scholarly journals Application of Genotyping-by-Sequencing on Semiconductor Sequencing Platforms: A Comparison of Genetic and Reference-Based Marker Ordering in Barley

PLoS ONE ◽  
2013 ◽  
Vol 8 (10) ◽  
pp. e76925 ◽  
Author(s):  
Martin Mascher ◽  
Shuangye Wu ◽  
Paul St. Amand ◽  
Nils Stein ◽  
Jesse Poland
Keyword(s):  
Genotyping By Sequencing ◽  
Semiconductor Sequencing ◽  
Sequencing Platforms

scholarly journals A sorghum Practical Haplotype Graph facilitates genome-wide imputation and cost-effective genomic prediction

2019 ◽  
Author(s):  
Sarah E. Jensen ◽  
Jean Rigaud Charles ◽  
Kebede Muleta ◽  
Peter Bradbury ◽  
Terry Casstevens ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Genomic Prediction ◽  
Sequence Data ◽  
Input Sequence ◽  
Genotyping By Sequencing ◽  
Cost Effective ◽  
Genome Wide ◽  
Variant Information ◽  
Sequencing Platforms ◽  
Low Coverage

AbstractSuccessful management and utilization of increasingly large genomic datasets is essential for breeding programs to increase genetic gain and accelerate cultivar development. To help with data management and storage, we developed a sorghum Practical Haplotype Graph (PHG) pangenome database that stores all identified haplotypes and variant information for a given set of individuals. We developed two PHGs in sorghum, one with 24 individuals and another with 398 individuals, that reflect the diversity across genic regions of the sorghum genome. 24 founders of the Chibas sorghum breeding program were sequenced at low coverage (0.01x) and processed through the PHG to identify genome-wide variants. The PHG called SNPs with only 5.9% error at 0.01x coverage - only 3% lower than its accuracy when calling SNPs from 8x coverage sequence. Additionally, 207 progeny from the Chibas genomic selection (GS) training population were sequenced and processed through the PHG. Missing genotypes in the progeny were imputed from the parental haplotypes available in the PHG and used for genomic prediction. Mean prediction accuracies with PHG SNP calls range from 0.57-0.73 for different traits, and are similar to prediction accuracies obtained with genotyping-by-sequencing (GBS) or markers from sequencing targeted amplicons (rhAmpSeq). This study provides a proof of concept for using a sorghum PHG to call and impute SNPs from low-coverage sequence data and also shows that the PHG can unify genotype calls from different sequencing platforms. By reducing the amount of input sequence needed, the PHG has the potential to decrease the cost of genotyping for genomic selection, making GS more feasible and facilitating larger breeding populations that can capture maximum recombination. Our results demonstrate that the PHG is a useful research and breeding tool that can maintain variant information from a diverse group of taxa, store sequence data in a condensed but readily accessible format, unify genotypes from different genotyping methods, and provide a cost-effective option for genomic selection for any species.

scholarly journals Feasibility Study of Semiconductor Sequencing for Noninvasive Prenatal Detection of Fetal Aneuploidy

2013 ◽  
Vol 59 (5) ◽  
pp. 846-849 ◽  
Author(s):  
Yuan Yuan ◽  
Fuman Jiang ◽  
Sang Hua ◽  
Bole Du ◽  
Yibin Hao ◽  
...  
Keyword(s):  
Maternal Plasma ◽  
Trisomy 13 ◽  
Personal Genome ◽  
Plasma Dna ◽  
Sequencing Technology ◽  
Fetal Aneuploidy ◽  
Prenatal Detection ◽  
Semiconductor Sequencing ◽  
Sequencing Platforms ◽  
Fetal Aneuploidies

