June 23-26, 2012
Nürnberg, Germany

Embargo:  00.01 hrs CEST Monday 25 June 2012

Nuremberg, Germany:  The first report of the diagnostic use of the technique of exome sequencing,  where short sequences of DNA are analysed, shows that it can give good results at low cost,  a researcher from The Netherlands will tell the annual conference of the European Society of Human Genetics today (Monday).    The scientists were able to perform a genetic diagnosis in around 20% of 100 cases of patients with intellectual disability (ID) and 50% of the 25 cases of blindness studied.  Not only is the exome test cheaper, but results are available more quickly than with Sanger sequencing[1], they say.   

Dr. Marcel Nelen, head of the Core Genome Analysis Laboratory of the Genetics Department at Radboud University Medical Centre, Nijmegen, will describe to delegates how he and colleagues at the University examined exome sequences from 262 patients with six heterogeneous diseases:  ID, blindness, deafness, movement disorders, cancer, and OXPHOS diseases[2].   In all, the researchers analysed about 500 exome sequences.   In the ID cases, exomes from the father, mother and the child were analysed; in all the other diseases, the exome data from the patient alone was filtered for known causative disease genes.

“The chances of finding a causal mutation in a single gene is small”, says Dr. Nelen, “but in a package containing more than 100 genes it is high, as our results from the blindness patients show. This new strategy means that we can analyse up to 20,000 genes with a single generic test, and the high throughput and lower cost means that we can test more for less money.  But before we implemented the test more widely in our laboratory we needed to be sure that it would give us reliable diagnostic results.”

Exons are short sequences of DNA representing the regions in genes that are translated into protein.   The human genome contains about 180,000 exons, constituting about 1% of the total genome.   While exome sequencing is only able to identify those conditions where protein function is affected, scientists believe that the exon regions contain about 85% of all disease-causing mutations.  And while Sanger sequencing looks at around 500 base pairs per analysis, NGS looks at millions of sequencing reactions per analysis.

The Dutch researchers were entering new territory and so needed to write the rulebook themselves.  “There were no best practice guidelines available for exome sequencing, and so we had to create diagnostic workflows, procedures and criteria.  What criteria did we have to set before we could authorise the outcome?  What type of informed consent was necessary?  How could we organise confirmation of our results?   All these questions had to be answered, and we undertook numerous discussions with clinical geneticists, researchers and ethicists before we could get started”, Dr. Nelen says.

The results then needed to be confirmed.  “We validated our results by using Sanger sequencing, the standard method of genetic diagnosis which has a very high sensitivity and specificity”, Dr. Nelen will say. In addition to ID and blindness, confirmed diagnostic results in the other diseases analysed to date were impressive.  In deafness disease-causing mutations were found in about 20% of cases, in movement disorders between 15 - 20%, and in OXPHOS diseases causal mutations were found in about 25% of the patients studied.     

“Although it is often not possible to treat their diseases, we should take into account that most of these patients will have had a long and worrying journey through different doctors and hospitals before they are diagnosed”, says Dr. Nelen.  “Exome sequencing can shorten that route, and it can also simplify the work of clinicians because they don't have to make a decision about which gene to test for - with 100 or more genes per disease, that can be a very difficult decision to make.  Exome sequencing tests for all the causative gene mutations at the same time, and that means that fast and accurate diagnoses can be made.  Even if there is no treatment available, such diagnoses can help parents, patients and clinicians to make well-informed decisions on treatment and care, as well as being able to plan for the future.”

A further advantage of the technique is its flexibility.  If a new, clinically relevant gene is discovered, it can be added to the testing list and the data reanalysed if necessary.  There are limits as to what exome sequencing can do, the researchers say, but these technical difficulties will diminish as the technique matures and evolves, and for now the fact that so many patients that can benefit from the technique, as opposed to time-consuming and costly Sanger  sequencing strategies, easily outweighs these disadvantages.

“We need to be able to reduce the price of the exome test yet further before we can offer it more widely”, Dr. Nelen will conclude.  “In the future I am sure that genome sequencing will become cheaper, and this is really the gold standard; it provides a single test that detects all possible pathogenic genetic variation, whereas exome sequencing still misses mutations due to its more limited nature.  But with whole genome sequencing currently costing on average €10 000 and an exome test between 10 and 20 times less we can see significant cost savings, and the less complex nature of the test  means that diagnostic results can be available much more quickly. Genetic diagnosis is becoming more and more important in the clinic and we believe that, as it develops, the exome technique will be one of the first tests to be considered by a doctor where a genetic disease is suspected. ”

(ends)

Abstract no:   C07.2
Session Monday, June 25, 1:15 pm    

[1] In Sanger sequencing, a single DNA fragment of about 500 base pairs, synthesised with polymerase chain reaction, is used as a template to generate a set of fragments that differ in length from each other by a single base. The fragments are then separated by size, and the bases at the end are identified, recreating the original sequence of the DNA fragment. 
[2]OXPHOS diseases are those where oxidative phosphorylation is disturbed. Oxidative phosphorylation is a metabolic pathway that produces ATP, the molecule that supplies energy to metabolism.   The manifestations of OXPHOS disease are very complex and can affect a variety of tissues or systems. 

