lalung ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Dna Profiling ◽  
Buccal Swab ◽  
Forensic Dna ◽  
Str Typing ◽  
Str Analysis ◽  
Dna Database ◽  
Autosomal Str ◽  
Dna Template ◽  
Reference Samples

Abstract Background DNA profiling has proven to be a valuable technique for identification of individuals in crime. Currently, the technique targets several short tandem repeat (STR) regions in human genome. However, increasing number of samples submitted for STR analysis may lead to delays due to the limited number of experienced analysts who might be available at any given moment and the time taken to complete lengthy DNA profiling procedures. This study was conducted to test the specificity, repeatability, reproducibility and robustness of Investigator® 24plex GO! kit for genotyping of reference samples submitted to the Royal Malaysian Police Forensic DNA Laboratory for DNA database. Material and methods In this study, Investigator® 24plex GO! kit was used to directly amplify STR loci from buccal swab cell of reference samples that had previously been STR typed using GlobalFiler™ Express kit. Capillary electrophoresis was carried out on a 3500xL Genetic Analyser using POP-4® Polymer. Amplified products were assigned to particular STR alleles using the GeneMapper ID-X version 1.4 software. Results Our study shows that STR profiles generated using Investigator® 24plex GO! gave concordance results with those previously obtained using the GlobalFiler™ Express kit. In addition, quality sensors included in the kit are of particular importance for determining the effectiveness of the PCR reaction and help to indicate the nature and quantity of DNA template for PCR amplification. Conclusion The Investigator® 24plex GO! kit is reliable for STR typing of reference samples.

PROGNOSIS IN NEWBORN INFANTS WITH X-CHROMOSOMAL ABNORMALITIES

PEDIATRICS ◽  
1971 ◽  
Vol 47 (4) ◽  
pp. 681-688
Author(s):  
Eleanor Eller ◽  
William Frankenburg ◽  
Mary Puck ◽  
Arthur Robinson
Keyword(s):  
Home Environment ◽  
Chromosomal Abnormalities ◽  
Newborn Infants ◽  
Evaluation Process ◽  
Chromosome Analysis ◽  
Pedigree Analysis ◽  
High Risk Group ◽  
The Past ◽  
Normal Limits ◽  
Growth Abnormalities

Sex-chromosomal aberrations occur with a relatively high frequency and have been associated with mental retardation, perceptual problems, psychopathology, and growth abnormalities. Identification of this possibly high risk group at birth enables the study of their growth and development to determine if and when they deviate from normal. Routine screening of the chromatin constitution of 21,214 consecutive newborn infants has identified 32 babies with gross X chromosome abnormalities. Three died in the newborn period. During the past 5 years, 27 children have been followed from birth. The evaluation process consists of semiannual and annual physical and developmental examinations, psychological testing, growth measurements, pedigree analysis, dermatoglyphic analysis, home environment evaluation, and, in mosaics, repeated chromosome analysis. The patients with 45,X karyotypes have classical physical signs. The other patients have normal phenotypes, although several have minor physical manifestations such as clinodactyly and epicanthic folds. Overall development in all except two patients has been within normal limits. In mosaics, there is a tendency for the abnormal cell line to disappear.

Application of Restriction Site-Associated DNA Sequencing (RAD-Seq) for Copy Number Variation and Triploidy Detection in Human

2021 ◽  
pp. 1-8
Author(s):  
Jian-Chun He ◽  
Shao-Ying Li ◽  
Wen-Zhi He ◽  
Jia-Jia Xian ◽  
Xiao-Yan Ma ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Cell Lines ◽  
Genome Sequencing ◽  
Copy Number ◽  
Restriction Site ◽  
Chromosomal Abnormalities ◽  
Copy Number Variations ◽  
Str Analysis ◽  
Tissue Samples ◽  
Low Pass

