TY - JOUR
T1 - SNPitty
T2 - An Intuitive Web Application for Interactive B-Allele Frequency and Copy Number Visualization of Next-Generation Sequencing Data
AU - van Riet, Job
AU - Krol, Niels M G
AU - Atmodimedjo, Peggy N
AU - Brosens, Erwin
AU - van IJcken, Wilfred F J
AU - Jansen, Maurice P H M
AU - Martens, John W M
AU - Looijenga, Leendert H
AU - Jenster, Guido
AU - Dubbink, Hendrikus J
AU - Dinjens, Winand N M
AU - van de Werken, Harmen J G
N1 - Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.
PY - 2018/3
Y1 - 2018/3
N2 - Exploration and visualization of next-generation sequencing data are crucial for clinical diagnostics. Software allowing simultaneous visualization of multiple regions of interest coupled with dynamic heuristic filtering of genetic aberrations is, however, lacking. Therefore, the authors developed the web application SNPitty that allows interactive visualization and interrogation of variant call format files by using B-allele frequencies of single-nucleotide polymorphisms and single-nucleotide variants, coverage metrics, and copy numbers analysis results. SNPitty displays variant alleles and allelic imbalances with a focus on loss of heterozygosity and copy number variation using genome-wide heterozygous markers and somatic mutations. In addition, SNPitty is capable of generating predefined reports that summarize and highlight disease-specific targets of interest. SNPitty was validated for diagnostic interpretation of somatic events by showcasing a serial dilution series of glioma tissue. Additionally, SNPitty is demonstrated in four cancer-related scenarios encountered in daily clinical practice and on whole-exome sequencing data of peripheral blood from a Down syndrome patient. SNPitty allows detection of loss of heterozygosity, chromosomal and gene amplifications, homozygous or heterozygous deletions, somatic mutations, or any combination thereof in regions or genes of interest. Furthermore, SNPitty can be used to distinguish molecular relationships between multiple tumors from a single patient. On the basis of these data, the authors demonstrate that SNPitty is robust and user friendly in a wide range of diagnostic scenarios.
AB - Exploration and visualization of next-generation sequencing data are crucial for clinical diagnostics. Software allowing simultaneous visualization of multiple regions of interest coupled with dynamic heuristic filtering of genetic aberrations is, however, lacking. Therefore, the authors developed the web application SNPitty that allows interactive visualization and interrogation of variant call format files by using B-allele frequencies of single-nucleotide polymorphisms and single-nucleotide variants, coverage metrics, and copy numbers analysis results. SNPitty displays variant alleles and allelic imbalances with a focus on loss of heterozygosity and copy number variation using genome-wide heterozygous markers and somatic mutations. In addition, SNPitty is capable of generating predefined reports that summarize and highlight disease-specific targets of interest. SNPitty was validated for diagnostic interpretation of somatic events by showcasing a serial dilution series of glioma tissue. Additionally, SNPitty is demonstrated in four cancer-related scenarios encountered in daily clinical practice and on whole-exome sequencing data of peripheral blood from a Down syndrome patient. SNPitty allows detection of loss of heterozygosity, chromosomal and gene amplifications, homozygous or heterozygous deletions, somatic mutations, or any combination thereof in regions or genes of interest. Furthermore, SNPitty can be used to distinguish molecular relationships between multiple tumors from a single patient. On the basis of these data, the authors demonstrate that SNPitty is robust and user friendly in a wide range of diagnostic scenarios.
KW - Algorithms
KW - Alleles
KW - Base Composition
KW - Biomarkers, Tumor
KW - Clinical Decision-Making/methods
KW - DNA Copy Number Variations
KW - Data Visualization
KW - Gene Dosage
KW - Gene Frequency/genetics
KW - High-Throughput Nucleotide Sequencing
KW - Humans
KW - Internet
KW - Loss of Heterozygosity
KW - Neoplasms/diagnosis
KW - Polymorphism, Single Nucleotide
KW - Web Browser
KW - Whole Exome Sequencing
U2 - 10.1016/j.jmoldx.2017.11.011
DO - 10.1016/j.jmoldx.2017.11.011
M3 - Article
C2 - 29305224
SN - 1525-1578
VL - 20
SP - 166
EP - 176
JO - The Journal of molecular diagnostics : JMD
JF - The Journal of molecular diagnostics : JMD
IS - 2
ER -