Note:   When obtaining outside comment, journalists are requested to ensure that their contacts are aware of the embargo on this release.

Notes to editors:  The European Society of Human Genetics uman Geneaims to promote research in basic and applied human and medical genetics, to ensure high standards in clinical practice and to facilitate contacts between all persons who share these aims, particularly those working in Europe.   It currently has about 2000 members from 72 countries.   About 2500 delegates are expected to attend this year's conference.

Embargo:  00.01 hrs CEST Tuesday 26 June 2012

Nuremberg, Germany: Genetic researchers have made an important step towards resolving the mystery of the causes of intrauterine fetal demise (IUFD), or stillbirth, where a baby dies in the womb after the 14th week of gestation. IUFD is responsible for 60% of perinatal mortality and occurs in about one in every two hundred pregnancies in Europe. Up to half of these stillbirths are unexplained. Now scientists from Italy, Germany, and the US have found that up to 8% [1] of these unexplained deaths may be caused by specific genetic heart conditions.

Ms Alice Ghidoni, a PhD student at the University of Pavia, Italy, will tell the annual conference of the European Society of Human Genetics today (Tuesday) that the group's research shows for the first time that cardiac channelopathies, hereditary diseases in which the heartbeat rhythm is disturbed, were likely to have played a causative role in some IUFD deaths . “Since we knew that 10-15% of sudden infant death syndrome cases carry genetic variants associated with long QT syndrome or Brugada syndrome[2], we decided to investigate whether sudden death due to malignant arrhythmias could underlie some cases of IUFD as well”, she will explain.

The researchers carried out molecular screening of stillborn fetuses where the cause of death remained unexplained after extensive post-mortem investigation. Informed consent was obtained from the parents.  They looked for mutations of three genes, two of them involved in long QT and one in both long QT and Brugada syndromes, and found three disease-causing variants that were present in the IUFD cases, but absent in more than 1000 ethnically-matched controls.

Genetic testing is still quite rare in IUFD, but it is an important tool for uncovering the causes of unexplained death, says Ms Ghidoni. “The most common causes of fetal death are chromosomal abnormalities, infections, fetal-maternal haemorrhages, and maternal diseases”, she says. “Most of these are relatively easy to identify. Since genetic screening is a long, expensive and complicated procedure, currently it is not routinely performed in cases where an autopsy has not shown the cause of death. However, such molecular investigation could be very useful to identify specific genetic defects occurring in the family, so that future pregnancies can be monitored with close clinical follow-up. In some cases, life-saving treatment could be given.”

Identification of a fetus with a gene mutation for a cardiac channelopathy allows for treatment for the mother with drugs such as beta-blockers, the same treatment that is given to adults who have been identified with long QT syndrome.  

Because the research was carried out by scientists from a number of different centres and countries, it was not possible to systematically collect parental DNA. However, as part of the planned expansion of the investigation, the researchers now intend to enlarge the study population further and to collect DNA from all family members.  Cardiac channelopathies run in families, so genetic testing will be able to identify not just those parents who are at risk of an affected pregnancy, but also all family members who may be unaware that they have a potentially fatal heart condition.

“We have also identified new candidate genes which may be linked to cardiac channelopathies, and we will investigate them in our follow-up work”, says Ms Ghidoni.  “Our current work shows that nearly 3% of IUFDs may be caused by a genetic variant with a cardiac disease-causing role, and another 5% by a variant that may predispose to disease. We believe that the new candidate genes may enlarge this field yet further. This is vitally important because we can then depict a clear picture of arrhythmic risk in perinatal life, both before and after birth.  

“We believe that it is very important to increase knowledge of these genetic disorders among paediatric cardiologists and gynaecologists and that genetic testing should be included in post-mortem analysis. Many more lives can be saved if there is sufficient awareness of these devastating conditions among healthcare professionals, as well as among the affected families who in many cases have already suffered enough,” Ms Ghidoni will conclude.

