scholarly journals DNA metabarcoding allows non-invasive identification of arthropod prey provisioned to nestling Rufous hummingbirds (Selasphorus rufus)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6596 ◽  
Author(s):  
Alison J. Moran ◽  
Sean W.J. Prosser ◽  
Jonathan A. Moran
Keyword(s):  
Alimentary Tract ◽  
Selasphorus Rufus ◽  
Non Invasive ◽  
Single Pellet ◽  
Wide Range ◽  
Dna Metabarcoding ◽  
Rufous Hummingbird ◽  
Almost All ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Hummingbirds consume sugars from nectar, sap and honeydew, and obtain protein, fat and minerals from arthropods. To date, the identity of arthropod taxa in hummingbird diets has been investigated by observation of foraging or examination of alimentary tract contents. Direct examination of nestling provisioning adds the extra complication of disturbance to the young and mother. Here, we show that arthropod food items provisioned to Rufous hummingbird (Selasphorus rufus) nestlings can be identified by a safe and non-invasive protocol using next-generation sequencing (NGS) of DNA from nestling fecal pellets collected post-fledging. We found that females on southern Vancouver Island (British Columbia, Canada) provisioned nestlings with a wide range of arthropod taxa. The samples examined contained three Classes, eight Orders, 48 Families, and 87 Genera, with from one to 15 Families being identified in a single pellet. Soft-bodied Dipterans were found most frequently and had the highest relative abundance; hard-bodied prey items were absent from almost all samples. Substantial differences in taxa were found within season and between years, indicating the importance of multi-year sampling when defining a prey spectrum.

NON-INVASIVE PREIMPLANTATION GENETIC TESTING (NIPGT) FOR ANEUPLOIDY AND STRUCTURAL REARRANGEMENTS USING NEXT GENERATION SEQUENCING (NGS) ON SPENT CULTURE MEDIA (SCM)

2021 ◽  
Vol 116 (3) ◽  
pp. e224-e225
Author(s):  
Dimitra Christopikou ◽  
Stephen Davies ◽  
Stavroula Zaxaria ◽  
Erika Tsorva ◽  
Andriani Karagianni ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Next Generation Sequencing ◽  
Culture Media ◽  
Structural Rearrangements ◽  
Next Generation ◽  
Preimplantation Genetic Testing ◽  
Non Invasive ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

scholarly journals Human Papillomavirus and the Development of Different Cancers

2016 ◽  
Vol 150 (3-4) ◽  
pp. 185-193 ◽  
Author(s):  
Ge Gao ◽  
David I. Smith
Keyword(s):  
Cervical Cancer ◽  
Squamous Cell Carcinomas ◽  
Human Papillomaviruses ◽  
Whole Genome ◽  
Physical Status ◽  
Cervical Cancers ◽  
Mate Pair ◽  
Almost All ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Human papillomaviruses (HPV) are responsible for the development of almost all cervical cancers. HPV is also found in 85% of anal cancer and in 50% of penile, vulvar, and vaginal cancers, and they are increasingly found in a subset of head and neck cancers, i.e., oropharyngeal squamous cell carcinomas (OPSCC). The model for how HPV causes cancer is derived from several decades of study on cervical cancer, and it is just presumed that this model is not only completely valid for cervical cancer but for all other HPV-driven cancers as well. Next-generation sequencing (NGS) has now provided the necessary tools to characterize genomic alterations in cancer cells and can precisely determine the physical status of HPV in those cells as well. We discuss recent discoveries from different applications of NGS in both cervical cancer and OPSCCs, including whole-genome sequencing and mate-pair NGS. We also discuss what NGS studies have revealed about the different ways that HPV can be involved in cancer formation, specifically comparing cervical cancer and OPSCC.

scholarly journals Diagnosis for choroideremia in a large Chinese pedigree by next-generation sequencing (NGS) and non-invasive prenatal testing (NIPT)

2017 ◽  
Vol 15 (3) ◽  
pp. 1157-1164 ◽  
Author(s):  
Li Zhu ◽  
Jingliang Cheng ◽  
Boxu Zhou ◽  
Chunli Wei ◽  
Weichan Yang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Prenatal Testing ◽  
Next Generation ◽  
Non Invasive ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

scholarly journals Is day 5 blastocyst better than day 6 blastocyst? Evidence from NGS-based PGT-A results

