79,813 results match your criteria next-generation sequencing


Cerebellar liponeurocytoma: clinical, histopathological and molecular features of a series of three cases, including one recurrent tumor.

Neuropathology 2022 Jan 18. Epub 2022 Jan 18.

IRCCS Neuromed, Pozzilli, Italy.

Cerebellar liponeurocytoma (CL) is an unusual tumor, histologically composed of a mixture of small to medium-sized, rounded neurocytic cells and a variable lipomatous component. Although CL was originally considered as a subtype of medulloblastoma, subsequent molecular studies demonstrated that this tumor was a distinct entity, exhibiting the tumor protein p53 gene (TP53) missense mutations in 20% of cases, chromosome 17 deletion, and the absence of mutations in the adenomatous polyposis coli gene (APC), the protein patched homolog gene (PTCH), the kinase insert domain receptor gene (KDR), and the β-catenin gene (CTNNB). Apart from these molecular features, little is known about the pathogenesis and the genetic landscape of CL to date. Read More

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January 2022

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.

Nature 2022 Jan 7. Epub 2022 Jan 7.

Department of Zoology, University of Oxford, Oxford, UK.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, whilst the second and third waves were driven by the Beta and Delta variants, respectively. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng Province, South Africa. Read More

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January 2022

The Skin and Nose Microbiome and Its Association with Filaggrin Gene Mutations in Pediatric Atopic Dermatitis.

Dermatology 2022 Jan 18:1-11. Epub 2022 Jan 18.

Department of Dermatology-Center of Pediatric Dermatology, Sophia Children's Hospital, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.

Background: Interactions between the skin barrier, immune system, and microbiome underlie the development of atopic dermatitis (AD).

Objective: To investigate the skin and nasal microbiome in relation to filaggrin gene (FLG) mutations.

Methods: A cross-sectional study including 77 children with difficult-to-treat AD. Read More

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January 2022

Final efficacy and safety data, and exploratory molecular profiling from the phase III ALUR study of alectinib versus chemotherapy in crizotinib-pretreated ALK-positive non-small-cell lung cancer.

ESMO Open 2022 Jan 15;7(1):100333. Epub 2022 Jan 15.

Department of Oncology, University of Turin, Orbassano, Italy. Electronic address:

Background: At the primary data cut-off, the ALUR study demonstrated significantly improved progression-free survival (PFS) and central nervous system (CNS) objective response rate (ORR) with alectinib versus chemotherapy in pretreated, advanced anaplastic lymphoma kinase (ALK)-positive non-small-cell lung cancer. We report final efficacy and safety data, and exploratory molecular profiling.

Patients And Methods: Patients who received prior platinum-doublet chemotherapy and crizotinib were randomized 2 : 1 to receive alectinib 600 mg twice daily (n = 79) or chemotherapy (pemetrexed 500 mg/m or docetaxel 75 mg/m, every 3 weeks; n = 40) until progressive disease, death or withdrawal. Read More

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January 2022

A clinical and integrated genetic study of isolated and combined dystonia in Taiwan.

J Mol Diagn 2022 Jan 15. Epub 2022 Jan 15.

Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan. Electronic address:

Dystonia is a clinically and genetically heterogeneous movement disorder. However, genetic causes of dystonia remain largely unknown in Asians. To address this, we applied an integrated two-step approach including gene dosage analysis and a next generation sequencing panel containing 72 known genes causative for dystonia and related movement disorders to 318 Taiwanese patients with isolated or combined dystonia. Read More

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January 2022

Poor Agreement Between Next-Generation DNA Sequencing and Bacterial Cultures in Orthopaedic Trauma Procedures.

J Bone Joint Surg Am 2022 Jan 18. Epub 2022 Jan 18.

Department of Orthopaedics, R Adams Cowley Shock Trauma Center, University of Maryland School of Medicine, Baltimore, Maryland.