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Abstract no. C16.4,
Tuesday 26 June, 11.00 hrs

(1) These figures differ from those in the abstract as they have been updated since it was submitted.
[2]Long QT and Brugada syndromes are conditions whereby an irregular heartbeat leads to syncopes, cardiac arrest and sudden death due to mutations in cardiac ionic channels able to induce arrhythmias.   They are best known for causing sudden unexplained death in young adults. While these syndromes can be identified through complete and accurate clinical evaluation and genetic testing, in most cases it is not until a sudden death has occurred that their existence is suspected.

Note:   When obtaining outside comment, journalists are requested to ensure that their contacts are aware of the embargo on this release.

Notes to editors:  The European Society of Human Genetics uman Geneaims to promote research in basic and applied human and medical genetics, to ensure high standards in clinical practice and to facilitate contacts between all persons who share these aims, particularly those working in Europe.   It currently has about 2000 members from 72 countries.   About 2500 delegates are expected to attend this year's conference.

Embargo:  13.15 hrs CEST Sunday 24 June 2012

Nuremberg, Germany: The use of genome-wide array analysis[1] in parents whose children are suspected of having a genetic disease shows that the parents frequently  also have previously undetected genetic abnormalities, a researcher from The Netherlands told the annual conference of the European Society of Human Genetics today (Sunday).  Being aware of this is important to parents because it means that their risk of having another affected child is significantly increased. 

Dr. Nicole de Leeuw, a clinical laboratory geneticist in the Department of Human Genetics of the Radboud University Nijmegen Medical Centre in Nijmegen, and colleagues performed genome-wide SNP[2] array analysis in 6,500 patients and 1,874 parents. The patients had intellectual disability and/or congenital abnormalities, and the parents of those in whom an aberration was detected were tested in a similar way to determine whether they had the same aberration as their child. Mosaic aberrations, where both genetically normal and abnormal cells are present in an individual, were not only found in one in every 300 patients, but in one in every 270 parents as well.  “These abnormalities occurred more frequently than we had expected”, said Dr. de Leeuw.  “Armed with this knowledge, we can try to understand not only why, but also how genetic disease arises in individuals, and this can help us to provide better genetic counselling.”

Analysis of patients' genomes showed 6.5% de novo (spontaneously arising) genomic imbalances, 9.1% of rare, inherited imbalances, and 0.8% of X-linked abnormalities.  Moreover, with the additional data from their SNP array test results, the researchers were able to subsequently find pathogenic mutations in recessive disease genes, uniparental disomies (where a single chromosome is doubled leading to two genetically identical ones), and mosaic aneuploidies (an extra or missing chromosome in some of the cells of the body) in about 30 patients.

“In at least seven families, these findings meant that  what we had thought of as a spontaneously arising, non-inherited genetic abnormality in a child was in fact already present in some form in the parent”, said Dr. de Leeuw. “Furthermore, when we tested in different cell lines - for example, DNA from blood and that from a mouth swab - we often found that results varied. This is because mosaic aberrations can occur in cells in some organs and not in others, and underlines the importance of not just relying on one type of cell line for this kind of genetic diagnosis.”

In two cases these tissue-dependent differences changed over time, and the researchers believe that this was due to an attempt by the body to correct and rescue the situation. “Such rescue attempts are best known in cases of trisomy, where there are three chromosomes instead of two in a cell, or monosomy, where there is only one.  In both these cases, the body may try to correct the situation by respectively deleting or adding (doubling) a chromosome.  Such rescue mechanisms may be more common than we expected, and by using genome-wide SNP array analysis it will help us to reveal them. For some patients, it would be particularly interesting if we could test multiple samples of these patients over time”, said Dr. de Leeuw.

The majority of genetic diseases are not treatable, but in some cases a special diet may reduce the severity of the symptoms ,for example, in phenylketonuria (PKU) or in coeliac disease, in others the same can be obtained by periodic examination of certain organs (for example in Down syndrome or Marfan syndrome). Sometimes hormone treatment will be of benefit to the patient, for example growth hormone treatment in Turner syndrome.  For most patients with a genetic disorder, there is no cure, but knowing the genetic cause of their disease may help and improve the care for these patients through knowledge about other patients with the same disease. And if the family is at risk of a genetic disease, couples considering having children can be better informed as to their options, the researchers say.

“By using genome-wide array analysis to look for imbalances in the human genome, we will uncover more and more accurate findings in patients.  This will not only increase our knowledge of genetic disorders and the human genome in general, but if we can also collect the clinical features of these patients in a structured and uniform way, the information will become increasingly valuable.   Fortunately, this is becoming easier due to advances in tools and software applications, and many professionals in the academic and commercial world have agreed to collaborate in order to substantially increase the genotype/phenotype collection and make these anonymised data publicly available to medical professionals in order to improve patient care worldwide”, Dr. de Leeuw concluded.

