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GV Newsletter - July 2022

 
 


We all had a wonderful time at HGM2022! We hope you did as well and made friends and new collaborations!

Here are the photos for all of you to see
https://www.hugo-hgm2022.org/About/ConferenceGallery2022.aspx">https://www.hugo-hgm2022.org/About/ConferenceGallery2022.aspx
 
Looking forward to the next HUGO Meeting!

Karen, Eran and Charles
The Conference Secretariat

ORTRA LTD.
P. O. Box 9352
Tel-Aviv 6109202, Israel
Tel: +972-3-6384444
Fax: +972-3-6384455
 

 view the program
 
We’re excited to let you know the program for veptc 2022 is now available and registration is open!  The 6th annual Variant Effect Prediction Training Course - veptc 2022  will be held 20 to 22 Sept 2022 in Nicosia, Cyprus!   

This year for the first time we will offer a hybrid course: an in-person and a virtual option. In-person atte ndance is encouraged for the most interactive workshop experience.

In-person attendees have the option to select a Basic or Advanced workshop for "Ensembl Genome Browser", "UCSC Genome Browser" and "ACMG variant grading (inc. cancer)".

Visit the website to learn more and to register (in-person places are limited), earlybird ends 31st July: veptc.variome.org
 
https://hugo-international.us1.list-manage.com/track/click?u=8b89ab9930fa0d9d5f17116d3&id=82064b8cc0&e=557fa9242e">

secure your place & find out more
 
New HVNC members
 
HUGO has completed the nomination process for new members of the HUGO “HGVS Variant Nomenclature Committee”.
 
After a call in January, HUGO received nine applications for membership of the “HGVS Variant Nomenclature Committee” (HVNC). The first step of the process was a meeting of the current HVNC members who evaluated the applications received. Based on the application letter, the CV, the applicants' expertise, the interest fields represented, and the expertise of the sitting committee members, the applications were rated. The HVNC selected four and proposed to the HUGO board to appoint these as new members for a four-year term (2022-2026). On May 23, the HUGO board met and accepted the HVNC proposal and nominated Marina DiStefano (USA), Rachel Taylor (UK), Jeroen Laros (Netherlands) and Alex Wagner (USA) as new HVNC members.
 
A new call for HVNC members will be released early 2024. Interested? Please make a note in your agenda to make sure you do not forget to apply. The current committee esp. lacks members representing Asia, Africa and South-America.
 
With the new nominations the current HVNC members are: Raymond Dalgleish (UK), Reece Hart (USA), Peter Causey Freeman (UK), Terence Murphy (USA), Ros Hastings (UK), Marina DiStefano (USA), Rachel Taylor (UK), Jeroen Laros (Netherlands), Alex Wagner (USA) and Johan den Dunnen (Netherlands, chair).
 
 
THANK YOU leaving HVNC members
 
With the nomination of four new members of the HUGO “HGVS Variant Nomenclature Committee”, we also have some leaving members.
 
First, we need to thank Anne-Francoise Roux (France), who joined the committee in 2014. Over the many years she served in the committee, Anne-Francoise represented the diagnostic testing laboratories, paying special attention to the practical implications of the HGVS nomenclature recommendations. Also, a thank you to Peter Taschner (Netherlands). Peter was a member of the committee from day 1, representing the gene variant databases (formerly known as LSDBs), with a special focus on the practicalities of the HGVS nomenclature for storing and retrieving variants in genomic databases. Besides being an active curator for several LOVD-powered gene variant databases, Peter was also instrumental in the development of the first on-line tool to check and generate HGVS variant descriptions, the Mutalyzer tool set (www.Mutalyzer.nl).
 
Anne-Francoise and Peter, on behalf of HUGO and the genetics community, thank you very much for dedicating part of your precious spare time to the important topic of HGVS nomenclature!! 

As small token of appreciation HUGO offers the leaving members a 50% discount on a 2-year membership to HUGO.
 


Congratulations
 to our HUGO Pathogenicity committee co-chair, Melissa Cline, who has been featured in a GA4GH article; a beautiful piece on some of the work she has recently published!
 
https://ctkd304.na1.hubspotlinks.com/Ctc/2J+113/ctKd304/VVFMJr3NpdPrW8TwY7J3tZyrVW2gkVcw4K_0YpN6klYVQ5nKvpV3Zsc37CgLk8W9fBTtg3_y3WHW78KVzc3sSlcxW6jNyvx5rYWMpW1FZ3rd15ZcnkW2pngk42hM4lDW238x884L1__FW8YF3G72wn8SsW6-QkkP1gryGHW1byN832C7YDCW4jVqLJ6X9gwTW2r4gg-">How a bot beamed from California to Japan may prevent cancer patients from losing their breasts unnecessarily
Too many women are getting unnecessary mastectomies and other invasive procedures because of a knowledge gap in cancer gene mutations. A new study offers a path to closing the gap, thanks to the data-sharing innovation of federated analysis.
 
 

Congratulations
 to our HUGO Education committee co-chair, Dhavendra Kumar, for the publication of the new book 'Genomic Medicine - Skills and Competencies'. This book is relevant in keeping with the HUGO Genomic Education mission/ objectives. It is part of the large series on 'Genomic and Precision Medicine in Clinical Practice'.
 
 
Genomic Variant Analysis and Clinical Interpretation
Virtual course
 
This is an ongoing course is designed to provide in-depth understanding of concepts as well as hands-on exposure to genomic variant analysis and clinical interpretation and would have online lectures during weekends (Saturday and Sunday) as well as assignments for weekdays (Monday - Friday).
 
Full details: http://gvaci.genomes.in">http://gvaci.genomes.in 
 
"The Future of Genetics in Angola"
30 June – 01 July 2022
College of Medicine - Universidade Agostinho Neto (Hybrid)
 
The Genetics Department of the Faculty of Medicine of the University Agostinho Neto (AG_FMUAN) is proud to announce its II International Genetics Symposium under the slogan "The Future of Genetics in Angola" on Thursday 30th June and Friday 1st July 2022, in a hybrid format (in-person and online). We expect to have a successful event, with around 200 expert guests and speakers, both national and international. The event is part of the scientific agenda of the International Center for Genetic Engineering and Biotechnology (ICGBE), of which Angola is a member state.
 
Full details: https://www.labiogene.com/copy-of-home">https://www.labiogene.com/copy-of-home
 
Genomics for Clinicians 
1st week, July 2022
Virtual
 
Genomics for Clinicians is an online introductory course for clinicians on genomics and genomic applications in clinical medicine. The course is designed for clinicians, genetic counsellors, nurses and nursing students to provide an overview of genomics and applications in clinical settings.
 
The course will commence in July 1st week
Online course with 5 sessions. The sessions can be taken online, at your convenience.
 
Full details: https://guardian.genomes.in/events/genomics-for-clinicians">https://guardian.genomes.in/events/genomics-for-clinicians
 
Board of Genetic Counselling India - 7th Annual International Conference
01-03 July, 2022
Ahmedabad, India (Hybrid)

 
This conference aims to promote education among genetic counsellors, doctors, health care providers, and students about current topics in genetics, genomics, and genetic counselling. The conference is expected to have 20 International speakers who are experts in genomic medicine/ genetic counselling and over 500 physical and 3000 online delegates from across the globe.
 
The science of genetics is influencing medicine at a rapid pace. The chief intent of the conference is to connect the practitioners from different specialties with the counsellors, diagnostic companies and researchers using latest advances and experiences shared by renowned speakers.
Genetic counselling can help in understanding the genetic predisposition, determine the right genetic test and help in early and accurate diagnosis. A genetic test can help establish a clinical diagnosis, identify the likely causative mutation, understand the disease progression, opt for rehabilitation (wherever possible), guide targeted therapy (if available) and help tailor patient care thus enabling a better quality of life. This further creates an opportunity for families to make informed healthcare and reproductive decisions.
 
Full details: http://www.bgciconference.com/registration.html
 
Bioinformatics Open Source Conference (BOSC)
13-14 July 2022
Wisconsin, USA (Hybrid)

 

BOSC 2022 will take place July 13-14, 2022, as part of ISMB 2022. The meeting will be held both in person in Madison, Wisconsin, USA (following safety protocols), and simultaneously online.

