scholarly journals Result of Prospective Validation of the Trisomy Test® for the Detection of Chromosomal Trisomies

Diagnostics ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 138 ◽  
Author(s):  
Sekelska ◽  
Izsakova ◽  
Kubosova ◽  
Tilandyova ◽  
Csekes ◽  
...  
Keyword(s):  
Prospective Study ◽  
Pregnant Women ◽  
Genome Sequencing ◽  
Prenatal Screening ◽  
Prenatal Testing ◽  
Screening Tests ◽  
Whole Genome ◽  
Noninvasive Prenatal Testing ◽  
Bioinformatic Pipeline ◽  
Low Coverage

Noninvasive prenatal testing (NIPT) is one of the most common prenatal screening tests used worldwide. Trisomy Test® belongs to NIPT tests based on low-coverage whole-genome sequencing. In our prospective study, 7279 samples of pregnant women collected during approximately two years were analyzed. In this cohort, 117 positive cases for trisomies 21, 18, and 13 were reported. An in-house designed bioinformatic pipeline and proprietary biostatistical approach was used for the detection of trisomies. The pooled sensitivity and specificity of our test reached 99.12% and 99.94%, respectively. The proportion of repeatedly uninformative results after repeated blood draws was 1.11%. Based on the presented results, we can confirm that the Trisomy Test® is fully comparable with other commercial NIPT tests available worldwide.

scholarly journals 353 ASAS-EAAP Talk: Low-coverage whole-genome sequencing in local livestock breeds

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 81-82
Author(s):  
Joaquim Casellas ◽  
Melani Martín de Hijas-Villalba ◽  
Marta Vázquez-Gómez ◽  
Samir Id Lahoucine
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Error Rate ◽  
Allele Frequencies ◽  
Paternity Testing ◽  
Sequencing Error ◽  
Whole Genome ◽  
Genomic Evaluation ◽  
Sequencing Error Rate ◽  
Low Coverage

Abstract Current European regulations for autochthonous livestock breeds put a special emphasis on pedigree completeness, which requires laboratory paternity testing by genetic markers in most cases. This entails significant economic expenditure for breed societies and precludes other investments in breeding programs, such as genomic evaluation. Within this context, we developed paternity testing through low-coverage whole-genome data in order to reuse these data for genomic evaluation at no cost. Simulations relied on diploid genomes composed by 30 chromosomes (100 cM each) with 3,000,000 SNP per chromosome. Each population evolved during 1,000 non-overlapping generations with effective size 100, mutation rate 10–4, and recombination by Kosambi’s function. Only those populations with 1,000,000 ± 10% polymorphic SNP per chromosome in generation 1,000 were retained for further analyses, and expanded to the required number of parents and offspring. Individuals were sequenced at 0.01, 0.05, 0.1, 0.5 and 1X depth, with 100, 500, 1,000 or 10,000 base-pair reads and by assuming a random sequencing error rate per SNP between 10–2 and 10–5. Assuming known allele frequencies in the population and sequencing error rate, 0.05X depth sufficed to corroborate the true father (85,0%) and to discard other candidates (96,3%). Those percentages increased up to 99,6% and 99,9% with 0,1X depth, respectively (read length = 10,000 bp; smaller read lengths slightly improved the results because they increase the number of sequenced SNP). Results were highly sensitive to biases in allele frequencies and robust to inaccuracies regarding sequencing error rate. Low-coverage whole-genome sequencing data could be subsequently integrated into genomic BLUP equations by appropriately constructing the genomic relationship matrix. This approach increased the correlation between simulated and predicted breeding values by 1.21% (h2 = 0.25; 100 parents and 900 offspring; 0.1X depth by 10,000 bp reads). Although small, this increase opens the door to genomic evaluation in local livestock breeds.

scholarly journals Expanded noninvasive prenatal testing for fetal aneuploidy and copy number variations and parental willingness for invasive diagnosis in a cohort of 18,516 cases

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Yunsheng Ge ◽  
Jia Li ◽  
Jianlong Zhuang ◽  
Jian Zhang ◽  
Yanru Huang ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
High Risk ◽  
Pregnant Women ◽  
Copy Number ◽  
Prenatal Testing ◽  
Copy Number Variations ◽  
Trisomy 13 ◽  
Noninvasive Prenatal Testing ◽  
Predictive Values ◽  
Parental Willingness

