Tag: LoF

An FGFR2 mutation as the potential cause of a new phenotype including early-onset osteoporosis and bone fractures: a case report | BMC Medical Genomics

Anamnesis vitae A 13 year old male born was as result of the VII pregnancy, from unrelated parents. Other pregnancies resulted in: I-II silent miscarriage in the second trimester; III – female, born in 2003 (III-3 Fig. 1) that has the following phenotypic features: genu valgum, hip dysplasia, combined thoracolumbar scoliosis,…

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r – How to keep ggplot x axis order when plotting with colour?

This question already has answers here: Closed 26 mins ago. Given a matrix mat with a column “rplau”, how to ensure ggplot keeps the same order as the factors / colour are considered as string? For instance, when plotting, I’d like 928:1852 to follow after 1:927. How to do that?…

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Groundbreaking ‘Gnocchi’ map reveals hidden secrets of the human genome

In a recent study published in Nature, researchers in the United  States aggregated and processed 76,156 human genomes to construct a genomic constraint map named “genomic non-coding constraint of haploinsufficient variation” (Gnocchi) for the whole genome. They found that non-coding constrained regions in the genome were rich in known regulatory…

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Map of disease-causing mutations in neurodevelopmental disorders and cancer revealed

Experimental design overview. a Two independent sgRNAs and associated HDR variant libraries are designed at the 5′ and 3′ end of each exon. b The sgRNA, together with the HDR template library are transfected into LIG4-KO Cas9-expressing HAP1 cells. HDR utilizes the library as a template for repair of the…

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Does GNOMAD use all LOFTEE LoF filters?

Does GNOMAD use all LOFTEE LoF filters? 0 Hi all, I have some lof variants and I want to know if they have already been detected in GNOMAD (I am essentially curious if my lof variants are novel). In order to make this comparison to GNOMAD I have run my…

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Loftee no splice site annotations

Loftee no splice site annotations 1 Hello! I am using Loftee in my VEP pipeline and after some fights with my code everything works now, but the splice site annotations…meaning that I dont get them. There is no error at all, but my vcf files do not contain a single…

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Where do these snpeff annotation come from?

Where do these snpeff annotation come from? 0 I am annotating a VCF with annotation from snpeff, which I want to use eventually to parse for predicted loss of function variants I want to understand the annotation better and document how they are happening. I run this command: snpEff “hg38″…

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Most large structural variants in cancer genomes can be detected without long reads

JaBbA v1 outperforms previous CN algorithms We enhanced our previous JaBbA (v0.1; ref. 4) model with several methodological innovations to increase robustness to read depth waviness, improve algorithm convergence and enforce junction balance for allele-specific as well as total CN (Extended Data Fig. 1a–d and Methods). We also rigorously defined…

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How to make 4-column annotation file

How to make 4-column annotation file 1 Hi everyone, I’ve been following regenie to perform analyses. In its 2nd step a 4-column annotation file is needed. The format is 1:55039839:T:C PCSK9 LoF 1:55039842:G:A PCSK9 missense According to snpEFF documentation, its output is in vcf format, which I think might be…

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Orthogonal Validation: A Means To Strengthen Gene Editing and Gene Modulation Research

From RNA interference (RNAi) to CRISPR, there are several methods that researchers can use to manipulate gene function, each with its own strengths and weaknesses. Orthogonal validation – the synergistic use of different methods – makes genetic perturbation studies more robust. Utilizing complementary methods, including RNAi and CRISPR-knockout, -interference and…

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The genomic footprint of whaling and isolation in fin whale populations

Samples and sequencing Tissue samples from 50 fin whales (Balaenoptera physalus) were collected using a standard protocol to obtain skin biopsies from free-ranging cetacean species, which use a small stainless-steel biopsy dart deployed from a crossbow or rifle73,74. These samples were collected throughout the Eastern North Pacific (ENP; N = 30, represented…

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Nuclear genetic control of mtDNA copy number and heteroplasmy in humans

Overview of mtSwirl Here we develop mtSwirl, a scalable pipeline for mtCN and variant calling which makes calls relative to an internally generated per-sample consensus sequence before mapping all calls back to GRCh38. In addition to GRCh38 reference files and WGS data, the mtSwirl pipeline takes as input nuclear genome…