At present, low-pass whole-genome sequencing (WGS) is frequently used in clinical research and in the screening of copy number variations (CNVs). However, there are still some challenges in the detection of triploids. Restriction site-associated DNA sequencing (RAD-Seq) technology is a reduced-representation genome sequencing technology developed based on next-generation sequencing. Here, we verified whether RAD-Seq could be employed to detect CNVs and triploids. In this study, genomic DNA of 11 samples was extracted employing a routine method and used to build libraries. Five cell lines of known karyotypes and 6 triploid abortion tissue samples were included for RAD-Seq testing. The triploid samples were confirmed by STR analysis and also tested by low-pass WGS. The accuracy and efficiency of detecting CNVs and triploids by RAD-Seq were then assessed, compared with low-pass WGS. In our results, RAD-Seq detected 11 out of 11 (100%) chromosomal abnormalities, including 4 deletions and 1 aneuploidy in the purchased cell lines and all triploid samples. By contrast, these triploids were missed by low-pass WGS. Furthermore, RAD-Seq showed a higher resolution and more accurate allele frequency in the detection of triploids than low-pass WGS. Our study shows that, compared with low-pass WGS, RAD-Seq has relatively higher accuracy in CNV detection at a similar cost and is capable of identifying triploids. Therefore, the application of this technique in medical genetics has a significant potential value.

scholarly journals Evaluation of variable numbers of tandem repeat as molecular epidemiological markers of Mycobacterium tuberculosis in Japan

2007 ◽  
Vol 56 (8) ◽  
pp. 1052-1057 ◽  
Author(s):  
Takayuki Wada ◽  
Shinji Maeda ◽  
Atsushi Hase ◽  
Kazuo Kobayashi
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tandem Repeat ◽  
Tandem Repeats ◽  
Allelic Diversity ◽  
Rflp Analysis ◽  
Strain Typing ◽  
Beijing Family ◽  
Discrimination Power ◽  
Family Based ◽  
Vntr Analysis

Using 243 Mycobacterium tuberculosis isolates obtained in 2001 in Osaka City, Japan, the discriminatory power of variable numbers of tandem repeats (VNTRs) of 12 standard mycobacterial interspersed repetitive units (MIRUs) was assessed. The biggest cluster defined by MIRU-VNTRs consisted of 57 (23.5 %) isolates and they belonged to the Beijing family based on spoligotyping. When additional VNTR loci were included in the MIRU-VNTR analysis, the 57 originally clustered strains were further differentiated by the addition of Queen's University Belfast (QUB)-VNTRs, but not exact tandem repeat-VNTR. The allelic diversity of additional VNTR loci such as VNTR 3232 (QUB-3232), VNTR 2163a (QUB-11a), VNTR 2163b (QUB-11b) and VNTR 1982 (QUB-18) was high in the 57 strains. When the 243 M. tuberculosis isolates were analysed using 16-locus VNTR (the 12 standard MIRUs and the 4 QUB loci) and IS6110 RFLP, the respective Hunter–Gaston discriminatory indexes were 0.9966 and 0.9971. The discrimination power of 16-locus VNTR was equal to that of IS6110 RFLP analysis. If appropriate loci are added to the standard MIRU analysis, VNTR genotyping could be a valuable tool for strain typing and epidemiological research of M. tuberculosis in Japan.

Does supplemental interphase FISH analysis to standard chromosom analysis improve the detection of myelodysplastic syndrome?

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 7060-7060 ◽  
Author(s):  
Benjamin Joseph Lang ◽  
Carol Minyon ◽  
Neelam Dhiman ◽  
Saurabh Gupta ◽  
Stella Wenceslao ◽  
...  
Keyword(s):  
Chromosomal Abnormalities ◽  
Statistical Significance ◽  
Chromosome Analysis ◽  
Diagnostic Value ◽  
Fish Analysis ◽  
Retrospective Data ◽  
Trisomy 8 ◽  
Prognostic Information ◽  
Monosomy 7 ◽  
Interphase Fish

