Tag: gnomAD

gnomad api

gnomad api 0 I have installed the source code for gnomad api from broadinstitute.github.io/gnomad_methods/#gnomad. I would like to run the utils.constraint in that package and then use compute_pli to calculate pLi score for the set of genes I have just like how it shows for individual genes in the online…

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Randomized phase II study of preoperative afatinib in untreated head and neck cancers: predictive and pharmacodynamic biomarkers of activity

Study objectives and endpoints The main objective consisted in identifying predictive biomarkers of efficacy by exploring correlation between baseline potential biomarkers and radiological and metabolic responses to afatinib. Secondary objectives were to identify potential pharmacodynamic biomarkers, to evaluate the efficacy and safety of afatinib and to assess the metabolic and…

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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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Convert bed file from hg19 to GRCH38

Convert bed file from hg19 to GRCH38 1 Hello everyone! I have a list of over 500,000 rs and I would like to obtain the coordinates (BED file) on the GRCH38 reference genome. I am using the UCSC Table Browser tool, but unfortunately, it doesn’t find 90,000 rs, and since…

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Study uncovers vast genomic diversity in Aboriginal Australian communities

In a recent study published in the journal Nature, researchers investigated the previously underrepresented genomic diversity of four Aboriginal Australian communities. They used population-scale whole-genome (WGS) long-read sequencing. Study findings revealed unique alleles comprised of insertion-deletion variants, variable copy number regions, and structural variants, 62% of which are novel to…

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The landscape of genomic structural variation in Indigenous Australians

Cohorts Saliva and/or blood samples were collected from consenting individuals among four NCIG-partnered communities: Tiwi Islands (comprising the Wurrumiyanga, Pirlangimpi and Millikapiti communities), Galiwin’ku, Titjikala and Yarrabah, between 2015 and 2019. Non-Indigenous comparison data, generated from unrelated Australian individuals of European ancestry, was drawn from two existing biomedical research cohorts:…

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Advancements in Genome Sequencing Unveil Unexplored Non-Coding Regions

A recent study published in Nature demonstrates the potential of genomic sequencing in exploring non-coding regions of the genome. Until now, the focus has primarily been on coding regions that make up a small percentage of the genome. However, researchers have recognized the importance of non-coding regions in complex human…

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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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Large-scale DNA sequence resource reveals new regions of the human genome under natural selection

BOSTON – Every human’s genome has millions of genetic variants, but most have little to no effect, making it difficult for clinicians to make medical diagnoses based on genetic differences. Using patterns of variation from tens of thousands of individuals with whole-genome sequence data, a team led by investigators at…

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Researchers develop approach to study rare gene variant pairs that contribute to disease

BOSTON – Each gene in the human genome has two copies. When researchers detect two mutations within a particular gene in a patient’s genome, it can be difficult or expensive to determine if those two mutations are present in the same copy of the gene (“in cis”) or different copies…

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Human hg38 chr6:31,165,200-31,165,800 UCSC Genome Browser v457

     Custom Tracks ac4C-RIP-seq peaks, hESC CTL-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC CTL-2hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-2hidedensesquishpackfull    Mapping and Sequencing Base Positionhidedensefull p14 Fix Patcheshidedensesquishpackfull p14 Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19…

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A genomic mutational constraint map using variation in 76,156 human genomes

Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Siwei Chen, Laurent C. Francioli, Julia K. Goodrich, Ryan L. Collins, Masahiro Kanai, Qingbo Wang, Jessica Alföldi, Nicholas A. Watts, Christopher Vittal, Timothy Poterba, Michael W. Wilson, Yekaterina Tarasova, William Phu, Riley Grant, Mary T. Yohannes, Namrata Gupta, Irina M. Armean, Samantha M. Baxter, Sarah E. Calvo, Katherine R. Chao, Sinéad Chapman, Beryl B. Cummings, Phil Darnowsky, Patrick…

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Genomics England hiring PhD Bioinformatics Intern in London, England, United Kingdom

Company DescriptionGenomics England partners with the NHS to provide whole genome sequencing diagnostics. We also equip researchers to find the causes of disease and develop new treatments – with patients and participants at the heart of it all. Our mission is to continue refining, scaling, and evolving our ability to…

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PhD Bioinformatics Intern Job in Greater London, Pharmaceuticals & Life Sciences Career, Intern/Graduate Jobs in Genomics England

