Categories
Tag: SNV
cfDNA Standards For Molecular Testing
Multiplexed ctDNA fragments (~150bp) mixed with nucleosomally fragmented wildtype cfDNA background in human plasma. The cell-derived ctDNA fragments are generated by Anchor’s unique multiplexed gene-editing method and are nucleosomally fragmented to around 150bp. The cell-derived variants are suitable for both the amplicon-based and capture-based methods. The synthetic ctDNA fragments are…
Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma
Whole-genome sequencing (WGS) analysis of early and advanced adenocarcinomas Whole-genome short read and long read sequencing datasets of 76 lung cancer specimens were analyzed. The datasets included newly generated data for 48 early small-sized lung adenocarcinoma cases (collectively called “Early-Ad” hereafter). These cases included 26 AIS (9 and 17 cases…
Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases | Genome Medicine
Our cohort comprises 34 families in which a presumably autosomal recessive disease defied molecular diagnosis by clinical exome sequencing (short-read sequencing-based) and reanalysis performed on the index individual for each family (Fig. 1). The index patient in each family was subjected to an average of 10 × depth lrWGS except for Family F8602…
Liquid Biopsy Uses ctDNA to Predict Recurrence of Hodgkin Lymphoma
A Stanford Medicine-led, international study of hundreds of samples from patients with classic Hodgkin lymphoma (cHL) has shown that levels of tumor DNA circulating in the blood can identify those individuals who are responding well to treatment and those who are likely to experience a disease recurrence. The study results suggest…
ASEReadCounter output wrong number of coverage
ASEReadCounter output wrong number of coverage 0 Hi, I am using ASEReadCounter to count the number of reads per variant in a BAM file. For some positions, it will report 1 read covered(1 refCount or 1 altCount) while there is no read covered at those positions after checking it in…
A Trimodal Approach to Interrogate Breast Cancer
Sponsored content brought to you by Along with advances in single-cell sequencing and multiomic analysis, researchers are able to more precisely decode the stages of human cancers—from precursor to development of invasive cancer—to more accurately inform therapeutic approaches. With more than 2 million global cases of breast cancer diagnosed annually,…
Bioconductor Code: SNPRelate
SNPRelate: Parallel computing toolset for relatedness and principal component analysis of SNP data ==== ![GPLv3](http://www.gnu.org/graphics/gplv3-88×31.png) [GNU General Public License, GPLv3](http://www.gnu.org/copyleft/gpl.html) [![Availability](http://www.bioconductor.org/shields/availability/release/SNPRelate.svg)](http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html) [![Years-in-BioC](http://www.bioconductor.org/shields/years-in-bioc/SNPRelate.svg)](http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html) [![R](https://github.com/zhengxwen/SNPRelate/actions/workflows/r.yml/badge.svg)](https://github.com/zhengxwen/SNPRelate/actions/workflows/r.yml) ## Features Genome-wide association studies are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed SNPRelate (R…
SNPs of a specific mouse strain
Hi, I wonder how can I get SNPs for a particular mouse strain like C57BL6. I have downloaded a mouse reference vcf from ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels/mgp_REL2021_snps.rsID.vcf.gz Its header is #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 129P2_OlaHsd 129S1_SvImJ 129S5SvEvBrd A_J AKR_J B10.RIII BALB_cByJ BALB_cJ BTBR_T+_Itpr3tf_J BUB_BnC3H_HeH C3H_HeJ C57BL_10J C57BL_10SnJ C57BL_6NJ…
Analyzing somatic mutations by single-cell whole-genome sequencing
Failla, G. The aging process and cancerogenesis. Ann. N. Y. Acad. Sci. 71, 1124–1140 (1958). Article CAS PubMed Google Scholar Szilard, L. On the nature of the aging process. Proc. Natl Acad. Sci. USA 45, 30–45 (1959). Article CAS PubMed PubMed Central Google Scholar Vijg, J. & Dong, X. Pathogenic…
Help finding the correct file version for dbSNP VCF ID replacement
Tried to use dbSNP version 156 using bcftools to replace the ID field in a reference VCF which originally contains a different position ID format. It seems the bcftools command did not work because a numeric chromosome column format in the #CHROM field which might not be compatible with bcftools…
New diagnostic workflow improves detection of 5q-spinal muscular atrophy
5q-spinal muscular atrophy (5q-SMA) is one of the more common types of spinal muscular atrophy (SMA) affecting around one in ten thousand individuals worldwide. Currently, tests are unable to detect all pathogenic genetic variants leading to 5q-SMA. However, researchers were able to reliably identify patients with 5q-SMA within a diagnostic…
GATK SelectVariants –remove-unused-alternates dropping real INDELs?