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Reply to: Re-evaluating evidence for adaptive mutation rate variation

replying to L. Wang et al. Nature doi.org/10.1038/s41586-023-06314-y (2023) Wang and colleagues1 argue that our report2 of lower mutation rates in gene bodies, essential genes and regions marked by H3K4me1 must result from DNA sequencing errors. We appreciate the issues raised by them and by other colleagues3. Although we overlooked…

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reference annotation for the human and mouse genomes in 2023

D942–D949 Nucleic Acids Research, 2023, Vol. 51, Database issue Published online 24 November 2022 doi.org/10.1093/nar/gkac1071 GENCODE: reference annotation for the human and mouse genomes in 2023 Adam Frankish 1,* , Sı́lvia Carbonell-Sala2 , Mark Diekhans 3 , Irwin Jungreis 4,5 , Jane E. Loveland 1 , Jonathan M. Mudge1 ,…

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Warning in 1st line in SnpEff files

Hello, I’ve got VCF files that I wish to annotate with SnpEff and then use SnpSift to add further annotations such as dbSNP, GWASCatalog, ClinVar, etc. I run SnpEff by typing the following command java -Xmx8g -jar snpEff.jar hg19 -chr -lof -hgvs -geneID -sequenceOntology -canon -csvStats sample_001.csv -stats sample_001.html input_001.vcf…

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PLSCR1 identified as a potent anti-SARS-CoV-2 factor in COVID-19 immunity

In a recent study published in Nature, researchers identified the anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) function of phospholipid scramblase 1 (PLSCR1), a cell-autonomous restriction factor induced by interferon-gamma (IFNγ). Its identification will help enhance the understanding of protective immunity in the human IFN response. The study used genome-wide…

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Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank

Ethics statement This study relied on analyses of genetic data from the UKB cohort, which was collected with informed consent obtained from all participants. Data for this study were obtained under the UKB applications licence number 66995. All data used in this research are publicly available to registered researchers through…

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The impact of rare protein coding genetic variation on adult cognitive function

The UKB is approved by the North West Multi-centre Research Ethics Committee (www.ukbiobank.ac.uk/learn-more-about-uk-biobank/about-us/ethics). The current study was conducted under UKB application no. 26041. The data in the UKB were collected after written informed consent was obtained from all participants. The Human Research Committee of the MGB approved the Biobank research…

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Reconstruction of the personal information from human genome reads in gut metagenome sequencing data –

Topic participation The examine protocol was accredited by the ethics committees of Osaka College and associated medical establishments in addition to the Translational Well being Science and Know-how Institute (Faridabad). Japanese people (n = 343) for whom intestine metagenome shotgun sequencing had been carried out in earlier research had been included on…

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Reconstruction of the personal information from human genome reads in gut metagenome sequencing data

Subject participation The study protocol was approved by the ethics committees of Osaka University and related medical institutions as well as the Translational Health Science and Technology Institute (Faridabad). Japanese individuals (n = 343) for whom gut metagenome shotgun sequencing were performed in previous studies were included in this study46,47,48. Among these…

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GENCODE – Mouse Release M32 Statistics

Statistics about the GENCODE Release M32 The statistics derive from the gtf file that contains only the annotation of the main chromosomes. For details about the calculation of these statistics please see the README_stats.txt file. General stats Total No of Genes 56953 Protein-coding genes 21565 – readthrough genes (not included)…

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Solved Step 0: Clean Data Obtain data from Kaggle G. Remove

Transcribed image text: Step 0: Clean Data Obtain data from Kaggle G​. Remove all duplicates. For the attribute “class”, change 0 to -1 so that -1 represents normal and +1 represents fraud. After this, the resulting dataset should contain 473 fraud and 283253 normal transactions. Step 1: Scale Time \&…

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The info column of raw-snps-filtered.ann.vcf file showing more than one gene for a single position of RNA editing sites.