Company Description Genomics England partners with the NHS to provide whole genome sequencing diagnostics. We also equip researchers to find the causes of disease and develop new treatments – with patients and participants at the heart of it all. Our mission is to continue refining, scaling, and evolving our…

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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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Identification of constrained sequence elements across 239 primate genomes

De novo assembly and repeat-masking To maximize the species diversity of primates in our analyses, we newly sequenced and assembled the genomes of 187 different primate species, initially presented in refs. 11,23, for which no other reference genome assembly was available. In brief, each individual was sequenced with 150 bp paired…

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GATK Mutect2 mouse dbSNP vcf files recommendations for mouse whole exome data

GATK Mutect2 mouse dbSNP vcf files recommendations for mouse whole exome data 0 Dear all, Is there any best practice for the mouse snp indel vcf files using GATK Mutect2 for mouse whole exome data? For mm10, it seems have several available, for mm39, it seems the newest is from…

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Exome-wide benchmark of difficult-to-sequence regions using short-read next-generation dna sequencing

doi: 10.1093/nar/gkad1140. Online ahead of print. Atsushi Hijikata  1 , Mikita Suyama  2 , Shingo Kikugawa  3 , Ryo Matoba  3 , Takuya Naruto  4 , Yumi Enomoto  4 , Kenji Kurosawa  4   5 , Naoki Harada  6 , Kumiko Yanagi  7 , Tadashi Kaname  7 , Keisuke Miyako  8 , Masaki Takazawa  8 , Hideo Sasai  8   9 , Junichi…

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EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2023 | Nucleic Acids Research

Abstract The European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) is one of the world’s leading sources of public biomolecular data. Based at the Wellcome Genome Campus in Hinxton, UK, EMBL-EBI is one of six sites of the European Molecular Biology Laboratory (EMBL), Europe’s only intergovernmental life sciences organisation. This…

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Functional filter for whole-genome sequencing data identifies HHT and stress-associated non-coding SMAD4 polyadenylation site variants >5 kb from coding DNA

Summary Despite whole-genome sequencing (WGS), many cases of single-gene disorders remain unsolved, impeding diagnosis and preventative care for people whose disease-causing variants escape detection. Since early WGS data analytic steps prioritize protein-coding sequences, to simultaneously prioritize variants in non-coding regions rich in transcribed and critical regulatory sequences, we developed GROFFFY,…

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Clinical, genetic and structural delineation of RPL13-related spondyloepimetaphyseal dysplasia suggest extra-ribosomal functions of eL13

Clinical and radiographic findings The most common features were mild to moderate short stature, delayed carpal bone ossification and epimetaphyseal dysplasia in the lower limbs. Height ranged from −5,8 to −1,2 SDS. A summary of the clinical observations can be found in Table 1 and Fig. 2, while the radiological…

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High Prevalence of Von Willebrand Disease Estimated Using Large-Scale Genetic Data

The estimated prevalence of von Willebrand disease (VWD) based on large-scale genetic data is considerably higher than expected, according to research published in NPJ Genomic Medicine. “According to previous studies, VWD prevalence is estimated to vary between 0.6% and 1.3%, even though on the basis of cases referred to specialized…

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Mutation of key signaling regulators of cerebrovascular development in vein of Galen malformations

Adams, R. H. & Eichmann, A. Axon guidance molecules in vascular patterning. Cold Spring Harb. Perspect. Biol. 2, a001875 (2010). Article  PubMed  PubMed Central  Google Scholar  Fish, J. E. & Wythe, J. D. The molecular regulation of arteriovenous specification and maintenance. Dev. Dyn. 244, 391–409 (2015). Article  CAS  PubMed  Google…

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Help with coshing mutations for oncoplot

Help with coshing mutations for oncoplot 0 I am interested in plotting mutations using the oncoplot function. I want to show the mutational landscape of leukemia patients involved in my research. I have generated .maf files to use with the maftools package, I also have excel files with variant classification data….