I’m using a VCF that is generated by GenotypeGVCFs (so doing calibration based on a larger cohort of samples) and my goal is to only extract variants of interest to one specific sample. The VCF in the subset tends to include some variants that were present in the original joint…
A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources
40,039 MAGs reconstructed from large-scale genome-resolved metagenomics To reconstruct previously unexplored bacterial and archaeal genomes, we performed a large-scale single-sample metagenomic assembly on 3304 soil metagenomes across the globe (Fig. 1a), including 363 metagenomes from the in-house dataset and 2941 from publicly available metagenomes. The soil samples were mainly collected from…
filtering SNV/INDEL in tumor-only WGS samples
filtering SNV/INDEL in tumor-only WGS samples 0 Dear all, To the cancer genomics community on Biostars that worked with tumor-only samples, a question please : which criteria do you apply to identify the most reliable somatic mutations ? I would appreciate having your suggestions. <> my colleagues performed somatic mutation…
Bioinformatics Research Associate, Genomics and Genetics
Job:Bioinformatics Research Associate, Genomics and Genetics 0 @jp-carter-15371 Last seen 7 hours ago Nashville, TN The Bioinformatics Research Associate is part of the Creative Data Solutions (CDS) Shared Resource at Vanderbilt University and is a key individual contributor responsible for performing bioinformatics analyses of genomic data sets, developing and implementing…
Quantification of rare somatic single nucleotide variants by droplet digital PCR using SuperSelective primers
Primary samples and nucleic acid extraction A cohort of 48 patients diagnosed with advanced adenoma (AAD), defined by size > 20 mm, or colorectal carcinoma (CRC) were collected between 2013 and 2016. The study was approved by the institutional ethics committee of Hospital General Universitario de Alicante (Ref. CEICPI2013/01), and written informed consent…
Beginner help with sequencing data
Beginner help with sequencing data 0 Sorry for the extremely basic nature of this question but I’m a bit lost here despite spending a couple days reading and troubleshooting. I recently submitted a bacterial strain for WGS via Nanopore sequencing. What I got back was a single FASTA file containing…
Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data
Study design Experiments were performed in accordance with the New Zealand Animal Welfare Act (1999) and institutional guidelines provided by the University of Auckland Animal Ethics Committee, which reviewed and approved these experiments under application R1003. We did not use any specific randomisation process to allocate animals to a particular…
Element Biosciences’ NGS Tech, App Stories to Be Featured at ASHG
Element Biosciences, the developer of the AVITI benchtop sequencer, will be sharing details about its technology and discussing customer stories at the annual meeting of the American Society of Human Genetics (ASHG) annual meeting. Element is a silver sponsor of the meeting, which will be held November 1–5 in Washington,…
No samples in .vcf file.
I am trying to convert my vcf file into a BED format file. When I use this command: plink –vcf merge.bacteria.vcf.gz –make-bed –out merge.bacteria.vcf.bed I get the following error stating: PLINK v1.90b6.21 64-bit (19 Oct 2020) www.cog-genomics.org/plink/1.9/(C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License…
Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients
Paired tumor and normal DNA samples from 30 patients were subjected to WES at four ZPM laboratories with subsequent data analysis performed at five ZPM bioinformatic institutions (Fig. 1). DNA was originally derived from fresh-frozen samples that had been analyzed by WES within the multicenter MASTER (Molecularly Aided Stratification for…
Labcorp hiring Genomics/bioinformatics Intern in San Diego, California, United States
The Center of Excellence (CoE) in Data Science and Bioinformatics at LabCorp Information Technology department applies various data science disciplines (including artificial intelligence, machine learning, graph databases, statistics, bioinformatics, and natural language processing) to our clinical, operational and financial challenges, and creates opportunities to enhance the value of our offerings…
Simulation of undiagnosed patients with novel genetic conditions
Simulated patient initialization We simulate patients for each of the 2134 diseases in Orphanet20 (orphadata.org, accessed October 29, 2019) that do not correspond to a group of clinically heterogeneous disorders (i.e., Orphanet’s “Category” classification31), have at least one associated phenotype, and have at least one causal gene. For Orphanet diseases…
Prospects of Whole Genome Sequencing in Animal Breeding
Prospects of Whole Genome Sequencing in Animal Breeding The development of high-throughput sequencing technologies has revolutionized animal genetics and genomics. The widespread use of whole-genome sequencing (WGS) allows detection of a full range of common and rare genetic variants of different types across almost the entire genome which facilitates rare…