This year, BOSC and Bio-Ontologies will join forces for part of a day! The joint session will include talks chosen from abstracts plus keynote speaker Melissa Haendel.

Keynote speaker Jason Williams‘s talk will be a joint BOSC/Education COSI keynote.

The BOSC 2022 program will also include a panel about Building and Sustaining Inclusive Open Science Communities.
 

Full details: https://www.open-bio.org/events/bosc-2022/ 
 
Human and Mammalian Genetics and Genomics: The 63rd McKusick Short Course
18-28 July, 2022
Bar Harbor, US (Hybrid)

 
Offered annually for over 60 years, the ‘Short Course’ is a 2-week program consisting of an immersive set of lectures, workshops, tutorials and demonstrations to understand the breadth of modern human genetics. The faculty includes leaders in contemporary genetics and genomics from Johns Hopkins, The Jackson Laboratory and other institutions around the world. The course covers basic science, clinical and translational aspects of human genetics and genomics, and runs the gamut from gene and variant discovery in Mendelian and complex disease, genome biology, the molecular basis of genetic disease, the use of animal models of human disease to understand pathophysiology, as well as genetic disease treatment and therapy. Workshops and lectures also cover bioinformatics, population genetics, genome manipulation, mutagenesis and phenotyping. 
This course includes daily lectures in the mornings and evenings as well as afternoon mini-symposia, workshops, tutorials, demonstrations and a poster session. There is special emphasis on student-faculty interaction. The faculty is diverse in terms of disciplines and the students in terms of stage of career and fields of concentration. This diversity makes for an enriching experience for all. Although the course schedule is quite full, there is time set aside to enjoy the natural beauty of Mt. Desert Island and Acadia National Park.
 
Full details: https://www.jax.org/education-and-learning/education-calendar/2022/july/human-and-mammalian-genetics-and-genomics-the-63rd-mckusick-short-course
 

13th Annual Meeting of the Cancer Genomics Consortium (CGC) 
31 July - 3 Aug, 2022
St Louise, Missouri , US

...

Posted by on in News
GV Newsletter - June 2022

 
 


We all had a wonderful time at HGM2022! We hope you did as well and made friends and new collaborations!

Here are the photos for all of you to see
https://www.hugo-hgm2022.org/About/ConferenceGallery2022.aspx">https://www.hugo-hgm2022.org/About/ConferenceGallery2022.aspx
 
Looking forward to the next HUGO Meeting!

Karen, Eran and Charles
The Conference Secretariat

ORTRA LTD.
P. O. Box 9352
Tel-Aviv 6109202, Israel
Tel: +972-3-6384444
Fax: +972-3-6384455
 

 view the program
 
We’re excited to let you know the program for veptc 2022 is now available and registration is open!  The 6th annual Variant Effect Prediction Training Course - veptc 2022  will be held 20 to 22 Sept 2022 in Nicosia, Cyprus!   

This year for the first time we will offer a hybrid course: an in-person and a virtual option. In-person atte ndance is encouraged for the most interactive workshop experience.

In-person attendees have the option to select a Basic or Advanced workshop for "Ensembl Genome Browser", "UCSC Genome Browser" and "ACMG variant grading (inc. cancer)".

Visit the website to learn more and to register (in-person places are limited), earlybird ends 31st July: veptc.variome.org
 
https://hugo-international.us1.list-manage.com/track/click?u=8b89ab9930fa0d9d5f17116d3&id=82064b8cc0&e=557fa9242e">

secure your place & find out more
 
New HVNC members
 
HUGO has completed the nomination process for new members of the HUGO “HGVS Variant Nomenclature Committee”.
 
After a call in January, HUGO received nine applications for membership of the “HGVS Variant Nomenclature Committee” (HVNC). The first step of the process was a meeting of the current HVNC members who evaluated the applications received. Based on the application letter, the CV, the applicants' expertise, the interest fields represented, and the expertise of the sitting committee members, the applications were rated. The HVNC selected four and proposed to the HUGO board to appoint these as new members for a four-year term (2022-2026). On May 23, the HUGO board met and accepted the HVNC proposal and nominated Marina DiStefano (USA), Rachel Taylor (UK), Jeroen Laros (Netherlands) and Alex Wagner (USA) as new HVNC members.
 
A new call for HVNC members will be released early 2024. Interested? Please make a note in your agenda to make sure you do not forget to apply. The current committee esp. lacks members representing Asia, Africa and South-America.
 
With the new nominations the current HVNC members are: Raymond Dalgleish (UK), Reece Hart (USA), Peter Causey Freeman (UK), Terence Murphy (USA), Ros Hastings (UK), Marina DiStefano (USA), Rachel Taylor (UK), Jeroen Laros (Netherlands), Alex Wagner (USA) and Johan den Dunnen (Netherlands, chair).
 
 
THANK YOU leaving HVNC members
 
With the nomination of four new members of the HUGO “HGVS Variant Nomenclature Committee”, we also have some leaving members.
 
First, we need to thank Anne-Francoise Roux (France), who joined the committee in 2014. Over the many years she served in the committee, Anne-Francoise represented the diagnostic testing laboratories, paying special attention to the practical implications of the HGVS nomenclature recommendations. Also, a thank you to Peter Taschner (Netherlands). Peter was a member of the committee from day 1, representing the gene variant databases (formerly known as LSDBs), with a special focus on the practicalities of the HGVS nomenclature for storing and retrieving variants in genomic databases. Besides being an active curator for several LOVD-powered gene variant databases, Peter was also instrumental in the development of the first on-line tool to check and generate HGVS variant descriptions, the Mutalyzer tool set (www.Mutalyzer.nl).
 
Anne-Francoise and Peter, on behalf of HUGO and the genetics community, thank you very much for dedicating part of your precious spare time to the important topic of HGVS nomenclature!! 

As small token of appreciation HUGO offers the leaving members a 50% discount on a 2-year membership to HUGO.
 


Congratulations
 to our HUGO Pathogenicity committee co-chair, Melissa Cline, who has been featured in a GA4GH article; a beautiful piece on some of the work she has recently published!
 
https://ctkd304.na1.hubspotlinks.com/Ctc/2J+113/ctKd304/VVFMJr3NpdPrW8TwY7J3tZyrVW2gkVcw4K_0YpN6klYVQ5nKvpV3Zsc37CgLk8W9fBTtg3_y3WHW78KVzc3sSlcxW6jNyvx5rYWMpW1FZ3rd15ZcnkW2pngk42hM4lDW238x884L1__FW8YF3G72wn8SsW6-QkkP1gryGHW1byN832C7YDCW4jVqLJ6X9gwTW2r4gg-">How a bot beamed from California to Japan may prevent cancer patients from losing their breasts unnecessarily
Too many women are getting unnecessary mastectomies and other invasive procedures because of a knowledge gap in cancer gene mutations. A new study offers a path to closing the gap, thanks to the data-sharing innovation of federated analysis.
 
 

Congratulations
 to our HUGO Education committee co-chair, Dhavendra Kumar, for the publication of the new book 'Genomic Medicine - Skills and Competencies'. This book is relevant in keeping with the HUGO Genomic Education mission/ objectives. It is part of the large series on 'Genomic and Precision Medicine in Clinical Practice'.
 
 
Genomic Variant Analysis and Clinical Interpretation
Virtual course
 
This is an ongoing course is designed to provide in-depth understanding of concepts as well as hands-on exposure to genomic variant analysis and clinical interpretation and would have online lectures during weekends (Saturday and Sunday) as well as assignments for weekdays (Monday - Friday).
 
Full details: http://gvaci.genomes.in">http://gvaci.genomes.in 
 
"The Future of Genetics in Angola"
30 June – 01 July 2022
College of Medicine - Universidade Agostinho Neto (Hybrid)
 
The Genetics Department of the Faculty of Medicine of the University Agostinho Neto (AG_FMUAN) is proud to announce its II International Genetics Symposium under the slogan "The Future of Genetics in Angola" on Thursday 30th June and Friday 1st July 2022, in a hybrid format (in-person and online). We expect to have a successful event, with around 200 expert guests and speakers, both national and international. The event is part of the scientific agenda of the International Center for Genetic Engineering and Biotechnology (ICGBE), of which Angola is a member state.
 