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Senior Bioinformatician – Centogene, Berlin or Remote

Senior Bioinformatician – Centogene, Berlin or Remote Senior Bioinformatician Centogene Berlin or Remote, Germany Your tasks and responsibilities: We are looking for senior Bioinformatician to join in the R&D bioinformatics team in either Berlin or remotely from all over the world. You will be responsible for developing new bioinformatics pipelines…

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Advisor/Sr. Advisor – Bioinformatics – Relocation Assistance job with Lilly

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease,…

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Lilly Advisor/Sr. Advisor – Bioinformatics in New York, NY | 883515845

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease,…

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St. Jude Children’s Research Hospital hiring Senior Bioinformatics Analyst/Bioinformatics Analyst in Memphis, Tennessee, United States

St. Jude Children’s Research Hospital is looking for a highly motivated Senior Bioinformatics Analyst/Bioinformatic Analyst to contribute to genetic research projects in the Department of Epidemiology and Cancer Control. Our research leverages comprehensive biomedical data from childhood cancer survivors participating in two world-leading cohort studies, CCSS (ccss.stjude.org/ ) and SJLIFE…

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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…

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Final Highlights from the 2023 ASHG Annual Meeting

When it comes to covering a conference as large as the annual meeting of the American Society of Human Genetics (ASHG), one of the biggest challenges is capturing the full breadth of content in a handful of stories. Last week, GEN’s editorial team published three special edition newsletters covering the…

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Add r-bsgenome-hsapiens-ucsc-hg38-masked and r-dnamcrosshyb.

* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg38-masked): New variable. Change-Id: Ic1b646a3bd3b7262dd82f0972961c2e89628e90b — gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) Toggle diff (51 lines) diff –git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d79236ea26..ac09a079b4 100644 — a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -68,6 +68,42 @@ (define-module (gnu packages bioconductor) ;;; Annotations +(define-public r-bsgenome-hsapiens-ucsc-hg38-masked + (package + (name “r-bsgenome-hsapiens-ucsc-hg38-masked”) +…

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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…

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Structural Variants in gnomAD v4

Today, we are thrilled to announce the release of genome-wide structural variants (SVs) for 63,046 unrelated samples with genome sequencing (GS) data. All site-level information for 1,199,117 high-quality SVs discovered in these samples is browsable in the gnomAD browser (gnomAD SV v4) and downloadable from the gnomAD downloads page. For…

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gnomAD v4 released

News:gnomAD v4 released 0 The #gnomAD team is proud to announce the release of gnomAD v4! The v4 dataset includes 730,947 exomes & 76,215 genomes, which is ~5x larger than the v2 & v3 releases combined, & includes nearly 120K indivs of non-European genetic ancestry t.co/YKXIFlZwSi #ASHG23 (1/11) pic.twitter.com/hp6zO3xWW9 —…

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ftsj3 Summary

Gene Symbol:  ftsj3 Gene Name:  FtsJ RNA methyltransferase homolog 3 Synonyms: ( Nomenclature history ) Gene Function: Putative SAM-dependent rRNmethyltransferase SPB1 Protein Function : Probable…

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Download stats for annotation package MafH5.gnomAD.r3.0.GRCh38

Download stats for annotation package MafH5.gnomAD.r3.0.GRCh38 This page was generated on 2023-10-26 21:49:21 -0400 (Thu, 26 Oct 2023). Note that MafH5.gnomAD.r3.0.GRCh38 doesn’t belong to the current release or devel version of Bioconductor anymore. Number of downloads for annotation package MafH5.gnomAD.r3.0.GRCh38, year by year, from 2023 back to 2009 (years with…

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NCT/DKFZ MASTER handbook of interpreting whole-genome, transcriptome, and methylome data for precision oncology

Patient characteristics and tissue context The clinical interpretation of molecular alterations starts with evaluating relevant patient characteristics and the tissue context in which a genetic profile occurs. The former relates, in particular, to previous therapies, in addition to disease stage and clinical performance status. For example, prior targeted therapies warrant…

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Long-read sequencing to reclassify variants of uncertain significance in IRDs

(Image Credit: AdobeStock/XaMaps) Reviewed by Debarshi Mustafi, MD, PhD Long-read sequencing technology may be emerging as an option to streamline haplotype analysis in cases in which genetic testing of family members is unfeasible to provide a complete genetic diagnosis,1 according to Debarshi Mustafi, MD, PhD, senior author, from the Department…

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Confirming called variants

Confirming called variants 0 Hello, I performed whole exome analysis using GATK pipeline. After annotation of variant using annovar, I performed these steps: Filtered variants that have passed all filters Using Gnomad_exome_all, looked for variants less than 0.01 Then tried to confirm if these variants are also present in bam…

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Activity 3 instructions-1 – Name: _____________________________ Gene name: ______________________

Name: _____________________________ Gene name: ______________________ Activity 3 instructions. You have two patients who have undergone Whole Exome Sequencing analysis. Their genetic results came back and both patients have a genetic variant in the same medically actionable gene. Patient #1 has a different variant than Patient #2. Use publicly available databases…