2021 ◽  
Author(s):  
Ting Zhang
Keyword(s):  
Maternal Age ◽  
Embryo Implantation ◽  
Trophectoderm Biopsy ◽  
Preimplantation Genetic Testing ◽  
Non Invasive ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Ploidy Status ◽  
Better Than ◽  
Euploid Embryo

Abstract Background Aneuploidy is the principal genetic factor leading to the failure of embryo implantation. For most patients who accept the non-preimplantation genetic testing (PGT) cycle, non-invasive methods to select euploid embryos with the best pregnancy potential are desirable Methods This retrospective study recruited women undergoing PGT for aneuploidy (PGT-A) with trophectoderm biopsy from January 2019 to December 2020. The ploidy status of embryos was determined by next generation sequencing (NGS). Results Altogether 2531 blastocysts from 839 PGT-A cycles were evaluated. The euploid rate of day 5 blastocysts seemed to be significantly higher than that of day 6 blastocysts, either from the same ovarian stimulation (OS) cycles (49.9% vs 35.7%, P < 0.001) or from different OS cycles (48.2% vs 27.8%, P < 0.001). Both the younger maternal age (adjusted OR = 0.917, 95% CI: 0.892–0.944, P < 0.001) and day 5 stage (adjusted OR = 1.735, 95% CI: 1.415–2.127, P < 0.001) were independently associated with the greater euploid rate of blastocysts. However, after single euploid embryo transfer, the clinical outcomes of day 5 blastocysts were comparable to those of day 6 blastocysts, no matter whether they were from the same OS cycles or not. Conclusions Our results revealed that day 5 blastocysts possess a higher euploid rate than day 6 blastocysts independent of the OS cycles. Giving priority to a day 5 blastocyst over day 6 blastocyst will increase the likelihood to select single euploid embryo for transfer in non-PGT cycles.

scholarly journals Next-generation sequencing in neuropathological diagnosis of infections of the nervous system

2016 ◽  
Author(s):  
Steven L. Salzberg ◽  
Florian Breitwieser ◽  
Anupama Kumar ◽  
Haiping Hao ◽  
Peter Burger ◽  
...  
Keyword(s):  
Spinal Cord ◽  
Nervous System ◽  
Next Generation Sequencing ◽  
Large Scale ◽  
Infectious Agent ◽  
Next Generation ◽  
Dna And Rna ◽  
Wide Range ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Objective: To determine the feasibility of next-generation sequencing (NGS) microbiome approaches in the diagnosis of infectious disorders in brain or spinal cord biopsies in patients with suspected central nervous system (CNS) infections. Methods: In a prospective-pilot study, we applied NGS in combination with a new computational analysis pipeline to detect the presence of pathogenic microbes in brain or spinal cord biopsies from ten patients with neurological problems indicating possible infection but for whom conventional clinical and microbiology studies yielded negative or inconclusive results. Results: Direct DNA and RNA sequencing of brain tissue biopsies generated 8.3 million to 29.1 million sequence reads per sample, which successfully identified with high confidence the infectious agent in three patients, identified possible pathogens in two more, and helped to understand neuropathological processes in three others, demonstrating the power of large-scale unbiased sequencing as a novel diagnostic tool. Validation techniques confirmed the pathogens identified by NGS in each of the three positive cases. Clinical outcomes were consistent with the findings yielded by NGS on the presence or absence of an infectious pathogenic process in eight of ten cases, and were non-contributory in the remaining two. Conclusions: NGS-guided metagenomic studies of brain, spinal cord or meningeal biopsies offer the possibility for dramatic improvements in our ability to detect (or rule out) a wide range of CNS pathogens, with potential benefits in speed, sensitivity, and cost. NGS-based microbiome approaches present a major new opportunity to investigate the potential role of infectious pathogens in the pathogenesis of neuroinflammatory disorders.

scholarly journals Identification of Germline Cancer Predisposition Variants During Clinical Ctdna Testing

2021 ◽  
Author(s):  
Leigh Anne Stout ◽  
Nawal Kassem ◽  
Cynthia Hunter ◽  
Santosh Philips ◽  
Milan Radovich ◽  
...  
Keyword(s):  
Circulating Tumor Dna ◽  
Variant Allele Frequency ◽  
Germline Variants ◽  
Non Invasive ◽  
Invasive Method ◽  
Selection For ◽  
Ctdna Analysis ◽  
Next Generation Sequencing Ngs ◽  
Tumor Dna ◽  
Generation Sequencing