Background: Next-generation DNA sequencing (NGS) detects bacteria-specific DNA corresponding to the 16S ribosomal RNA gene and can identify bacterial presence with greater accuracy than traditional culture methods. The clinical relevance of these findings is unknown. The purpose of the present study was to compare the results from bacterial culture and NGS in order to characterize the potential use of NGS in orthopaedic trauma patients. Read More

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January 2022

Hearing Impairment in South Africa and the Lessons Learned for Planetary Health Genomics: A Systematic Review.

OMICS 2022 Jan;26(1):2-18

Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.

Hearing impairment (HI) is a silent planetary health crisis that requires attention worldwide. The prevalence of HI in South Africa is estimated as 5.5 in 100 live births, which is about 5 times higher than the prevalence in high-income countries. Read More

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January 2022

Genetic Analysis of Pediatric Pancreatoblastoma: A Case Report.

Pancreas 2021 Nov-Dec 01;50(10):1445-1449

From the Department of Hepatobiliary and Pancreatic Surgery, the Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital.

Abstract: Pediatric pancreatoblastoma (PBL) is a rare disease, and the treatment of which is diverse. The molecular alteration in pancreatoblastoma is not very clear. A 7-year-old female who presented with intermittent abdominal pain, anorexia, and abdominal mass was admitted in our hospital. Read More

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January 2022

Diagnostic yield of exome sequencing in fetuses with multisystem malformations: systematic review and meta-analysis.

Ultrasound Obstet Gynecol 2022 Jan 18. Epub 2022 Jan 18.

BCNatal, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain.

Objective: To determine the diagnostic yield of exome sequencing (ES) above chromosomal microarray analysis (CMA) or karyotype in fetuses with multiple multisystem structural anomalies (at least two major anomalies from different anatomical systems).

Method: This is a systematic review conducted in accordance with PRISMA criteria. All studies identified in PubMed, Ovid Medline and Web of Science, describing ES, whole genome and next-generation sequencing in fetuses with multisystem malformation. Read More

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January 2022

Sex differences in microRNA expression in first and third trimester human placenta†.

Biol Reprod 2021 Dec 7. Epub 2021 Dec 7.

Maternal and fetal pregnancy outcomes related to placental function vary based on fetal sex, which may be due to sexually dimorphic epigenetic regulation of RNA expression. We identified sexually dimorphic miRNA expression throughout gestation in human placentae. Next-generation sequencing identified miRNA expression profiles in first and third trimester uncomplicated pregnancies using tissue obtained at chorionic villous sampling (n = 113) and parturition (n = 47). Read More

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December 2021

Characterization of the novel HLA-C*16:184 allele by next-generation sequencing.

HLA 2022 Jan 17. Epub 2022 Jan 17.

CHU de Reims, Laboratoire d'immunologie, Pôle de biologie médicale et pathologie, Reims, France.

HLA-C*16:184 differs from HLA-C*16:02:01:01 by one nucleotide substitution at position 737 in exon 3. This article is protected by copyright. All rights reserved. Read More

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January 2022

Genetic diversity and population structure of rice (Oryza sativa L.) landraces from Kerala, India analyzed through genotyping-by-sequencing.

Mol Genet Genomics 2022 Jan 18. Epub 2022 Jan 18.

Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periye (PO), Kasaragod, Kerala, 671316, India.

Researchers stand at the vanguard of advancement and application of next-generation sequencing technology for developing dominant strategies for the sustainable management of genetically diverse crops. We attempt to fill the existing research lacuna in the molecular characterization of potent rice landraces in Kerala. Genotyping-by-sequencing (GBS) was performed on 96 Kerala rice accessions to identify single-nucleotide polymorphisms (SNPs), to examine the genetic diversity, population structure, and to delineate linkage disequilibrium (LD) pattern. Read More

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January 2022

Value of the loss of heterozygosity to BRCA1 variant classification.

NPJ Breast Cancer 2022 Jan 17;8(1). Epub 2022 Jan 17.

