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GV/ HVP Newsletter - August 2019

The Community Consultation call for proposal SVD-WG008 (RefSeq)
 has been open since 20th July and will close on Monday 30th September 2019. The proposal suggests to extend the HGVS recommendations by specifying what sequences can be used as a reference sequence. See
A sequence variant is defined in the context of a reference sequence which must be referred to by means of a unique sequence identifier. Because a reference sequence defines the numbering system and default state of a sequence (e.g. coding transcript, non-coding transcript), reference sequences have to follow specific requirements which seem "obvious" but were not yet defined. This proposal lists all the essential requirements.
Whether your opinion is positive or negative, we would appreciate your honest opinion. Please email any comments or suggestions to with the Subject: SVD-WG008.
If you would like to be on the community consultation e-mail list, please register with the GV office: - Subject: SVD-WG discussion list


Meeting report: the 2019 Human Genome Meeting (HGM2019) of the Human Genome Organization (HUGO) was held in Seoul, Korea, from 24 to 26 April 2019, at Ewha Woman’s University.


Describing exon deletions/duplications
During the last "Variant Effect Prediction Training Course" (May 29-31, Moscow, Russia) the importance of correctly describing the variants detected using HGVS nomenclature was discussed extensively. One of the examples covered was the description of MLPA-detected deletions/duplications, many struggle with this. During the course the "Reading Frame Checker", offered per gene by the "Global Variome shared LOVD" (, was pointed out as a useful support tool. The reading frame checker can be used to check the predicted consequences of a deletion or duplication of one or more exons being "in frame" or "out of frame". The reading frame checker also gave exon-based variant descriptions but these unfortunately did not follow HGVS recommendations. Since modification according to the developer was "simple" and modification should not take "more than a month" the LOVD-team left with the promise to modify the tool. Modification has now been completed and the GVsharedLOVD can be used to generate HGVS compliant exon deletion/duplication variant description like c.(93+1_94-1)_(649+1_650-1)del.


The BRCA Challenge and ENIGMA consortia are pleased to announce the publication of "Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants", Hum Mutat. 2019 Jul 11. This paper reports on the results of the CAGI5 ENIGMA challenge for predicting the clinical significance of BRCA variants.  In this challenge, six teams predicted the clinical significance of 326 BRCA variants, which had recently been interpreted by ENIGMA but for which the interpretations were not yet published.  The six teams submitted predictions from fourteen methods, which were then assessed through comparison with the unpublished interpretation.  The best performance was achieved by the LEAP methods by Color Genomics.  These methods were able to successfully leverage private information, including an internal database of genetic testing results and a subscription to HGMD.  While the results of this experiment yielded many lessons for the scientific community, the biggest lesson is that there is still private information that is valuable in variant interpretation.  To the extent that such information can be made public, science will benefit, as will genetic testing patients by extension.

Help us improve the quality of genetic testing data by contributing to the BRCA Exchange!   The BRCA Exchange makes high quality data available to the international public. This free-of-charge resource allows researchers, testing companies, and clinicians access a consistent, shared data set regardless of where or how the test is done. BRCA Exchange data is checked by experts in the field, so clinicians can be confident that they are accessing the best information possible when helping patients. Monthly data releases, alongside expertly designed collection methods, also provide clinicians with updated, complete public information on each variant in the BRCA Exchange.  To support this effort, we are running on online fundraising drive through the month of October, which is Breast Cancer Awareness month.  For more information, please see



InSiGHT is submitting its variant interpretation committees to ClinGen as Expert Panels for the MMR genes and APC. They have done a lot of work identifying and reconciling discordant interpretations of these genes on ClinVar and building specific modifications of the ACMG guidelines for the MMR genes and APC.  All variants not reviewed in the last 2 years are being addressed again through literature and other searches. . The team are testing the tool "Mastermind" to assist in this task. The gene specific modifications are to be submitted to ClinGen, with a batch of variants addressed by the modifications, to see if they align with the assignments of pathogenicity as gauged by the well-tried InSiGHT criteria - especially for the MMR genes.

Finlay Macrae, Secretary to InSiGHT, would like to thank Sherry Yin, Lachlan O'Connell and Matthew Daly. As final year medical students doing their research projects in variant interpretation, they have been fabulous and so helpful for to InSiGHT.

Ethics Checklist for Database Curators and Submitters

These guidelines have now been published on the HVP website. 