BACKGROUND Noninvasive prenatal detection of common fetal aneuploidies with cell-free DNA from maternal plasma has been achieved with high-throughput next-generation sequencing platforms. Turnaround times for previously tested platforms are still unsatisfactory for clinical applications, however, because of the time spent on sequencing. The development of semiconductor sequencing technology has provided a way to shorten overall run times. We studied the feasibility of using semiconductor sequencing technology for the noninvasive detection of fetal aneuploidy. METHODS Maternal plasma DNA from 13 pregnant women, corresponding to 4 euploid, 6 trisomy 21 (T21), 2 trisomy 18 (T18), and 1 trisomy 13 (T13) pregnancies, were sequenced on the Ion Torrent Personal Genome Machine sequencer platform with 318 chips. The data were analyzed with the T statistic method after correcting for GC bias, and the T value was calculated as an indicator of fetal aneuploidy. RESULTS We obtained a mean of 3 524 401 high-quality reads per sample, with an efficiency rate of 77.9%. All of the T21, T13, and T18 fetuses could be clearly distinguished from euploid fetuses, and the time spent on library preparation and sequencing was 24 h. CONCLUSIONS Semiconductor sequencing represents a suitable technology for the noninvasive prenatal detection of fetal aneuploidy. With this platform, sequencing times can be substantially reduced; however, a further larger-scale study is needed to determine the imprecision of noninvasive fetal aneuploidy detection with this system.

scholarly journals Genome-Wide Marker Analysis for Traits of Economic Importance in Asian Seabass Lates calcarifer

2021 ◽  
Vol 9 (3) ◽  
pp. 282
Author(s):  
Nguyen Nguyen ◽  
Pham Khang
Keyword(s):  
Body Weight ◽  
Complex Traits ◽  
Prediction Accuracy ◽  
Genetic Parameters ◽  
Growth Traits ◽  
Genotyping By Sequencing ◽  
Lates Calcarifer ◽  
Asian Seabass ◽  
Genome Wide ◽  
Sequencing Platforms

To date, it is not known whether animal breeding values in Asian seabass (Lates calcarifer) can be estimated using single nucleotide polymorphisms (SNPs) generated from new high-throughput genotyping by sequencing platforms. The principal aim of the present study was to assess the genomic prediction accuracy for growth traits, survival, cannibalism, and disease resistance against Streptococcus iniae in this species L. calcarifer. Additionally, this study attempted to identify markers associated with the five traits studied as well as to understand if the genotype data can be used to estimate genetic parameters for these complex traits. The genomic best linear unbiased prediction (gBLUP) method was used to analyze 11,084 SNPs and showed that the prediction accuracies for growth traits (weight and length) were high (0.67–0.75). By contrast, these estimates for survival were low (0.25). Multi-locus mixed model analyses identified four SNPs significantly associated with body weight (p < 5 × 10−8 or −log10p> = 5). There were, however, no significant associations detected for other traits. Similarly, the SNP heritability was moderate, while the estimates for other traits were approximated to zero and not significant. Genetic correlations between body weight and standard length were close to unity. Collectively, the results obtained from this study suggest that genotyping by sequencing platforms can provide informative DNA markers to conduct genome-wide association analysis, estimation of genetic parameters, and evaluation of genomic prediction accuracy for complex traits in Asian seabass.

scholarly journals Detection of Tumor Recurrence via Circulating Tumor DNA Profiling in Patients with Localized Lung Cancer: Clinical Considerations and Challenges

Cancers ◽  
2021 ◽  
Vol 13 (15) ◽  
pp. 3759
Author(s):  
Bryan Ulrich ◽  
Anne Pradines ◽  
Julien Mazières ◽  
Nicolas Guibert
Keyword(s):  
Lung Cancer ◽  
Residual Disease ◽  
Lung Cancer Screening ◽  
Circulating Tumor Dna ◽  
Definitive Treatment ◽  
Curative Intent ◽  
Screening Programs ◽  
Adjuvant Therapies ◽  
Sequencing Platforms ◽  
Tumor Dna

Approximately 30% of patients with non-small-cell lung cancer (NSCLC) present with localized/non-metastatic disease and are eligible for surgical resection or other “treatment with curative intent”. Due to the high prevalence of recurrence after treatment, adjuvant therapy is standard care for most patients. The effect of adjuvant chemotherapy is, however, modest, and new tools are needed to identify candidates for adjuvant treatments (chemotherapy, immunotherapy, or targeted therapies), especially since expanded lung cancer screening programs will increase the rate of patients detected with localized NSCLC. Circulating tumor DNA (ctDNA) has shown strong potential to detect minimal residual disease (MRD) and to guide adjuvant therapies. In this manuscript, we review the technical aspects and performances of the main ctDNA sequencing platforms (TRACERx, CAPP-seq) investigated in this purpose, and discuss the potential of this approach to guide or spare adjuvant therapies after definitive treatment of NSCLC.

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