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IJMS | Free Full-Text | Whole-Genome Sequencing of 502 Individuals from Latvia: The First Step towards a Population-Specific Reference of Genetic Variation

1. Introduction Human population genetics benefitted from the completion of the human genome sequence [1], which was further advanced by creating the reference of global genome variation [2] and, finally, the establishment of regional references assessing fine details of local variation in whole-genome sequences. Although European populations are relatively well…

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BioSpace hiring Advisor/Sr. Advisor – Bioinformatics in Cambridge, MA

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our 35,000 employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of…

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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…

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Genotyping, sequencing and analysis of 140,000 adults from Mexico City

Recruitment of study participants The MCPS was established in the late 1990s following discussions between Mexican scientists at the National Autonomous University of Mexico (UNAM) and British scientists at the University of Oxford about how best to measure the changing health effects of tobacco in Mexico. These discussions evolved into…

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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…

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Is SeqSQC compatible with hg38?

Is SeqSQC compatible with hg38? 1 @d0d83382 Last seen 8 hours ago Switzerland Dear Bioconductor team, I am contacting you because for my PhD project we have done whole genome sequencing with 30x coverage of 50 patients. We got the fastq files from the sequencing facility and now I am…

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Weirdness in annotation (missing allele frequencies)

Hello everyone! I am trying to get the gnomad allele frequencies of variants in the VCF files (I share the screenshot of one example which allele frequency I want to have). I used the following protocols and operations: protocols=”gnomad211_genome,gnomad211_exome,clinvar_20221231,dbnsfp42a,avsnp150,refGene” operations=”f,f,f,f,f,g” I have two sets of AF values, I believe one…

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Diagnostic genome sequencing improves diagnostic yield: a prospective single-centre study in 1000 patients with inherited eye diseases

Introduction Although protein-coding regions represent only 1–2% of the human genome, they harbour an estimated 85% of annotated pathogenic variants.1 2 Despite these numbers, genome sequencing (GS) usually achieves a higher diagnostic yield than sequencing approaches that focus on exonic regions, not least because of its more homogeneous coverage3 4…

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Human Genomics Team Leader at European Molecular Biology Laboratory (EMBL)

About the team/job Recent advances in technology and analysis have revealed significant opportunities to further our understanding of the diversity and impact of human genetics (such as the first full length telomere-to-telomere human genome and the first release of the human pangenome). As a result, we are excited to launch…

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Researchers identify a rare cause of male infertility and discover a potential cure

In a recent study published in the eBioMedicine journal, researchers investigated the genetic underpinning of asthenozoospermia, the leading cause of male fertility. Study: Deficiency in AK9 causes asthenozoospermia and male infertility by destabilising sperm nucleotide homeostasis. Image Credit: WHITE MARKERS/Shutterstock.com Their multidisciplinary examinations were able to identify adenylate kinase 9 (AK9), an enzyme…

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Bioconductor – MafH5.gnomAD.v3.1.1.GRCh38

DOI: 10.18129/B9.bioc.MafH5.gnomAD.v3.1.1.GRCh38     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see MafH5.gnomAD.v3.1.1.GRCh38. Minor allele frequency data from gnomAD version 3.1.1 for GRCh38 Bioconductor version: 3.13 Store minor allele frequency data from the Genome Aggregation Database (gnomAD version 3.1.1) for the human genome…

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Investigation of blood group genotype prevalence in Korean population using large genomic databases

Previous studies have attempted to elucidate the distribution of RBC antigen phenotypes and genotypes in the Korean population. However, conventional serological methods have proven challenging for examining a wide range of RBC antigens because of the considerable cost, time, and effort required to verify an individual’s RBC antigens using antisera…

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Is a PON necessary for tumor-normal matched Mutect2?

Is a PON necessary for tumor-normal matched Mutect2? 1 I’m a bit confused on whether or not i should include GATK’s public PON (either 1000g_pon.hg38.vcf.gz since I aligned with hg38), make my own from my normal samples, or just leave it and not include a PON. I am planning on…

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Downstream analysis on multi-sample or single-sample VCF files?

Downstream analysis on multi-sample or single-sample VCF files? 0 Hello, I use GATK best practices in my analysis (mainly dnaseq pipeline) and as it is suggested the pipeline calls genotypes on all the samples together and at the end creates an “allSamples.vcf.gz” file. At this stage one approach would be…

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Liftover GRCh37 to hg38 1kg/GATK.

