Tag: ClinGen

De novo variants underlying monogenic syndromes with intellectual disability in a neurodevelopmental cohort from India

Russell PSS, Nagaraj S, Vengadavaradan A, Russell S, Mammen PM, Shankar SR, et al. Prevalence of intellectual disability in India: a meta-analysis. World J Clin Pediatr. 2022;11:206–14. Article  PubMed  PubMed Central  Google Scholar  Winnepenninckx B, Rooms L, Kooy RF. Mental retardation: a review of the genetic causes. Br J Dev…

Continue Reading De novo variants underlying monogenic syndromes with intellectual disability in a neurodevelopmental cohort from India

Geisinger College of Health Sciences

GenomeConnect is an online registry designed by the NIH-funded Clinical Genome Resource (ClinGen) for people who are interested in sharing de-identified genetic and health information to improve our understanding of the relationship between genes and human health. Investigators at Geisinger are helping to lead this initiative and invite you to…

Continue Reading Geisinger College of Health Sciences

Criteria for better assessment of rare genetic variants that can lead to hereditary colorectal cancer

APC gene, APC protein, and criteria boundaries and genotype-phenotype correlations. Representation of the APC gene (bottom) and its main protein product (middle) on the reference sequence NM_000038.6 (non-coding exon 1 not shown). The figure shows on the top the boundaries for the application of PVS1, BS3 and BP1 and genotype-phenotype…

Continue Reading Criteria for better assessment of rare genetic variants that can lead to hereditary colorectal cancer

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…

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

Greenphire, Florence Healthcare Team Up; Illumina Partnerships; Oxford Nanopore Develops New Data Technology

November 29, 2023 | Greenphire and Florence Healthcare announce a technology partnership; Illumina and Veracyte join together in a multi-year agreement; Oxford Nanopore Technologies collaborates with Fabric Genomics and Saphetor to develop data technology for research; more.  Greenphire and Florence Healthcare announced a technology partnership that integrates two of the…

Continue Reading Greenphire, Florence Healthcare Team Up; Illumina Partnerships; Oxford Nanopore Develops New Data Technology

Estimating the proportion of nonsense variants undergoing the newly described phenomenon of manufactured splice rescue

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17:405–24. Article  PubMed  Google Scholar  Abou…

Continue Reading Estimating the proportion of nonsense variants undergoing the newly described phenomenon of manufactured splice rescue

Application of CNV-seq technology | IJWH

Introduction Ultrasound soft markers refer to small nonspecific variations in foetal structure found in prenatal ultrasound that are often associated with abnormal chromosome number or pathogenic copy number variations (CNVs).1,2 Common ultrasound soft markers include nuchal translucency (NT) thickness, nuchal fold (NF) thickness, nasal bone dysplasia, choroid plexus cyst, intracardiac…

Continue Reading Application of CNV-seq technology | IJWH

The Imageable Genome | Nature Communications

For the Imageable Genome project, we developed a data pipeline that identifies texts containing radiotracers, recognizes and extracts names of radiotracers from texts, filters for clinically relevant radiotracers and their associated targets, and translates protein names, i.e. of radiotracer targets, to names of the coding genes. We then downloaded the…

Continue Reading The Imageable Genome | Nature Communications

Can adding RNA sequencing to germline genetic testing improve accuracy and clinical sensitivity over time compared to DNA sequencing alone?

In a recent study published in the Journal of American Medical Association (JAMA) Oncology, researchers from California investigated the diagnostic outcomes of concurrent sequencing of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) to detect the predisposition to hereditary cancer in 43,524 individuals. They found that adding RNA sequencing to germline…

Continue Reading Can adding RNA sequencing to germline genetic testing improve accuracy and clinical sensitivity over time compared to DNA sequencing alone?

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…

Continue Reading ftsj3 Summary

Curation in ClinVar

Expert curation of variants Expert curated variants are submitted to ClinVar by ClinGen-approved expert panels. Read more about expert panels in ClinVar. NCBI staff do not curate variant classifications. Our staff work closely with submitters to ensure that each record submitted to ClinVar reflects the submitter’s assertion about the variant….

