scholarly journals QTLseqr: An R package for bulk segregant analysis with next-generation sequencing

2017 ◽  
Author(s):  
Ben N. Mansfeld ◽  
Rebecca Grumet
Keyword(s):  
Next Generation Sequencing ◽  
Bulk Segregant Analysis ◽  
Statistical Significance ◽  
Simulation Method ◽  
R Package ◽  
List Type ◽  
Next Generation ◽  
Snp Data ◽  
R Packages ◽  
Generation Sequencing

1AbstractNext Generation Sequencing Bulk Segregant Analysis (NGS-BSA) is efficient in detecting quantitative trait loci (QTL). Despite the popularity of NGS-BSA and the R statistical platform, no R packages are currently available for NGS-BSA. We present QTLseqr, an R package for NGS-BSA that identifies QTL using two statistical approaches: QTL-seq and G’. These approaches use a simulation method and a tricube smoothed G statistic, respectively, to identify and assess statistical significance of QTL. QTLseqr, can import and filter SNP data, calculate SNP distributions, relative allele frequencies, G’ values, and log10(p-values), enabling identification and plotting of QTL. The source code is available at https://github.com/bmansfeld/QTLseqr.Core ideasAn R package that performs Next Generation Sequencing Bulk Segregant Analysis was developedTwo methods for analysis are provided: QTL-seq and G’The QTLseqr package is quick and produces publication quality figures and tables

scholarly journals 112 Axonal polyneuropathy with onset in young adulthood due to TUBB3 mutation

2019 ◽  
Vol 90 (e7) ◽  
pp. A36.2-A36
Author(s):  
Po Sheng Yang ◽  
Kimberley K Forrest ◽  
Ian B Wilson
Keyword(s):  
Next Generation Sequencing ◽  
Axonal Neuropathy ◽  
Extraocular Muscles ◽  
Diagnostic Process ◽  
List Type ◽  
Next Generation ◽  
Sensorimotor Polyneuropathy ◽  
Axonal Polyneuropathy ◽  
Congenital Fibrosis ◽  
Generation Sequencing

IntroductionThe TUBB3 gene encodes the protein Beta-tubulin isotype III, a component of the microtubule cytoskeleton. Mutations in this gene have been associated with axonal polyneuropathy, however usually associated with congenital fibrosis of the extraocular muscles (CFOEM) and other abnormalities of cerebral development.1 2 We report a case of isolated neuropathy associated with a TUBB3 mutation.MethodsCase report - clinical information and next generation sequencing results were obtained.ResultsA 64 year old man presented with a severe, progressive, length dependent sensorimotor polyneuropathy which commenced in his late twenties. There was no clinical involvement of the extraocular muscles and cognition was normal. Family history was limited, but there were no other members affected.The patient had previously been extensively investigated including sural nerve biopsy, which confirmed axonal neuropathy without a specific diagnosis. Intravenous immunoglobulins and steroids had been trialled without benefit.A neuromuscular gene panel utilising next generation sequencing was performed and demonstrated heterozygosity for a variant of the TUBB3 gene (D417N substitution).Case series describing TUBB3 mutations show a large heterogeneity in phenotypic expression depending on the amino acid substitution.2–4 There is also heterogeneity in patients with D417N mutations, although a small number have been reported to develop a polyneuropathy without CFOEM1.ConclusionsThis case strengthens previous reports that TUBB3 mutation can be associated with a pure, axonal, sensorimotor polyneuropathy and highlights the use of next generation sequencing in streamlining the diagnostic process.ReferenceTischfield M, et al. Human TUBB3 mutations perturb microtubule dynamics, kinesin interactions, and axon guidance. Cell 2010;140(1):pp.74–87.Ncbi.nlm.nih.gov. (2019). Congenital fibrosis of the extraocular muscles - Conditions - GTR - NCBI. [online] Available at: https://www.ncbi.nlm.nih.gov/gtr/conditions/CN043677/ [Accessed 14 Feb. 2019].Omim.org. (2019). OMIM Entry - * 602661 - TUBULIN, BETA-3; TUBB3. [online] Available at: https://www.omim.org/entry/602661 [Accessed 14 Feb. 2019].Krupa, K. and Bekiesinska-Figatowska, M. (2013). Congenital and Acquired Abnormalities of the Corpus Callosum: A Pictorial Essay. BioMed Research International, 2013, pp.1–14.

