Tag: gnomAD

AWS launches Amazon Omics for precision medicine

To enhance clinical insights at the point of care and help identify the best treatment or prevention options for patients, Amazon Web Services has launched a service that utilizes artificial intelligence (AI), machine learning, and other AWS and partner products and services to run IT-heavy bioinformatics workflows.  WHY IT MATTERS…

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Datasets | TogoVar

Variant frequencies for which you can apply for use of individual-level data∗1 to the NBDC human databases∗2 Click the links at the Included controlled-access datasets to apply for use of individual-level data ∗1:fastq/bam/cel files and/or lists of genotype data etc.∗2:Japanese Genotype-phenotype Archive (JGA) / AMED Genome group sharing Database (AGD)…

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Genome-wide identification of disease-causing copy number variations in 450 individuals with anorectal malformations

CNV analysis After the application of quality filter step I (gender mismatch), two patients were excluded. Through step II (call rate <98%), 40 patients were discarded and after step III (exceeded double of standard deviation), 12 more patients were excluded. In the remaining 396 individuals with ARM, a total of…

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Bioconductor – MafH5.gnomAD.v3.1.1.GRCh38 (development version)

DOI: 10.18129/B9.bioc.MafH5.gnomAD.v3.1.1.GRCh38     This is the development version of MafH5.gnomAD.v3.1.1.GRCh38; for the stable release version, see MafH5.gnomAD.v3.1.1.GRCh38. Minor allele frequency data from gnomAD version 3.1.1 for GRCh38 Bioconductor version: Development (3.16) Store minor allele frequency data from the Genome Aggregation Database (gnomAD version 3.1.1) for the human genome version…

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Human hg38 chr7:73,678,750-73,740,129 UCSC Genome Browser v435

Use drop-down controls below and press refresh to alter tracks displayed.Tracks with lots of items will automatically be displayed in more compact modes.    Custom Tracks H3K27ac Meta NeuN SCZhidedensesquishpackfull H3K27ac NeuN SCZ del_CRDhidedensesquishpackfull H3K27ac NeuN SCZ del_CRD_del_peakshidedensesquishpackfull H3K27ac Tissuehidedensesquishpackfull H3K27ac Tissue BDhidedensesquishpackfull H3K27ac Tissue BD del_CRDhidedensesquishpackfull H3K27ac Tissue BD…

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iPSCs derived from infertile men carrying complex genetic abnormalities can generate primordial germ-like cells

Patients and controls The patient 1 was 38 years old and consulted for infertility after he and his partner had been trying to conceive for 2 years. The patient was the first child of unrelated parents, and he had four brothers and five sisters whose fertility status could not be determined…

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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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Samtools Htslib Issues

Issue Title State Comments Created Date Updated Date How to get a specific chromosome open 1 2022-07-14 2022-07-18 tabix returns row from VCF file multiple times open 4 2022-07-11 2022-07-18 Modified base parsing failure failure closed 0 2022-07-01 2022-07-18 extract genotype information open 1 2022-06-24 2022-07-18 sam_hdr_remove_lines is inefficient if…

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Annotating with CADD, gnomad, Clinvar & dbNSFP on UKB RAP – Feature Requests

dint May 9, 2022, 1:33pm #1 i’m just wondering if you can specify cadd, gnomad, clinvar and dbNSFP options when annotating with hail on dxjupyterlab_spark_cluster o the UKB RAP? From the hail website, the following command can be used on your matrix file to annotate with these features: db =…

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VCV000038126.28 Observations – ClinVar – NCBI

1 SCV000301220.2 Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) Pathogenic reviewed by expert panel curation Breast-ovarian cancer, familial, susceptibility to, 2 (unknown ) germline Variant allele predicted to encode a truncated non-functional protein. 1 SCV000785901.2 Counsyl Pathogenic criteria provided,single submitter clinical testing Breast-ovarian cancer, familial, susceptibility to,…

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Polygenic Risk Score Performance Improved With Expression-Related Rare Variant Insights

NEW YORK – A team from Stanford University and other centers in the US and China have demonstrated that polygenic risk scores (PRS) based on common variants can be bolstered by incorporating clues from rare variants linked to significant gene expression shifts, dubbed expression outliers. “As individual PRS estimates are…

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Obtain equivalent variant ids (chr-pos-ref-alt) for GRCh37 and GRCh38