Full details: https://www.labiogene.com/copy-of-home">https://www.labiogene.com/copy-of-home
 
Genomics for Clinicians 
1st week, July 2022
Virtual
 
Genomics for Clinicians is an online introductory course for clinicians on genomics and genomic applications in clinical medicine. The course is designed for clinicians, genetic counsellors, nurses and nursing students to provide an overview of genomics and applications in clinical settings.
 
The course will commence in July 1st week
Online course with 5 sessions. The sessions can be taken online, at your convenience.
 
Full details: https://guardian.genomes.in/events/genomics-for-clinicians">https://guardian.genomes.in/events/genomics-for-clinicians
 
Board of Genetic Counselling India - 7th Annual International Conference
01-03 July, 2022
Ahmedabad, India (Hybrid)

 
This conference aims to promote education among genetic counsellors, doctors, health care providers, and students about current topics in genetics, genomics, and genetic counselling. The conference is expected to have 20 International speakers who are experts in genomic medicine/ genetic counselling and over 500 physical and 3000 online delegates from across the globe.
 
The science of genetics is influencing medicine at a rapid pace. The chief intent of the conference is to connect the practitioners from different specialties with the counsellors, diagnostic companies and researchers using latest advances and experiences shared by renowned speakers.
Genetic counselling can help in understanding the genetic predisposition, determine the right genetic test and help in early and accurate diagnosis. A genetic test can help establish a clinical diagnosis, identify the likely causative mutation, understand the disease progression, opt for rehabilitation (wherever possible), guide targeted therapy (if available) and help tailor patient care thus enabling a better quality of life. This further creates an opportunity for families to make informed healthcare and reproductive decisions.
 
Full details: http://www.bgciconference.com/registration.html
 
Bioinformatics Open Source Conference (BOSC)
13-14 July 2022
Wisconsin, USA (Hybrid)

 

BOSC 2022 will take place July 13-14, 2022, as part of ISMB 2022. The meeting will be held both in person in Madison, Wisconsin, USA (following safety protocols), and simultaneously online.

This year, BOSC and Bio-Ontologies will join forces for part of a day! The joint session will include talks chosen from abstracts plus keynote speaker Melissa Haendel.

Keynote speaker Jason Williams‘s talk will be a joint BOSC/Education COSI keynote.

The BOSC 2022 program will also include a panel about Building and Sustaining Inclusive Open Science Communities.
 

Full details: https://www.open-bio.org/events/bosc-2022/ 
 
Human and Mammalian Genetics and Genomics: The 63rd McKusick Short Course
18-28 July, 2022
Bar Harbor, US (Hybrid)

 
Offered annually for over 60 years, the ‘Short Course’ is a 2-week program consisting of an immersive set of lectures, workshops, tutorials and demonstrations to understand the breadth of modern human genetics. The faculty includes leaders in contemporary genetics and genomics from Johns Hopkins, The Jackson Laboratory and other institutions around the world. The course covers basic science, clinical and translational aspects of human genetics and genomics, and runs the gamut from gene and variant discovery in Mendelian and complex disease, genome biology, the molecular basis of genetic disease, the use of animal models of human disease to understand pathophysiology, as well as genetic disease treatment and therapy. Workshops and lectures also cover bioinformatics, population genetics, genome manipulation, mutagenesis and phenotyping. 
This course includes daily lectures in the mornings and evenings as well as afternoon mini-symposia, workshops, tutorials, demonstrations and a poster session. There is special emphasis on student-faculty interaction. The faculty is diverse in terms of disciplines and the students in terms of stage of career and fields of concentration. This diversity makes for an enriching experience for all. Although the course schedule is quite full, there is time set aside to enjoy the natural beauty of Mt. Desert Island and Acadia National Park.
 
Full details: https://www.jax.org/education-and-learning/education-calendar/2022/july/human-and-mammalian-genetics-and-genomics-the-63rd-mckusick-short-course
 

13th Annual Meeting of the Cancer Genomics Consortium (CGC) 
31 July - 3 Aug, 2022
St Louise, Missouri , US

...

Posted by on in News
GV Newsletter - May 2022

 
President-Elect of HUGO


The HUGO Executive Board is pleased to announce the appointment of Ada Hamosh as the next HUGO President. Effective immediately, Ada will serve as Vice President and will step into the shoes of Charles Lee as President of HUGO on March 31st, 2023. 

Typically, the outgoing President stays on the Executive Board for an additional year. However, Charles Lee would like to step down. We are pleased to announce that John Burn will take on this role in March 2023.
 
Ada and John bring a lot of experience and great enthusiasm, please join us in welcoming them!
 


What a remarkable Human Genome Meeting in Tel Aviv this was! We want to thank those of you who attended for joining us. 
 
Above is a photo from the wrap-up, right after we heard Prof. Ed Liu’s inspiring words about where genomics is going in the future. We will send you a link to all the photos from the meeting, as well as links to the recordings for those who registered, to ensure you can hear the talks you missed from the concurrent sessions, or if you were unable to attend.
 
Congratulations to the poster prize winners: Lukasz S. Kaczmarczyk, Simon Fishilevich, Hagai Levi, Lior Ankol Redlich, Christina Canavati, Yael Shalev Ezra

         Looking forward to meet you at future HUGO HGM meetings!
         Karen Avraham (Tel Aviv)


 
 

view the program
 
We’re excited to let you know the program for veptc 2022 is now available and registration is open!  The 6th annual Variant Effect Prediction Training Course - veptc 2022  will be held 20 to 22 Sept 2022 in Nicosia, Cyprus!   

This year for the first time we will offer a hybrid course: an in-person and a virtual option. In-person attendance is encouraged for the most interactive workshop experience.

In-person attendees have the option to select a Basic or Advanced workshop for "Ensembl Genome Browser", "UCSC Genome Browser" and "ACMG variant grading (inc. cancer)".

Visit the website to learn more and to register (in-person places are limited), earlybird ends 31st July: veptc.variome.org
 
https://hugo-international.us1.list-manage.com/track/click?u=8b89ab9930fa0d9d5f17116d3&id=82064b8cc0&e=557fa9242e">

secure your place & find out more
 
Call for nomination of members of The International Standing Committee of Human Cytogenomic Nomenclature:
 
The present Committee (Laura K. Conlin, Johan T. den Dunnen, Rosalind J. Hastings, Jin-Yeong Han, Nils Mandahl, Jean McGowan-Jordan, Sarah Moore, Cynthia C. Morton) was elected in the spring of 2018, with Jean McGowan-Jordan as Chair. The Committee elected a new Chair, Rosalind Hastings, following the publication of ISCN 2020. There are three vacancies on the ISCN Committee that now need to be elected. To facilitate continuity and maintain geographic distribution of the committee, new members are required from the Asia (1), Europe or Americas (1), Africa and Australia/New Zealand/Oceania (1).
 
The position is non-remunerable and for a period of four years in the first instance. Most meeting are held remotely and expenses are paid for any in-person meetings. An excellent working knowledge of English is essential
 
Interested applicants should have an extensive background in ISCN and experience of reporting complex cytogenomic results. The applicant should either be a head of department; section or a senior member of department. 
 
Applicants should submit a short CV plus a supporting letter explaining how they could contribute to the committee to ros.hastings@ouh.nhs.uk?subject=NOMINATION%3A%20The%20International%20Standing%20Committee%20of%20Human%20Cytogenomic%20Nomenclature">ros.hastings@ouh.nhs.uk. The CV should be no longer than one A4 page in length. All nomination must be made or seconded by a Head or Section Head of a diagnostic laboratory. Self- nominations will not be accepted.
 