Liftover GRCh37 to hg38 1kg/GATK. 1 I need to liftover a few variants from GRCh37 to hg38 1kg/GATK. UCSC lifover does not have this reference genome version available. I have tried with the standard hg38 but conversations are wrong. Where can I find GRCh37 to hg38 1kg/GATK chain files or…

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Purpose, Principles, Applications and more

DNA sequencing is a laboratory technique used to determine the order of nucleotides (adenine, cytosine, guanine, and thymine) in a DNA molecule. It is a fundamental tool in molecular biology and genetics, with a wide range of applications in fields such as genomics, medicine, forensics, and evolutionary biology. There are…

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Bioinformaticist (Scott) – (Job Number: 3258449) at Mass General Brigham in Mei Mass Eye And Ear Main Building Boston, Boston 1070276

!*! A talented bioinformaticist with experience in genomics is sought to join the Massachusetts Eye and Ear Bioinformatics Center (MBC) of the Ocular Genomics Institute (OGI) at Mass Eye and Ear (MEE) and Harvard Medical School. The mission of the OGI is to improve our understanding of the genetic causes…

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From where can I obtain vcf files of healthy exomes

From where can I obtain vcf files of healthy exomes 2 I want to do a simulation analysis for my project which requires benchmarking on a cohort of 200-300 exomes of healthy people. I tried to download such data from GnomAD or the 1000 Genome project but each VCF contains…

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gnomAD v2 Track Settings problem

Hello, In the UCSC Genome Browser “Genome Aggregation Database (gnomAD) Genome and Exome Variants v2.1 Track Settings” I noticed, that it is not possible to truly “Clear all” from the “Exclude variants with these FILTER values:” list. When pressing the “Clear all” button or manually disabling every filter, and…

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Pipeline to analyse variant calls against clinvar and gnomad

I am looking for a freelancer to help me build a pipeline for variant calls analysis against clinvar and gnomad. The project requires both single-sample and multi-sample analysis. Skills and Experience: – Proficiency in variant calls analysis – Experience with clinvar and gnomad databases – Strong knowledge of bioinformatics and…

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Challenging interpretation of germline TP53 variants based on the experience of a national comprehensive cancer centre

Subjects TP53 gene was investigated in 880 consecutive oncology patients referred for molecular genetic testing at our national centres (Department of Laboratory Medicine, Semmelweis University and Department of Molecular Genetics, National Institute of Oncology) between 2021 and 2022. This cohort consisted of patients with potential hereditary tumour predisposition. Their genetic…

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GWAS Links Gene Variant to Parkinson’s Disease Risk in People of African Ancestry

NEW YORK — Through a genome-wide association study, an international team of researchers has found a novel Parkinson’s disease gene variant among people of African ancestry that is not seen among Europeans. The researchers believe that this variant in the GBA1 gene — which encodes β-glucocerebrosidase, a protein known to…

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The role of chromosome 20p11.2 deletions

In a recent study posted to the medRxiv* preprint server, a group of researchers identified large deletions in individuals with unexplained hyperinsulinism (HI), thereby elucidating the potential dysregulation of Forkhead box protein A2 (FOXA2) expression and its implications for syndromic HI. Study: Chromosome 20p11.2 deletions cause congenital hyperinsulinism via the likely…

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Multiparameter prediction of myeloid neoplasia risk

Data acquisition UKB is a large-scale biomedical database and research resource containing genetic, lifestyle and health information from half a million UK participants. UKB has approval from the North West Multicentre Research Ethics Committee (11/NW/0382) and all participants provided written informed consent. The present study has been conducted under approved…

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East Asian people found to have more variants in DDC gene: Study | Highest frequency for cause of AADC deficiency in all ethic groups

People in East Asia have a higher frequency of variants in the DDC gene — the cause of aromatic l-amino acid decarboxylase (AADC) deficiency — than do those in any other ethnic groups across the world, a new study has found. Interestingly, while Koreans had the lowest carrier frequency among East…

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gatk – A bash script for running on a bunch of bam files

I have some bam files in this directory /data/Continuum/WES/results/ I want to run GATK mutation calling over bam files I googled and I realised for one function, I can do this cd /data/Continuum/WES/vcf/ for file in *.bam ; do ./gatk CollectSequencingArtifactMetrics -I /data/Continuum/WES/results/NG-27280_CLTSS_LTS_0017_lib506243_7661_2_MarkedDup.bam -O NG-27280_CLTSS_LTS_0017_lib506243_7661_2_MarkedDup –FILE_EXTENSION .txt -R resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta done;…