Obtain equivalent variant ids (chr-pos-ref-alt) for GRCh37 and GRCh38 0 Hi all, I want to obtain the equivalent variant id (chr-pos-ref-alt) from GRCh38 in GRCh37. This is to deal with some variants poorly lifted over. To exemplify, see the variant gnomad.broadinstitute.org/variant/10-17838942-A-G?dataset=gnomad_r3 It has two equivalents in GRCh37. I want to…

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Genetic and chemotherapeutic influences on germline hypermutation

DNM filtering in 100,000 Genomes Project We analysed DNMs called in 13,949 parent–offspring trios from 12,609 families from the rare disease programme of the 100,000 Genomes Project. The rare disease cohort includes individuals with a wide array of diseases, including neurodevelopmental disorders, cardiovascular disorders, renal and urinary tract disorders, ophthalmological…

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Bioinformatics Data Engineer in Boston, MA for Dana-Farber Cancer Institute

Details Posted: 27-Apr-22 Location: Boston, Massachusetts Salary: Open Categories: Staff/Administrative Internal Number: 2022-26005 Located in Boston and the surrounding communities, Dana-Farber Cancer Institute (DFCI) brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people…

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Bioinformatics Analyst II – Remote in Danville, PA for Geisinger

Details Posted: 22-Apr-22 Location: Danville, Pennsylvania Type: Full Time Salary: Open Categories: Operations Job Summary Primary accountability is to leverage the organization’s data assets exome sequencing data (>180,000 individuals) from MyCode Community Health Initiative to improve quality, efficiency and generate knowledge specifically in the field of bioinformatics within health research….

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Where are the GnoMAD gnomes in Darksiders 2?

Darksiders II Darksiders II is an action role-playing hack and slash action-adventure video game developed by Vigil Games and published by THQ. It is the sequel to Darksiders and was released in August 2012 for Microsoft Windows, PlayStation 3, Xbox 360 and as a launch title for Wii U upon…

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subpopulations available in MafH5.gnomAD.v3.1.1.GRCh38

subpopulations available in MafH5.gnomAD.v3.1.1.GRCh38 1 @b14a6f0d Last seen 16 hours ago United States Are subpopulation MAFs available for gnomADv.3.1.1 with any package, like they are in MafDb.gnomAD.r2.1.hs37d5? I’m trying to use Genomic Scores to obtain all variants in a genomic range with MAF in any subpopulation >= cutoff. I tried…

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bedtools -u not giving unique files

bedtools -u not giving unique files 1 The following are the steps Im following: First step to extract sample using bed file is this (here the bedfile is input bedfile converted to Hg38): tabix -h -R Hg19_to_Hg38_sorted.bed.gz gnomad.genomes.v{g_version}.hgdp_tgp.chr{chr}.vcf.bgz | perl {vcftools} -c {sample_name} > {sample_name}_out.vcf’ output({sample_name}_out.vcf’) chr2 113982416 rs56177103 TATAAAATAAAATAAA…

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Today is about raising awareness about rare diseases

Aisha, a migrant from Guinea, plays with her baby daughter at a park in the Tunisian town of Medenine – Copyright AFP/File GIANLUIGI GUERCIA Today is Rare Disease Day, which is the globally coordinated movement on rare diseases, working towards equity in social opportunity, healthcare, and access to diagnosis and…

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rs532111960 RefSNP Report – dbSNP

Help Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When…

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rs9789283 RefSNP Report – dbSNP

Help Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When…

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Ensembl VEP gnomAD annotated allele frequencies different from gnomAD browser

I’ve annotated some variants using VEP, and was looking at the minor allele frequencies. Some of the variants had very different MAFs in the annotation than I expected (I expected MAF < 1%, whereas some annotated MAFs were >50%). I looked up the same variants on the gnomAD v3 browser,…

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Mitochondrial DNA variation across 56,434 individuals in gnomAD

Genomic databases of allele frequency are extremely helpful for evaluating clinical variants of unknown significance; however, until now, databases such as the Genome Aggregation Database (gnomAD) have focused on nuclear DNA and have ignored the mitochondrial genome (mtDNA). Here we present a pipeline to call mtDNA variants that addresses three…

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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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New resource tracks genetic variations in Han Chinese populations | Spectrum

Yongyuan Dai / Getty Images Researchers in China have cataloged genetic variations among nearly 3,000 Chinese people and constructed a comprehensive new reference genome for this population. The resource, which is called NyuWa and is freely available online, could help researchers discern the effects of genetic variants found in…

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Ethnic Diversity of DPD activity and the DPYD Gene