Department of Medical Biology and Pathology, Gustave Roussy, Cancer Genetics Laboratory, Gustave Roussy, Villejuif, France.

At least 10% of the BRCA1/2 tests identify variants of uncertain significance (VUS) while the distinction between pathogenic variants (PV) and benign variants (BV) remains particularly challenging. As a typical tumor suppressor gene, the inactivation of the second wild-type (WT) BRCA1 allele is expected to trigger cancer initiation. Loss of heterozygosity (LOH) of the WT allele is the most frequent mechanism for the BRCA1 biallelic inactivation. Read More

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January 2022

Efficacy of pembrolizumab and comprehensive CD274/PD-L1 profiles in patients previously treated with chemoradiation therapy as radical treatment in bladder cancer.

J Immunother Cancer 2022 Jan;10(1)

Department of Urology, Osaka Medical and Pharmaceutical University, Takatsuki, Japan.

Background: Chemoradiation therapy (CRT) has been increasingly reported as a possible alternative to total cystectomy (TC) for localized bladder cancer (BC). Pembrolizumab is the standard of care for platinum-refractory metastatic urothelial carcinoma, although it is unknown whether the efficacy of pembrolizumab in patients previously treated with curative CRT varies from the results of benchmark trials.

Methods: We retrospectively assessed whether the survival benefit of pembrolizumab differs between patients previously treated with TC or CRT as radical treatment. Read More

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January 2022

Experience analysing over 190,000 embryo trophectoderm biopsies using a novel FAST-SeqS preimplantation genetic testing assay.

Reprod Biomed Online 2021 Jun 30. Epub 2021 Jun 30.

Invitae, 1400 16th St, San Francisco CA 94103, USA.

Research Question: Is FAST-SeqS an accurate methodology for preimplantation genetic testing for whole-chromosome aneuploidy (PGT-A)? What additional types of chromosomal abnormalities can be assessed? What are the observed aneuploidy rates in a large clinical cohort?

Design: FAST-SeqS, a next-generation sequencing (NGS)-based assay amplifying genome-wide LINE1 repetitive sequences, was validated using reference samples. Sensitivity and specificity were calculated. Clinically derived trophectoderm biopsies submitted for PGT-A were assessed, and aneuploidy and mosaicism rates among biopsies were determined. Read More

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ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines.

Genome Med 2022 Jan 18;14(1). Epub 2022 Jan 18.

Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.

Background: Identification of clinically significant genetic alterations involved in human disease has been dramatically accelerated by developments in next-generation sequencing technologies. However, the infrastructure and accessible comprehensive curation tools necessary for analyzing an individual patient genome and interpreting genetic variants to inform healthcare management have been lacking.

Results: Here we present the ClinGen Variant Curation Interface (VCI), a global open-source variant classification platform for supporting the application of evidence criteria and classification of variants based on the ACMG/AMP variant classification guidelines. Read More

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January 2022

MODY5 Hepatocyte Nuclear Factor 1ß (HNF1ß)-Associated Nephropathy: experience from a regional monogenic diabetes referral centre in Singapore.

J Investig Med High Impact Case Rep 2022 Jan-Dec;10:23247096211065626

Clinical Research Unit, Khoo Teck Puat Hospital, Singapore.

From our monogenic diabetes registry set-up at a secondary-care diabetes center, we identified a nontrivial subpopulation (~15%) of maturity-onset diabetes of the young (MODY) among people with young-onset diabetes. In this report, we describe the diagnostic caveats, clinical features and long-term renal-trajectory of people with mutations (HNF1B-MODY). Between 2013 and 2020, we received 267 referrals to evaluate MODY from endocrinologists in both public and private practice. Read More

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January 2022

Genomic Correlates of Unfavorable Outcome in Locally Advanced Cervical Cancer Treated with Neoadjuvant Chemoradiation.

Cancer Res Treat 2022 Jan 17. Epub 2022 Jan 17.

Department of Radiology, Shandong Cancer Hospital affiliated to Shandong University, Jinan, China.