Continue Reading Curation in ClinVar

ClinVar Partners with ClinGen to Review & Curate Submitted Records

Do you currently use or submit clinical variation data? NCBI now has a new mechanism to improve ClinVar data quality. Since ClinVar’s founding over 10 years ago, the amount of information in this free resource has expanded dramatically with submissions from research and clinical laboratories all over the world. Because…

Continue Reading ClinVar Partners with ClinGen to Review & Curate Submitted Records

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…

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

Specifications of the ACMG/AMP guidelines for ACADVL variant interpretation

. 2023 Jul 26;140(3):107668. doi: 10.1016/j.ymgme.2023.107668. Online ahead of print. May Flowers  1 , Alexa Dickson  2 , Marcus J Miller  3 , Elaine Spector  4 , Gregory Mark Enns  5 , Heather Baudet  6 , Marzia Pasquali  7 , Lemuel Racacho  8 , Kianoush Sadre-Bazzaz  9 , Ting Wen  9 , Melissa Fogarty  9 , Raquel Fernandez  10 , Meredith A…

Continue Reading Specifications of the ACMG/AMP guidelines for ACADVL variant interpretation

Exploring the molecular and clinical spectrum of COVID-19-related acute necrotizing encephalopathy in three pediatric cases

Messiah SE, Xie L, Mathew MS, Delclos GL, Kohl HW 3rd, Kahn JS. Results of COVID-19 surveillance in a large United States pediatric healthcare system over one year. Child (Basel). 2021;8:752. Google Scholar  Cloete J, Kruger A, Masha M, du Plessis NM, Mawela D, Tshukudu M, et al. Paediatric hospitalisations…

Continue Reading Exploring the molecular and clinical spectrum of COVID-19-related acute necrotizing encephalopathy in three pediatric cases

refget v2.0 links the hidden dictionaries of

image: How refget works view more  Credit: Stephanie Li / GA4GH   A widely-used tool that finds the exact references needed to pinpoint differences in our DNA just got a refresh. On 17 July, the Standards Steering Committee of the Global Alliance for Genomics and Health (GA4GH) voted to release refget v2.0….

Continue Reading refget v2.0 links the hidden dictionaries of

Otago University Study Offers Genetic Test Certainty

Findings from a new international study look set to improve rates of diagnosis for patients undergoing genetic testing in Aotearoa New Zealand and around the world. The research, published in one of the world’s most prestigious medical journals, could pave the way for earlier intervention in the treatment of patients…

Continue Reading Otago University Study Offers Genetic Test Certainty

refget v2.0 links the hidden dictionaries of DNA

How refget works. Credit: Stephanie Li / GA4GH A widely-used tool that finds the exact references needed to pinpoint differences in our DNA just got a refresh. On 17 July, the Standards Steering Committee of the Global Alliance for Genomics and Health (GA4GH) voted to release refget v2.0. With better…

Continue Reading refget v2.0 links the hidden dictionaries of DNA

A biallelic variant in COX18 cause isolated Complex IV deficiency associated with neonatal encephalo-cardio-myopathy and axonal sensory neuropathy

Kadenbach B, Hüttemann M. The subunit composition and function of mammalian cytochrome c oxidase. Mitochondrion. 2015;24:64–76. Article  CAS  PubMed  Google Scholar  Brischigliaro M, Zeviani M. Cytochrome c oxidase deficiency. Biochim Biophys Acta Bioenerg. 2021;1862:148335. Article  CAS  PubMed  Google Scholar  Sacconi S, Trevisson E, Pistollato F, Baldoin MC, Rezzonico R, Bourget…

Continue Reading A biallelic variant in COX18 cause isolated Complex IV deficiency associated with neonatal encephalo-cardio-myopathy and axonal sensory neuropathy

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…

Continue Reading A framework for individualized splice-switching oligonucleotide therapy

Genomenon Accelerates Quest to Curate Entire Human Genome With Boston Genetics Acquisition

NEW YORK – In acquiring longtime partner Boston Genomics this week, Genomenon is stepping up its efforts to become the first entity to curate the entire human genome, though it may be the only one to have declared such an intention. By adding Cambridge, Massachusetts-based Boston Genetics’ team of about…

Continue Reading Genomenon Accelerates Quest to Curate Entire Human Genome With Boston Genetics Acquisition

Bioinformatics Startup Geneyx Builds Business on Whole-Genome, Long-Read Sequencing Analysis

NEW YORK – This month’s announcement that Oxford Nanopore Technologies would integrate its Epi2Me cloud-based analysis platform with Geneyx’s software to automate analysis and clinical reporting of long-read sequencing data represents the continuation of an ongoing growth strategy for Israeli bioinformatics startup Geneyx. Chief Product Officer Hagar Mor Shaked said…

Continue Reading Bioinformatics Startup Geneyx Builds Business on Whole-Genome, Long-Read Sequencing Analysis