Abstract Next-generation sequencing (NGS) of circulating tumor DNA (ctDNA) is a non-invasive method to guide therapy selection for cancer patients. ctDNA variant allele frequency (VAF) is commonly reported and may aid in discerning whether a variant is germline or somatic. We report on the fidelity of VAF in ctDNA as a predictor for germline variant carriage. Two patient cohorts were studied. Cohort 1 included patients with known germline variants. Cohort 2 included patients with any variant detected by the ctDNA assay with VAF of 40–60%. In cohort 1, 36 of 91 (40%) known germline variants were identified through ctDNA analysis with a VAF of 39-87.6%. In cohort 2, 111 of 160 (69%) variants identified by ctDNA analysis with a VAF between 40–60% were found to be germline. Therefore, variants with a VAF between 40–60% should induce suspicion for germline status but should not be used as a replacement for germline testing.

scholarly journals The Emerging Roles of RNA Modifications in Glioblastoma

Cancers ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 736 ◽  
Author(s):  
Zhen Dong ◽  
Hongjuan Cui
Keyword(s):  
Tumor Type ◽  
Messenger Rnas ◽  
Rna Modifications ◽  
Transfer Rnas ◽  
Pathological Mechanism ◽  
Fast Development ◽  
Living Organisms ◽  
Almost All ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Glioblastoma (GBM) is a grade IV glioma that is the most malignant brain tumor type. Currently, there are no effective and sufficient therapeutic strategies for its treatment because its pathological mechanism is not fully characterized. With the fast development of the Next Generation Sequencing (NGS) technology, more than 170 kinds of covalent ribonucleic acid (RNA) modifications are found to be extensively present in almost all living organisms and all kinds of RNAs, including ribosomal RNAs (rRNAs), transfer RNAs (tRNAs) and messenger RNAs (mRNAs). RNA modifications are also emerging as important modulators in the regulation of biological processes and pathological progression, and study of the epi-transcriptome has been a new area for researchers to explore their connections with the initiation and progression of cancers. Recently, RNA modifications, especially m6A, and their RNA-modifying proteins (RMPs) such as methyltransferase like 3 (METTL3) and α-ketoglutarate-dependent dioxygenase alkB homolog 5 (ALKBH5), have also emerged as important epigenetic mechanisms for the aggressiveness and malignancy of GBM, especially the pluripotency of glioma stem-like cells (GSCs). Although the current study is just the tip of an iceberg, these new evidences will provide new insights for possible GBM treatments. In this review, we summarize the recent studies about RNA modifications, such as N6-methyladenosine (m6A), N6,2′O-dimethyladenosine (m6Am), 5-methylcytosine (m5C), N1-methyladenosine (m1A), inosine (I) and pseudouridine (ψ) as well as the corresponding RMPs including the writers, erasers and readers that participate in the tumorigenesis and development of GBM, so as to provide some clues for GBM treatment.

scholarly journals Molecular and Genetic Mechanism of Non-Syndromic Congenital Cataracts. Mutation Screening in Spanish Families

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 580
Author(s):  
Celia Fernández-Alcalde ◽  
María Nieves-Moreno ◽  
Susana Noval ◽  
Jesús M. Peralta ◽  
Victoria E. F. Montaño ◽  
...  
Keyword(s):  
De Novo ◽  
Mutation Screening ◽  
Disease Genes ◽  
De Novo Mutations ◽  
Congenital Cataracts ◽  
Pathogenic Variants ◽  
Unknown Significance ◽  
Almost All ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Our purpose was to identify mutations responsible for non-syndromic congenital cataracts through the implementation of next-generation sequencing (NGS) in our center. A sample of peripheral blood was obtained from probands and willing family members and genomic DNA was extracted from leukocytes. DNA was analyzed implementing a panel (OFTv2.1) including 39 known congenital cataracts disease genes. 62 probands from 51 families were recruited. Pathogenic or likely pathogenic variants were identified in 32 patients and 25 families; in 16 families (64%) these were de novo mutations. The mutation detection rate was 49%. Almost all reported mutations were autosomal dominant. Mutations in crystallin genes were found in 30% of the probands. Mutations in membrane proteins were detected in seven families (two in GJA3 and five in GJA8). Mutations in LIM2 and MIP were each found in three families. Other mutations detected affected EPHA2, PAX6, HSF4 and PITX3. Variants classified as of unknown significance were found in 5 families (9.8%), affecting CRYBB3, LIM2, EPHA2, ABCB6 and TDRD7. Mutations lead to different cataract phenotypes within the same family.

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