Purpose: Neoadjuvant therapy modality can increase the operability rate and mitigate pathological risks in locally advanced cervical cancer, but treatment response varies widely. It remains unclear whether genetic alterations correlate with the response to neoadjuvant therapy and disease-free survival in locally advanced cervical cancer.

Materials And Methods: A total of 62 locally advanced cervical cancer (stage IB-IIA) patients who received neoadjuvant chemoradiation plus radical hysterectomy were retrospectively analyzed. Read More

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January 2022

SARS-CoV-2 and the role of orofecal transmission: a systematic review.

F1000Res 2021 24;10:231. Epub 2021 Mar 24.

Centre for Evidence Based Medicine, University of Oxford, Oxford, OX2 6GG, UK.

Background: Modes of transmission of SARS-CoV-2 are of key public health importance. SARS-CoV-2 has been detected in the feces of some COVID-19 patients, suggesting the possibility that the virus could, in addition to droplet and fomite transmission, be transmitted via the orofecal route.

Methods: This review is part of an Open Evidence Review on Transmission Dynamics of COVID-19. Read More

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Biological system considerations for application of toxicogenomics in next-generation risk assessment and predictive toxicology.

Toxicol In Vitro 2022 Jan 13:105311. Epub 2022 Jan 13.

ScitoVation, 100 Capitola Drive, Suite 106, Durham, NC 27713, United States of America.

There is increasing interest in using modern 'omics technologies, such as whole transcriptome sequencing, to inform decisions about human health safety and chemical toxicity hazard. High throughput methodologies using in vitro assays offer a path forward in reducing or eliminating animal testing. However, many aspects of these technologies need assessment before they will gain the trust of regulators and the public as viable alternative test methods for human health and safety. Read More

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January 2022

Incidence, Clinicopathologic Features, and Genetics of in situ Follicular Neoplasia: A Comprehensive Screening Study in a Japanese Cohort.

Histopathology 2022 Jan 17. Epub 2022 Jan 17.

Department of Pathology, University of Yamanashi.

Aims: In situ follicular neoplasia (ISFN) is a histologically recognisable neoplastic proliferation of follicular lymphoma (FL)-like B cells confined to the germinal centres. While some ISFNs are associated with overt FL, others are incidentally identified as isolated or pure forms in individuals without evidence of overt FL. The prevalence of incidentally found isolated ISFN is approximately 3% in Europe; however, no screening study has been conducted in Asia. Read More

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January 2022

Real-world data of off-label drug use in patients with actionable genomic alterations on next-generation sequencing.

Invest New Drugs 2022 Jan 17. Epub 2022 Jan 17.

Division of Hematology and Medical Oncology, Mays Cancer Center, University of Texas Health San Antonio MD Anderson Cancer Center, Texas, USA.

Introduction We analyzed the outcomes of patients with advanced cancers in our institution treated with off-label drugs targeting actionable genomic alteration based on next-generation sequencing who did not qualify for clinical trials. Purposes Our study endpoint was objective tumor response or stable disease at 16 weeks or later after treatment initiation. Methods Sixteen patients were included, 8 treated with immune checkpoint inhibitors targeting PD-L1 expression or TP53 mutations and 8 with other drugs. Read More

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January 2022

Review of genome sequencing technologies in molecular characterization of influenza A viruses in swine.

J Vet Diagn Invest 2022 Jan 17:10406387211068023. Epub 2022 Jan 17.

School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.

The rapidly evolving antigenic diversity of influenza A virus (IAV) genomes in swine makes it imperative to detect emerging novel strains and track their circulation. We analyzed in our review the sequencing technologies used for subtyping and characterizing swine IAV genomes. Google Scholar, PubMed, and International Nucleotide Sequence Database Collaboration (INSDC) database searches identified 216 studies that have utilized Sanger, second-, and third-generation sequencing techniques to subtype and characterize swine IAV genomes up to 31 March 2021. Read More

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January 2022

DNA-repair status should be assessed in treatment-emergent neuroendocrine prostate cancer before platinum-based therapy.