The nominations of potential new Committee members shall be by email. Nominations for candidates including their name, affiliation, postal address and e-mail address should be e-mailed to the Chair at ros.hastings@ouh.nhs.uk before June 17, 2022, after which the list of nominated candidates will be published with the call for voting. Ballots for voting can be requested from the Chair at ros.hastings@ouh.nhs.uk?subject=NOMINATION%3A%20The%20International%20Standing%20Committee%20of%20Human%20Cytogenomic%20Nomenclature">ros.hastings@ouh.nhs.uk after June 17, 2022, by including your name, affiliation, postal address, and email. The election ballots with voting procedures will then be distributed after July 22, 2022 to the requested address. Instructions for returning the ballots will accompany the ballot requests.
 
Genomic Variant Analysis and Clinical Interpretation
Virtual course
 
This is an ongoing course is designed to provide in-depth understanding of concepts as well as hands-on exposure to genomic variant analysis and clinical interpretation and would have online lectures during weekends (Saturday and Sunday) as well as assignments for weekdays (Monday - Friday).
 
Full details: http://gvaci.genomes.in">http://gvaci.genomes.in 
 
International Data Week 2022
20-23 June 2022
Seoul, South Korea (Hybrid)

 
This landmark event will bring together data scientists, researchers, industry leaders, entrepreneurs, policymakers, and data stewards from disciplines across the globe to explore how best to exploit the data revolution to improve science and society through data-driven discovery and innovation. IDW 2022 combines the 19th RDA Plenary Meeting, the biannual meeting of this international member organization working to develop and support global infrastructure facilitating data sharing and reuse, and SciDataCon 2022, the scientific conference addressing the frontiers of data in research organized by CODATA and WDS.

Full details: https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhumanvariomeproject.us1.list-manage.com%2Ftrack%2Fclick%3Fu%3D0634203d6f80b6aabccbff98e%26id%3Dd49b7cab12%26e%3Dd5da02100c&data=04%7C01%7Cjohn.burn%40newcastle.ac.uk%7Cf86dceba63a1469ff8870">https://www.rd-alliance.org/plenaries/rda-19th-plenary-meeting-part-international-data-week-20%E2%80%9323-june-2022-seoul-south-korea
 
 
"The Future of Genetics in Angola"
30 June – 01 July 2022
College of Medicine - Universidade Agostinho Neto (Hybrid)
 
The Genetics Department of the Faculty of Medicine of the University Agostinho Neto (AG_FMUAN) is proud to announce its II International Genetics Symposium under the slogan "The Future of Genetics in Angola" on Thursday 30th June and Friday 1st July 2022, in a hybrid format (in-person and online). We expect to have a successful event, with around 200 expert guests and speakers, both national and international. The event is part of the scientific agenda of the International Center for Genetic Engineering and Biotechnology (ICGBE), of which Angola is a member state.
 
Full details: https://www.labiogene.com/copy-of-home">https://www.labiogene.com/copy-of-home
 
Genomics for Clinicians 
1st week, July 2022
Virtual
 
Genomics for Clinicians is an online introductory course for clinicians on genomics and genomic applications in clinical medicine. The course is designed for clinicians, genetic counsellors, nurses and nursing students to provide an overview of genomics and applications in clinical settings.
 
The course will commence in July 1st week
Online course with 5 sessions. The sessions can be taken online, at your convenience.
 
Full details: https://guardian.genomes.in/events/genomics-for-clinicians">https://guardian.genomes.in/events/genomics-for-clinicians
 
SAVE THE DATE - GA4GH 10th Plenary Meeting
22-23 September 2022
Barcelona


Full details of registration with be announced soon
 


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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GV Newsletter - March 2022

 


SUBMIT YOUR ABSTRACT! 
 

We would like to invite you to attend the Human Genome Meeting (HGM 2022) The Next Frontiers in Genomics - which will take place at the Dan Panorama Hotel in Tel Aviv, Israel on May 23-25, 2022. This will be a hybrid meeting. HGM 2022 will have, with your help, a captivating program of plenary lectures, symposia, workshops, poster presentations, lectures and social events. Our scientific program will cover a wide range of topics in human genomics to share the most up-to-date research trends, results, information and databases, which often sparks off new collaboration opportunities.

We plan to create a memorable, extraordinary conference in Tel Aviv, which is considered to be the liveliest city in the region - The City that Never Sleeps. This will be the very first time that an HGM is held in Israel and we look forward to welcome its participants to Tel Aviv for an experience of a lifetime.

Our sessions will cover the following:

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Posted by on in News
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/

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Posted by on in News
GV Newsletter - December 2021

 


More information, please visit: https://www.hugo-hgm2022.org/
 
One activity of HVP/GV that has continued under the new organization of HUGO is a working group of Genetics Journals Editors. Chaired by Garry Cutting (Human Mutation), the group meets monthly online to discuss topics of mutual interest. A key focus has been the adoption of HGVS nomenclature for variant descriptions in all publications. As a first step, the group conducted a pilot study to evaluate the workload imposed by requiring authors to verify variant compliance with HGVS nomenclature using public software. The two primary software tools are Mutalyzer and Variant Validator.  Editorial staff at Human Genetics and Genetics in Medicine conducted the pilot and reporting that the burden of variant validation to editorial staff to editorial staff was minimal. 

Earlier this year the group published their result along with guidelines for implementing variant validation: Higgins et al. (2020). Verifying nomenclature of DNA variants in submitted manuscripts: Guidance for journals. Hum Mutat. 2021 42: 3-7 (https://onlinelibrary.wiley.com/doi/epdf/10.1002/humu.24144">https://onlinelibrary.wiley.com/doi/epdf/10.1002/humu.24144).

The manuscript recommends that journals require authors check variant descriptions using online tools like Mutalyzer (www.Mutalyzer.nl) or Variant Validator (www.variantvalidator.org). One metric to evaluate adoption of these guidelines is traffic at the websites that offer variant validation tools. The Mutalyzer team shared the the figure below. Based on unique IP addresses the number of monthly variant check requests nearly tripled when the Guidelines paper was published online. 

The Variant Validator group reported that prior to December 2019, the batch analysis was only being used sporadically. Since the Pilot Project, we are seeing above 500 users a month at least, and since the paper was released, this has increased to around 800-1000 users a month.
 
These are remarkable results, illustrating that journals can be instrumental in the adoption of genomics standards that improve the quality of variant data published.

 

HUGO Gene Nomenclature Committee recommendations for the designation of gene fusions

 
The HUGO Gene Nomenclature Committee (HGNC) has recently published a new recommendation that fusion genes be designated using a double colon (e.g.BCR::ABL) (Bruford et al., 2021). Fusion genes are a common feature in the causation of particular tumour types, and can arise as a consequence of reciprocal translocations, such as are seen in Burkitt lymphoma (BL) and in chronic myeloid leukaemia (CML). CML is now known to result from the creation of a fusion gene, at the breakpoint, comprising the 5′ part of the BCR gene at 22q11 with the 3′ part of the ABL1 tyrosine kinase-encoding gene from 9q34. The abnormal protein expressed from this fusion gene displays increased tyrosine kinase activity. To date, almost 1000 gene fusions have been found by genomic characterization of breakpoints in cytogenetically identified aberrations, balanced as well as unbalanced, in various leukaemias, lymphomas, and solid tumours.

There has never been a generally recommended, standardised way to denote gene fusions. Instead, multiple notations have been used with varying popularity over time, the most common designation being SYMBOL-SYMBOL, followed by SYMBOL/SYMBOL. However, both designations have shortcomings. Hyphens are already used in the designation of readthrough transcripts (e.g.INS-IGF2), of members of protein complexes (e.g., MRE11-RAD50-NBN), or within some gene symbols (e.g.TRX-CAT1-2). Similarly, the forward slash is used by the International System for Human Cytogenomic Nomenclature (ISCN) to denote different clones, both constitutionally (mosaicism) and in cancer cells, and the Human Genome Variation Society (HGVS) guidelines also use a forward slash to indicate mosaicism. It is also used in the literature in place of “either/or” (e.g.BRCA1/2), to denote involvement of alternative genes in a fusion (e.g.SS18-SSX1/SSX2), and in pathway and complex descriptions (e.g., RAS/RAF/MAPK).

