scholarly journals Calculation of Fetal Fraction for Non-Invasive Prenatal Testing

BioTech ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 17
Author(s):  
Matthew Cserhati
Keyword(s):  
Length Distribution ◽  
Prenatal Testing ◽  
Estimation Methods ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Main Method ◽  
Advantages And Disadvantages ◽  
Non Invasive ◽  
The Difference ◽  
Fetal Fraction

Estimating the fetal fraction of DNA in a pregnant mother’s blood is a risk-free, non-invasive way of predicting fetal aneuploidy. It is a rapidly developing field of study, offering researchers a plethora of different complementary methods. Such methods include examining the differences in methylation profiles between the fetus and the mother. Others include calculating the average allele frequency based on the difference in genotype of a number of single-nucleotide polymorphisms. Differences in the length distribution of DNA fragments between the mother and the fetus as well as measuring the proportion of DNA reads mapping to the Y chromosome also constitute fetal fraction estimation methods. The advantages and disadvantages of each of these main method types are discussed. Moreover, several well-known fetal fraction estimation methods, such as SeqFF, are described and compared with other methods. These methods are amenable to not only the estimation of fetal fraction but also paternity, cancer, and transplantation monitoring studies. NIPT is safe, and should aneuploidy be detected, this information can help parents prepare mentally and emotionally for the birth of a special needs child.

Sex Differences in Childhood Associations between DNA Markers and General Cognitive Ability

2007 ◽  
Vol 28 (3) ◽  
pp. 161-164 ◽  
Author(s):  
Rosalind Arden ◽  
Nicole Harlaar ◽  
Robert Plomin
Keyword(s):  
Sex Differences ◽  
Single Nucleotide Polymorphisms ◽  
Cognitive Ability ◽  
Dna Markers ◽  
Community Sample ◽  
Nucleotide Polymorphisms ◽  
General Cognitive Ability ◽  
Single Nucleotide ◽  
The Difference

Abstract. An association between intelligence at age 7 and a set of five single-nucleotide polymorphisms (SNPs) has been identified and replicated. We used this composite SNP set to investigate whether the associations differ between boys and girls for general cognitive ability at ages 2, 3, 4, 7, 9, and 10 years. In a longitudinal community sample of British twins aged 2-10 (n > 4,000 individuals), we found that the SNP set is more strongly associated with intelligence in males than in females at ages 7, 9, and 10 and the difference is significant at 10. If this finding replicates in other studies, these results will constitute the first evidence of the same autosomal genes acting differently on intelligence in the two sexes.

scholarly journals Significant Associations of lncRNA H19 Genotypes with Susceptibility to Childhood Leukemia in Taiwan

2021 ◽  
Vol 14 (3) ◽  
pp. 235
Author(s):  
Jen-Sheng Pei ◽  
Chao-Chun Chen ◽  
Wen-Shin Chang ◽  
Yun-Chi Wang ◽  
Jaw-Chyun Chen ◽  
...  
Keyword(s):  
Confidence Interval ◽  
Childhood Leukemia ◽  
Healthy Controls ◽  
Nucleotide Polymorphisms ◽  
Wild Type ◽  
Single Nucleotide ◽  
Genotypic Distribution ◽  
Heterozygous Variant ◽  
Significant Difference ◽  
The Difference

The purpose of our study was to investigate whether genetic variations in lncRNA H19 were associated with susceptibility to childhood leukemia. Two hundred and sixty-six childhood leukemia patients and 266 healthy controls were enrolled in Taiwan, and two single nucleotide polymorphisms (SNPs), rs2839698 and rs217727, in H19 were genotyped and analyzed. There was a significant difference in the genotypic distribution of rs2839698 between patients and healthy controls (p = 0.0277). Compared to the wild-type CC genotype, the heterozygous variant CT and homozygous variant TT genotypes were associated with significantly increased risks of childhood leukemia with an adjusted odd ratio (OR) of 1.46 (95% confidence interval (CI), 1.08–2.14, p = 0.0429) and 1.94 (95%CI, 1.15–3.31, p = 0.0169), respectively (pfor tread = 0.0277). The difference in allelic frequencies between childhood leukemia patients and controls was also significant (T versus C, adjusted OR = 1.53, 95%CI, 1.13–1.79, p = 0.0077). There were no significant differences in the genotypic and allelic distributions of rs217727 between cases and controls. Interestingly, the average level of H19 rs2839698 was statistically significantly higher for patients with CT and TT genotypes than from those with the CC genotype (p < 0.0001). Our results indicate that H19 SNP rs2839698, but not rs217727, may serve as a novel susceptibility marker for childhood leukemia.