Epidemiology and analysis of SARS-CoV-2 Omicron subvariants BA.1 and 2 in Taiwan
Prevalence of Omicron subvariants between December 2021 and January 2023 in Taiwan BA.1 and BA.2 and their sublineages entered Taiwan in December 2021 and January 2022, respectively (Supplementary Table S1 and Fig. 1). These two Omicron lineages did not cause COVID-19 outbreaks until March and April 2022 (Supplementary Table S1 and…
RNAseq based variant dataset in a black poplar association panel | BMC Research Notes
Dickmann DI, Kuzovkina J. Poplars and willows of the world, with emphasis on silviculturally important species. In: Isebrands JG, Richardson J, editors. Poplars and willows: trees for society and the environment. Wallingford: CABI; 2014. Google Scholar Imbert E, Lefèvre F. Dispersal and gene flow of Populus nigra (Salicaceae) along a…
Rapid, tunable, and multiplexed detection of RNA using convective array PCR
Integrating reverse transcription in caPCR We first introduced an RT step to the standard caPCR assay. caPCR is performed using a set of 4 heaters that clamp on either face of a cartridge containing a toroidal chamber filled with the PCR reaction mixture4. By setting heaters on one side of…
mbQTL: An R/Bioconductor Package for Microbial Quantitative Trait Loci (QTL) Estimation
Motivation: In recent years, significant strides have been made in the field of genomics, with the commencement of large-scale studies aimed at collecting host mutational profiles and microbiome data. The amalgamation of host gene mutational profiles in both healthy and diseased subjects with microbial abundance data holds immense promise in…
Genomic profiling of post-transplant lymphoproliferative disorders using cell-free DNA
Diagnosing post-transplant lymphoproliferative disorder (PTLD) is challenging and often requires invasive procedures. Analyses of cell-free DNA (cfDNA) isolated from plasma is minimally invasive and highly effective for genomic profiling of tumors. We studied the feasibility of using cfDNA to profile PTLD and explore its potential to serve as a screening…
Genomic profiling of post-transplant lymphoproliferative disorders using cell-free DNA | Journal of Hematology & Oncology
The median age of the patients was 55 years (range 13–74). Median time between SOT and PTLD was 95 months (range 2–338). Most patients had stage IV disease (n = 13, 76%) with a median metabolic tumor volume (MTV) of 302 mL (range 5–2070 mL). Lactate dehydrogenase (LDH) levels ranged from 210 to 5068 (Additional file…
Roche hiring Principal Scientist I Bioinformatics in Mississauga, Ontario, Canada
The PositionRoche Sequencing Solutions (RSS), a business within Roche Diagnostics, focused on developing a disruptive Next-Generation Sequencing (NGS) platform along with a portfolio of reagents, assays and informatics solutions for multiple disease areas. We are looking for a Principal Bioinformatics Scientist in the NGS Algorithms and Applications team to support…
Genetic Cancer Hereditary Cancer Mutations Susceptibility To Cancer Genetic Changes
Genetic Cancers: Welcome back to “The Science Of Health”, ABP Live’s health column. Last time, in the health column, we discussed the difference between small cell lung cancers and non-small cell lung cancers, and explained why small cell lung cancers are less common than non-small cell lung cancers, despite the…
SNPred outperforms other ensemble-based SNV pathogenicity predictors and elucidates the challenges of using ClinVar for evaluation of variant classification quality.
Abstract Background: Current single nucleotide variants (SNVs) pathogenicity prediction tools assess various properties of genetic variants and provide a likelihood of causing a disease. This information aids in variant prioritization – the process of narrowing down the list of potential pathogenic variants, and, therefore, facilitating diagnostics. Assessing the effectiveness of…
The identification and genetic characteristics of Quang Binh virus from field-captured Culex tritaeniorhynchus (Diptera: Culicidae) from Guizhou Province, China | Parasites & Vectors
Mosquito species field collection and composition A total of 32,177 mosquitoes were collected from 15 counties of Guizhou Province, China. These mosquitoes were sampled from various locations, such as pig pens, cattle pens, trees, houses and other places. Among the collection sites, the largest portion of mosquitoes was obtained from…
Identification of transgene insertion site using Illumina DNA Sequencing
Identification of transgene insertion site using Illumina DNA Sequencing 0 I would like to request some help. We isolated some mutants with interesting phenotypes serendipitously when trying to generate mutants by targeted integration of a deletion cassete in a yeast. We confirm by PCR that the integration of the deletion…
SNPs that have the same position and alleles, which rsnumber to pick?