scholarly journals genBaRcode: a comprehensive R-package for genetic barcode analysis

2019 ◽  
Vol 36 (7) ◽  
pp. 2189-2194 ◽  
Author(s):  
Lars Thielecke ◽  
Kerstin Cornils ◽  
Ingmar Glauche
Keyword(s):  
User Interface ◽  
Next Generation Sequencing ◽  
Error Correction ◽  
Graphical User Interface ◽  
R Package ◽  
Next Generation ◽  
Analysis Strategies ◽  
Genetic Sequences ◽  
Reproducible Analysis ◽  
Generation Sequencing

Abstract Motivation Genetic barcodes have been established as an efficient method to trace clonal progeny of uniquely labeled cells by introducing artificial genetic sequences into the corresponding genomes. The assessment of those sequences relies on next generation sequencing and the subsequent analysis aiming to identify sequences of interest and correctly quantifying their abundance. Results We developed the genBaRcode package as a toolbox combining the flexibility of digesting next generation sequencing reads with or without a sophisticated barcode structure, with a variety of error-correction approaches and the availability of several types of visualization routines. Furthermore, a graphical user interface was incorporated to allow also less experienced R users package-based analyses. Finally, the provided tool is intended to bridge the gap between generating and analyzing barcode data and thereby supporting the establishment of standardized and reproducible analysis strategies. Availability and implementation The genBaRcode package is available at CRAN (https://cran.r-project.org/package=genBaRcode).

scholarly journals Refinement of microbiota analysis of specimens from patients with respiratory infections using next-generation sequencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hiroaki Ikegami ◽  
Shingo Noguchi ◽  
Kazumasa Fukuda ◽  
Kentaro Akata ◽  
Kei Yamasaki ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Respiratory Infections ◽  
Statistical Significance ◽  
Bacterial Species ◽  
Bacterial Flora ◽  
Lung Abscess ◽  
Next Generation ◽  
Causative Agents ◽  
Sanger Method ◽  
Generation Sequencing

AbstractNext-generation sequencing (NGS) technologies have been applied in bacterial flora analysis. However, there is no standardized protocol, and the optimal clustering threshold for estimating bacterial species in respiratory infection specimens is unknown. This study was conducted to investigate the optimal threshold for clustering 16S ribosomal RNA gene sequences into operational taxonomic units (OTUs) by comparing the results of NGS technology with those of the Sanger method, which has a higher accuracy of sequence per single read than NGS technology. This study included 45 patients with pneumonia with aspiration risks and 35 patients with lung abscess. Compared to Sanger method, the concordance rates of NGS technology (clustered at 100%, 99%, and 97% homology) with the predominant phylotype were 78.8%, 71.3%, and 65.0%, respectively. With respect to the specimens dominated by the Streptococcus mitis group, containing several important causative agents of pneumonia, Bray Curtis dissimilarity revealed that the OTUs obtained at 100% clustering threshold (versus those obtained at 99% and 97% thresholds; medians of 0.35, 0.69, and 0.71, respectively) were more similar to those obtained by the Sanger method, with statistical significance (p < 0.05). Clustering with 100% sequence identity is necessary when analyzing the microbiota of respiratory infections using NGS technology.

P–557 Trophectoderm biopsy technique and rate of mosaicism in human blastocysts

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
C W Chan ◽  
Z Q Tee ◽  
A Y X Lim ◽  
M W Lim ◽  
C S S Lee
Keyword(s):  
Next Generation Sequencing ◽  
Statistical Significance ◽  
Laser Pulses ◽  
Trophectoderm Biopsy ◽  
Next Generation ◽  
Biopsy Technique ◽  
Group 2 ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Group 1