7060 Background: Our objective was to evaluate whether the addition of interphase FISH analysis to standard chromosome analysis (CA) improves the detection of chromosomal abnormalities in patients with work up for myelodysplastic syndromes (MDS), acute myeloid leukemia, and myelodysplastic/myeloproliferative disorders and thereby increases diagnostic and prognostic information. We performed a retrospective data review of all MDS orders between January and September 2015 at our institution and evaluated concurrent tests for discrepancies between CA and FISH results. Our aim was to evaluate best practices with regard to diagnostic test utilization, specifically to assess the diagnostic and prognostic value of FISH in addition to CA for patients with potential and known MDS. Methods: Retrospective data review of concurrent test orders of CA and myelodysplastic FISH panel were reviewed. The myelodysplastic FISH panel consists of screening for monosomy 5/deletion 5q, monosomy 7/deletion 7q, CEP7, trisomy 8, and D20S108 (20q12). The results of CA and FISH results were analyzed using a chi-square test to evaluate statistical significance. Results: A total of 1121 samples were queried, of which 55 were excluded due to inability to perform CA and limited diagnostic value of accompanying standalone FISH data on the 4 markers tested in this study. Analysis of the eligible 1066 samples showed that the standalone CA had significantly higher sensitivity (p < 0.0001) in detecting abnormal cases (N = 247, 23.17%) as compared to standalone FISH analysis (N = 180, 16.89%). Overall, 173 (16.23%) cases were determined to be abnormal by both methods. CA correctly interpreted 1059 of 1066 cases (99.34%).Only 7 samples were interpreted as normal by CA but were found to be abnormal by FISH. This results in overall 0.66% (2.76% of the abnormal cases) of abnormalities that would have been missed by CA only. Conclusions: These findings suggest that FISH studies with 4 markers used in this study provide limited additional utility in cases with a complete CA.

Correlation of Prenatal Diagnosis and Pathology Findings Following Dilation and Evacuation for Fetal Anomalies

2016 ◽  
Vol 141 (2) ◽  
pp. 267-273
Author(s):  
Carolin A. Boecking ◽  
Eleanor A. Drey ◽  
Jennifer L. Kerns ◽  
Walter E. Finkbeiner
Keyword(s):  
Body Wall ◽  
Chromosomal Abnormalities ◽  
Ultrasound Examination ◽  
Chromosome Analysis ◽  
Congenital Defect ◽  
Second Trimester ◽  
Fetal Anomalies ◽  
Pathologic Findings ◽  
Clinical Diagnoses ◽  
Prenatal Imaging

Context.—Despite increased use of dilation and evacuation in the setting of fetuses with developmental anomalies, the pathology examination of fragmented specimens obtained by this technique has been understudied. Objectives.—To correlate pathologic findings in second-trimester fetal dilation and evacuation specimens with prenatal diagnoses established through ultrasound and/or chromosome studies to determine the value of pathology examination for supplementing or correcting clinical diagnoses. Design.—In this retrospective study, clinical and pathology findings were correlated in 448 dilation and evacuation specimens performed for second-trimester termination of pregnancy for fetal anomalies discovered on ultrasound examination (278 cases) or chromosome analysis (170 cases). Results.—In 109 of the 170 cases with chromosomal abnormalities (64%), pathologists identified at least 1 congenital defect associated with the respective karyotype. In 278 cases with ultrasound-detected anomalies, pathologists confirmed the major congenital defect in 116 fetal specimens (42%). Evaluating for congenital central nervous system and body wall/diaphragm pathologic findings proved challenging owing to tissue disruption. However, taking all categories into account, pathology studies corrected ultrasound diagnoses in 152 of 413 cases (37%) and yielded additional diagnostic findings in 137 cases (33%). Conclusions.—In a substantial number of cases, examination of fragmented fetuses corrected or refined prenatal diagnoses, demonstrating a role for detailed pathology examination of dilation and evacuation specimens in quality control of prenatal imaging studies and for potentially aiding subsequent genetic counseling.

scholarly journals Two rare cases of acute myeloid leukemia with t(8;16)(p11.2;p13.3) and 1q duplication: case presentation and literature review