scholarly journals Non-invasive prenatal testing: what an obstetrician needs to know

2020 ◽  
Vol 9 (12) ◽  
pp. 5200
Author(s):  
Mishu Mangla
Keyword(s):  
Health Care Providers ◽  
Prenatal Screening ◽  
Prenatal Testing ◽  
High Sensitivity ◽  
Target Population ◽  
Care Providers ◽  
Advantages And Disadvantages ◽  
Non Invasive ◽  
Primary Health Care Providers ◽  
First Choice

No field in obstetrics has seen such fast advancement, as the field of prenatal screening and diagnosis. A wide variety of tests are available today, and this at times becomes confusing both for the patient and the treating doctor that which screening test would be best suited in the given circumstances. Non-invasive prenatal screening, with its numerous advantages is rapidly becoming the test of first choice, especially in the affording set of population.  Although, the test has a very high sensitivity and a very good positive predictive value, this too suffers from some disadvantages which should be clear to the obstetrician ordering the test. A good knowledge about the test, the ideal target population in which this should be offered as the primary screening tool and limitations of the test should be known to all practicing obstetricians and primary health care providers. The current review aims to provide a simplified and updated knowledge regarding non-invasive prenatal testing (NIPT), its major advantages and disadvantages and summarizes the role of ultrasound in patients with negative NIPT.

Advantages and Disadvantages of Different Implementation Strategies of Non-Invasive Prenatal Testing in Down Syndrome Screening Programmes

2015 ◽  
Vol 18 (5) ◽  
pp. 260-271 ◽  
Author(s):  
Elke Mersy ◽  
Christine E.M. de Die-Smulders ◽  
Audrey B.C. Coumans ◽  
Luc J.M. Smits ◽  
Guido M.W.R. de Wert ◽  
...  
Keyword(s):  
Down Syndrome ◽  
Implementation Strategies ◽  
Prenatal Testing ◽  
Advantages And Disadvantages ◽  
Non Invasive ◽  
Down Syndrome Screening

scholarly journals Java GUI application for comparing the levels of biometric security: Fingerprint vs. Iris

2021 ◽  
Vol 69 (3) ◽  
pp. 676-686
Author(s):  
Komlen Lalović ◽  
Mitko Bogdanoski
Keyword(s):  
Comparative Analysis ◽  
Iris Recognition ◽  
Scientific Data ◽  
Body Parts ◽  
Main Method ◽  
Software Application ◽  
Java Programming ◽  
Advantages And Disadvantages ◽  
Iris Biometrics ◽  
The Difference

Introduction/purpose: The main purpose of this paper is to present a novel Java GUI - based software application for a comparative analysis of fingerprint and iris biometrics. Methods: The first part of this work is realized in Java Programming language. in the GUI framework named swing while the rest of the paper shows in detail the advantages and disadvantages of both systems and gives scientific data on when fingerprint and iris recognition can be used to enable top level security. The main method here is a well known comparative analysis. Results: The results were obtained for both fingerprint and iris biometrics, showing the difference between the two. Conclusion: Different types of biometrics, based on body parts formed at different age, are given as well as the comparison of their security levels.

scholarly journals Combination of Fetal Fraction Estimators Based on Fragment Lengths and Fragment Counts in Non-Invasive Prenatal Testing

2019 ◽  
Vol 20 (16) ◽  
pp. 3959 ◽  
Author(s):  
Juraj Gazdarica ◽  
Rastislav Hekel ◽  
Jaroslav Budis ◽  
Marcel Kucharik ◽  
Frantisek Duris ◽  
...  
Keyword(s):  
State Of The Art ◽  
Prenatal Testing ◽  
The State ◽  
Accurate Estimation ◽  
Special Focus ◽  
Dna Fragments ◽  
Sources Of Information ◽  
Non Invasive ◽  
Genomic Locations ◽  
Fetal Fraction

The reliability of non-invasive prenatal testing is highly dependent on accurate estimation of fetal fraction. Several methods have been proposed up to date, utilizing different attributes of analyzed genomic material, for example length and genomic location of sequenced DNA fragments. These two sources of information are relatively unrelated, but so far, there have been no published attempts to combine them to get an improved predictor. We collected 2454 single euploid male fetus samples from women undergoing NIPT testing. Fetal fractions were calculated using several proposed predictors and the state-of-the-art SeqFF method. Predictions were compared with the reference Y-based method. We demonstrate that prediction based on length of sequenced DNA fragments may achieve nearly the same precision as the state-of-the-art methods based on their genomic locations. We also show that combination of several sample attributes leads to a predictor that has superior prediction accuracy over any single approach. Finally, appropriate weighting of samples in the training process may achieve higher accuracy for samples with low fetal fraction and so allow more reliability for subsequent testing for genomic aberrations. We propose several improvements in fetal fraction estimation with a special focus on the samples most prone to wrong conclusion.