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Rare Disease Variants ID’d in Literature Not Always Found in Accessible Databases

Nearly a quarter of variants reported to be pathogenic for X-linked Creatine Transporter Deficiency in articles available in PubMed are not present in public variant databases, according to a new analysis in BMC Genomics. Researchers from the US National Institutes of Health and the Frederick National Laboratory for Cancer Research…

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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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Advisor/Sr. Advisor – Bioinformatics job in Cambridge at Lilly Company

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our 35,000 employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of…

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Evidence from adults seeking treatment reveals intriguing oligogenic patterns

Obesity is a complex disorder that is dependent on environmental and genetic factors. Severe obesity, which is otherwise known as class III obesity, is a chronic condition that increases the risk of mortality and morbidity. Current estimates indicate that the healthcare costs of individuals with severe obesity are 40% greater…

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Potential immunosuppressive clonal hematopoietic mutations in tumor infiltrating immune cells in breast invasive carcinoma

Our approach for identifying potential immunosuppressive CH mutations in TII consisted of four stages as shown in Fig. 2. (1) We selected protein altering mutations, which are more likely to be pathogenic than non-coding and synonymous mutations. (2) Clonally expanded somatic mutations in TII were identified based on variant allele fraction…

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Genome-wide prediction of disease variant effects with a deep protein language model

This study did not require any ethical approval. ESM1b In this study, we have leveraged and expanded the use of ESM1b, a protein language model developed by MetaAI20. The code and pretrained parameters for ESM1b (and other ESM models) were taken from the model’s official GitHub repository at github.com/facebookresearch/esm. Throughout…

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Deloitte hiring Bioinformatics Consultant – Python | NextFlow – Federal Health Sector in Atlanta, Georgia, United States

In this age of disruption, organizations need to navigate the future with confidence by tapping into the power of data analytics, robotics, and cognitive technologies such as Artificial Intelligence (AI). Our Strategy & Analytics portfolio helps clients leverage rigorous analytical capabilities and a pragmatic mindset to solve the most complex…

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Annovar and the ‘Otherinfo’ column in VCF inputs

Hi all, I am relatively new to bioinformatics research and am trying to use annovar on a vcf file I inherited from another person. I am running the following line of code: perl /project/annovar/table_annovar.pl \ –vcfinput exome_calls_pass_step2_normalized.vcf \ /project/annovar/humandb/ \ -buildver hg19 \ -out exome_calls_pass_step2_normalized_anno \ -remove \ -protocol refGene,genomicSuperDups,avsnp147,esp6500siv2_all,1000g2015aug_all,exac03,gnomad_exome,gnomad_genome,cadd13,dbnsfp33a,mpc,bravo,…

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VEP run with –af_gnomadg refuses to provide allele frequencies for extremely rare variants

VEP run with –af_gnomadg refuses to provide allele frequencies for extremely rare variants 0 Here are some examples. Now, I will grant you these are all extremely rare but not unknown. HGVSg gnomADg_AF actual chr20:g.63400308G>A 1.97088e-05 chr20:g.63400728C>A 1.31465e-05 chr20:g.63401127G>A 6.57263e-06 chr20:g.63402766G>A 2.6276e-05 chr20:g.63402967G>A 6.57082e-06 chr20:g.63403148G>A 1.97114e-05 chr20:g.63403351C>T 6.56927e-06 chr20:g.63403638G>A 1.31524e-05…

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ClearanceJobs hiring Bioinformatics Engineer with Security Clearance in Atlanta, Georgia, United States

In this age of disruption, organizations need to navigate the future with confidence by tapping into the power of data analytics, robotics, and cognitive technologies such as Artificial Intelligence (AI). Our Strategy & Analytics portfolio helps clients leverage rigorous analytical capabilities and a pragmatic mindset to solve the most complex…

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matching gnomAD allele frequency

matching gnomAD allele frequency 0 Is there a way to find the allele frequency of gnomAD db with the rsID of my SNP data using gnomAD db in Python or R? If there is a specific rsID, I want to get the total allele frequency and east asian allele frequency…

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Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification

Human study The study was approved by the institutional review boards (Ethics Commission of the Medical Faculty of Technical University Munich (protocol 193/17S) and Ethics Committee of the Medical Faculty of Heidelberg University (protocol S-206/2011)) and all patients provided written informed consent under these protocols. The study was conducted in…

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Bioconductor – MafDb.gnomAD.r2.1.hs37d5 (development version)

DOI: 10.18129/B9.bioc.MafDb.gnomAD.r2.1.hs37d5   This is the development version of MafDb.gnomAD.r2.1.hs37d5; for the stable release version, see MafDb.gnomAD.r2.1.hs37d5. Minor allele frequency data from gnomAD release 2.1 for hs37d5 Bioconductor version: Development (3.18) Store minor allele frequency data from the Genome Aggregation Database (gnomAD release 2.1) for the human genome version hs37d5….

