HVP Shared Database
Last year saw a considerable increase in the use of LOVD databases (numbers for Leiden/HVP hosted installations only):
- The number of monthly page views increased from approximately 350,000 to almost 450,000 with the number of unique monthly visitors (each institute counted as one visitor) increased by 20,000.
- The use of LOVD, api, computer requests for information increased from 4,000,000 to >39,000,000.
Statistics for the HVP shared gene variant database show a substantial increase as well:
- The number of submitters, people actively sharing data with the HVP database, has grown in 2017 from 1046 to 1431.
- The total number of variants in the database increased from 377,974 (49,238 unique) to 549,140 (79,224 unique), the number of individuals for which data were shared from 156,577 to 285,424
Total numbers (# installations, # individuals, # variants) for all public LOVD installations can be found on the LOVD website (http://www.lovd.nl/3.0/public_list)
Impressive numbers! We would like to thank all the LOVD team and it’s users for all their hard work.
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A great start to 2018 as Dutch data now being shared with LOVD. Some time ago, the 9 Dutch clinical labs decided to share all classified variants which each other. They have now made an even bigger step and shared this data with the world.
The project was initiated by the (Vereniging Klinisch Genetische Laboratoriumdiagnostiek, http://www.vkgl.nl), the Dutch association of laboratories for Clinical Genetics. Headed by Dr. Marielle van Gijn (UMC, Utrecht), the project first collected the data in a national repository built on Molgenis software, and checked whether variant classifications between labs agreed.
The Dutch database currently contains over 90,000 classified variants. The variants for which there was consensus, roughly 28,000 classifications (>10,000 unique), have now been shared with the HVP shared database (LOVD). The variants can be found at https://databases.lovd.nl/shared, go to the Variants tab, select top option (View all genomic variants) and query for Owner "VKGL" (last column on the right). Soon all variants will be publically shared with both the HVP shared and ClinVar database.Our compliments and congratulations to the Dutch initiative. Which country is next?
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Friday June 15, Milan (Italy)
Teach the Teacher: HGVS nomenclature
A course on HGVS nomenclature, organised with financial support of the European Society of Human Genetics (ESHG), in collaboration with the Human Variome Project (HVP and the ESHG Education Committee.
HGVS nomenclature, currently supported by the HGVS, HVP, HUGO and GA4GH, is the language by which diagnostic reports as well as scientific reports on human genetic variation are drafted. Understanding this language and knowing how to use it is crucial for mutual understanding between geneticists and for the accuracy of diagnostic and scientific reporting in Human and Medical Genetics. A correct use of the HGVS recommendations prevents miscommunication and ensures that variants can be efficiently retrieved from existing data repositories facilitating variant annotation and classification.
The aim of the course is to give participants a detailed overview of the HGVS nomenclature. i.e. the recommendations for the description of sequence variants (Den Dunnen et al., 2017, Hum.Mutat. 37:564,;http://varnomen.HGVS.org). The course will have a “Teach the Teacher” format, i.e. after the course participants should be able to teach HGVS nomenclature to others. Registration to the course is free, but limited to 16-20 participants. Participants will be selected based on their willingness to act as a local (national) teacher and their expertise in the field. In addition we want to make sure participants are spread internationally, covering all continents on the globe.
The entire course will be recorded (sound and video) and used to develop educational tools on HGVS nomenclature, including an e-learning module.
To register, please send a letter (max. A4) with your contact details and your motivation
ultimately April 15, 2018 to:
ESHG Education Committee
att. Johan den Dunnen
VarNomen@HGVS.org
Subject: HGVS course
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Save the Date!
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Topical article – Genomic Medicine, Without Borders: Which Strategies Should Developing Countries Employ to Invest in Precision Medicine? A New "Fast-Second Winner" Strategy
By Mitropoulos, K. et al. (DOI: 10.1089/omi.2017.014)
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