SNPs that have the same position and alleles, which rsnumber to pick? 0 When trying to match snps to rs number based on position I came across this problem. There are multiple SNPs on the same position with the same alleles and they are not synonyms or merged into each…
Dual CRISPR-Cas3 is a promising tool to induce a gigantic genomic deletion and restore dystrophin protein
In a recent study published in Stem Cell Reports, researchers evaluated the use of a dual clustered regularly interspaced short palindromic repeats (CRISPR)-Cas3 system for inducing multi-exon skipping (MES) among Duchenne muscular dystrophy (DMD)-patient-derived induced pluripotent stem cells (iPSCs). Study: Dual CRISPR-Cas3 system for inducing multi-exon skipping in DMD patient-derived iPSCs. Image…
Mitochondrial DNA study offers several new findings, reveals confounding factor in previous research
Pervasive nuclear genetic control over common mtDNA heteroplasmies. a, Quality control (QC)-passing mtDNA heteroplasmies in UKB and AoU. From the inside: mtDNA positions of poly-C tracts; genomic annotations (orange, HVR; yellow, rRNA genes; blue, tRNA genes; purple, coding genes); heteroplasmic SNV counts (red); heteroplasmic indel counts (black). The teal arc…
Principal Scientist II Bioinformatics – Hiring Now at F. Hoffmann-La Roche Ltd in Mississauga, ON
We are searching for a persistent Principal Scientist II Bioinformatics to join our energetic team at F. Hoffmann-La Roche Ltd in Mississauga, ON.Growing your career as a Full Time Principal Scientist II Bioinformatics is an incredible opportunity to develop key skills.If you are strong in leadership, critical thinking and have…
Experts Call for Better FDA Policing of Direct-to-Consumer Polygenic Risk Scores
NEW YORK—Experts have called for US Food and Drug Administration regulation of direct-to-consumer (DTC) tests that use a polygenic risk score (PRS) to estimate an individual’s disease risk. PRS are genome-wide measures of individuals’ genetic propensities for diseases that, combined with other lifestyle factors, can give a better idea of…
Bioinformatics Scientist – Baylor Genetics
SUMMARY: Bioinformatics scientist responsible for designing, developing, evaluating, maintaining, and optimizing genomic/genetic data, workflows, and tools, as well as visualizing and communicating key results to stakeholders. QUALIFICATIONS: Education: Master’s or higher degree in Bioinformatics, Computer Science or genetic/genomic relate biological Science and/with two (2) years of experience on genomic data…
A HiFi movement : Isoform-resolved cell atlases
Cellular cartography has been just as important for biologists to navigate the complex topography of living systems as was the mapping of the earth’s landscapes for explorers hundreds of years ago. While much has been learned about cellular identities and functions through gene expression analysis, one of the main drivers…
I tried to upload vcf of SV from HiFi CNV and pbsv into Franklin (by genoox)
I tried to upload vcf of SV from HiFi CNV and pbsv into Franklin (by genoox) 0 Hi I tried to upload vcf of SV from HiFi CNV and pbsv into Franklin (by genoox). For inherited disease family case, I used 1 file of merged vcf for SNV from Deeptrio,…
theta parameter file was not given
Strelka error: theta parameter file was not given 0 Hi guys, I’m trying to run strelka2 somatic workflow on my matched normal-tumor samples, but I keep running into the following error: [TaskManager] Launching command task: ‘CallGenome+callGenomeSegment_chromId_002_chr3_0015’ from sub-workflow ‘CallGenome’ [TaskRunner:CallGenome+callGenomeSegment_chromId_002_chr3_0015] Task initiated on local node [TaskManager] [ERROR] Failed to complete…
Principal Scientist I Bioinformatics job with F. Hoffmann-La Roche AG
The Position Roche Sequencing Solutions (RSS), a business within Roche Diagnostics, focused on developing a disruptive Next-Generation Sequencing (NGS) platform along with a portfolio of reagents, assays and informatics solutions for multiple disease areas. We are looking for a Principal Bioinformatics Scientist in the NGS Algorithms and Applications team to…
Senior Principal Bioinformatics Scientist, NGS Algorithms job with F. Hoffmann-La Roche AG
The Position Roche Sequencing Solutions (RSS), a business within Roche Diagnostics, focused on developing a disruptive Next-Generation Sequencing (NGS) platform along with a portfolio of reagents, assays and informatics solutions for multiple disease areas. We are looking for a Principal Bioinformatics Scientist in the NGS Algorithms and Applications team to…
Postdoc in single-cell cancer omics bioinformatics to Karolinska Institutet
Do you want to contribute to top quality medical research? Do you want to work in the exciting field of single-cell cancer genomics and contribute to improve our understanding of how tumors evolve to treat them more effectively? A postdoc position in single-cell cancer omics bioinformatics is immediately available in…
Proton and alpha radiation-induced mutational profiles in human cells
Determining proton and helium ion fraction, and irradiating the cell lines The dosage of radiation was determined experimentally in order to achieve between 40 and 50% lethality (corresponding to 50% to 60% clonogenic survival), independently across the two types of particle beams (Fig. 1a,b). Figure 1 Overview of the experimental design….
Senior Principal Scientist Bioinformatics job with F. Hoffmann-La Roche AG
The Position Roche Sequencing Solutions (RSS), a business within Roche Diagnostics, focused on developing a disruptive Next-Generation Sequencing (NGS) platform along with a portfolio of reagents, assays and informatics solutions for multiple disease areas. We are looking for a Principal Bioinformatics Scientist in the NGS Algorithms and Applications team to…
How to extract read counts at the mutation locations
I have a scDNAseq dataset having multiple FASTQ files for multiple single cells. samtools was used after aligning FASTQ files with BWA to hg19 reference to produce bam files. I have already identified 36 SNV mutation sites and I want to use mpileup to extract read counts (Total read count…
Why does Ensembl VEP provide HGVSg for some variants and not others?