Abstract Background Noninvasive prenatal testing (NIPT) has been wildly used to screen for common aneuplodies. In recent years, the test has been expanded to detect rare autosomal aneuploidies (RATs) and copy number variations (CNVs). This study was performed to investigate the performance of expanded noninvasive prenatal testing (expanded NIPT) in screening for common trisomies, sex chromosomal aneuploidies (SCAs), rare autosomal aneuploidies (RATs), and copy number variations (CNVs) and parental willingness for invasive prenatal diagnosis in a Chinese prenatal diagnosis center. Methods A total of 24,702 pregnant women were retrospectively analyzed at the Women and Children’s Hospital from January 2013 to April 2019, among which expanded NIPT had been successfully conducted in 24,702 pregnant women. The high-risk expanded NIPT results were validated by karyotype analysis and chromosomal microarray analysis. All the tested pregnant women were followed up for pregnancy outcomes. Results Of the 24,702 cases, successful follow-up was conducted in 98.77% (401/446) of cases with common trisomies and SCAs, 91.95% (80/87) of RAT and CNV cases, and 76.25% (18,429/24,169) of cases with low-risk screening results. The sensitivity of expanded NIPT was 100% (95% confidence interval[CI], 97.38–100%), 96.67%(95%CI, 82.78–99.92%), and 100%(95%CI, 66.37–100.00%), and the specificity was 99.92%(95%CI, 99.87–99.96%), 99.96%(95%CI, 99.91–99.98%), and 99.88% (95%CI, 99.82–99.93%) for the detection of trisomies 21, 18, and 13, respectively. Expanded NIPT detected 45,X, 47,XXX, 47,XXY, XYY syndrome, RATs, and CNVs with positive predictive values of 25.49%, 75%, 94.12%, 76.19%, 6.45%, and 50%, respectively. The women carrying fetuses with Trisomy 21/Trisomy 18/Trisomy 13 underwent invasive prenatal diagnosis and terminated their pregnancies at higher rates than those at high risk for SCAs, RATs, and CNVs. Conclusions Our study demonstrates that the expanded NIPT detects fetal trisomies 21, 18, and 13 with high sensitivity and specificity. The accuracy of detecting SCAs, RATs, and CNVs is still relatively poor and needs to be improved. With a high-risk expanded NIPT result, the women at high risk for common trisomies are more likely to undergo invasive prenatal diagnosis procedures and terminate their pregnancies than those with unusual chromosome abnormalities.

scholarly journals Comparison between Enzyme Immunoassays Performed on Samples of Dried Blood and Serum for Toxoplasmosis Prenatal Screening: Population-based Study

2021 ◽  
Vol 43 (05) ◽  
pp. 351-356
Author(s):  
Bárbara Araújo Marques ◽  
Ericka Vianna Machado Carellos ◽  
Vânia Maria Novato Silva ◽  
Fernando Henrique Pereira ◽  
Maria Regina Lage Guerra ◽  
...  
Keyword(s):  
Pregnant Women ◽  
Prenatal Screening ◽  
Dried Blood Spots ◽  
Population Based ◽  
Minas Gerais ◽  
Immunoglobulin M ◽  
Screening Tests ◽  
Reference Test ◽  
Screening Programs ◽  
Blood Spots

Abstract Objective Most prenatal screening programs for toxoplasmosis use immunoassays in serum samples of pregnant women. Few studies assess the accuracy of screening tests in dried blood spots, which are of easy collection, storage, and transportation. The goals of the present study are to determine the performance and evaluate the agreement between an immunoassay of dried blood spots and a reference test in the serum of pregnant women from a population-based prenatal screening program for toxoplasmosis in Brazil. Methods A cross-sectional study was performed to compare the immunoassays Imunoscreen Toxoplasmose IgM and Imunoscreen Toxoplasmose IgG (Mbiolog Diagnósticos, Ltda., Contagem, Minas Gerais, Brazil)in dried blood spots with the enzyme-linked fluorescent assay (ELFA, BioMérieux S.A., Lyon, France) reference standard in the serum of pregnant women from Minas Gerais Congenital Toxoplasmosis Control Program. Results The dried blood spot test was able to discriminate positive and negative results of pregnant women when compared with the reference test, with an accuracy of 98.2% for immunoglobulin G (IgG), and of 95.8% for immunoglobulin M (IgM). Conclusion Dried blood samples are easy to collect, store, and transport, and they have a good performance, making this a promising method for prenatal toxoplasmosis screening programs in countries with continental dimensions, limited resources, and a high prevalence of toxoplasmosis, as is the case of Brazil.

Sign in / Sign up

Export Citation Format

Share Document