To avoid further potential confusion arising from the multiple possible meanings of hyphens and forward slashes, HGNC consulted with a group of experts and proposed the use of a double colon (::). which denotes break and reunion in ISCN nomenclature, and was first established in the HGVS variant guidelines to indicate transcript fusions.
This new standard has already attracted attention from others, with one group proposing future extensions to the standard (Wagner et al., 2021) and the authors of a new review on round cell sarcomas having embraced the new standard (Kallen and Hornick, 2021).

 

References:

  • Bruford EA, Antonescu CR, Carroll AJ, Chinnaiyan A, Cree IA, Cross NCP, et al. (2021) HUGO Gene Nomenclature Committee (HGNC) recommendations for the designation of gene fusions. Leukemia, 35:3040-3043. DOI: 10.1038/s41375-021-01436-6

  • Kallen ME, Hornick JL (2021) From the ashes of "Ewing-like" sarcoma: A contemporary update of the classification, immunohistochemistry, and molecular genetics of round cell sarcomas. Semin Diagn Pathol, published online ahead of print. DOI: 10.1053/j.semdp.2021.10.002

  • Wagner AH, Akkari Y, Li M, Roy A, Tsuchiya K, Raca G (2021) Recommendations for future extensions to the HGNC gene fusion nomenclature. Leukemia, published online ahead of print. DOI: 10.1038/s41375-021-01458-0




HGVS nomenclature Q&A 
 
The third HGVS nomenclature online Q&A session took place on November 9th.  Not many participants were present live, but it was still an entertaining session. Johan den Dunnen posted questions on HGVS nomenclature which participants answered using the DirectPoll platform. As in previous sessions, no participant was able to answer all questions correctly.
 
Want to give it a try?  The questions are available on Socrative (https://api.socrative.com/rc/iLc982), classroom HGVSonline3). 
 
Joining live is much more fun: the next online Q&A session will be on January 11, 3pm GMT. Want to join? Please register:
(https://us02web.zoom.us/meeting/register/tZAqcO-urjkrH9UoMfHbIxL9f58jFQhXDVuo">https://us02web.zoom.us/meeting/register/tZAqcO-urjkrH9UoMfHbIxL9f58jFQhXDVuo).
 
One of the questions was:
           Who knows variant NC_045512.2:g.23604C>G?  What is it?
           Do you know? (for the right answer see the end of the Newsletter)


  
If you have any comments, suggestions or questions you would like answered for these sessions, please let us know. 
 
Interested to support the HGVS nomenclature work? Please consider sponsoring one of the bi-monthly meetings. For details, please contact amy@variome.org">amy@variome.org. Of course, we will acknowledge sponsorship in advertisement and during the meeting.


 

UCSC researchers double-down on data sharing’s key role in global health 

Scientists present framework for freely and safely sharing health data on a global scale in a brand new, open access journal 

Titled “https://www.cell.com/cell-genomics/fulltext/S2666-979X(21)00036-7" target="_blank" rel="noopener" style="color: rgb(38, 171, 226); font-weight: normal; text-decoration: underline;" title="mailto:https://www.cell.com/cell-genomics/fulltext/S2666-979X(21)00036-7">GA4GH: International policies and standards for data sharing across genomic research and healthcare,” first author and GA4GH vice-chair Heidi Rehm and GA4GH community co-authors present the organization’s strategies for addressing some of the most pressing challenges of the genomic data revolution. The authors present the GA4GH toolkit of secure, interoperable technical standards and policy frameworks, their relevance to key domains of research and clinical care, and the organization’s future plans. 

Genomics Institute and Baskin Engineering Associate Research Scientist Melissa Cline, who is a GA4GH Steering Committee member and GA4GH Driver Project Champion for the BRCA Challenge, was co-author on the showcase paper, which provides a high-level overview of the GA4GH organization, deliverables, and strategy for enabling interoperability across the international genomics landscape. Dr. Cline is also a co-author on the commentary article “https://www.cell.com/cell-genomics/fulltext/S2666-979X(21)00039-2" target="_blank" rel="noopener" style="color: rgb(38, 171, 226); font-weight: normal; text-decoration: underline;">International federation of genomic medicine databases using GA4GH standards” and the technology article "https://www.cell.com/cell-genomics/fulltext/S2666-979X(21)00034-3" target="_blank" rel="noopener" style="color: rgb(38, 171, 226); font-weight: normal; text-decoration: underline;">The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification”, and one of the GA4GH contributors featured in “https://www.cell.com/cell-genomics/fulltext/S2666-979X(21)00043-4" target="_blank" rel="noopener" style="color: rgb(38, 171, 226); font-weight: normal; text-decoration: underline;">Voices of GA4GH members: Collaborating in technology and policy development”.





Announcing GA4GH Special Issue in Cell Genomics
 
This issue is the culmination of an incredible effort from the global GA4GH contributor community and includes ten papers. “The entire GA4GH community has come together across time and space to deliver the resources described in this special issue,” said GA4GH CEO Peter Goodhand. “It represents an important milestone in the evolution of this organization.”
 
 
Read GA4GH Press Release
 
Read GA4GH Special Issue
 
 




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)
 



HGVS nomenclature Q&A 

The question was:
           Who knows variant NC_045512.2:g.23604C>G?  What is it?
           Do you know? (for the right answer see the end of the Newsletter)


[ Variant NC_045512.2:g.23604C>G is the most discussed variant in 2021, 
it is the SARS-CoV-2 delta variant. ]
 
 
 
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GV Newsletter - October 2021



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

We are proud to announce that Professor Johan den Dunnen has been bestowed upon the royal title of "Officer of the Order of Orange-Nassau" by the King of the Netherlands, represented by the mayor of Leiden, Mr. H. Lenferink. Johan received this royal recognition for: his dedication to make the latest genomic technologies available to researchers through the Leiden Genome Technology Center (LGTC), his research in particular on muscular dystrophies and the development of the exon skipping therapy, his efforts to get to an international standard for the description of genetic variants (the HGVS nomenclature), his commitment to the public sharing of genetic variant data through establishing the Leiden Open Variation Database (LOVD) platform, his enthusiasm to share his knowledge on DNA and genomic technologies with students of any background, and his role in the initiation of "LeveDNA!", a Dutch foundation to explain everything about DNA to the layman. These contributions to science and society were highlighted in an entertaining speech by the mayor, after which he pinned on the medal.
 
Johan den Dunnen officially retired in July of this year and celebrated his retirement and his achievements of the last few decades with a small group of family and close colleagues last Thursday, September 30.

 
 


HGVS nomenclature Q&A sessions have started!
 
The sessions start with a brief welcome from Johan den Dunnen, chair of the HGVS nomenclature committee. Next, a series of prepared questions for the participants to answer using the DirectPoll system. Participants are able to see each other’s answers anonymously. After each question, the answers are revealed and explained.  We want to hold these sessions, giving people a chance to practice and discuss in a safe environment. After the prepared questions, there is time for participants to ask specific questions directly.
 
For those interested to give it a try, the Q&A session is available aftwewards using Socrative, classroom HGVSonline (https://api.socrative.com/rc/ibPQGW).
 
 
Our next session will take place on Tuesday 26th October at 8am UTC. We have alternated the timings of each session to accommodate all time zones. For your time zone, please click here
 
To register for the next session, please click here. You can also see this event listed on the Human Genome Organisation’s(HUGO) Facebook page. We record the meeting for those not able to join. 
 
 
The questions from the Q&A session will be taken from those we receive daily and be a mix of simple and more complex cases. The idea is that you train yourself and learn HGVS nomenclature by applying the recommendations. For those not able to participate, the questions will be available afterwards using the Socrative platform (www.Socrative.com, classroom to be announced).  For the 'questions from participants' session, everybody is encouraged to send questions to VarNomen@HGVS.org so we can prepare. Of course, we will also allow you to ask questions 'live'.
 
 
If you have any comments, suggestions or questions you would like answered for these sessions, please let us know. 
 