2020 ◽  
Author(s):  
Meng Liu ◽  
Yuan Ren ◽  
Xianfu Wang ◽  
Xianglan Lu ◽  
Ming Li ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Chromosomal Abnormalities ◽  
Chromosome Analysis ◽  
Recurrent Event ◽  
Chromosome 1 ◽  
Comparative Genome Hybridization ◽  
Array Comparative Genome Hybridization ◽  
Acute Myeloid

Abstract Background: Acute myeloid leukemia (AML) is a complex hematological disease characterized by genetic and clinical heterogeneity. The identification and understanding of chromosomal abnormalities are important for the diagnosis and management of AML patients. Compared to recurrent chromosomal translocations in AML, t(8;16)(p11.2;p13.3) can be found in any age group, but is very rare and typically associated with poor prognosis. Methods: Conventional cytogenetic studies were performed among 1,824 AML patients from our oncology database in the last 20 years. Fluorescence in situ hybridization (FISH) was carried out to demonstrate the translocation fusion. Array comparative genome hybridization (aCGH) was carried out to further characterize the duplication of chromosomes.Results: We identified three AML patients with t(8;16)(p11.2;p13.3) by chromosome analysis. Two of the three patients with additional 1q duplication were detected by FISH and aCGH. aCGH characterized a 46.7 Mb and 49.9 Mb gain of chromosome 1 at bands q32.1q44 in these two patients, respectively. One patient achieved a complete remission (CR) but relapsed three months later. The other patient never experienced a CR and died two years after diagnosis. Conclusion: 1q duplication were detected in two of three AML patients with t(8;16)(p11.2;p13.3), suggesting that 1q duplication can be a recurrent event in AML patients with t(8;16). In concert with the findings of previous studies of similar patients, our work suggests that 1q duplication may also be an unfavorable prognostic factor of the disease.

scholarly journals Clinical Application of Chromosomal Microarray Analysis for Fetuses with Craniofacial Malformations

2020 ◽  
Author(s):  
Chenyang Xu ◽  
Yanbao Xiang ◽  
Xueqin Xu ◽  
Lili Zhou ◽  
Huanzheng Li ◽  
...  
Keyword(s):  
Microarray Analysis ◽  
Genetic Basis ◽  
Chromosomal Abnormalities ◽  
Chromosome Analysis ◽  
Chromosomal Microarray ◽  
Chromosomal Microarray Analysis ◽  
Molecular Technique ◽  
Craniofacial Malformations ◽  
Pathogenic Cnvs ◽  
Clinically Significant

Abstract Background This study aimed to evaluate the applicability of chromosomal microarray analysis (CMA) for prenatal diagnosis of craniofacial malformations (CFMs). We also investigated the potential correlations between chromosomal abnormalities and CFMs. To this end, 118 fetuses with CFMs were enrolled in the study and underwent both G-banded chromosome analysis and CMA. Results Of the 118 cases in this study, 39.8% were isolated CFMs (47/118) whereas 60.2% were non-isolated CFMs (71/118). The detection rate of chromosomal abnormalities or submicroscopic chromosomal abnormalities in non-isolated CFM fetuses was significantly higher than that in isolated CFM fetuses (26/71 vs. 7/47, p = 0.01). Compared to the 16 fetuses (16/104; 15.4%) with pathogenic chromosomal abnormalities detected by karyotype analysis, CMA identified a total of 33 fetuses (33/118; 28.0%) with clinically significant findings. These 33 fetuses included cases with aneuploidy abnormalities (14/118; 11.9%), microdeletion/microduplication syndromes (9/118; 7.6%), and other pathogenic CNVs only (10/118; 8.5%). We further explored the CNV/phenotype correlation and found a series of clear or suspected dosage-sensitive CFM genes. Conclusion CMA is a rapid and reliable molecular technique to identify fetal chromosomal aberrations associated with CFMs. Identification of the genetic basis of CFMs contributes to the understanding of their pathogenesis and etiology.

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