Correlation between Z score, fetal fraction, and sequencing reads in non-invasive prenatal testing

2017 ◽  
Vol 37 (9) ◽  
pp. 943-945 ◽  
Author(s):  
Marie Balslev-Harder ◽  
Stine R. Richter ◽  
Susanne Kjaergaard ◽  
Peter Johansen
Keyword(s):  
Prenatal Testing ◽  
Z Score ◽  
Non Invasive ◽  
Fetal Fraction

scholarly journals Comparison of single nucleotide polymorphisms and microsatellites in non-invasive genetic monitoring of a wolf population

2012 ◽  
Vol 64 (1) ◽  
pp. 321-335 ◽  
Author(s):  
Elena Fabbri ◽  
R. Caniglia ◽  
Nadia Mucci ◽  
H.P. Thomsen ◽  
K. Krag ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Error Rates ◽  
Snp Genotyping ◽  
Genetic Monitoring ◽  
Taqman Probe ◽  
Degraded Dna ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Non Invasive ◽  
Probe Assay

Single nucleotide polymorphisms (SNPs) which represent the most widespread source of sequence variation in genomes, are becoming a routine application in several fields such as forensics, ecology and conservation genetics. Their use, requiring short amplifications, may allow a more efficient genotyping of degraded DNA. We provide the first application of SNP genotyping in an Italian non-invasive genetic monitoring project of the wolf. We compared three different techniques for genotyping SNPs: pyrosequencing, SNaPshot? and TaqMan? Probe Assay in Real-Time PCR. We successively genotyped nine SNPs using the TaqMan Probe Assay in 51 Italian wolves, 57 domestic dogs, 15 wolf x dog hybrids and 313 wolf scats collected in the northern Apennines. The obtained results were used to estimate genetic variability and PCR error rates in SNP genotyping protocols compared to standard microsatellite analysis. We evaluated the cost, laboratory effort and reliability of these different markers and discuss the possible future use of VeraCode, SNPlex and Fluidigm EP1 system in wild population monitoring.

scholarly journals In silico analysis of single nucleotide polymorphisms (SNPs) in human FOXC2 gene

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 243
Author(s):  
Mohammed Nimir ◽  
Mohanad Abdelrahim ◽  
Mohamed Abdelrahim ◽  
Mahil Abdalla ◽  
Wala eldin Ahmed ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Conservation Score ◽  
Interaction Network ◽  
In Silico Analysis ◽  
Gene Interaction ◽  
Nucleotide Polymorphisms ◽  
Gene Interaction Network ◽  
Single Nucleotide ◽  
Functional Studies ◽  
Advantages And Disadvantages

Introduction: Lymphedema is an abnormal accumulation of interstitial fluid, due to inefficient uptake and reduced flow, leading to swelling and disability, mostly in the extremities. Hereditary lymphedema usually occurs as an autosomal dominant trait with allelic heterogeneity. Methods: We identified single nucleotide polymorphisms (SNPs) in the FOXC2 gene using dbSNP, analyzed their effect on the resulting protein using VEP and Biomart, modelled the resulting protein using Project HOPE, identified gene – gene interactions using GeneMANIA and predicted miRNAs affected and the resulting effects of SNPs in the 5’ and 3’ regions using PolymiRTS. Results: We identified 473 SNPs - 429 were nsSNPs and 44 SNPs were in the 5’ and 3’ UTRs. In total, 2 SNPs - rs121909106 and rs121909107 - have deleterious effects on the resulting protein, and a 3D model confirmed those effects. The gene – gene interaction network showed the involvement of FOXC2 protein in the development of the lymphatic system. hsa-miR-6886-5p, hsa-miRS-6886-5p, hsa-miR-6720-3p, which were affected by the SNPs rs201118690, rs6413505, rs201914560, respectively, were the most important miRNAs affected, due to their high conservation score. Conclusions: rs121909106 and rs121909107 were predicted to have the most harmful effects, while hsa-miR-6886-5p, hsa-miR-6886-5p and hsa-miR-6720-3p were predicted to be the most important miRNAs affected. Computational biology tools have advantages and disadvantages, and the results they provide are predictions that require confirmation using methods such as functional studies.

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