Interested to support the HGVS nomenclature work? Please consider sponsoring one of the bi-monthly meetings. For details, please contact amy@variome.org">amy@variome.org. Of course, we will acknowledge sponsorship in advertisement and during the meeting.
 
 

HGVS nomenclature

On Friday October 8, the Sequence Variant Description working group (SVD-WG) had its first online meeting. On the table were subjects like; the collaboration between HGVS, HVP/GV and HUGO, membership of the SVD-WG of the new HUGO Nomenclature Standards committee, the Terms of reference of the SVD-WG, membership of the working group and the election of new members. In addition, the SVD-WG discussed the comments that were received for Community Consultation proposal SVD-WG010 (http://varnomen.hgvs.org/bg-material/consultation/svd-wg010/">http://varnomen.hgvs.org/bg-material/consultation/svd-wg010/), the var-distance proposal. The working group decided that more time was needed to discuss the comments received and a final decision remains pending.
 
 

NEW members for HGVS nomenclature committee

The HGVS nomenclature committee, the Sequence Variant Description working group (SVD-WG), is looking for new members. In a next newsletter we will give details on when and how to apply.
 

Do you want to get involved? 
Please prepare to apply!

 

Variant Effect Prediction Training Course

21 - 23 September 2021

Online

The 5th Variant Effect Prediction Training Course was held from the 21st -23rd September. Originally scheduled to take place in Barcelona in 2020 it was postponed due to COVID-19 and was transformed from an in-person to a virtual course this year.  Three days of live streaming, connected 280 attendees from 40 countries and 105 cities for 3 days packed with expert speakers and interesting sessions.

The three-day program covered many themes related to variant interpretation starting with the “basics” (nature and possible consequences of variants in DNA, RNA and protein; description in HGVS nomenclature) and followed by applications for robust variant classification as well as overarching topics such as the MANE project, the use of HPO terms, gene/disease specific databases and the importance of data sharing initiatives. One of the main points of the course was the presentation of the limitations of NGS diagnostics, as a lecture and workshop. Furthermore we were lucky to have speakers from the major genome browsers UCSC and Ensembl, as well as leading scientists in their field, who presented their state-of-the-art lectures and workshops and thank them for taking time to join us. Many sessions include interactive polling and problem solving, this was in most cases the starting point of lively discussions and in addition to the specific questions of the participants about the presentations, ethical issues of genome analyses were also discussed.
 

Global Variome’s mission to increase capacity is being realised through conferences and training courses such as these.  If you missed out on the live course you can still register for on-demand viewing at veptc.variome.org or signup to the mailing list to be kept informed about the next course.

We would like to sincerely thank all our speakers and participants with a special mention to our sponsor Qiagen.

We hope that you can all join us again at our next course.

...

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GV Newsletter - August 2021



We are now formally sharing the news that the 25th Human Genome Meeting has been postponed to 23-25 May 2022, due to the COVID-19 pandemic.
 
More information, please visit: https://www.hugo-hgm2022.org/
 
 

Proposal SVD-WG010 (var distance) is now closed. The nomenclature committee will evaluate the comments received and make a decision as soon as possible.


Click here to view the proposal
 
Thank you
On behalf of the Sequence Variant Description Working Group,
Johan den Dunnen (chair)
 


HGVS nomenclature Q&A sessions (by Johan den Dunnen)

Tuesday August 24, we had the second one-hour online HGVS nomenclature session. People from different parts of the world joined at 3 pm (GMT) to work with HGVS nomenclature. After a short introduction, participants with different levels of experience had to answer nomenclature-based questions using the DirectPoll system. After each question, it was explained why a particular answer was correct or not. Following the online session everybody learned a bit more about applying the HGVS nomenclature recommendations in practice. Although I could not check, I don’t think a single participant answered them all correctly. At the end of the session there was time for participants to ask questions directly and discuss  nomenclature related issues.
 
While following the online session live is more attractive, it is possible to give it a try afterwards. For this, we use the Socrative platform, where you can find the questions, answers and an explanation of the correct answer. To give it a try, go to Socrative and select classroom HGVSonline2 (https://api.socrative.com/rc/vKH4rQ">https://api.socrative.com/rc/vKH4rQ). Over 200 people have tried the Q&A of the first online session, available as classroom HGVSonline.
 
Questions to be discussed next time are taken from the questions we receive daily (at VarNomen@HGVS.org). In addition, by checking the questions answered in Socrative, we get a nice overview of the parts of HGVS nomenclature which are problematic, meaning they need additional attention. If you have a question regarding HGVS nomenclature you would like to be discussed, please email!

 
Our next session will take place on Tuesday 26th October, at 8am UTC. We have alternated the timings of each session to accommodate all time zones. For your time zone, please click here
 
To register for the next session, please click here. You can also see this event listed on the Human Genome Organisation’s(HUGO) Facebook page. We record the meeting for those not able to join. 
 
 
 
Interested to support the HGVS nomenclature work? Please consider sponsoring one of the bi-monthly meetings. For details, please contact amy@variome.org">amy@variome.org. Of course, we will acknowledge sponsorship in advertisement and during the meeting.
 
As part of the newly merged HUGO, we have reorganised our committee structure. One of our committees will be the HUGO Nomenclature Standards Committee, which will  promote the use of internationally developed and agreed standards in genomic research.
 
The committee is supported by several working groups, each focusing on a specific Standards topic. The currently approved working groups include:
- the HUGO Gene Nomenclature Committee (HGNC)
- the HGVS nomenclature Sequence Variant Description working group (SVD-WG)
- The ISCN Standards committee

The ISCN Standing Committee welcomes an inclusion of a representative on the HUGO Nomenclature Standards Committee. For more information on the ISCN Standards committee, please click here 

 
 
LOVD security improved by hackers

Not all hackers are bad. In fact, there are large groups of so-called "white hat hackers" that attempt to break into online systems not to cause damage, but to report vulnerabilities to their owners. Often these white hat hackers are rewarded small "bounties", either gifts or financial compensations for their efforts. A large majority of white hat hackers are from developing countries and use these bounties to fund their studies. This July, LOVD sent out an invitation (a "bug bounty program") which caused some 15 white hat hackers to scan LOVD and the LOVD website for vulnerabilities. Several small issues were found, as well as two vulnerabilities that attackers could potentially use to set up a successful breach of LOVD security. Although no breach had actually occurred, all vulnerabilities were fixed and everyone who reported an issue received financial compensation.
 
DECIPHER v11.6 Released DatabasE of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources

You can also view this on the web at:https://www.deciphergenomics.org/about/news

It is now possible to query Matchmaker Exchange through DECIPHER to find matches for small copy-number variants that overlap a gene, in addition to sequence variants. Matchmaker exchange allows the federated discovery of potential matching patients in connected databases. DECIPHER currently supports the searching for patient matches in PhenomeCentral, MyGene2, GeneMatcher, RD-Connect and Broad-seqr. When DECIPHER users query Matchmaker Exchange, overlapping phenotypes are now highlighted in the interface to enable relevant patient matches to more easily be identified.

On plots of individual patients' height, weight, and head circumference (visible to depositors who enter this information), the points representing individual observations are now connected with curves instead of lines, to better approximate the likely pattern of growth.

The genome browser tracks menu has been updated so that the available tracks are grouped to allow users to more easily find tracks of interest. The tracks menu can be accessed by clicking on the word "Tracks" in the top left of the genome browser.

It is now possible for DECIPHER depositors to copy a patient's phenotypes and associated HPO codes. Click on "Show simple term list" to view this information (this is only visible for patients in your own projects). This development helps enable interfacing with electronic health records and family tree programs.
 

BRCA Exchange Release 50

We are excited to announce that Release 50 of BRCA Exchange will soon be live with more than 67K variants!!! Thanks to our collaboration with the ENIGMA Consortium, this release offers new data on laboratory functional assays. We anticipate that this release will go live in roughly two weeks.
 
Like recipes for chefs, functional assays are standardized processes that laboratory-based researchers use as their common language. Researchers use assays to measure and discuss how much a variant impacts “normal” biological function at a molecular level. This is why functional assays are considered a rich source of information that can help people understand and manage their potential genetic risk for cancer.
 