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A diverse ancestrally-matched reference panel increases genotype imputation accuracy in a underrepresented population

In the present study, we enrolled 412 participants from the Southeast Asian Brugada syndrome cohort (ClinicalTrials.gov number, NCT04232787). The study was approved by the Institutional Review Board (IRB) of the Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand (IRB No. 431/58). All methods were performed in accordance with relevant guidelines/regulations. Informed…

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GATK GetPileupSummaries Java heap space

GATK GetPileupSummaries Java heap space 1 I am using GATK GetPileSummaries in the following way: GENOME=”/FILES/HUMAN_REFERENCES/hg19.fa” RECBAM=”/FILES/${patient_id}/${patient_id}.recalibrated.bam” intervals_list=”/FILES/HUMAN_REFERENCES/wgs_calling_regions.v1.interval_list” GERM=”/FILES/HUMAN_REFERENCES/small_exac_common_3-hg19.vcf” PON=”/FILES/HUMAN_REFERENCES/Mutect2-WGS-panel- b37-hg19.vcf”export GERM=”/FILES/HUMAN_REFERENCES/af-only-gnomad-hg19.raw.sites.vcf” VCF=”/FILES/${patient_id}/${patient_id}.recalibrated.vcf” OUTPUT=”/FILES/${patient_id}/${patient_id}.getpileupsummaries.table” srun /mnt/beegfs/apptainer/images/gatk4.sif gatk GetPileupSummaries \ -I $RECBAM \ -L $GERM \ -O $OUTPUT \ -V $GERM Resulting in the following error: 16:37:40.248 INFO NativeLibraryLoader – Loading…

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GATK GetPileUpSummariesUsage

GATK GetPileUpSummariesUsage 0 Hi, I am doing variant calling using as reference hg19. After Gatk Mutect with PON Mutect2-WGS-panel-b37.vcf transformed into Mutect2-WGS-panel-b37-hg19.vcf and germline af-only-gnomad.raw.sites.vcf to af-only-gnomad.hg19.raw.sites.vcf (with Picard LiftOver). After doing Mutect2 next step is GATK GetPileUpSummaries, that has this usage from GATK website: gatk GetPileupSummaries \ -I tumor.bam…

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vcf variant selection

vcf variant selection 1 I have vcf files that I want to convert into .bed files with plink to use for proxy search. One issue I am having is that each variant id must be unique. In these vcf’s, the multi-allelic variants are formatted as bi-allelic records. Here is an…

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PON and germline files for Mutect2 Tumor-only mode

Hi! I am applying Mutect2 in tumor-only.mode having hg19 as reference and samples resulting of targeted sequencing (not only coding gene parts but also some non coding regions), I found this: console.cloud.google.com/storage/browser/gatk-best-practices/somatic-b37%2F;tab=objects?prefix=&forceOnObjectsSortingFiltering=false. This bundle is used for b37 which is equivalent to hg19 (not 100% similar). export PON=”/filepath/Mutect2-WGS-panel-b37-hg19.vcf” export GERM=”/filepath/af-only-gnomad-hg19.raw.sites.vcf”…

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NM_000475.5(NR0B1):c.521G>C (p.Arg174Pro) AND multiple conditions – ClinVar

Description This sequence change replaces arginine, which is basic and polar, with proline, which is neutral and non-polar, at codon 174 of the NR0B1 protein (p.Arg174Pro). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with…

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GATK BaseRecalibrator known-sites vcf file

Hi, I am trying to run GATK’s BaseRecalibrator on a BAM file created with the hg19 reference sequence downloaded from UCSC website. For the –known-sites option I would like to use either a gnomAD .vcf file or a dbSNP .vcf, downloaded from their respective websites. The analysis works if I…

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Bioinformatics Consultant with Security Clearance Atlanta, GA – Jobs in USA – jobs –

Job Description In this age of disruption, organizations need to navigate the future with confidence by tapping into the power of data analytics, robotics, and cognitive technologies such as Artificial Intelligence (AI). Our Strategy & Analytics portfolio helps clients leverage rigorous analytical capabilities and a pragmatic mindset…

