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News
Detecting Contamination and Cross-Talk in Sequencing Data
3+ day, 26+ min ago (128+ words) Table 1: Summary of contamination types in NGS data, with characteristic data signatures and recommended analytical detection tools. Reads with unexpected or mismatched index combinations Unique dual index audit, per-library read-count review A systematic approach for evaluating a sample flagged for…...
Unique Molecular Identifiers and Duplicate Removal
3+ day, 26+ min ago (156+ words) Mapped 5' start position Mapped start position and UMI sequence Distinguishes independent molecules at the same position Appropriate for WGS germline variant calling Yes, with added overhead Appropriate for deep targeted panel sequencing No; removes genuine fragments Yes, via consensus calling…...
Controls, Replicates, and Batch Effects in Sequencing Experiments
3+ day, 26+ min ago (214+ words) Table 1: Common control types in NGS experiments, their diagnostic purpose, and the failure mode each detects. Benchmarks variant calling against an established truth set Run-level instrument failure or cluster density issues Figure 1: In a confounded design, condition and batch are…...
AI Identifies Disease-Relevant Genetic Variants
3+ day, 5+ hour ago (596+ words) More than two decades after scientists first sequenced the entire human genome — all 3 billion “letters,” or base pairs, of DNA code — the meaning of much of this code remains a mystery. Researchers at UC Berkeley have created a new genomic language…...
Stress Alters the Structure of Support Cells in the Brain’s Fear Center
4+ day, 4+ hour ago (221+ words) A new study led by UCLA Health researchers has identified a specific type of brain cell and a tiny structure on its surface that changes when the body is under stress, which may help explain why stress can lead to…...
Predictive Tools Can Confuse Rare Mutations With Dangerous Ones
6+ day, 5+ hour ago (523+ words) When a patient has their DNA read, it gets compared against a reference version of the human genome. It allows geneticists and rare disease experts to look at a list of places where the patient's DNA differs. Most variations will…...
Oxford Nanopore Sequencing: Principles, Performance, and Applications
1+ week, 5+ day ago (388+ words) Nanopore sequencing read length is constrained by the length of the input DNA fragment, not the chemistry. In principle, the pore will continue reading for as long as the molecule threading through it remains intact. Practical limits arise from sample…...
Epigenetic Changes Cause a Stress Gene To Become "Stuck On" in Schizophrenia
2+ week, 4+ day ago (330+ words) Experts at the University of Sydney have found that a gene involved in regulating the body’s response to stress switches on more easily in the brains of people who live with schizophrenia. The study, published in the American Journal of…...
Younger Lung Cancer Patients More Likely To Have Targetable Genetic Changes
2+ week, 5+ day ago (619+ words) A large international analysis of 14,246 people with non-small cell lung cancer (NSCLC) has found that younger adults were more likely than older adults to have genetic changes that can be matched with existing targeted treatments. The findings come from a…...
Scientists Map Epigenetic Changes in "Asleep" Cancer Cells
3+ week, 2+ day ago (499+ words) Now, a new study not only redefines our understanding of senescence but also illustrates how to prevent its harmful effects. The findings, published in Life Science Alliance, reveal that senescence unfolds in stages—not all at once as previously thought…...