Why does Ensembl VEP provide HGVSg for some variants and not others? 0 docker run \ -u 1000:1000 \ -v $HOME/vep_data:/data \ -v $HOME/vep_data:/.vep \ -v $PWD:/opt/foo ensemblorg/ensembl-vep \ vep \ -i /opt/foo/{input} \ -o /opt/foo/{output} \ –cache \ –force_overwrite \ –fork {threads} \ –format vcf \ –buffer_size 5000 \…
Cracking cancer: Using long-read RNA sequencing for cancer neoantigen discovery
When developing effective personalized immunotherapies, such as cancer vaccines, a pivotal factor lies in uncovering tumor neoantigens that can serve as crucial therapeutic targets. Traditionally, neoantigen discovery heavily relied on short-read sequencing technology, with a predominant focus on neoantigens resulting from single-nucleotide variants (SNVs). However, recent advancements have unveiled the…
Principal Scientist I Bioinformatics Job Opening in Santa Clara, CA at Roche Holdings Inc.
The Position Roche Sequencing Solutions (RSS), a business within Roche Diagnostics, focused on developing a disruptive Next-Generation Sequencing (NGS) platform along with a portfolio of reagents, assays and informatics solutions for multiple disease areas. We are looking for a Principal Bioinformatics Scientist in the NGS Algorithms and Applications team to…
Sequential intrahost evolution and onward transmission of SARS-CoV-2 variants
Emergence of a novel BA.1 sublineage through intrahost evolution We performed genomic analysis of serially collected nasopharyngeal (NP) and anterior nares (AN) samples from an immunocompromised patient (P1) with diffuse B-cell lymphoma and persistent SARS-CoV-2 Omicron BA.1 replication between December 2021 and March 2022. Over a 12-week period, we documented…
Characterization of metagenome-assembled genomes from the International Space Station | Microbiome
Metagenome-assembled bacterial genomes Out of the 42 ISS metagenomes submitted at NCBI, only PMA-treated metagenomes (n = 21) representing the viable/intact cells were used for generating bacterial MAGs. Characteristics of MAGs (n = 46) such as genome size (2.6 to 6.6 Mb), completeness, contamination percentage, the average mean coverage, number…
Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum
CRISPR editing of DNA polymerase δ To increase the genetic repertoire of P. falciparum parasites in culture, we aimed to generate parasites with impaired 3ʹ−5ʹ proof-reading activity from the catalytic subunit of DNA polymerase δ (PF3D7_1017000) in order to increase the level of basal spontaneous mutations, based on prior work…
JPM | Free Full-Text | Determination of the Duplicated CYP2D6 Allele Using Real-Time PCR Signal: An Alternative Approach
1. Introduction The Cytochrome P450 (CYP) superfamily of enzymes are involved in the metabolism of a range of xenobiotics and their evolution parallels the need for host protection against environmental and food-produced toxins [1,2]. One critically important member is the CYP2D6 hepatic enzyme owing to its involvement in the metabolism…
Splitting of VCF file of CSQ field in the INFO column to tabular format.
VCF file will be having seven fixed columns and INFO column. Chromosome, position, ID, ref, alt, qual, filter, and INFO column. This INFO column will be having the variant related information. In the INFO column CSQ field will be having multiple fields – 82 fields fixed with the delimeter “|”…
Generating variant read count matrix, total read count matrix and binary/ternary mutaion matrix for SNV from scDNAseq FASTQ files
Generating variant read count matrix, total read count matrix and binary/ternary mutaion matrix for SNV from scDNAseq FASTQ files 0 Leung et al., 2017 paper mentioned in Fig 1 data processing for CRC patients was sequenced as single cell for both SNV (with MDA WGA) and CNA (with DOP-PCR) parallelly….
Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater
Wastewater sample collection, RNA extraction, and sequencing Houston Water collected and provided weekly 24-hour time-weighted composite influent (raw wastewater) samples from 39 wastewater treatment plants (WWTPs) in Houston covering a service area of approximately 580 miles2 and serving over 2.3 million people. In total, 2637 samples were analyzed. Untreated wastewater…
Pre-test and post-test genetic counseling
Introduction The yield of genetic prenatal diagnosis has been notably improved by introducing whole genome chromosomal microarray (CMA) analysis, which is now recommended in all cases with structural anomalies,1 allowing an additional diagnostic yield as compared to karyotyping of up to 10%.2,3 Moreover, recent data suggest that the expected diagnostic…
Prevalence of BRCA homopolymeric indels in an ION Torrent-based tumour-to-germline testing workflow in high-grade ovarian carcinoma
Patients cohort Among consecutive patients who underwent BRCA tumour testing through ION Torrent-based sequencing between August 2017 and February 2022, we retrospectively selected 222 high-grade ovarian cancer (HGOC) patients with the following histological subtypes: 203 serous (HGSOC), seven endometrioid, five clear-cell and seven with mixed histotypes. Since NGS BRCA1/2 tumour…
Activation of the urotensin-II receptor by remdesivir induces cardiomyocyte dysfunction
Study design The overall goal of this study was to explore the molecular mechanisms of remdesivir-related cardiotoxicity in anti-COVID-19 therapy. We first performed the GPCR screening using major anti-COVID-19 drugs as ligands (n = 3 per GPCR). We validated the results of GPCR screening by concentration-response analysis and determined the EC50 and…
Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk
Development and benchmarking of MEGAnE Accurate variant genotyping is required for statistical genetics. To enable both discovery and accurate MEV genotyping from genomes studied using short reads, we developed a new bioinformatic tool, mobile element genotype analysis environment (MEGAnE; Supplementary Note). Compared to SVs resolved by long reads, MEGAnE discovers…
How do I use the new human pangenome reference to discover SNV and SV.
We are excited to announce a collection of new human reference genome sequences that reflect much more global diversity! t.co/a39cFG8dOu — Human Pangenome Reference Consortium (@HumanPangenome) May 10, 2023 My favorite T2T/Pangenome discovery so far: a multi-megabase inverted segmental duplication on the short arm of chr14 that explains the mechanism…
Principal scientist bioinformatics – Urgent Role at Roche in Washington DC
We are looking to hire a resourceful Principal scientist bioinformatics to join our incredible team at Roche in Washington DC.Growing your career as a Full Time Principal scientist bioinformatics is an incredible opportunity to develop excellent skills.If you are strong in presentation, adaptability and have the right mindset for the…
Evidence of international transmission of mobile colistin resistant monophasic Salmonella Typhimurium ST34
Three samples of S. 4,[5],12:i:-, all isolated in 2010, harbored mcr-3.1. Two were from human stool and the other was from ready-to-eat frozen food. Phenotypic characterization confirmed that all three isolates were resistant to colistin, all with MIC and MBC of 8 µg/ml. WGS of H1-012, H1-014 and H1-120 were analyzed…
Bioconductor – SICtools
DOI: 10.18129/B9.bioc.SICtools This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SICtools. Find SNV/Indel differences between two bam files with near relationship Bioconductor version: 3.12 This package is to find SNV/Indel differences between two bam files with near relationship in a way…
Convergent genomic diversity and novel BCAA metabolism in intrahepatic cholangiocarcinoma
Multi-omics analyses of the ICC samples Following multiregional sampling of primary ICC cases, we performed multi-omics analyses, including genome, transcriptome, proteome, and metabolome analysis. We used 10 (67 samples), 11 (88 samples), 10 (49 samples) and 10 (49 samples) ICC cases for WES, whole-transcriptome sequencing, proteomic analysis, and metabolomic analysis,…
What are the advantages of using the T2T as a reference vs GRCh38 today?
enter link description hereOnter, The advantages of (T2T) CHM13v2 over (GRC) GRCh38.p14 are myraid and extend into over a dozen fields. The second question you ask is a minor subset of that first, huge question. To date, even dedicated peer reviewed manuscripts on this subject have struggled to present all…
Roche hiring Principal Scientist II Bioinformatics in Mississauga, Ontario, Canada
The PositionRoche Sequencing Solutions (RSS), a business within Roche Diagnostics, focused on developing a disruptive Next-Generation Sequencing (NGS) platform along with a portfolio of reagents, assays and informatics solutions for multiple disease areas. We are looking for a Principal Bioinformatics Scientist in the NGS Algorithms and Applications team to support…
Anyone familiar with ICGC’s DCC data releases?
