Tag: SNV

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…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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*,…

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How to handle VCFs from the same sample but using different aligners and variant callers?

Hi, I’m using whole-exome sequencing (WES) for somatic variant calling. During the process, I tried to follow the approach described here: pubmed.ncbi.nlm.nih.gov/28420412/ Basically my workflow is as follows: FASTQ preprocessing: Using 2 aligners (BWA-MEM, Bowtie2) BAM calibration Variant calling: Using 3 software (Mutect2, Strelka2, Lancet) Variant filtering: I keep just…

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The Biostar Herald for Tuesday, September 21, 2021

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

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Phylogeographic reconstruction of the marbled crayfish origin

Procambarus fallax collections and PCR genotyping Animals were collected from various wild populations (Table S1) in compliance with state and local regulations (Georgia department of natural resources scientific collection permit 115621108, state of Florida collection permits S-19-10 and S-20-04). DNA was isolated from abdominal muscle tissue using SDS-based extraction and precipitation…

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Alternate nucleotide is more frequent than reference nucleotide. OMG I’m dizzy. How do I stop the twirl?

This is due to the fact that the very reference genomes that we use for re-alignment are themselves based on individuals who carry rare risk alleles. Thus, when we call variants against these genomes, we are, at many loci, comparing against rare disease risk alleles. As the best/worst example (depending…

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ZhaozzReal/SNV_IPA: Detect SNV-associated intronic polyadenylation events from standard RNAseq data

Description Somatic single nucleotide variants (SNVs) in cancer genome affect gene expression through various mechanisms depending on their genomic location. In this study, we found that somatic SNVs near splice site are associated with abnormal intronic polyadenylation (IPA) . Here we give examples to show how to detect SNV-associated IPA…

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Is it possible to detect of SNVs and InDels in low coverage WGS (5-10X) data?

Is it possible to detect of SNVs and InDels in low coverage WGS (5-10X) data? 2 Hello, the Biostar community, What I know about low coverage WGS (or shallow WGS) data is that it is an economic technique for genomic copy number detection in the realms of tumor diagnosis or…

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Gene mutation analysis in papillary thyroid carcinoma

Introduction Thyroid tumors are the most common malignant tumors of the endocrine system, and their incidence has been increasing in the recent decades. Currently, there are some target drugs that can effectively treat PTC, and next-generation sequencing (NGS) can be used for targeted therapy. In order to make better informed…

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Bioconductor – BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major

DOI: 10.18129/B9.bioc.BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major     Full genome sequences for Homo sapiens (UCSC version hg38, based on GRCh38.p12) with injected major alleles (dbSNP151) Bioconductor version: Release (3.13) Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with major allele injected from dbSNP151, and stored in Biostrings…

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Calculate the fraction of genome that is feature X

Calculate the fraction of genome that is feature X 2 I am trying to calculate enrichment of Structural variant breakpoints and SNV locations in genomic features (exon, intron, 5’UTR…) in a non-human genome. To know whether a feature is over/underrepresented in a SV/SNV dataset, I first need to know the…

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Dissecting Cancer with Single-cell DNA Sequencing & Multi-omics | Learning Center

CANCER & SINGLE-CELL ANALYSIS The heterogeneity and dynamism of cancer present formidable challenges to understanding and treating the disease. As discussed in the last section, tumor evolution often leads to considerable genetic variation across clones. But the complexity of tumors does not stop at the level of DNA. Intratumoral phenotypic…

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How to merge multiple patient’s vcf files (indel and snv) with different IDs?

How to merge multiple patient’s vcf files (indel and snv) with different IDs? 0 Hi all, I have some VCF files for my patients, each patient has 2 files( indel.vcf , snv.vcf) and I want to merge these file by the script bellow: java -jar gatk-package-4.2.0.0-local.jar MergeVcfs -I /PATH_TO_patient1_ID_indel.vcf -I…

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Need suggestions about pathogenicity prediction of gdc level 3 SNV file

Hi, I am trying to figure out which tool is most accurate in terms of pathogenicity prediction of TCGA SNVs level 3 data. TCGA offers SIFT, PolyPhen, and IMPACT scores for different kinds of mutations. SIFT, and PolyPhen cover mainly “Missense Mutation”, while IMPACT categorizes every kind of mutation into…

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Change chromosome notation in dbSNP VCF file

Change chromosome notation in dbSNP VCF file 0 Hiii, I have downloaded dbSNP VCf file from [ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/] The format is as follows: #CHROM POS ID REF ALT QUAL FILTER INFO 1 10019 rs775809821 TA T . . RS=775809821;RSPOS=10020;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000020005000002000200;GENEINFO=DDX11L1:100287102;WGT=1;VC=DIV;R5;ASP 1 10039 rs978760828 A C . . RS=978760828;RSPOS=10039;dbSNPBuildID=150;SSR=0;SAO=0;VP=0x050000020005000002000100;GENEINFO=DDX11L1:100287102;WGT=1;VC=SNV;R5;ASP 1 10043 rs1008829651 T…

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Parsing snp result

Parsing snp result 1 I am trying to parse dbSNP results into data frame in python, I got the result as “bytes” and I wonder if there is a way to parse it into dataframe. I tried multiple xml packages (xml, lxml) but they are not able to separate the…

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