scholarly journals A GENE FEATURE ENUMERATION APPROACH FOR DESCRIBING HLA ALLELE POLYMORPHISM

2015 ◽  
Author(s):  
Steven J. Mack
Keyword(s):  
Sequence Polymorphism ◽  
Untranslated Regions ◽  
Nucleotide Polymorphism ◽  
Allele Polymorphism ◽  
Hla Polymorphism ◽  
Hla Genotyping ◽  
The Individual ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Gene Feature

HLA genotyping via next generation sequencing (NGS) poses challenges for the use of HLA allele names to analyze and discuss sequence polymorphism. NGS will identify many new synonymous and non- coding HLA sequence variants. Allele names identify the types of nucleotide polymorphism that define an allele (non-synonymous, synonymous and non-coding changes), but do not describe how polymorphism is distributed among the individual features (the flanking untranslated regions, exons and introns) of a gene. Further, HLA alleles cannot be named in the absence of antigen-recognition domain (ARD) encoding exons. Here, a system for describing HLA polymorphism in terms of HLA gene features (GFs) is proposed. This system enumerates the unique nucleotide sequences for each GF in an HLA gene, and records these in a GF enumeration notation that allows both more granular dissection of allele-level HLA polymorphism, and the discussion and analysis of GFs in the absence of ARD-encoding exon sequences.

Molekulare Blutgruppenbestimmung

2017 ◽  
Vol 7 (02) ◽  
pp. 87-94
Author(s):  
Christoph Gassner
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Next Generation Sequencing ◽  
Blood Transfusion ◽  
International Society ◽  
In Silico ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Molekulare Analyse ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

ZusammenfassungDie erste molekulare Analyse einer menschlichen Blutgruppe erfolgte 1983 mittels eines Restriktions-Fragment-Längen-Polymorphismus (RFLP) am System Xg. Seither wurden in unzähligen Studien die molekularen Ursachen für Blutgruppen und deren Antigene erforscht,und das resultierende Wissen für eine ständige Verbesserung der entsprechenden Analysemethoden verwendet. Die Untersuchung kausaler Punktmutationen (Single Nucleotide Polymorphism, SNP) aller 36 von der International Society for Blood Transfusion (ISBT) anerkannten Blutgruppensysteme erlaubt heute eine der Serologie ebenbürtige, exakte Vorhersage der Blutgruppenantigene. In Patienten wird die molekulare Blutgruppenbestimmung bevorzugt in Form von Einzelprobenanalytik für die Diagnose von RhD-Varianten eingesetzt, um damit transfusionsrelevante Entscheidungen bezüglich RhD zu treffen und um die Rh-Prophylaxe noch zielsicherer zu steuern. An Spenderproben und im Hochdurchsatz ermöglicht die Blutgruppen-Genotypisierung die Schaffung einer ausreichenden Anzahl von Spender-Datensätzen, um immunisierte Patienten bestverträglich zu transfundieren oder deren Immunisierung bereits im Ansatz zu vermeiden. Gleichzeitig werden heutzutage an den gleichen Proben zusätzlich eine Vielzahl weiterer SNPs zur Identifikation von Spendern mit seltener Negativität für hochfrequente Antigene getestet. Derartig umfassende Spender-Datensätze werden bereits ideal genutzt für „In-silico-Kreuzproben“ eingesetzt. Next Generation Sequencing (NGS) ist auch in der Transfusionsmedizin der „neue Stern am Horizont“ und wird vermutlich innert weniger Jahre eine wichtige Rolle in der Analyse kompletter Blutgruppengenome (chronischer) Empfänger spielen. Blutgruppenbestimmung als frühestes Beispiel echter personalisierter Medizin wird in ihrer molekularen Version mit dazu beitragen, den gebührenden Platz der Transfusionsmedizin in der modernen Medizin zu behaupten.

scholarly journals miPIE: NGS-based Prediction of miRNA Using Integrated Evidence

2018 ◽  
Author(s):  
R.J. Peace ◽  
M. Sheikh Hassani ◽  
J.R. Green
Keyword(s):  
De Novo ◽  
Genomic Sequence ◽  
Prediction Performance ◽  
Data Sets ◽  
Mirna Prediction ◽  
Individual Contributions ◽  
The Individual ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

