№ files_lp_4_process_3_100934
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Open-access research article presenting the implementation and continuous improvement of VariantValidator and VariantFormatter for standardising genetic variant nomenclature in literature, clinical reports, and databases to ensure consistent, accurate, and traceable variant descriptions for diagnostic purposes.
Year: 2024
Region / Institution: University of Manchester, University of Leicester, Leiden University Medical Center, Johns Hopkins University, Massachusetts General Hospital
Subject: Genetic variant nomenclature, bioinformatics, rare disease diagnostics
Document type: Research article
Authors: Peter J. Freeman, John F. Wagstaff, Ivo F.A.C. Fokkema, Garry R. Cutting, Heidi L. Rehm, Angela C. Davies, Johan T. den Dunnen, Liam J. Gretton, Raymond Dalgleish
Target audience: Clinical scientists, geneticists, bioinformaticians
Methodology / Tools: VariantValidator, VariantFormatter, REST API, HGVS nomenclature standards
Key databases: ClinVar, Leiden Open Variation Database (LOVD), Universal Transcript Archive (UTA)
Integration: Genomics workflows, omics platforms, journal publishing systems
Data coverage: Human genome builds GRCh37 and GRCh38, RefSeq and Ensembl transcripts
Updates: Continuous development since 2018, support for RNA descriptions, iterative user-driven improvements
Publication date: 2024
Price: 8 / 10 USD
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ACMG/AMP Classification Rules Specified for BRCA1 & BRCA2 ENIGMA Variant Curation Expert Panel, Classification Criteria V1.2 2024-11-18
Year: 2024
Region / City: N/A
Topic: BRCA1 & BRCA2 variant classification
Document type: Classification guidelines
Organization / Institution: ACMG/AMP, ENIGMA
Author: Variant Curation Expert Panel
Target audience: Geneticists, researchers, healthcare professionals
Period of validity: N/A
Approval date: 2024-11-18
Modification date: N/A
Make-to-Order Production for Sales Kits with Variant Configuration (4OC_US)
Year: 2022
Region / City: Not specified
Topic: Variant Configuration, Make-to-Order Production, Sales Kits
Document Type: Test Script
Organization / Institution: SAP
Author: Not specified
Target Audience: SAP users involved in testing variant configuration and make-to-order production processes
Effective Period: Not specified
Approval Date: Not specified
Date of Changes: Not specified
Contextual Description: Detailed test procedure for make-to-order production of sales kits using advanced variant configuration in SAP S/4HANA for a customer-specific robot bundle configuration.
ACMG/AMP Classification Rules Specified for BRCA1 & BRCA2ENIGMA Variant Curation Expert Panel, Classification Criteria V1.0 2023-04-27
Year: 2023
Region / City: Global
Topic: Variant Classification
Document Type: Technical Specification
Organization / Institution: ACMG/AMP, ENIGMA Variant Curation Expert Panel
Author: Unknown
Target Audience: Researchers, Geneticists, Clinicians
Period of Validity: Ongoing
Approval Date: 2023-04-27
Date of Changes: None
Supplemental Materials: Whole Exome Sequencing, Intraocular Pressure Analysis, and Sample and Variant Quality Control Methods
Section: Supplemental Materials
Abbreviations: IOP; MEE/RHC; QC; GSA; PCA; LD; MAF; PC; WES; BAM; VCF; EUR; AFR; AMR; EAS; SAS; GQ; SNPs; MAD; GTEx; Non-PAR; Indels; HWE; AB; GWAS; FAME; GC; QTL; eQTL; CLPP; FDR; OHTN; RINT
Methodology: Whole exome sequencing and statistical genetic analysis
Sequencing Platform: NovaSeq S4 flow cell (2x151bp)
Library Preparation Kit: KAPA Hyper Prep with Library Amplification Primer Mix (KK8504)
Capture Kit: IDT XGen hybridization and wash kit
Custom Bait: TWIST Biosciences exome bait