Anyone familiar with ICGC’s DCC data releases? 0 Hi all, As part of my project, I wanted to find recurrent somatic mutations in cancer, but not only coding regions, I want to assess the whole genome for noncoding somatic mutations -> Thus I need WGS data. My supervisor directed me…
Minimal residual disease monitoring in NSCLC
Background Cell-free DNA (cfDNA) refers to fragments of DNA released into the circulation by endothelial cells and white blood cells by active release or passively through apoptosis and necrosis.1,2 The fraction of cfDNA that originates from tumor is known as circulating tumor DNA (ctDNA). In 2016 the first commercial ctDNA…
Sanger Sequencing Market is expected to undergo a CAGR of 18.50%
Data Bridge Market Research analyses that the sanger sequencing market which was USD 1.92 billion in 2021, would rocket up to USD 7.47 billion by 2029, and is expected to undergo a CAGR of 18.50% during the forecast period 2022 to 2029. In addition to the market insights such as…
1000 genomes hg38 with dbSNP rsid
1000 genomes hg38 with dbSNP rsid 1 Hi, Anyone know where I can download the latest version of 1000 Genomes, on build hg38, in VCF format (or PLINK format), that ALSO contains the dbSNP RSid in the VCF ID field? I looked at the IGSR website, dbSNP, UCSC, etc. So…
using GRanges metadata to constrain overlap searches between objects
I have two sets of genomic data, one a list of SNPs and another a list of ChIP-seq-type peaks, each drawn from the same set of multiple samples. I’d like to be able to ask, for each sample, which SNPs overlap with the peaks in the same sample – and…
Cancer genomics and transcriptomics | EMBL-EBI Training
This course will focus on the analysis of data from genomic studies of cancer. It will also highlight the application of transcriptomic analysis and single-cell technologies in cancer. Talks and interactive sessions will give an insight into the bioinformatic concepts required to analyse such data, whilst practical sessions will enable…
The human story behind human genome sequencing
Hidden in the nuclei of your cells, DNA molecules lie tightly coiled, harbouring the genetic secrets that make you who you are. Thanks to advancements in clinical genomics, it is now possible to unravel your DNA’s code, allowing scientists to better understand and treat genetic conditions. What is a genome?…
Tecan and Oxford Nanopore build alliance to create automated, seamless and fully compatible nanopore sequencing library preparation for any-length fragments of native DNA/RNA
The Tecan Group and Oxford Nanopore Technologies plc (Oxford Nanopore) today announce their collaboration to drive easier high-throughput nanopore library preparation in an automated, hands-free fashion. The result is a fully walkaway automated workflow for Oxford Nanopore’s Ligation Sequencing Kit XL V14 protocol (LSK114) with Tecan’s DreamPrep® NGS solutions. The…
Do we have any disease specific SNVs database?
Do we have any disease specific SNVs database? 0 Hi, I have a general question. I was looking for some resources to bring some connection between SNVs and protein activity. I know that there are some softwares like ANNOVAR which can be used to prioritized the SNVs in terms of…
A CRISPR/Cas12a-assisted array for Helicobacter pylori DNA analysis in saliva
. 2023 Jan 25;1239:340736. doi: 10.1016/j.aca.2022.340736. Epub 2022 Dec 23. Affiliations Expand Affiliations 1 Department of Health Inspection and Quarantine, School of Public Health, Fujian Medical University, Fuzhou, Fujian, 350122, PR China. 2 College of Chemistry, Key Laboratory of Analysis and Detecting Technology, Food Safety MOE, Fuzhou University, Fuzhou, 350002,…
Genotyping approach to predict Coa and Cob antigens
Introduction The Colton (CO) blood group system (ISBT No. 015) currently consists of four antigens; a high prevalence antigen, Coa with its antithetical antigen, Cob, and the other high prevalence antigens, Co3 and Co4.1 The CO antigens are carried on red blood cell (RBC) water transporter, aquaporin-1 (AQP1), encoded by…
how to seperate VEP INFO column into seperate columns
I have a vcf files like below: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT treatmentSample chr1 857100 . C T 1756.06 PASS AC=2;AF=1;AN=2;DP=60;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=29.27;SOR=1.812;CSQ=chr1:857100|T|SNV|ENSG00000228794|ENST00000445118|LINC01128||1|MODIFIER|non_coding_transcript_exon_variant||||5/5|||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,60:60:99:1770,180,0 Does anyone know how to seperate INFO columns into different columns? And also how to separate treatmentSample column following the FORMAT ORDER? I…
Bridging biological cfDNA features and machine learning approaches: Trends in Genetics
Early detection (pancreatic cancer) cfMeDIP-seq, 5hmC sequencing LR elastic-net Hierarchical clustering, t-SNE, LR with elastic-net penalization Methylation (5mC-5hmC) 208 (72/136) 24-feature 5mC, 27-features 5hmC, 51-features combined model SML, UML Combined 5mC and 5hmC AUC of 0.997 (sensitivity 0.938, specificity 0.955) Median total reads: 17.4 M, 0.8 nonduplicate mapping rate pms.cd120.com/PDAC/index.html…
AGBT Sessions Shine Spotlight on Long-Read Sequencing
This story includes reporting by Huanjia Zhang. NEW YORK – As the reigning Nature Methods method of the year, long-read sequencing featured prominently in many of the talks at this year’s Advances in Genome Biology and Technology meeting, held in Hollywood, Florida, last week. Pacific Biosciences presented new data from…
The Carbon Footprint Impact of Cloud Solutions
