High-throughput sequencing platform established by sensor measurement technology for the detection of TSC1 and TSC2 genes in prenatal diagnosis

Measurement ◽  
2020 ◽  
Vol 160 ◽  
pp. 107828
Author(s):  
Qiuxia Xu ◽  
Min Wang ◽  
Sujing Huang ◽  
Lin Xu ◽  
Hongqiong Guan ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Measurement Technology ◽  
Sequencing Platform ◽  
Sensor Measurement

scholarly journals Application of High-Throughput Sequencing in the Diagnosis of Inherited Thrombocytopenia

2018 ◽  
Vol 24 (9_suppl) ◽  
pp. 94S-103S ◽  
Author(s):  
Qi Wang ◽  
Lijuan Cao ◽  
Guangying Sheng ◽  
Hongjie Shen ◽  
Jing Ling ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Gene Sequencing ◽  
Hereditary Diseases ◽  
Sequencing Platform ◽  
Pathogenic Variants ◽  
Diagnosis Method ◽  
Inherited Thrombocytopenia ◽  
Thrombotic Diseases ◽  
Next Generation Sequencing Ngs

Inherited thrombocytopenia is a group of hereditary diseases with a reduction in platelet count as the main clinical manifestation. Clinically, there is an urgent need for a convenient and rapid diagnosis method. We introduced a high-throughput, next-generation sequencing (NGS) platform into the routine diagnosis of patients with unexplained thrombocytopenia and analyzed the gene sequencing results to evaluate the value of NGS technology in the screening and diagnosis of inherited thrombocytopenia. From a cohort of 112 patients with thrombocytopenia, we screened 43 patients with hereditary features. For the blood samples of these 43 patients, a gene sequencing platform for hemorrhagic and thrombotic diseases comprising 89 genes was used to perform gene detection using NGS technology. When we combined the screening results with clinical features and other findings, 15 (34.9%) of 43patients were diagnosed with inherited thrombocytopenia. In addition, 19 pathogenic variants, including 8 previously unreported variants, were identified in these patients. Through the use of this detection platform, we expect to establish a more effective diagnostic approach to such disorders.

Noninvasive prenatal diagnosis empowered by high-throughput sequencing

2012 ◽  
Vol 32 (4) ◽  
pp. 401-406 ◽  
Author(s):  
Rossa W. K. Chiu ◽  
Y. M. Dennis Lo
Keyword(s):  
Prenatal Diagnosis ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Noninvasive Prenatal Diagnosis

scholarly journals A high-throughput sequencing test for diagnosing inherited bleeding, thrombotic, and platelet disorders

Blood ◽  
2016 ◽  
Vol 127 (23) ◽  
pp. 2791-2803 ◽  
Author(s):  
Ilenia Simeoni ◽  
Jonathan C. Stephens ◽  
Fengyuan Hu ◽  
Sri V. V. Deevi ◽  
Karyn Megy ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Genetic Test ◽  
Targeted Sequencing ◽  
Sequencing Platform ◽  
Key Points ◽  
Platelet Disorders

Key Points Developed a targeted sequencing platform covering 63 genes linked to heritable bleeding, thrombotic, and platelet disorders. The ThromboGenomics platform provides a sensitive genetic test to obtain molecular diagnoses in patients with a suspected etiology.

scholarly journals jackalope: a swift, versatile phylogenomic and high-throughput sequencing simulator

2019 ◽  
Author(s):  
Lucas A. Nell
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Population Genomics ◽  
R Package ◽  
Gene Trees ◽  
Sequencing Platform ◽  
Genomic Variants ◽  
Pacific Biosciences ◽  
Wide Range ◽  
Reference Genomes

AbstractHigh-throughput sequencing (HTS) is central to the study of population genomics and has an increasingly important role in constructing phylogenies. Choices in research design for sequencing projects can include a wide range of factors, such as sequencing platform, depth of coverage, and bioinformatic tools. Simulating HTS data better informs these decisions. However, current standalone HTS simulators cannot generate genomic variants under even somewhat complex evolutionary scenarios, which greatly reduces their usefulness for fields such as population genomics and phylogenomics. Here I present the R package jackalope that simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. Genomic variants can be simulated using phylogenies, gene trees, coalescent-simulation output, population-genomic summary statistics, and Variant Call Format (VCF) files. jackalope can simulate single, paired-end, or mate-pair Illumina reads, as well as reads from Pacific Biosciences. These simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates. It can read reference genomes from FASTA files and can simulate new ones, and all outputs can be written to standard file formats. jackalope is available for Mac, Windows, and Linux systems.

scholarly journals High-throughput sequencing of murine immunoglobulin heavy chain transcripts using single side unique molecular identifiers on an Ion Torrent PGM