We want to give a shout out to the many people who contributed so much work and thought to this functionality, especially team members Michael Parsons and Zack Fischmann. #heritablecancer #knowyourrisk #BRCA  
 
 
GA4GH

The Global Alliance for Genomics and Health (GA4GH) has approved a policy for the return of clinically actionable genomic research results, the first such policy approved by an international body. Click here for more information.
 
13th Conference of the AfSHG & 1st Conference of the Tanzania Society of Human Genetics
Dar es Salaam, Tanzania • August 30 - September 5
For more information, see the event page
 
Harnessing biological data: from molecular
processes to human health

Basel, Switzerland • September 13 - 15
For more information, see the event page
 
The VIII International Conference of Cardiovascular Genomic Medicine  Tickets, Thu 16 Sep 2021 at 12:00 | Eventbrite

For more informationclick here  

For the the agenda,  click here

 
 


The 5th Variant Effect Prediction Training Course
is open for registration!
 
Earlybird registration ends 19th of July so register now to make a saving!

This year the course will be an immersive virtual experience and will take place from the 21st to the 23rd of September 2021.  Core topics will be delivered live with ample opportunity for Q & A; some topics will be on-demand.  

Participants will have access to recordings after the course.

Expected Participants are people working in a DNA laboratory including clinical diagnostic labs involved in DNA sequencing data analysis.

VEPTC 2021 will be a fully immersive virtual event using the Attendify platform.
 

The course will include:

  • Variants in the genome, position & possible consequences
  • NGS: what method to apply (gene panel, WES or WGS) and where technology fails
  • NGS limitations: sequencing technologies / calling variants (SNV+CNV+SV)
  • CNV calling/ analysis: applications and challenges
  • SNV calling/ analysis: applications and challenges
  • HGVS Nomenclature; describing variants
  • Human Phenotype Ontology (HPO)
  • Integration of phenotypic and genomic data to diagnose patients with rare diseases 
  • Annotating variants
  • Variant Classification (ACMG recs.)
  • Prediction tools
  • Ensembl Genome Browser
  • UCSC Genome Browser
  • Future developments
  • Qiagen variant interpretation workshop
  • & more…

VIEW THE PROGRAM HERE: https://veptc.variome.org/program.html 

We invite you to register, and submit an abstract for consideration as a virtual poster (only if you wish) and look forward to your participation.  

REGISTER HERE: https://veptc.variome.org/registration.html

Further details about the event may be found on the website:  veptc.variome.org
 
8th International Workshop on ​Genome
Privacy and Security (GenoPri'21)

Virtual • September 22
For more information, see the event page
 
20th Precision Medicine World Conference (PMWC)
Pittsburgh, USA • September 23 - 24
For more information, see the event page
 

GA4GH 9th Plenary

registration is now open!


GA4GH 9th Plenary will be held virtually on September 28–29. We are excited to continue engaging our global community in advancing data sharing for the benefit of human health and medicine. GA4GH 9th Plenary is a free event and, as always, open to the public.
 
For more information, see the event page
 
6th International Virtual G2MC Conference
Virtual • September 29
For more information, see the event page
 
2021 Conference on Precision Psychiatry
Virtual • September 30 - October 1
For more information, see the event page
 


We go virtual in 2021! EHTG's 5th Meeting was cancelled because of the Covid-19 pandemic. This year we are back and will host our annual Meeting on October 8 and 9 2021 as an online congress
 
You can already register for the event or become a member and enjoy complimentary registration for the meeting. Abstract submission is now open.
 
 
Next Generation Sequencing Bioinformatics
Virtual • October 18 - 22
For more information, see the event page
 
 
 


We welcome you to the 14th International Congress of Human Genetics (ICHG2022)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 13 – 17 February 2022.
 
Warm regards
Raj Ramesar and Charles Rotimi
(Co-Chairs LOC/ICHG 2021)
 
 
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Twitter
Website
Email
 
 
 







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GV Newsletter - July 2021

https://mailchi.mp/6d44df00cc88/hugo-newsletter-april-4928346?e=93495c83ac

 



We are now formally sharing the news that the 25th Human Genome Meeting has been postponed to 23-25 May 2022, due to the COVID-19 pandemic.
 
More information, please visit: https://www.hugo-hgm2022.org/
 
 


Proposal SVD-WG010 (var distance) is now open for Community Consultation. You are invited to review and comment on this proposal.  
 
Click here to view the proposal

 
Deadline for comments - Friday 30th July- comments to VarNomen@HGVS.org">VarNomen@HGVS.org

 
Thank you
On behalf of the Sequence Variant Description Working Group,
Johan den Dunnen (chair)
 


HGVS nomenclature Q&A sessions have started!
 
On June 22, we started an experiment, an online HGVS nomenclature session. We thank those who dared to attend the first session; there is always the danger of technical issues. But not this time, everything went smoothly. We had a mix of experienced users and nomenclature beginners who enjoyed the chance to practice and discuss relevant nomenclature issues.
 
The session started with a brief welcome from Johan den Dunnen, chair of the HGVS nomenclature committee. Next, were a series of prepared questions for the participants to answer using the DirectPoll system. Participants were able to see each other’s answers anonymously. After each question, the answers were revealed and explained. Was it easy? Certainly not. One question in particular was answered incorrectly by all, even from the experienced users of the group. But this is why we wanted to hold these sessions, giving people a chance to practice and discuss in a safe environment. After the prepared questions, there was time for participants to ask specific questions directly.
 
For those interested to give it a try, the Q&A session is available using Socrative, classroom HGVSonline (https://api.socrative.com/rc/ibPQGW).
 
 
Our next session will take place on Tuesday 24th August, at 3pm UTC. We have alternated the timings of each session to accommodate all time zones. For your time zone, please click here
 
To register for the next session, please click here. You can also see this event listed on the Human Genome Organisation’s(HUGO) Facebook page. We record the meeting for those not able to join. 
 
 
The questions from the Q&A session will be taken from those we receive daily and be a mix of simple and more complex cases. The idea is that you train yourself and learn HGVS nomenclature by applying the recommendations. For those not able to participate, the questions will be available afterwards using the Socrative platform (www.Socrative.com, classroom to be announced).  For the 'questions from participants' session, everybody is encouraged to send questions to VarNomen@HGVS.org so we can prepare. Of course, we will also allow you to ask questions 'live'.
 
 
If you have any comments, suggestions or questions you would like answered for these sessions, please let us know. 
 
Interested to support the HGVS nomenclature work? Please consider sponsoring one of the bi-monthly meetings. For details, please contact amy@variome.org">amy@variome.org. Of course, we will acknowledge sponsorship in advertisement and during the meeting.
 
 

 

UNESCO Online Database Training Course

Financially supported by a grant from UNESCO, Global Variome is organising an "Online training course in curation of human gene/disease databases". Interested students from all over the world applied earlier this year. A Global Variome committee has now selected the 16 participants that are allowed to enter the course. Selected participants come from 12 different countries: Argentina, Cameroon, Egypt, Ethiopia, India, Malaysia, Mexico, Nigeria, Romania, Senegal, Turkey and South Africa.
 
The online training sessions will be held on Mondays over the next few months. To accommodate the 13-hour time difference between the participant's home countries, there will be alternating morning and afternoon sessions (based on UTC). Sessions will be recorded and made available for the participants who are unable to join. Between sessions participants will have to complete specific tasks focussing on a gene/disease they have selected. At the end of the course the participants will be curator for one of the genes in the "Global Variome shared LOVD" (http://databases.lovd.nl/shared">http://databases.lovd.nl/shared). The first session will start July 19, 8 am (UTC).

 
SVD-WG: thank you Donna Maglott!

Donna MaglottThe HGVS nomenclature committee, the Sequence Variant Description working group (SVD-WG), is a group of experts guarding the nomenclature recommendations. The committee currently exists of eight members and three observers (representing HGVS, GV/HVP and HUGO). Until now, membership of the committee has been assigned on an ad-hoc basis. The plan is to make membership of the HGVS nomenclature committee a more open process where candidates apply for membership and committee members serve a specified term time. The plan is to start this process
later in the year, under the umbrella of the new HUGO, where the three organisations supporting the HGVS nomenclature have started to collaborate more closely.
 
