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GV Newsletter - November 2020



GVshared LOVD 2019 

(Usage of the “Global Variome shared LOVD” databases, the primary LOVD installation maintained by Global Variome (, again showed a strong growth in 2019. The number of submitters, people actively sharing data, increased from 2134 (2018) to 2527 (2019). The total number of variants in the GVsharedLOVD increased from 1.05 million to 1.65 million (unique variants from 184,000 to 255,000). The number of individuals/families for which data were shared increased from 988,000 to over 1.2 million. 

Total numbers across all public LOVD installations (# installations, # individuals, # variants) can be found on the LOVD website ( 

Web statistics for the LOVD installations hosted in Leiden (i.e. mainly the “Global Variome shared LOVD”) also showed a steady increase to 500,000 page views per month (2019 total 5.8 million). The number of unique monthly visitors (institutes mostly counted as one visitor) increased to 30,000. While in 2018 79,000 different users visited the LOVD databases, this number doubled to 159,000 in 2019. Annual use of the LOVD api, computer requests for information, increased to over 125 million. 



We would appreciate your input... 

Proposal SVD-WG009 (conversion) 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 - October 31st 2020 - comments to 

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




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Get in Line at the DNA Bank

In the same year that Vernon Ingram first showed us that changes to a single amino acid in a protein can cause disease or disorder in humans, Johan den Dunnen was born. Growing up in a time when scientific advances in the realm of human genetics were on rapid fire (do the names Meselson, StahlLejeune, Guthrie and Nirenberg ring a bell?), he was inspired to study biology. Johan went on to complete his PhD in the Netherlands examining the evolution of eye-lens crystallin genes, before his research took him toward the area of genetic disease - specifically Duchenne muscular dystrophy.

As well as being an academic (currently a Professor of Medical Genome Technology at Leiden University Medical Centre), Johan, is part of another group within the community. The group boasts members such as Ozzy Osbourne, Elvis Presley, Larry King, and Glenn Close.

What they have in common (unfortunately we're not announcing a supergroup to rival the Traveling Wilburys) is that they have all had their genome sequenced.

Since the completion of the Human Genome Project in 2003, a developing commercial market has allowed an increasing number of individuals to have their genome sequenced. While for James Watson - joint discoverer of DNA - it came at a cost of around $1 million dollars, but by the time Steve Jobs sought information about his own genome to aid his cancer treatment, the cost had fallen to around $100,000.

Today genetics is not just for the wealthy. Today individuals can have access to their own genomic blueprint for around $1,000 USD.

When the "Publish or Perish" model does more harm than good

If you're an academic or on your way down a related path, the term "publish or perish" needs no further explanation. For those outside the circle, the pressure to generate multiple high quality research publications in rapid succession may not seem unusual. How else will the worldwide science community know what you are working on? What other channels exist to share interesting pieces of data or breakthrough results?

The flip side of the argument often points out that focussing on publication quantity has detrimental effects on publication quality. This side of the argument is fuelled by reports highlighting careless mistakes in scientific literature, low reproducibility rates in repeat experiments and extreme cases of academic misconduct and the falsification of results. While all of this sounds like a horror story for scientists to deal with, what are the real implications of these errors outside of the lab? A recently published article in the Atlantic outlined one such example in a disconcerting scenario encountered by Heidi Rehm.

In addition to her role on the International Scientific Advisory Committee for the Human Variome Project, Heidi Rehm is also the Chief Laboratory Director at Partners' Laboratory for Molecular Medicine and Associate Professor of Pathology at Brigham & Women's Hospital and Harvard Medical School. Rehm's position sees her routinely provide reports on patient samples sent to Partners Laboratory from healthcare professionals around the country.

The particular situation described by Heidi Rehm pertains to a foetal blood test which returned a result indicating a variant in PTPN11, a gene which can signify an increased risk of Noonan syndrome. Using the tools at her disposal, Heidi Rehm scoured the scientific literature, finding a paper which classified the specific variant as pathogenic and indeed likely to cause Noonan syndrome. Naturally, the report she returned detailed this finding.

Since the particular sample in question crossed Heidi Rehm's path, further research by a separate group uncovered a high prevalence of the PTPN11 variant among particular ethnic groups who show no sign of the genetic disease, resoundingly disproving the earlier classification of the variant as pathogenic. The original paper that Rehm referenced was wrong.