2017 ◽  
Author(s):  
Jean-Philippe Bürckert ◽  
William J. Faison ◽  
Axel R. S. X. Dubois ◽  
Regina Sinner ◽  
Oliver Hunewald ◽  
...  
Keyword(s):  
High Throughput ◽  
Heavy Chain ◽  
High Throughput Sequencing ◽  
Gene Segment ◽  
Personal Genome ◽  
Sequencing Platform ◽  
Ion Torrent Pgm ◽  
Indel Detection ◽  
Processing Strategies ◽  
Nucleotide Insertions

AbstractWith the advent of high-throughput sequencing (HTS), profiling immunoglobulin (IG) repertoires has become an essential part of immunological research. Advances in sequencing technology enable the IonTorrent Personal Genome Machine (PGM) to cover the full-length of IG mRNA transcripts. Nucleotide insertions and deletions (indels) are the dominant errors of the PGM sequencing platform and can critically influence IG repertoire assessments. Here, we present a PGM-tailored IG repertoire sequencing approach combining error correction through unique molecular identifier (UID) barcoding and indel detection through ImMunoGeneTics (IMGT), the most commonly used sequence alignment database for IG sequences. Using artificially falsified sequences for benchmarking, we found that IMGT efficiently detects 98% of the introduced indels through gene-segment frameshifts. Undetected indels are either located at the ends of the sequences or produce masked frameshifts with an insertion and deletion in close proximity. IMGT’s indel correction algorithm resolves up to 87% of the tested insertions, but no deletions. The complementary determining regions 3 (CDR3s) are returned 100% correct for up to 3 insertions or 3 deletions through conservative culling. We further show, that our PGM-tailored unique molecular identifiers results in highly accurate HTS datasets if combined with the presented data processing. In this regard, considering sequences with at least two copies from datasets with UID families of minimum 3 reads result in correct sequences with over 99% confidence. The protocol and sample processing strategies described in this study will help to establish benchtop-scale sequencing of IG heavy chain transcripts in the field of IG repertoire research.

scholarly journals IROme, a New High-Throughput Molecular Tool for the Diagnosis of Inherited Retinal Dystrophies

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Daniel F. Schorderet ◽  
Alexandra Iouranova ◽  
Tatiana Favez ◽  
Leila Tiab ◽  
Pascal Escher
Keyword(s):  
Retinitis Pigmentosa ◽  
Molecular Diagnosis ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequence Variant ◽  
Sequence Variants ◽  
Sequencing Platform ◽  
Capture Assay ◽  
Retinal Dystrophies ◽  
Exon Capture

The molecular diagnosis of retinal dystrophies is difficult because of the very important number of genes implicated and is rarely helped by genotype-phenotype correlations. This prompted us to develop IROme, a custom designed in solution-based targeted exon capture assay (SeqCap EZ Choice library, Roche NimbleGen) for 60 retinitis pigmentosa-linked genes and three candidate genes (942 exons). Pyrosequencing was performed on a Roche 454 GS Junior benchtop high-throughput sequencing platform. In total, 23 patients affected by retinitis pigmentosa were analyzed. Per patient, 39.6 Mb were generated, and 1111 sequence variants were detected on average, at a median coverage of 17-fold. After data filtering and sequence variant prioritization, disease-causing mutations were identified inABCA4,CNGB1,GUCY2D,PROM1,PRPF8,PRPF31,PRPH2,RHO,RP2, andTULP1for twelve patients (55%), ten mutations having never been reported previously. Potential mutations were identified in 5 additional patients, and in only 6 patients no molecular diagnosis could be established (26%). In conclusion, targeted exon capture and next-generation sequencing are a valuable and efficient approach to identify disease-causing sequence variants in retinal dystrophies.

scholarly journals Efficient discovery of potently neutralizing SARS-CoV-2 antibodies using LIBRA-seq with ligand blocking

2021 ◽  
Author(s):  
Andrea R Shiakolas ◽  
Nicole Johnson ◽  
Kevin J Kramer ◽  
Naveenchandra Suryadevara ◽  
Daniel Wrapp ◽  
...  
Keyword(s):  
High Throughput ◽  
Neutralizing Antibodies ◽  
High Throughput Sequencing ◽  
Therapeutic Antibody ◽  
Sequencing Platform ◽  
Large Numbers ◽  
Ligand Interactions ◽  
Antibody Discovery ◽  
Small Set

SARS-CoV-2 therapeutic antibody discovery efforts have met with notable success but have been associated with a generally inefficient process, requiring the production and characterization of exceptionally large numbers of candidates for the identification of a small set of leads. Here, we show that incorporating antibody-ligand blocking as part of LIBRA-seq, the high-throughput sequencing platform for antibody discovery, results in efficient identification of ultra-potent neutralizing antibodies against SARS-CoV-2. LIBRA-seq with ligand blocking is a general platform for functional antibody discovery targeting the disruption of antigen-ligand interactions.

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