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GV Newsletter - February 2022

 


More information, please visit: https://www.hugo-hgm2022.org/
 
 
 

We are saddened to learn of the passing of Dr. Tom Caskey, a former HUGO President (1993-95) and a global pioneer in genomics. 
 
Here is the posted obituary: https://www.legacy.com/us/obituaries/washingtonpost/name/c-casky-obituary?id=32256748">https://www.legacy.com/us/obituaries/washingtonpost/name/c-casky-obituary?id=32256748 
 

ANNOUNCEMENT

VEPTC Course 2022
 
The organising committee is pleased to announce that a Variant Effect Prediction Training Course (VEPTC) will be held again in 2022. The course will take place in Cyprus at the end of September 2022 as a face-to-face course, the exact date will be announced soon. However, due to the ongoing pandemic situation and better accessibility of potential participants, we plan to offer the course in a hybrid format.
 
We are happy to be able to win Andreas Hadjisavvas (The Cyprus Institute of Neurology and Genetics) as a local host and look forward to being able to offer an in-person course again, of course in compliance with all necessary hygiene regulations and subject to local pandemic regulations.
 
Like the previous courses, the course will cover a broad spectrum regarding variant interpretation and will be a mix of theory and practice presented by invited expert speakers (link to the program of the previous VEPTC 2021: https://veptc.variome.org/). Practical sessions and interactive workshops will be complemented by lectures to give participants a comprehensive overview of the state of the art in variant interpretation.
 
The expected participants are molecular geneticists, clinical geneticists, genetics researchers, molecular diagnostics labs, data analysts, medical specialists with interests in genomics or generally speaking anyone interpreting DNA variants on a regular basis.
 
Andreas Laner on behalf of the VEPTC Organizing Committee
 
CALL FOR MEMBERS!
 HGVS nomenclature

 
The HGVS Variant Nomenclature Committee (HVNC) is looking for new members. The main activity of the committee is to dhttps://humanvariomeproject.us1.list-manage.com/track/click?u=0634203d6f80b6aabccbff98e&id=265d192058&e=1602850b00">efine the standard for the unambiguous description of all sequence variants at the DNA, RNA and protein level, the so called HGVS nomenclature standard. The current standard can be found at the HGVS nomenclature website, www.HGVS.org/varnomen. A summary of the 2021 activities of the committee are reported elsewhere in this Newsletter.
 
Interested in the work of the HVNC? Willing to spend some spare time and join the committee? Please apply to become a member. HVNC members should together represent interested communities, including gene/disease specific database curators, central repositories, clinical geneticists, commercial diagnostic laboratories, bioinformaticians, scientific journals, etc.  Applications should include a motivation letter detailing relevant expertise and interests in HGVS nomenclature (max. 1-page A4) and a CV.
 
Applications should be mailed before March 1 to the HUGO office: amy@variome.org. Applications will be evaluated by the HVNC, and new members proposed to the HUGO board. New members will be appointed by the HUGO board. The term of membership of the HVNC will be for 4 years. Each member should attend a minimum of 50% of HVNC meetings over an 18-month period, otherwise they will forfeit their position.
 


HGVS nomenclature in 2021
 
The recommendations for the description of variants in DNA, RNA and protein sequences, HGVS nomenclature, is now under the wings of HUGO as the HGVS Variant Nomenclature Committee (HVNC), a member of the HUGO Nomenclature Standards Committee (HNSC). The committee wrote a Terms of Reference which was sent to the HUGO office for approval. The committee welcomed two new members; Ros Hastings (Oxford, UK) succeeded Jean McGowan-Jordan as the ISCN representative and Terence Murphy (NCBI, USA) succeeded Donna Maglott as representative of the major databases (EBI/NCBI). A call for new HVNC members will be published early 2022 (see elsewhere in this Newsletter).
 
The committee finalised an update of the accepted “Reference Sequences”. With active input from committee members Pete Causey-Freeman, Raymond Dalgleish, Reece Hart and extensive discussions with EBI and Genomics England LTD, Ensembl reference sequences (ENSG, ENST, ENSP) are now accepted as approved reference sequences. The HVNC completed the Community Consultation call for SVD-WG010 (var distance) suggesting changes to the nomenclature. Given the comments received, the proposal needs further improvements before it can be accepted. A modified proposal is in preparation. No new version of the HGVS nomenclature was released, the latest version remains v20.05.
 
Raymond Dalgleish, Pete Freeman and Johan den Dunnen, as members of the HVP Genetics Journals working group, co-authored a paper promoting the use of HGVS nomenclature: Higgins et al. (2021). “Verifying nomenclature of DNA variants in submitted manuscripts: Guidance for journals”. Hum.Mutat. 42(1), 3-7.
 
The SVD-WG chair, Johan den Dunnen (Leiden, NL), received ~160 questions about HGVS nomenclature (e-mail and facebook) all of which have been answered. Based on the questions received, 26 facebook posts were made, mirrored on the HGVS/HUGO twitter. Mostly triggered by questions or remarks received, a range of improvements were made to the HGVS nomenclature website (varnomen.hgvs.org), correcting errors, adding examples and improving explanation.
 
HGVS nomenclature website usage increased again showing 15-20% more daily visitors (peaking at 783 in November). Annual totals for 2021 are 692,443 pageviews (632k in 2020) in 209,112 sessions (185k in 2020), from 117,807 visitors (103k in 2020). The graphs show an expected weekly fluctuation and top 10 of visitor countries.
 