Liquid Handling Systems: Agilent Bravo; Hamilton Starlet
Quantification Method: qPCR; Invitrogen Quant-It broad range dsDNA assay
Genotyping Platform: Global Screening Array (GSA)
Software: PLINK 1.9; PLINK 2.0; R; Python; Hail v0.2
Reference Panel: 1000 Genomes Project Phase 3
Ancestry Groups: European (EUR); African (AFR); Admixed American (AMR); East Asian (EAS); South Asian (SAS)
Statistical Analysis: Analysis of variance (aov in R); Tukey honest significant difference test
Quality Control Criteria: Sample-level and variant-level QC including genotype missingness, heterozygosity, relatedness (PI_HAT), sex concordance, ancestry inference, BAM and VCF metrics
ClinGen Somatic Cancer Variant Curation Expert Panel (SC-VCEP) Application
Note: Year
Trans, Non-binary, Intersex & Gender Variant Group Lead Facilitator Job Description
Year: 2023
Region / city: Bristol
Topic: Job Description, Peer Support, Trans and Non-binary Community
Document type: Job Description
Organization: SARSAS
Author: SARSAS
Target audience: Trans, non-binary, intersex, or gender variant individuals seeking a facilitating role
Period of validity: 6th February 2023 to end July 2023
Approval date: 6th February 2023
Modification date: None
Historic Technical Passport Variant
Note: Year
Document Type: Technical Passport
Issuing Organization: RACB
Author: RACB Sport
Target Audience: Car manufacturers, car enthusiasts, regulatory bodies
Clinical and Molecular Description of Sickle Cell Disease Due to HBB Variant HbS
Year: Not specified
Country of origin: Surinam
Institution: The Hemoglobin University
Authors: Bento C; Traeger-Synodinos J; Kountouris P; et al.
Thematic area: Hematology; Hemoglobinopathies; Molecular genetics
Document type: Case report submission form
Gene: HBB
Protein variant: p.Glu7Val
cDNA variant: c.20A>T
Variant name: HbS
Database accession: HbVar ID 226; IthaID 824
Phenotype: Abnormal Doppler; organ failure due to vaso-occlusive crisis; skeletal dysplasia
Alpha genotype: -alpha3.7/-alpha3.7
Beta genotype: betaS/betaS
Age at evaluation: 56 years
Age at diagnosis: 2 months
Sex at birth: Female
Family history: Two sisters carriers of HbS
Clinical history: Hydroxyurea treatment from childhood until 54 years; uncomplicated pregnancy at 23 years; exchange transfusion started at 54 years
Hematological parameters before transfusion: Reported at age 53 years (Hb, MCV, MCH, RBC, Hct, Ret, RDW)
Iron status: Ferritin 35 µg/L
Blood smear: Target cells at normal iron indicative of alpha-thalassemia trait
Biochemical studies: Capillary electrophoresis (Sebia); HPLC (Trinity PHR)
Molecular studies: Sanger sequencing of exon 1 of HBB gene
Transfusion status: Exchange transfusion from age 54 years
Test 3. Module 3 Spotlight 2 Variant 11
Note: Year
Context: Educational exercise for learning English vocabulary and sentence structure, focusing on animals and abilities.
Table S1. cgMLST targets differing between ST23 and the ST2695 variant identified in Bresso outbreak in 2018
Year: 2018
Region / City: Bresso
Topic: cgMLST targets, bacterial strain variation
Document Type: Table
Organization: Not specified
Author: Not specified
Target Audience: Researchers in molecular biology, genetics, and epidemiology
Period of validity: Not specified
Date of approval: Not specified
Date of changes: Not specified
Test on Present Simple and Present Continuous, Variant I & II
Year: Not specified
Region / City: Not specified
Subject: English language test
Document type: Educational test
Author: Not specified
Target audience: English learners
Validity period: Not specified
Approval date: Not specified
Modification date: Not specified
Topics: Standardising VariantValidator Variant