Contributed Commentary by Mladen Lazarevic, Seven Bridges February 3, 2023 | Researchers turn to bioinformatics computing to analyze large datasets and tackle issues ranging from precision medicine solutions in oncology to novel drug therapies. This is especially true of genomic data and bioinformatics analysis. While those in the life sciences…
Study demonstrates intrahost MPXV variation within a single lesion
In a recent study published in Emerging Infectious Diseases, researchers reported on the clinical and molecular characteristics of monkeypox (MPX) virus (MPXV) infections in Finland. Study: Intrahost Monkeypox Virus Genome Variation in Patient with Early Infection, Finland, 2022. Image Credit: ART-ur/Shutterstock Background Ever since 2022, an unprecedented MPXV outbreak has…
A Solve-RD ClinVar-based reanalysis of 1,522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing
Purpose: Within the Solve-RD project (solve-rd.eu/), the ERN-ITHACA (European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies) aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for…
Hypersaline Lake Urmia: a potential hotspot for microbial genomic variation
Physico-chemical features of Lake Urmia Sampling was performed during the period of lowest rainfall and input volume in the year when the lake water reached the highest salt concentration (locations shown in Fig. 1, Supplementary Table S1). The measured ionic composition of the collected brine showed the typical composition of halite-dominated…
Detecting de novo SNV with vcftools
Detecting de novo SNV with vcftools 1 Hi, all. I have a raw whole genome sequence data of a kind of fish trio: father, mother and offspring. I would like to know how many SNV loci there are in the child but not in the parent (i.e. de novo SNV…
Senior Scientist Applied Bioinformatics Job In San Francisco, CA 94103| TechCareers
At Bristol Myers Squibb, we are inspired by a single vision – transforming patients’ lives through science. In oncology, hematology, immunology and cardiovascular disease – and one of the most diverse and promising pipelines in the industry – each of our passionate colleagues contribute to innovations that drive meaningful change….
BAM file and no RNAME or POS information? : bioinformatics
Newbie here. Please, play nice. I got possession of a set of 4 .bam files that stores the exome of an individual, around 400 MB each. I used samtools to generate a 2.4 GB .sam file out of one of the .bam files, and I found it contains lines with…
Table – PMC
PMC full text: Copyright/LicenseRequest permission to reuse This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. Summary of SNV class by matrix. Matrix Pinnable Variants…
Color hiring Software Engineer, Bioinformatics in Remote
About Color Color’s mission is to help people lead the healthiest lives that science and medicine can offer. We launched in April 2015 with a simple, affordable genetic test to help people understand their risk for hereditary cancer. In 2017, we added coverage for hereditary heart conditions. Between them, cancer…
Design and implementation of a novel pharmacogenetic assay for the identification of the CYP2D6*10 genetic variant | BMC Research Notes
Methods The study was conducted at the Human Genetics Unit, Faculty of Medicine, University of Colombo. It was an experimental study, where a novel assay was designed for the targeted variant, and a cohort of hormone receptor positive breast cancer patients were genotyped for the CYP2D6*10 variant using the optimized…
Comparison of CNV analysis methods: Array CGH vs NGS
Rare genetic disorders are caused by variants in major functional genes. Most are SNV or INDEL variants, but SVs, such as CNVs or chromosomal variants, can also be the cause. Recently, a large-scale study has also been published showing that CNVs were identified in 11-12% more infants and children with…
A genomic mutation spectrum of collecting duct carcinoma in the Chinese population
This article was originally published here BMC Med Genomics. 2022 Jan 3;15(1):1. doi: 10.1186/s12920-021-01143-2. ABSTRACT BACKGROUND: Renal collecting duct carcinoma (CDC) is a rare and lethal subtype of renal cell carcinoma (RCC). The genomic profile of the Chinese population with CDC remains unclear. In addition, clinical treatments are contradictory. In…
Systems biology analysis of human genomes points to key pathways conferring spina bifida risk
Significance Genetic investigations of most structural birth defects, including spina bifida (SB), congenital heart disease, and craniofacial anomalies, have been underpowered for genome-wide association studies because of their rarity, genetic heterogeneity, incomplete penetrance, and environmental influences. Our systems biology strategy to investigate SB predisposition controls for population stratification and avoids…
What is the single nucleotide polymorphism database ( dbsnp )?
The Single Nucleotide Polymorphism Database (dbSNP) is a free public archive for genetic variation within and across different species developed and hosted by the National Center for Biotechnology Information (NCBI) in collaboration with the National Human Genome Research Institute (NHGRI). Furthermore, are there any databases for single nucleotide polymorphisms?As there…
Reliability of Cell-Free DNA (cfDNA) Next Generation Sequencing in Predicting Chromosomal Structural Abnormalities and Cytogenetic-Risk Stratification of Patients with Myeloid Neoplasms
Oral and Poster Abstracts 617. Acute Myeloid Leukemias: Biomarkers, Molecular Markers and Minimal Residual Disease in Diagnosis and Prognosis: Poster III Translational Research Maher Albitar, MD1*, Andrew Ip, MD, MSc2, Andre H. Goy, MD3*, Jeffrey Justin Estella, BS, MS1*, Ivan De Dios, BS1*,…