 
 
HGVS nomenclature presentations were given at several national and international meetings / courses / workshops but all online. In addition, June 2021 a series of bi-monthly online HGVS nomenclature Q&A sessions were started. So far four one-hour sessions have been completed. The interactive Q&A sessions use the DirectPoll system (www.DirectPoll.com), allowing participants to answer about 15-20 questions per session. In addition, using so called Socrative classrooms (www.Socrative.com), questions and answers have been made available for users which were not able to join the live online session. Up to over 200 users per classroom have so far used this option to test their knowledge on HGVS nomenclature.
 
 
 

We are thrilled to announce the new BRCA Exchange blog! This patient-oriented This patient-oriented blog will address topics that are commonly asked about in online patient support networks, including: types of genetic tests, genetic data privacy, and how you can learn if there's anything new on your variant. We welcome any suggestions for new topics.

https://brcaexchange.org/blog/

 

We have just completed a new data release from the main programme of the 100,000 Genomes Project, consisting of rare disease and cancer participants.
Data Release Version 14 provides clinical data for 90,259 participants, and 118,448 genomes from 86,997 of these participants. Of these genomes, 75,526 are rare disease genomes (from 72,726 participants) and 42,922 are cancer genomes (from 14,271 participants).




To help you use this data and understand what is available, we have published a data release noteThis release note is accessible both inside and outside the Research Environment on the help pages.

What’s new in this data release?
This release has a significant increase in the number of participants because we have re-introduced participants that were previously excluded due to having expired child consent (turned 16 without reconsenting as adults). Consultation confirmed that these participants should not be removed as ineligible participants provided that we do not include any new data from after the age of 16, so secondary data for these participants has been trimmed.
Secondly, this release includes the Mental Health Services Data Set (MHSDS) from NHS Digital, currently covering the period 2016-2019. This new dataset is based on a different data model to previous mental health data in the Research Environment, please refer to the data release note for full details.

 
 
 
 
 
Joint Dutch/UK Clinical Genetics Societies and Cancer Genetics Group Meeting
07-10 March, 2022
Rotterdam, Netherlands 
 
The 8th Joint Dutch/UK Clinical Genetics Societies and Cancer Genetics Groups meeting is being held on 7-8th March 2022 in Rotterdam. The program includes invited presentations on all topics across the field of clinical genetics. The central theme of the 8th joint meeting will be: “Next Generation Genetics”. 
 
Full details: https://www.clingensoc.org/events/joint-dutchuk-clinical-genetics-societies-and-cancer-genetics-group-meeting/
 
 
Progress in Genomic Medicine Implementation: Research Priorities and Population Health Impact
17 March, 2022, 11:00 am -12:00 pm ET
Virtual

 
This seminar will provide an overview of progress and ongoing challenges in genomic medicine in the last two decades and outlines research initiatives at the National Human Genome Research Institute that seek to advance the evaluation and implementation of new genome discoveries into clinical care and population health.
 
Full details: https://www.cdc.gov/genomics/events/progress_in_genomic_medicine_2022.html
 

Genomics of Rare Disease – Wellcome Connecting Science

28–29 March 2022
Wellcome Genome Campus, UK

The 16th in Wellcome Connecting Science’s series of meetings on rare diseases will present an exciting blend of genomic science and clinical medicine. This meeting will explore how cutting-edge genomic research translates into clinical care and informs our understanding of the biology of rare disease.

This year’s meeting will discuss how the use of diverse genomes can help drive precision medicine and more equitable healthcare benefits. They will also focus on non-Mendelian forms of rare disease and new approaches to treat rare disease.  They will also discuss how high-throughput functional assays can improve the interpretation of variants and discuss the ongoing challenges and opportunities in implementing genomics in mainstream healthcare systems across the world.

Abstract deadline | 02 February 2022   |    Registration deadline | 22 March 2022

Full details – https://coursesandconferences.wellcomeconnectingscience.org/event/genomics-of-rare-disease-20220328/

 
Primary Care and Public Health 2022
11-12 May 2022
Birmingham, UK

 
Primary Care and Public Health is a key annual event for GPs, federations, CCGs, primary care and community pharmacists, nurses, midwives, allied health professionals, and healthcare managers in primary care, community care, public and prison health.
 
Full details: https://www.genomicseducation.hee.nhs.uk/events/primary-care-and-public-health-2020/
 
 

Digital Health World Congress 2022
17-18 May 2022
London, UK

 
We are excited to announce this year’s keynotes and speakers for at the annual conference Digital Health World Congress 2022 in London, UK. These include HUMA, Oracle, IBM, Google, ORCHA,Thrive Wearables and many more!

Registration deadline | 17 May 2022
Full details: https://digitalhealthcareworldcongress.com/
 

 


We welcome you to the 14th International Congress of Human Genetics (ICHG2023) to be held in Cape, South Africa, proudly hosted by the African Society of Human Genetics (AfSHG) and the Southern African Society for Human Genetics (SASHG).
 
Taking into account the COVID-19 pandemic, we are formally sharing the news that the ICHG will be postponed to 22-26 February, 2023. 
 
Warm regards
Raj Ramesar and Charles Rotimi
(Co-Chairs LOC/ICHG 2023)
 
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