Results 61 to 70 of about 37,179 (261)

filter-specific-GATK

, 2014
filter-specific ...
Zhao, Wei, Jian-Feng Mao (427222), Mao, Jian-Feng, Gao, Jie, Jie Gao (10266), Baosheng Wang (427221), Wei Zhao (14321), Pei, Zhi-Yong, Jin Pan (411619), Wang, Baosheng, Zhi-Yong Pei (3265467), Pan, Jin, Wang, Xiao-Ru, Xiao-Ru Wang (12804)   +13 more
core   +1 more source

A Living Multi‐Omics PDX Biobank of High‐Risk Sarcomas Reveals ecDNA‐Driven Oncogene Amplification in Osteosarcoma and Enables Preclinical Precision Oncology

Advanced Science, EarlyView.
A living multi‐omics sarcoma PDX biobank is enriched for high‐risk disease and preserves key patient tumor features at histopathological and molecular levels. Integrated profiling reveals ecDNA‐driven oncogene amplification in osteosarcoma and preferential retention of ecDNA during PDX evolution.
Weisong Zhao, Zhiwei Cheng, Kai Tian, Mengxiong Sun, Zhuoying Wang, Ming Jiao, Jens Luebeck, Kaiyuan Zhu, Xiao Zhang, Dongqing Zuo, Hongsheng Wang, Chongren Wang, Jiakang Shen, Xiaojun Ma, Gangyang Wang, Zongyi Wang, Jing Han, Kaiyuan Liu, Haoran Mu, Weiqi Ma, Yongyong Ren, Shibing Guo, Huangxin Tu, Lingfeng Yu, Yining Tao, Yu Lv, Hui Lu, Owen S. Chapman, Rishaan Kenkre, Lukas Chavez, Zhengdong Cai, Yuqin Yang, Wei Sun, Yafei Jiang, Yingqi Hua   +34 more
wiley   +1 more source

Comparative Evaluation of Variant Calling Strategies for High-Density SNP Discovery in Polyploid Kiwifruit (Actinidia spp.)

Horticulturae
Single nucleotide polymorphisms (SNPs) are widely used for genetic diversity analysis, linkage mapping, genome-wide association studies (GWAS), and molecular marker development in crop plants.
Yumi Kim, Mockhee Lee, Daeil Kim
doaj   +1 more source

Agile parallel bioinformatics workflow management using Pwrake

BMC Research Notes, 2011
Background In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management.
Tanaka Masahiro, Sasaki Kensaku, Mishima Hiroyuki, Tatebe Osamu, Yoshiura Koh-ichiro   +4 more
doaj   +1 more source

Structural Variants in the Human Genome Associated With Gut Microbiome and Blood Metabolic Traits With Potential Causal Links

Advanced Science, EarlyView.
Based on a multi‐omics cohort of 2002 individuals comprising high‐depth whole‐genome and metagenomic sequencing data, blood metabolites, and detailed questionnaires, we identified 138 859 high‐confidence SVs, uncovering 36 significant SV–microbiome associations and 48 SV–blood metabolite associations.
Qun Zhou, Keqing Wang, Junhong Chen, Haoyu Wang, Xinjiang Tan, Xuanlin Huang, Zhiyin Lin, Xun Xu, Xin Jin, Shaoqiao Zhang, Liang Xiao, Yuanqiang Zou, Tao Zhang, Xiaomin Liu   +13 more
wiley   +1 more source

Fast and accurate DNASeq variant calling workflow composed of LUSH toolkit

Human Genomics
Background Whole genome sequencing (WGS) is becoming increasingly prevalent for molecular diagnosis, staging and prognosis because of its declining costs and the ability to detect nearly all genes associated with a patient's disease. The currently widely
Taifu Wang, Youjin Zhang, Haoling Wang, Qiwen Zheng, Jiaobo Yang, Tiefeng Zhang, Geng Sun, Weicong Liu, Longhui Yin, Xinqiu He, Rui You, Chu Wang, Zhencheng Liu, Zhijian Liu, Jin’an Wang, Xiangqian Jin, Zengquan He   +16 more
doaj   +1 more source

Halvade-RNA: Parallel variant calling from transcriptomic data using MapReduce. [PDF]

PLoS ONE, 2017
Given the current cost-effectiveness of next-generation sequencing, the amount of DNA-seq and RNA-seq data generated is ever increasing. One of the primary objectives of NGS experiments is calling genetic variants.
Dries Decap, Joke Reumers, Charlotte Herzeel, Pascal Costanza, Jan Fostier   +4 more
doaj   +1 more source

Concurrent Germline RB1 & Mosaic TP53 in a Child With Multiple Childhood Cancers

American Journal of Medical Genetics Part A, EarlyView.
ABSTRACT We report a patient with a pathogenic germline variant (PGV) in RB1 and somatic mosaicism for a pathogenic TP53 variant who developed three distinct types of childhood cancer: retinoblastoma, osteosarcoma, and myelodysplastic syndrome (MDS) before the age of 6 years.
Ole Haubjerg Nielsen, Ulrik Kristoffer Stoltze, Pernille Axél Gregersen, Marianne Hoffmann, Morten Lyng Høgild, Mette Klarskov Andersen, Lise Barlebo Ahlborn, Lisa Lyngsie Hjalgrim, Karin A. W. Wadt   +8 more
wiley   +1 more source

Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines

BMC Genomics, 2021
Background Next Generation Sequencing (NGS) is the fundament of various studies, providing insights into questions from biology and medicine. Nevertheless, integrating data from different experimental backgrounds can introduce strong biases.
Stephan Weißbach, Stanislav Sys, Charlotte Hewel, Hristo Todorov, Susann Schweiger, Jennifer Winter, Markus Pfenninger, Ali Torkamani, Doug Evans, Joachim Burger, Karin Everschor-Sitte, Helen Louise May-Simera, Susanne Gerber   +12 more
doaj   +1 more source

Variant detection and annotation workflows using the GATK pipeline

Journal of Animal Breeding and Genomics
Whole genome sequencing is a technology that detects nucleotide sequences across the entire DNA, which, in the past, was limited by high costs and time constraints. However, recent advancements in science and technology have significantly reduced these limitations.
Seunghwan Ko, Jeong Woen Shin, Yoonji Chung, Phuong Thanh N. Dinh, Young jae Choi, Jaeho Lee, Euiseo Hong, Woonyoung Jeong, Hayeong Oh, JuHyeok Kim, Seung Hwan Lee   +10 more
openaire   +1 more source