Plain Language Summary Fluoropyrimidine (FP; 5-FU, capecitabine) is a common chemotherapy used to treat many different cancers, including cancer of the colon and rectum, upper digestive tract, breast and head and neck. Cancer patients who receive FP chemotherapy are at risk of developing severe side effects from their treatment. A…

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Filtering of rare variants

Filtering of rare variants 1 Hello I have exome datasets from 6 samples, in which four are affected and two are non-affected. I did joint call genotyping for all the six samples and annotated the vcf file. From this annotated vcf file, I have to look for rare variants shared…

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gnomAD v3 link not working for download

gnomAD v3 link not working for download 1 your URL is wrong. $ wget -q -O – “https://storage.googleapis.com/gcp-public-data–gnomad/release/3.1.1/vcf/genomes/gnomad.genomes.v3.1.1.sites.chr1.vcf.bgz” | gunzip -c | head ##fileformat=VCFv4.2 ##hailversion=0.2.64-1ef70187dc78 ##FILTER=<ID=AC0,Description=”Allele count is zero after filtering out low-confidence genotypes (GQ < 20; DP < 10; and AB < 0.2 for het calls)”> ##FILTER=<ID=AS_VQSR,Description=”Failed VQSR filtering…

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rosetta fold vs alphafold 2

S. Both AlphaFold and Xu use simple folding engines L-BFGS (L- Broyden–Fletcher–Goldfarb– Shanno (BFGS)) and CNS (Crystallography and NMR System), respectively, i.e., improvements come from a better energy potential using distributional information. The phase problem is a problem, to the point that in the past decade, several structures, such as M-PMV…

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mixing hg38 and GRCh38 during variant calling

mixing hg38 and GRCh38 during variant calling 0 Hello everyone! I’ve been working on a variant calling pipeline for WES data and used a mix of hg38 and GRCh38 reference files after reading that hg38 is just an abbreviation of GRCh38, and that they refer to the same thing. But…

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gnomADc plugin instructions not working for VEP

Hi, I have installed VEP for offline use and I am trying to download the data for the gnomADc plugin. The instructions from VEP are as follows; genomes=”storage.googleapis.com/gnomad-public/release/3.0/coverage/genomes” genome_coverage_tsv=”gnomad.genomes.r3.0.coverage.summary.tsv.bgz” wget “${genomes}/${genome_coverage_tsv}” zcat “${genome_coverage_tsv}” | sed -e ‘1s/^locus/#chromtpos/; s/:/t/’ | bgzip > gnomADc.gz tabix -s 1 -b 2 -e 2 gnomADc.gz…

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Import VCF from GnomAD

Import VCF from GnomAD 1 Hi all, new to bioinformatics and have what I think is a pretty basic question. I’m attempting to use hail to import a vcf file from the gnomad website (gnomad.broadinstitute.org/downloads). I’ve successfully created a python session in the terminal and loaded hail, now just trying…

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How to calculate popmax values for gnomAD variants?

How to calculate popmax values for gnomAD variants? 0 I’m trying to use the gnomAD data to build a noise filter. We want to filter variants from our .vcf’s that have a popmax value greater than a certain threshold, but I’m having trouble figuring out how to calculate popmax. We’ve…

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Allele frequency for genes

Allele frequency for genes 0 Hello All, Where can i find allele frequency cut offs (or upper and lower range) for all the genes (for all the types of variants) to call variants polymorphic or rare in nature? Thank you for your time frequency gnomAD gene allele • 88 views…

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Annotate Structural variants with population specific allele frequency values

Annotate Structural variants with population specific allele frequency values 0 Hi, Has anyone tried filtering structural variants based on pupulation specific allele frequency (AF) values (for example gnomAD-SV or phase 3 1000 genome SV)? I have a set of SVs that I detected using a multipronged approach. For prioritising variants,…

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Bioinformatics Analyst II in Danville, PA for Geisinger

Job Summary Primary accountability is to leverage the organization’s data assets exome sequencing data (>180,000 individuals) from MyCode Community Health Initiative to improve quality, efficiency and generate knowledge specifically in the field of bioinformatics within health research. Performs and supervises complex data extraction, transformation, visualization, and summarization to support Research…

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Can someone explain the differences between various 1000 genome project and gnomad call sets? Also any straightforward PCA implementation on them?

I’ve been trying to delve into the data from whole genome sequencing, specifically by looking at the already existing data in the 1000 genome project and gnomad, and I have a lot of questions. Does gnomAD contain the 1000gp samples? I’ve found many vcf including these: ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/hd_genotype_chip/ ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/ ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/ gnomad.broadinstitute.org/downloads…

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