Newborn genome sequencing project identifies unanticipated disease risks

Due to the recent advancements in genome-scale sequencing, complete genomic sequencing of a newborn can be performed shortly after birth. Analysis of this sequence enables the detection of deleterious variants linked to monogenic diseases. Even though such a screening tool is currently available, it is associated with several ethical, evidentiary,…

Continue Reading Newborn genome sequencing project identifies unanticipated disease risks

Human hg38 chr10:21,513,475-21,525,682 UCSC Genome Browser v446

     Seq2science ChIP-seq hub ChIP-seqhidedensesquishpackfull    Mapping and Sequencing Base Positionhidedensefull p14 updated Fix Patcheshidedensesquishpackfull p14 updated Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19 Diffhidedensesquishpackfull INSDChidedensesquishpackfull LiftOver & ReMaphidedensesquishpackfull LRG Regionshidedensesquishpackfull Mappabilityhideshow Problematic Regionshidedensesquishpackfull new Recomb…

Continue Reading Human hg38 chr10:21,513,475-21,525,682 UCSC Genome Browser v446

Highly variable hearing loss due to POU4F3 (c.37del) is revealed by longitudinal, frequency specific analyses

ADSNHL is caused by a novel variant in POU4F3 (DFNA15) Targeted Sanger sequencing for known DFNA/B pathogenic variants in the NL population yielded no hits. Genome-wide genotyping and linkage analysis on one branch of the North American kindred yielded three equally positive “logarithm of the odds” scores (LOD = 2.08) suggestive of…

Continue Reading Highly variable hearing loss due to POU4F3 (c.37del) is revealed by longitudinal, frequency specific analyses

Index of /pub/clinvar

Name Last modified Size Parent Directory – ClinGen/ 2018-12-14 09:17 – document_archives/ 2014-04-24 08:19 – presentations/ 2021-06-23 17:39 – release_notes/ 2023-04-06 10:38 – submission_examples/ 2020-08-03 13:46 – submission_templates/ 2023-02-17 13:23 – tab_delimited/ 2023-04-10 15:02 – temp/ 2022-12-20 16:01 – vcf_GRCh37/ 2023-04-10 14:53 – vcf_GRCh38/ 2023-04-10 14:53 – xml/ 2023-04-10 15:02…

Continue Reading Index of /pub/clinvar

Advantages of genome sequencing in healthcare

Genome sequencing customises diagnostic procedures for diseases at a very nascent stage and provides personalised treatment In 1990, The Human Genome Project was started which took 13 years for sequencing 20,000 genes and to understand the relationship between the genes and their work together. The idea behind genome sequencing is…

Continue Reading Advantages of genome sequencing in healthcare

dbCNV: deleteriousness-based model to predict pathogenicity of copy number variations | BMC Genomics

MacDonald JR, Ziman R, Yuen RK, Feuk L, Scherer SW. The database of genomic variants: a curated collection of structural variation in the human genome. Nucleic Acids Res. 2014;42(Database issue):D986–992. Article  CAS  PubMed  Google Scholar  Zarrei M, MacDonald JR, Merico D, Scherer SW. A copy number variation map of the…

Continue Reading dbCNV: deleteriousness-based model to predict pathogenicity of copy number variations | BMC Genomics

Can genes expose more glaucoma in the population?

Glaucoma specialist and medical geneticist DR JANEY WIGGS revealed two new genes in juvenile early-onset glaucoma and dissected the value of polygenic risk scores when she delivered the Glaucoma Update Lecture at RANZCO’s 53rd Congress. Contemporary glaucoma researchers are using a genetic approach to understand the mechanisms of glaucoma. This…

Continue Reading Can genes expose more glaucoma in the population?

Human hg38 chr19:11,216,461-11,670,150 UCSC Genome Browser v442

     Custom Tracks 1806hidedensefull 468hidedensefull BT20hidedensefull BT474hidedensefull MCF7hidedensefull T47Dhidedensefull    Mapping and Sequencing Base Positionhidedensefull p13 Fix Patcheshidedensesquishpackfull p13 Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19 Diffhidedensesquishpackfull INSDChidedensesquishpackfull LiftOver & ReMaphidedensesquishpackfull LRG Regionshidedensesquishpackfull Mappabilityhideshow RefSeq Acchidedensesquishpackfull…

Continue Reading Human hg38 chr19:11,216,461-11,670,150 UCSC Genome Browser v442

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…

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