Donna Maglott (NCBI) has recently decided to step down as a member of the SVD-WG. Donna will be replaced by Terence Murphy (NCBI). From the start, Donna has been a very active and responsive member of the SVD-WG. Her input, expertise, commitment to standards, spirit of collaboration and the discussions within the committee have always been appreciated. Donna made essential contributions to the HGVS nomenclature recommendations as they are now. These recommendations are not perfect, they will probably never be, but they are of very high quality, serve a need and this is why they are applied as THE standard world-wide, especially in a diagnostic setting. Donna can be proud on having played an essential role towards this achievement.
 
Donna, on behalf of the SVD-WG, thank you very much, enjoy your well-deserved retirement!
 
 

File:Flag map of the United Arab Emirates.svg - Wikimedia CommonsUAE launches new Centre for Genomic Discovery
 

"The UAE has launched a 'first-of-its-kind' Centre for Genomic Discovery, which will help diagnose and treat patients with genetic disorders as well enhance local genomic research and train the country’s next generation of scientists"


For more information, click here 

 


"In response to the global COVID-19 pandemic, we are no able to organize the traditional conference and celebrate all together the 20th Gene Forum"

"This year's presentations will cover themes from the use of genomic data in personalized medicine and applications in healthcare, pharmacogenomics, regulatory genomics and molecular functions, population genomics and human microbiome interactions. Given the situation in the world, this year's Gene Forum will also have a session on COVID-19 research."
 
For more information, see the event page
 
 
BC2

Harnessing biological data: from molecular processes to human health


[BC]2 Basel Computational Biology Conference
13 – 15 September 2021
Congress Center Basel, Basel, CH


Early bird registration now open! 

For more information, see the event page 
 
 


The 5th Variant Effect Prediction Training Course
is open for registration!
 
Earlybird registration ends 19th of July so register now to make a saving!

This year the course will be an immersive virtual experience and will take place from the 21st to the 23rd of September 2021.  Core topics will be delivered live with ample opportunity for Q & A; some topics will be on-demand.  

Participants will have access to recordings after the course.

Expected Participants are people working in a DNA laboratory including clinical diagnostic labs involved in DNA sequencing data analysis.

VEPTC 2021 will be a fully immersive virtual event using the Attendify platform.
 

The course will include:

  • Variants in the genome, position & possible consequences
  • NGS: what method to apply (gene panel, WES or WGS) and where technology fails
  • NGS limitations: sequencing technologies / calling variants (SNV+CNV+SV)
  • CNV calling/ analysis: applications and challenges
  • SNV calling/ analysis: applications and challenges
  • HGVS Nomenclature; describing variants
  • Human Phenotype Ontology (HPO)
  • Integration of phenotypic and genomic data to diagnose patients with rare diseases 
  • Annotating variants
  • Variant Classification (ACMG recs.)
  • Prediction tools
  • Ensembl Genome Browser
  • UCSC Genome Browser
  • Future developments
  • Qiagen variant interpretation workshop
  • & more…

VIEW THE PROGRAM HERE: https://veptc.variome.org/program.html 

We invite you to register, and submit an abstract for consideration as a virtual poster (only if you wish) and look forward to your participation.  

REGISTER HERE: https://veptc.variome.org/registration.html

Further details about the event may be found on the website:  veptc.variome.org
 
 
 

GA4GH 9th Plenary

registration is now open!


GA4GH 9th Plenary will be held virtually on September 28–29. We are excited to continue engaging our global community in advancing data sharing for the benefit of human health and medicine. GA4GH 9th Plenary is a free event and, as always, open to the public.
 
For more information, see the event page
 


We go virtual in 2021! EHTG's 5th Meeting was cancelled because of the Covid-19 pandemic. This year we are back and will host our annual Meeting on October 8 and 9 2021 as an online congress
 
You can already register for the event or become a member and enjoy complimentary registration for the meeting. Abstract submission is now open.
 
 
 
 


We welcome you to the 14th International Congress of Human Genetics (ICHG2022)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 13 – 17 February 2022.
 
Warm regards
Raj Ramesar and Charles Rotimi
(Co-Chairs LOC/ICHG 2021)
 
 
Facebook
Twitter
Website
Email
 
 
 







This email was sent to amy@variome.org 
why did I get this?    unsubscribe from this list    update subscription preferences 
Human Variome Project · Centre for Life · Times Square · Newcastle Upon Tyne, Tyne and Wear NE1 4EP · United Kingdom 

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GV Newsletter - June 2021


https://twitter.com/humangenomeorg/status/1400363296725819392
 
Complete Human Genome Sequence

New Scientist Default Image
On June 26, 2000, the draft human genome sequence was announced. 21 years later, on May 27, 2021, the Telomere-to-Telomere (T2T) consortium has completed the human genome sequence! The remaining 8% of missing genetic data was added, capping the full sequence at 3.055Bbp!

Read the fill article here:
https://www.biorxiv.org/content/10.1101/2021.05.26.445798v1
 
 


NEW - HGVS nomenclature Q&A session
 
We receive a lot of questions regarding HGVS nomenclature. Currently, these questions are all answered by private e-mail, with some examples published on the nomenclature Facebook page

In order for users to gain real practical experience carrying out nomenclature tasks, we are going to try something NEW:
 
.
 
            bi-monthly online HGVS nomenclature Q&A sessions
 
The first meeting will take place on June 22, 8:00am GMT (check your own time zone here)
 
The meetings will be bi-monthly, on the 4th Tuesday of every 2nd month (even months). We will alternate the time of the meeting in order to allow people from either Asia+Australia, Europe+Africa or North+South America to follow the meeting during the day. We plan to record the meeting for those not able to join.
 
Meetings will take 60 minutes and have a standard format:
1) Short welcome (5 min)
2) Participants answer questions (35 min)
3) Questions from participants (15 min)
4) Close of meeting

For questions to be answered by participants we will use an online polling system (DirectPoll).  Questions will be taken from those we receive daily and be a mix of simple and more complex cases. The idea is that you train yourself and learn HGVS nomenclature by applying the recommendations. For those not able to participate, the questions will be available afterwards using the Socrative platform (www.Socrative.com, classroom to be announced).  For the 'questions from participants' session, everybody is encouraged to send questions to VarNomen@HGVS.org so we can prepare. Of course, we will also allow you to ask questions 'live'.
 
 
For HUGO members, participation will be free. Details for non-members to join will be shared later. To register your interest, please contact amy@variome.org
 
Interested to support the HGVS nomenclature work? Please consider sponsoring one of the bi-monthly meetings. For details, please contact amy@variome.org. Of course, we will acknowledge sponsorship in advertisement and during the meeting.

 
 


For more info click here
 
 


It's not too late to sign up to our Scientific Conference: Data Insights in a Pandemic. Taking place on 23rd June, the #HDRSciCon will be an exciting full day virtual event showcasing the latest advancements in health data science. 

 
 
 
https://www.ivvy.com.au/campaign/link/process/id/6e7fd0cc6cedef3f9014ed9e963270da/s/9c7b38a1e5345caad81d3f21e989566a/account/613/report/56626">VEPTC 2021 IMAGE
https://www.ivvy.com.au/campaign/link/process/id/6e7fd0cc6cedef3f9014ed9e963270da/s/9c7b38a1e5345caad81d3f21e989566a/account/613/report/56626">VEPTC2021 image

Don't miss your opportunity to learn - attend VEPTC 2021!

We are excited to announce that the next Variant Effect Prediction Training Course is now open for registration!

This year the course will be an immersive virtual experience and will take place from the 21st to the 23rd of Sept. 2021.  Core topics will be delivered live with ample opportunity for Q & A; some topics will be on-demand.  We invite you to register, and submit an abstract for consideration as a virtual poster (if you wish) and look forward to your participation.   

Expected Participants are people working in a DNA laboratory including clinical diagnostic labs involved in DNA sequencing data analysis.

To find out more please visit the website.
 

...