AbstractMethods for the de novo identification of microRNA (miRNA) have been developed using a range of sequence-based features. With the increasing availability of next generation sequencing (NGS) transcriptome data, there is a need for miRNA identification that integrates both NGS transcript expression-based patterns as well as advanced genomic sequence-based methods. While miRDeep2 does examine the predicted secondary structure of putative miRNA sequences, it does not leverage many of the sequence-based features used in state-of-the-art de novo methods. Meanwhile, other NGS-based methods, such as miRanalyzer, place an emphasis on sequence-based features without leveraging advanced expression-based features reflecting miRNA biosynthesis. This represents an opportunity to combine the strengths of NGS-based analysis with recent advances in de novo sequence-based miRNA prediction. We here develop a method, microRNA Prediction using Integrated Evidence (miPIE), which integrates both expression-based and sequence-based features to achieve significantly improved miRNA prediction performance. Feature selection identifies the 20 most discriminative features, 3 of which reflect strictly expression-based information. Evaluation using precision-recall curves, for six NGS data sets representing six diverse species, demonstrates substantial improvements in prediction performance compared to miRDeep2 and miRanalyzer. The individual contributions of expression-based and sequence-based features are also examined and we demonstrate that their combination is more effective than either alone.

scholarly journals Precision Medicine in Pediatric Cancer: Current Applications and Future Prospects

2018 ◽  
Vol 7 (4) ◽  
pp. 39 ◽  
Author(s):  
Atif Ahmed ◽  
Divya Vundamati ◽  
Midhat Farooqi ◽  
Erin Guest
Keyword(s):  
Pediatric Cancer ◽  
Pediatric Population ◽  
Current Status ◽  
Precision Oncology ◽  
Pediatric Tumors ◽  
Future Prospects ◽  
Clinical Scenarios ◽  
The Individual ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Precision oncologic medicine is an emerging approach for cancer treatment that has recently taken giant steps in solid clinical practice. Recent advances in molecular diagnostics that can analyze the individual tumor’s variability in genes have provided greater understanding and additional strategies to treat cancers. Although tumors can be tested by several molecular methods, the use of next-generation sequencing (NGS) has greatly facilitated our understanding of pediatric cancer and identified additional therapeutic opportunities. Pediatric tumors have a different genetic make-up, with a fewer number of actionable targets than adult tumors. Nevertheless, precision oncology in the pediatric population has greatly improved the survival of patients with leukemia and solid tumors. This review discusses the current status of pediatric precision oncology and the different clinical scenarios in which it can be effectively applied.

scholarly journals Fully Closed Genome Sequences of Five Type Strains of the Genus  Cronobacter and One Cronobacter sakazakii Strain: TABLE 1

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Deborah Moine ◽  
Mohamed Kassam ◽  
Leen Baert ◽  
Yanjie Tang ◽  
Caroline Barretto ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Source Tracking ◽  
Cronobacter Sakazakii ◽  
Nucleotide Polymorphism ◽  
Genome Sequences ◽  
Single Nucleotide ◽  
Next Generation Sequencing Ngs ◽  
Type Strains ◽  
Reference Genomes ◽  
Generation Sequencing

Cronobacter is associated with infant infections and the consumption of reconstituted infant formula. Here we sequenced and closed six genomes of C. condimenti T , C. muytjensii T , C. universalis T , C. malonaticus T , C. dublinensis T , and C. sakazakii that can be used as reference genomes in single nucleotide polymorphism (SNP)-based next-generation sequencing (NGS) analysis for source tracking investigations.

scholarly journals Individual Oligogenic Background in p.D91A-SOD1 Amyotrophic Lateral Sclerosis Patients

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1843
Author(s):  
Giulia Gentile ◽  
Benedetta Perrone ◽  
Giovanna Morello ◽  
Isabella Laura Simone ◽  
Sebastiano Andò ◽  
...  
Keyword(s):  
Disease Diagnosis ◽  
Untranslated Regions ◽  
Slow Progression ◽  
Uncertain Significance ◽  
Progression Of Disease ◽  
Small Cohort ◽  
Next Generation Sequencing Ngs ◽  
Als Patients ◽  
Generation Sequencing ◽  
Lateral Sclerosis

The p.D91A is one of the most common ALS-causing SOD1 mutations and is known to be either recessive or dominant. The homozygous phenotype is characterized by prolonged survival and slow progression of disease, whereas the affected heterozygous phenotypes can vary. To date, no genetic protective factors located close to SOD1 have been associated with the mild progressive homozygous phenotype. Using Next Generation Sequencing (NGS), we characterized a small cohort of sporadic and familial p.D91A-SOD1 heterozygous (n = 2) or homozygous (n = 5) ALS patients, to reveal any additional contributing variant in 39 ALS-related genes. We detected unique sets of non-synonymous variants, four of which were of uncertain significance and several in untranslated regions of ALS-related genes. Our results supported an individual oligogenic background underlying both sporadic and familial p.D91A cases irrespective of their p.D91A mutant alleles. We suggest that a comprehensive genomic view of p.D91A-SOD1 ALS patients may be useful in identifying emerging variants and improving disease diagnosis as well as guiding precision medicine.

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