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Evolutionary histories of breast cancer and related clones

Data reporting No statistical methods were used to determine the sample size. The experiments were not randomized. Pathologists were blinded to the genetic alterations in each sample during histopathological evaluation. Participants and materials We enroled 207 female patients with breast cancer who underwent surgery at the Kyoto University Hospital and…

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python ‘gnomAD_DB’

python ‘gnomAD_DB’ 0 Hello. I have a question about ‘gnomAD_DB’ package of Python. How to save query result as csv file? This is my code. test_df = db.get_info_from_df(dummy_var_df, “AF”) I want to make the result of ‘test_df’ into a csv file. What should I do? test_df.to_csv(‘my_data.csv’, index = False) I…

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GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.

Hi, I am following the GATK best practices pipeline for variant calling starting from targeted sequencing bam and bai files using the hg19 reference. When applying GATK Mutect2 got the following error A USER ERROR has occurred: Input files reference and features have incompatible contigs: No overlapping contigs found. reference…

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how to filter based on FREQ from snpsift annotation for vcf files?

After annotating by snpsift, how could I filter based on FREQ? For example, a record with the following annotation, and I would like to filter based on GnomAD. How should I write the expression? Many thanks! Note there are four value, the first is the ref with frequency of 0.3163,…

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Liftover Archives | The Golden Helix Blog

The world has been making a shift to use GRCh38 human genome reference coordinates, but the transition has not been fast. Many of the mainstay human catalog projects are changing to use native GRCh38 catalogs, or are remapping their…

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Senior Bioinformatics Engineer in Manila Philippines – Career Connect

This is a remote position. We’re looking for someone with years of experience in machine learning and data science for a Hawaii-based health care company. Lead the development of new bioinformatics algorithms, pipelines, and infrastructure in a cloud-based environment in support of the Company’s discovery platform Apply rigorous standards and…

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gnomAD Archives | The Golden Helix Blog

In this blog post, I am very excited to talk about The Broad Institute’s release of the latest version of gnomAD, v 3.1.2, which is now available for use as an annotation source in your SVS or VarSeq projects….

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Access age metadata for gnomAD, HGDP + 1KG dataset

Access age metadata for gnomAD, HGDP + 1KG dataset 0 Hi all, I recently downloaded the HGDP + 1KG dataset from the gnomAD website (gnomad.broadinstitute.org/downloads#v3-hgdp-1kg). I am trying to find out the age of the patients at the time of the analysis, but I cannot find this info in the…

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A framework for individualized splice-switching oligonucleotide therapy

Patients The WGS and clinical data of 235 patients with A-T were provided by the Global A-T Family Data Platform of ATCP. Our access to the data was approved by the Data Access Committee of ATCP. Selected patients with A-T enrolled at the Manton Center for Orphan Disease Research under…

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Principal Bioinformatics Engineer Job Opening in Waltham, MA at BIO-TECHNE

Job Details Level:    Experienced Job Location:    Waltham MA – Waltham, MA Position Type:    Full Time Education Level:    Graduate Degree Salary Range:    Undisclosed Travel Percentage:    Up to 10% Job Shift:    Day Job Category:    Research Description Principal Bioinformatics Engineer   The Opportunity Exosome Diagnostics, a Bio-Techne brand (NASDAQ: TECH), is a global…

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Accurate sequencing of DNA motifs able to form alternative (non-B) structures

Matthias H. Weissensteiner1,11,12, Marzia A. Cremona2,3,4,11, Wilfried M. Guiblet1,5, Nicholas Stoler6, Robert S. Harris1, Monika Cechova1,7,13, Kristin A. Eckert4,8, Francesca Chiaromonte4,9,10, Yi-Fei Huang1,4 and Kateryna D. Makova1,4 1Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; 2Department of Operations and Decision Systems, Université Laval, Quebec, Quebec G1V0A6,…

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genotype frequency API/download

genotype frequency API/download 0 Hi! I have difficulties getting the genotype frequency for healthy people. I do not want to download VCF files from gnomAD, because I don’t have that much memory on my device. Can someone recommend me something else? I then have to compare the values with my…

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Using publicly available dataset as control for GWAS

Using publicly available dataset as control for GWAS 0 I am aware of the limitations, and potential false positives that can arise in using a publicly available dataset as a control for a GWAS-like SNP association analysis. I was wondering if it would be possible to use a vcf like…

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