Prostate 2022 Jan 17. Epub 2022 Jan 17.

Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China.

Objectives: This study sought to provide contemporary data from a multi-institution with respect to DNA-repair genes (DRGs) status and its impact on effects of platinum-based chemotherapy in treatment-emergent neuroendocrine prostate cancer (t-NEPC), for which little data exist.

Patients And Methods: All patients were retrospectively collected with eligible biopsied tissues for targeted next generation sequencing (NGS). The main outcomes were radiologic progression-free survival and overall survival according to Response Evaluation Criteria in Solid Tumors, version 1. Read More

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January 2022

Downregulation of HLA class II is associated with relapse after allogeneic stem cell transplantation and alters recognition by antigen-specific T cells.

Int J Hematol 2022 Jan 17. Epub 2022 Jan 17.

Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya, Aichi, 466-8560, Japan.

Genomic deletion of donor-patient-mismatched HLA alleles in leukemic cells is a major cause of relapse after allogeneic hematopoietic stem cell transplantation (HSCT). Mismatched HLA is frequently lost as an individual allele or a whole region in HLA-class I, however, it is downregulated in HLA-class II. We hypothesized that there might be a difference in T cell recognition capacity against epitopes associated with HLA-class I and HLA-class II and consequently such allogeneic immune pressure induced HLA alterations in leukemic cells. Read More

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January 2022

Analysis of Small RNA Sequencing Data in Plants.

Methods Mol Biol 2022 ;2443:497-509

Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India.

Over the past decades, next-generation sequencing (NGS) has been employed extensively for investigating the regulatory mechanisms of small RNAs. Several bioinformatics tools are available for aiding biologists to extract meaningful information from enormous amounts of data generated by NGS platforms. This chapter describes a detailed methodology for analyzing small RNA sequencing data using different open source tools. Read More

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January 2022

Managing High-Density Genotyping Data with Gigwa.

Methods Mol Biol 2022 ;2443:415-427

French Institute of Bioinformatics (IFB)-South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, France.

Next generation sequencing technologies enabled high-density genotyping for large numbers of samples. Nowadays SNP calling pipelines produce up to millions of such markers, but which need to be filtered in various ways according to the type of analyses. One of the main challenges still lies in the management of an increasing volume of genotyping files that are difficult to handle for many applications. Read More

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January 2022

Annotation of Protein-Coding Genes in Plant Genomes.

Authors:
Bhavna Hurgobin

Methods Mol Biol 2022 ;2443:309-326

La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Life Sciences, AgriBio Building, La Trobe University, Bundoora, VIC, Australia.

Advances in next-generation sequencing technologies and the lower sequencing costs are paving the way to more plant genome sequencing, assembly, and annotation projects. While genome assembly is the first step toward elucidating the genome structure of a species, it is the annotation of the protein-coding genes that provide meaningful information to biologists. However, genome annotation is not a trivial task. Read More

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January 2022

Trimming and Validation of Illumina Short Reads Using Trimmomatic, Trinity Assembly, and Assessment of RNA-Seq Data.

Methods Mol Biol 2022 ;2443:211-232

Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, Australia.

Next-generation sequencing (NGS) technologies can generate billions of reads in a single sequencing run. However, with such high-throughput comes quality issues which have to be addressed before undertaking downstream analysis. Quality control on short reads is usually performed at default settings due to a lack of in-depth understanding of a particular software's parameters and their effect if changed on the output. Read More

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January 2022

Using GenBank and SRA.

Methods Mol Biol 2022 ;2443:1-25

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

GenBank and the Sequence Read Archive (SRA) are comprehensive databases of publicly available DNA sequences. GenBank contains data for 480,000 named organisms, more than 176,000 within the embryophyta, obtained through submissions from individual laboratories and batch submissions from large-scale sequencing projects. SRA contains reads from next-generation sequencing studies from over 110,000 species. Read More

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January 2022