Abstract Study question Do different trophectoderm biopsy techniques affect mosaicism rate in human blastocysts? Summary answer No statistical significance was found between biopsy techniques and mosaicism rate. However, an increase in mosaicism rate was observed when the flicking technique was used. What is known already Mosaicism is defined as two or more distinct cell lines within an embryo. Recent advances in Next Generation Sequencing (NGS) technology with an increased sensitivity allows a higher accuracy in quantification of mosaic levels in biopsied cells. The incidence of mosaicism is widely debated as there are many attributing technical and biological factors. Since, trophectoderm biopsy is a technically challenging process, it is crucial to ensure that the both biopsied cells and blastocyst suffers minimal damage during biopsy. Study design, size, duration This is a prospective study involving 222 patients (age range= 18–44, mean age= 31.5) who underwent IVF cycles in Alpha IVF, Malaysia from March 2019 to August 2019. Six hundred and sixty-eight (668) of the blastocysts were biopsied on Day 5 (Group 1) while 177 blastocysts were biopsied on Day 6 (Group 2). The blastocysts in these groups were further categorised into their corresponding biopsy techniques: (A) laser+pulling; (B) laser+flicking; (C) flicking only. Participants/materials, setting, methods Blastocysts which were at least fair graded (Gardner, 1999) were biopsied and vitrified (Cryotec, Japan). The number of biopsied cells ranged from 5 to 10 cells. All biopsied trophectoderm samples were subjected to Preimplantation Genetic Testing for Aneuploidy (PGT-A) with Next Generation Sequencing (NGS) (Ion Torrent, USA). Chromosomal mosaicism analysis was done using ReproSeq Mosaic PGS w1.1 workflow. Trophectoderm biopsied sample which were tested to have 20% to 80% aneuploid cells were reported as mosaic. Main results and the role of chance In Group 1, the mosaicism rates for biopsy technique A, B and C were 23.3% (104/446), 28.2% (58/206) and 37.5% (6/16) respectively. In Group 2, the mosaicism rates for biopsy technique A, B and C were 14.6% (7/48), 19.5% (23/118) and 27.3% (3/11) respectively. There were no significant differences (p &gt; 0.05) in mosaicism rates between all study groups and subgroups. Limitations, reasons for caution Although no statistical significance was found between trophectoderm biopsy techniques and the prevalence of mosaicism, there is a trend of an increase in mosaicism rate when the flicking technique was used. Therefore, further studies with a larger sample size should be undertaken. Wider implications of the findings: Our study demonstrates a trend in the decrease of mosaicism rate when laser pulses was used to loosen the cell junction of targeted cells. Hence, in place of the flicking method alone, laser pulses should be applied during trophectoderm biopsy if our findings are confirmed in a larger controlled study. Trial registration number Not applicable

scholarly journals Population genomic SNPs from epigenetic RADs: gaining genetic and epigenetic data from a single established next-generation sequencing approach

2019 ◽  
Author(s):  
M. Crotti ◽  
C.E. Adams ◽  
K.R. Elmer
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
List Type ◽  
Summary Statistics ◽  
Next Generation ◽  
Population Genomic ◽  
Genome Wide ◽  
Generation Sequencing

SummaryEpigenetics is increasingly recognised as an important molecular mechanism underlying phenotypic variation. To study DNA methylation in ecological and evolutionary contexts, epiRADseq is a cost-effective next-generation sequencing technique based on reduced representation sequencing of genomic regions surrounding non-/methylated sites. EpiRADseq for genome-wide methylation abundance and ddRADseq for genome-wide SNP genotyping follow very similar library and sequencing protocols, but to date these two types of dataset have been handled separately. Here we test the performance of using epiRADseq data to generate SNPs for population genomic analyses.We tested the robustness of using epiRADseq data for population genomics with two independent datasets: a newly generated single-end dataset for the European whitefish Coregonus lavaretus, and a re-analysis of publicly available, previously published paired-end data on corals. Using standard bioinformatic pipelines with a reference genome and without (i.e. de novo catalogue loci), we compared the number of SNPs retained, population genetic summary statistics, and population genetic structure between data drawn from ddRADseq and epiRADseq library preparations.We find that SNPs drawn from epiRADseq are similar in number to those drawn from ddRADseq, with a 55-83% of SNPs being identified by both methods. Genotyping error rate was <5% in both approaches. For summary statistics such as heterozygosity and nucleotide diversity, there is a strong correlation between methods (Spearman’s rho > 0.88). Furthermore, identical patterns of population genetic structure were recovered using SNPs from epiRADseq and ddRADseq approaches.We show that SNPs obtained from epiRADseq are highly similar to those from ddRADseq and are equivalent for estimating genetic diversity and population structure. This finding is particularly relevant to researchers interested in genetics and epigenetics on the same individuals because using a single epigenomic approach to generate two datasets greatly reduces the time and financial costs compared to using these techniques separately. It also efficiently enables correction of epigenetic estimates with population genetic data. Many studies will benefit from a combinatorial approach with genetic and epigenetic markers and this demonstrates a single, efficient method to do so.

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