The info column of raw-snps-filtered.ann.vcf file showing more than one gene for a single position of RNA editing sites. 1 Hi All, I am first time trying to identify the RNA editing sites from (A TO I )changes.I have used GATK pipeline and at the very end when I have…

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Detection of biallelic loss of DNA repair genes in formalin-fixed, paraffin-embedded tumor samples using a novel tumor-only sequencing panel

Brown JS O’Carrigan B Jackson SP Yap TA Targeting DNA Repair in Cancer: Beyond PARP Inhibitors. Cancer Discov. 2017; 7: 20-37 Farmer H McCabe N Lord CJ Tutt AN Johnson DA Richardson TB Santarosa M Dillon KJ Hickson I Knights C Martin NM Jackson SP Smith GC Ashworth A Targeting…

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anomaly detection machine learning kaggle

What is Anomaly Detection? Anomaly detection, also known as outlier detection or novelty detection, is a method of identifying uncommon events, or data points that don’t conform to the expected pattern in a dataset. Anomaly detection is used in a wide range of applications, such as networking and security-related areas,…

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Whole-genome CRISPR activation for the identification of host factors controlling cellular interactions with SARS-CoV-2

In a recent study published in the PLOS Biology, researchers found that leucine-rich repeat-containing protein 15 (LRRC15), a toll-like receptor (TLR)-related cell surface receptor, blocked severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) binding. Study: Fibroblast-expressed LRRC15 is a receptor for SARS-CoV-2 spike and controls antiviral and antifibrotic transcriptional…

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The role of heteroplasmic mitochondrial DNA mutations on tumorigenesis and metabolism

The electron transport chain (ETC) activity in mammalian cells is necessary for survival and proliferation. The ETC is composed of ~100 subunits mostly encoded in the nuclear genome, but 13 essential subunits are in the mitochondrial genome (mtDNA). Accumulation of mutations in the mtDNA can lead to severe genetic defects…

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Basic research opens up new therapeutic opportunities for fighting leukemia

Genome-wide CRISPR/Cas9-based loss-of-function screen identifies genetic dependencies of STAT3Y640F-driven cells a) Schematic illustration of a competitive proliferation assay. b) Competitive proliferation assays of clonal Cas9-expressing STATY640F-driven HPC7 or c) clonal Cas9-HPC7 empty vector cells expressing IRF670 and sgRNAs targeting either Myb (positive control) or the Rosa26 locus (negative control). d)…

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GENCODE – Mouse Release M31 Statistics

Statistics about the GENCODE Release M31 The statistics derive from the gtf file that contains only the annotation of the main chromosomes. For details about the calculation of these statistics please see the README_stats.txt file. General stats Total No of Genes 56923 Protein-coding genes 21657 – readthrough genes (not included)…

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Availability of information on genes in Gnomad VCF data

Availability of information on genes in Gnomad VCF data 1 Hi , Im new to gnomad and genetics in general and i was wondering does the gnomad genome data that is downlaoded in the vcf format on variants contains information of what is the nearest gene and is the genomic…

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Natural variants of human SARM1 cause both intrinsic and dominant loss-of-function influencing axon survival

Selection of naturally occurring human SARM1 variants with potential for LoF We hypothesised that naturally occurring SARM1 coding variation that confers LoF exists in the general human population. Previous studies have shown that disruption of the SAM multimerization domains or catalytic TIR domain of SARM1 is more likely to cause…

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A Guide for Optimizing Arrayed CRISPR Screens

Loss-of-function (LOF) screens measure the phenotypic effects of gene disruptions, which helps researchers identify and validate gene targets for drug discovery. CRISPR-Cas9 technology has enabled great advances in LOF screening. While researchers typically use pooled CRISPR screens to assess fitness phenotypes, arrayed screens are amenable to a variety of functional…

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Loss of gene linked to differences in brain size

The work, from the Wellcome Sanger Institute, the French Institute of Health and Medical Research (Inserm), the University of Bourgogne Franche-Comté, and Beijing Genomics Institute (BGI)-Shenzhen, found that when there was a loss-of-function mutation in the mouse gene Magee2, it led to adult male mice having slightly enlarged brains. When…

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Inquiry related to vcf file and formatting

Hello everyone, I am trying to run predixcan software. But its showing error as segmentation fault implying that there is something wrong with my vcf files. I am sharing the header of vcf file. ##fileformat=VCFv4.1 ##INFO=<ID=LDAF,Number=1,Type=Float,Description=”MLE Allele Frequency Accounting for LD”> ##INFO=<ID=AVGPOST,Number=1,Type=Float,Description=”Average posterior probability from MaCH/Thunder”> ##INFO=<ID=RSQ,Number=1,Type=Float,Description=”Genotype imputation quality from…

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