Next generation sequencing (NGS), or massively paralleled sequencing, refers to a collective group of methods in which numerous sequencing reactions take place simultaneously, resulting in enormous amounts of sequencing data for a small fraction of the cost of Sanger sequencing. Typically short (50-250 bp), NGS reads are first mapped to a reference genome, and then variants are called from the mapped data. While most NGS applications focus on the detection of single nucleotide variants (SNVs) or small insertions/deletions (indels), structural variation, including translocations, larger indels, and copy number variation (CNV), can be identified from the same data. Structural variation detection can be performed from whole genome NGS data or "targeted" data including exomes or gene panels. However, while targeted sequencing greatly increases sequencing coverage or depth of particular genes, it may introduce biases in the data that require specialized informatic analyses. In the past several years, there have been considerable advances in methods used to detect structural variation, and a full range of variants from SNVs to balanced translocations to CNV can now be detected with reasonable sensitivity from either whole genome or t...Continue Reading
Letter: A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining
A tyrosine kinase created by fusion of the PDGFRA and FIP1L1 genes as a therapeutic target of imatinib in idiopathic hypereosinophilic syndrome
Progress in concurrent analysis of loss of heterozygosity and comparative genomic hybridization utilizing high density single nucleotide polymorphism arrays
Adverse prognostic significance of KIT mutations in adult acute myeloid leukemia with inv(16) and t(8;21): a Cancer and Leukemia Group B Study
First-line gefitinib in patients with advanced non-small-cell lung cancer harboring somatic EGFR mutations
A new chromosomal three-way rearrangement involving MLL masked by a t(9;19)(p11;p13) in an infant with acute myeloid leukemia
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data
New strategies and emerging technologies for massively parallel sequencing: applications in medical research
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection
ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information
Targeted next generation sequencing of clinically significant gene mutations and translocations in leukemia
ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing
Rational search for genes in familial cortical myoclonic tremor with epilepsy, clues from recent advances
ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly
A new generation of cancer genome diagnostics for routine clinical use: overcoming the roadblocks to personalized cancer medicine
Function of cancer associated genes revealed by modern univariate and multivariate association tests
Copy number changes of clinically actionable genes in melanoma, non-small cell lung cancer and colorectal cancer-A survey across 822 routine diagnostic cases
Goat domestication and breeding: a jigsaw of historical, biological and molecular data with missing pieces
Multicolor Fluorescence In Situ Hybridization (FISH) Approaches for Simultaneous Analysis of the Entire Human Genome
Whole-genome sequencing analysis of CNV using low-coverage and paired-end strategies is efficient and outperforms array-based CNV analysis.
TSD: A Computational Tool To Study the Complex Structural Variants Using PacBio Targeted Sequencing Data
Influence of validating the parental origin on the clinical interpretation of fetal copy number variations in 141 core family cases
Identification of T-DNA Insertion Site and Flanking Sequence of a Genetically Modified Maize Event IE09S034 Using Next-Generation Sequencing Technology
Critical assessment of bioinformatics methods for the characterization of pathological repeat expansions with single-molecule sequencing data.
Copy Number Variations in Amyotrophic Lateral Sclerosis: Piecing the Mosaic Tiles Together through a Systems Biology Approach
Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software
Location of Balanced Chromosome-Translocation Breakpoints by Long-Read Sequencing on the Oxford Nanopore Platform
Multi-gene panel testing for hereditary cancer predisposition in unsolved high-risk breast and ovarian cancer patients
Next-generation sequencing approaches for the study of genome and epigenome toxicity induced by sulfur mustard
Atypical Presentation of Bilateral Retinoblastoma with Floaters and Sub-Internal Limiting Membrane Seeds in an 11-Year-Old Asian Indian Male
Genome-Wide Analysis of Interchromosomal Interaction Probabilities Reveals Chained Translocations and Overrepresentation of Translocation Breakpoints in Genes in a Cutaneous T-Cell Lymphoma Cell Line
Comparative assessments of indel annotations in healthy and cancer genomes with next-generation sequencing data.
Integrative analysis of structural variations using short-reads and linked-reads yields highly specific and sensitive predictions.
Next-Generation Sequencing-Based Approaches for Mutation Mapping and Identification in Caenorhabditis elegans
Intronic Breakpoint Signatures Enhance Detection and Characterization of Clinically Relevant Germline Structural Variants.
Acute Myeloid Leukemia
Acute myeloid leukemia (AML) is a clinically and genetically heterogeneous disease with approximately 20,000 cases per year in the United States. AML also accounts for 15-20% of all childhood acute leukemias, while it is responsible for more than half of the leukemic deaths in these patients. Here is the latest research on this disease.
AML: Role of LSD1 by CRISPR (Keystone)
Find the latest rersearrch on the ability of CRISPR-Cas9 mutagenesis to profile the interactions between lysine-specific histone demethylase 1 (LSD1) and chemical inhibitors in the context of acute myeloid leukemia (AML) here.
Acute Myeloid Leukaemia & RNA
Acute myeloid leukaemia (AML) is a common hematological type of cancer. As the population ages, there has been a rise in the frequency of AML. RNA expression has been used to see if there are different genetic profiles that exist within AML and whether these may underpin the variations in survival rates. Here is the latest research on AML and RNA.