scholarly journals Cell Banking of hiPSCs: A Practical Guide to Cryopreservation and Quality Control in Basic Research

2020 ◽  
Vol 55 (1) ◽  
Author(s):  
Aya Shibamiya ◽  
Elisabeth Schulze ◽  
Dana Krauß ◽  
Christa Augustin ◽  
Marina Reinsch ◽  
...  
Keyword(s):  
Quality Control ◽  
Basic Research ◽  
Practical Guide ◽  
Cell Banking

scholarly journals The SEQC2 epigenomics quality control (EpiQC) study

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jonathan Foox ◽  
Jessica Nordlund ◽  
Claudia Lalancette ◽  
Ting Gong ◽  
Michelle Lacey ◽  
...  
Keyword(s):  
Quality Control ◽  
Reference Materials ◽  
Single Molecule ◽  
Bisulfite Sequencing ◽  
Basic Research ◽  
Control Group ◽  
Oxford Nanopore ◽  
Long Read ◽  
Genome Bisulfite Sequencing ◽  
High Concordance

Abstract Background Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA’s Epigenomics Quality Control Group. Results Each sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms. Conclusions The data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.

scholarly journals A fully automated approach for quality control of cancer mutations in the era of high-resolution whole genome sequencing

2021 ◽  
Author(s):  
Jacob Househam ◽  
William CH Cross ◽  
Giulio Caravagna
Keyword(s):  
Quality Control ◽  
Data Quality ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Large Scale ◽  
Control Method ◽  
Point Mutations ◽  
Basic Research ◽  
Whole Genome ◽  
Colorectal Cancer Patients

AbstractCancer is a global health issue that places enormous demands on healthcare systems. Basic research, the development of targeted treatments, and the utility of DNA sequencing in clinical settings, have been significantly improved with the introduction of whole genome sequencing. However the broad applications of this technology come with complications. To date there has been very little standardisation in how data quality is assessed, leading to inconsistencies in analyses and disparate conclusions. Manual checking and complex consensus calling strategies often do not scale to large sample numbers, which leads to procedural bottlenecks. To address this issue, we present a quality control method that integrates point mutations, copy numbers, and other metrics into a single quantitative score. We demonstrate its power on 1,065 whole-genomes from a large-scale pan-cancer cohort, and on multi-region data of two colorectal cancer patients. We highlight how our approach significantly improves the generation of cancer mutation data, providing visualisations for cross-referencing with other analyses. Our approach is fully automated, designed to work downstream of any bioinformatic pipeline, and can automatise tool parameterization paving the way for fast computational assessment of data quality in the era of whole genome sequencing.

HOW MUCH RESEARCH IS ENOUGH?

PEDIATRICS ◽  
1985 ◽  
Vol 75 (6) ◽  
pp. A82-A82
Keyword(s):  
Quality Control ◽  
Research Policy ◽  
Basic Research ◽  
Academic Science ◽  
Control Mechanisms ◽  
Natural Rate ◽  
Subsequent Research ◽  
Medical Researchers ◽  
Promising Avenue

Medical researchers are spluttering outrage. Last year Congress approved 6,500 new grants for them. But the Office of Management and Budget has now directed that only 5,000 be awarded, as the Administration requested in the first place. The researchers say the promise of their field has never been higher and more research will hasten the conquest of disease. So how much research is enough? A reasonable goal for basic research policy is to maximize the natural rate of discovery by leaving no promising avenue unfunded. But is there already too much money chasing too few good ideas? The quality-control mechanisms of academic science are so loose that they regularly fail to detect even outright fraud. The possibly doubtful quality of many research reports is evident from the rapidity with which most are forgotten. Only 36% of published scientific articles are cited two or more times in subsequent research reports. The rest—two-thirds of researchers' published output—may contribute only negligibly to the march of science.

scholarly journals The SEQC2 Epigenomics Quality Control (EpiQC) Study: Comprehensive Characterization of Epigenetic Methods, Reproducibility, and Quantification

2020 ◽  
Author(s):  
Jonathan Foox ◽  
Jessica Nordlund ◽  
Claudia Lalancette ◽  
Ting Gong ◽  
Michelle Lacey ◽  
...  
Keyword(s):  
Quality Control ◽  
Bisulfite Sequencing ◽  
Sequence Data ◽  
Basic Research ◽  
High Coverage ◽  
Genome Wide ◽  
Wide Range ◽  
Genome Bisulfite Sequencing ◽  
Mammalian Genomes ◽  
Primary Focus

AbstractDetection of DNA cytosine modifications such as 5-methylcytosine (5mC) and 5-hydroxy-methylcytosine (5hmC) is essential for understanding the epigenetic changes that guide development, cellular lineage specification, and disease. The wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research.We present a multi-platform assessment and a global resource for epigenetics research from the FDA’s Epigenomics Quality Control (EpiQC) Group. The study design leverages seven human cell lines that are publicly available from the National Institute of Standards and Technology (NIST) and Genome in a Bottle (GIAB) consortium. These genomes were subject to a variety of genome-wide methylation interrogation approaches across six independent laboratories. Our primary focus was on cytosine modifications found in mammalian genomes (5mC, 5hmC). Each sample was processed in two or more technical replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS, SPLAT), oxidative bisulfite sequencing (oxBS), Enzymatic Methyl-seq (EM-seq), Illumina EPIC targeted-methylation sequencing, and ATAC-seq. Each library was sequenced to high coverage on an Illumina NovaSeq 6000. The data were subject to rigorous quality assessment and subsequently compared to Illumina EPIC methylation microarrays. We provide a wide range of sequence data for commonly used genomics reference materials, as well as best practices for epigenomics research. These findings can serve as a guide for researchers to enable epigenomic analysis of cellular identity in development, health, and disease.

scholarly journals Meta-Analytic Methodology for Basic Research: A Practical Guide

2019 ◽  
Vol 10 ◽  
Author(s):  
Nicholas Mikolajewicz ◽  
Svetlana V. Komarova
Keyword(s):  
Basic Research ◽  
Practical Guide
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