The paper has also appeared online at Human Mutation.

Click here to view the paper

We encourage all memebers to:
1. Circulate it to their colleagues and students
2. Post on their web-site
3. Suggest the guide be used as a basis for discussion at up-coming national meetings and local workshops



Australian Genomics: A federated model for integrating genomics into mainstream healthcare.
As governments around the world invest heavily in genomic medicine, Australian Genomics is using a federated model to pave the way for the full integration of genomics into mainstream healthcare.
A new paper published in the American Journal of Human Genetics presents the first analysis of the model adopted by Australian Genomics when it was launched in 2016.

More for information, click here 




The Human Genome Variation Society meeting "Genotypes & Intermediate Phenotypes" will be held Tuesday 15th of October 2019 as a satellite to the American Society of Human Genetics' Meeting in Houston.
Genotype-phenotype correlations have long been an area of interest in genetic research. A subset of this topic involves “Intermediate phenotypes” or “endophenotypes”, which are heritable biological traits within complex conditions that are measurable and relate to the mechanism of the full heritable condition. They have been a source of ongoing study in neuro-psychiatric illness, cystic fibrosis, obesity, and other diseases. Intermediate phenotypes have been used to aid gene discovery and in the interpretation of GWAS studies of complex phenotypes. This meeting will explore new data on Intermediate Phenotypes in these contexts.

We invite you to learn and participate by attending this event and invite you to submit your abstracts as soon as possible, closing date 5th September 2019.

Further details may be found on the website.





We have arranged an informal meeting for those GV/HVP members attending ASHG in October in Houston:
Friday 18th October
2-3:30pm Houston time
Lobby of the ASHG venue, George R. Brown Convention Center



GA4GH 7th Plenary Meeting
October 21 – 23, 2019
Boston, USA

The GA4GH 7th Plenary Meeting will be held on October 21-23, 2019 at the Hynes Convention Center, Boston, USA. The 7th Plenary will bring together organizations and stakeholders from the genomics and health community for two days of keynotes, talks, updates, and workshops that will focus on advancing development work for the immediate data sharing needs of the community.

Global Globin 2020 Challenge (GG2020) Conference 2019

The third Global Globin 2020 Challenge (GG2020) Conference 2019 will be held at the UNESCO Headquarter, Paris from 28-30 October 2019. The theme for this year’s conference is "Enhancing Partnership in Genomic Capacity Towards Equitable Healthcare". Kindly save the date and please help to promote and disseminate the info to your contacts.  For further information about the conference, please contact or More information about the conference can be obtained at

Click here for more information



There is continued interest around on the new project: Global Familial Heart Challenge. However, the progress has been slow, largely due to lack of funding. An informal meeting of current and prospective members of GFHC is planned at the 7th International Cardiovascular Genomic Medicine Conference held in York, England from 4-5 December 2019. Leading members of the Indian team are joining. They have secured funding for systemic collection of phenotype data on familial and inherited cardiovascular diseases. The genotype information would also be included as it became available. The group will discuss different aspects of GFHC and explore funding options. The British Heart Foundation has launched a new funding stream related to health innovation, initially focused on heart failure.


The Human Genome Organisation (HUGO) is pleased to announce the 24th Annual Human Genome Meeting (HGM)will be held 5 - 8 April 2020 at the Perth Convention and Exhibition Centre, Perth, Western Australia. 

The committee are excited to confirm the below Plenary Speakers, as well as a wide range of Symposium Speakers, both local and international. We are aiming for a 50:50 gender representation at HGM2020. We are currently on track with equal numbers of male and female speakers and organising committee members.

Please click here to view the current Symposium Speakers.


Building upon the more technology-orientated biennial Mutation Detection meetings initiated by Prof. Richard Cotton in 1991, the symposium organised by The Human Variome Project will be held in picturesque Piran, on the Adriatic coast of Slovenia from 25 - 27 May 2020. Much has changed; in the earlier years the symposium reported on the application and evolution of existing DNA technologies, as well as the development of new DNA technologies for the detection, analysis and documentation of genetic variation. The NGS revolution has shifted our focus from technologies for detecting variants in DNA to the evaluation of the possible consequences of sequence variants. Consequently, we shifted the focus of the symposium to “detection, genome sequencing and interpretation”.  The symposium will be presented in plenary format with invited keynote speakers and selected abstracts.

Further details may be found on the website: 

Download the flyer to put up in your institute here


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