(ends)

Abstract no:   C04.5, 
Session: Sunday, June 24, 1:15 pm

[1] A DNA microarray (or gene chip) is a collection of microscopic DNA spots attached to a solid surface, used to measure the relative quantity of large numbers of genes simultaneously in multiple regions of a genome, thereby determining the DNA copy number. 
[2] A SNP (pronounced ”˜snip'), or single nucleotide polymorphism, is a relatively common DNA sequence variation, a change in  a single nucleotide ”” A, T, C or G ”” in the genome, without clinical consequences. Each person has about 3 million SNPs in his or her genome, a unique genetic signature. In a SNP microarray, the probes (small pieces of DNA) bind only to the complementary piece of DNA being analysed if it is an exact match, making it possible to determine the genotype (SNP composition) of a DNA sample in addition to the DNA copy number.

Note:   When obtaining outside comment, journalists are requested to ensure that their contacts are aware of the embargo on this release.

Notes to editors:  The European Society of Human Genetics uman Geneaims to promote research in basic and applied human and medical genetics, to ensure high standards in clinical practice and to facilitate contacts between all persons who share these aims, particularly those working in Europe.   It currently has about 2000 members from 72 countries.   About 2500 delegates are expected to attend this year's conference.

Embargo:  00.01 hrs CEST Saturday 23 June 2012

Nuremberg, Germany: The commonly-used epilepsy drug, valproic acid (VPA), can have a highly beneficial effect on some babies born with spinal muscular atrophy (SMA), the number one genetic killer during early infancy. But in about two-thirds of such cases it is either damaging or simply has no effect. Now, for the first time, researchers have found a way to identify which patients are likely to respond well to VPA prior to starting treatment. Their results have major implications, not just for SMA patients, but for other conditions treated with the drug such as migraine and epilepsy, and may even provide the conditions for turning VPA non-responders into responders, the researchers say.

Dr. Lutz Garbes, from the Institute of Human Genetics, University of Cologne, Germany, will tell the annual conference of the European Society of Human Genetics tomorrow (Sunday) that he and his colleagues had analysed blood RNA samples from a small group of SMA patients who had been treated with VPA.  They found, as expected, that only about one third of patients responded well.  In an attempt to discover whether blood sampling was the most appropriate test method to use, they also looked at VPA response in another tissue - fibroblasts (a type of skin cell). They found that the response in blood and in skin was the same in 60% of cases.

The researchers then generated pluripotent stem cells from fibroblasts of both a VPA responder and a non-responder, and differentiated them into GABAergic neurons (neurons that produce the amino acid GABA, the chief neurotransmitter in the mammalian nervous system).  These neurons, when treated with VPA, exhibited a similar response to that previously found in blood and fibroblasts.

“This indicates for the first time that response to VPA is the same among blood and skin and suggests that monitoring blood for VPA therapy is indeed feasible in central nervous system diseases”, says Dr. Garbes.  “But, even more importantly, by using the SMA patients' fibroblasts we were able to identify a decisive factor in the suppression of the positive response to VPA treatment.  Utilising transcriptome-wide microarray profiling*, we found that high levels of the fatty acid transporter protein CD36 are associated with the lack of positive response to treatment.

“The implications of this discovery are far-reaching.  First, we have been able to prove that monitoring blood is a reliable method for doctors to determine response to VPA treatment in many central nervous system diseases, since our findings are not specific to SMA.  Second, the identification of CD36 as the crucial factor in suppressing response to treatment provides a simple way of appraising whether a patient will respond to therapy before treatment starts.  And third, in the long run we may find a way to target CD36 in order to be able to change a non-VPA responder into a responder.”

Knowing that CD36 is a crucial factor here means that the current, potentially dangerous, ”˜trial and error' approach to VPA treatment is now obsolete, the researchers say.  Screening of patients for CD36 prior to treatment would mean that only those who would respond positively to VPA would be given it. This is important because, in some cases, VPA can cause life-threatening side-effects such as impairment of liver, blood cell and pancreatic function, especially in those just starting the treatment. “But we still do not understand how CD36 suppresses response to VPA, only that it does so,” says Dr. Garbes.  “A greater understanding of its effects could also lead to the detection of even better targets to overcome the problem. “

In the case of SMA, VPA works by inhibiting enzymes called histone deacetylase (HDACs) which are involved in regulating the packaging of DNA.  HDACs lead to a denser DNA packaging whereby protein production from genes is reduced.  Other enzymes called histone acetyltransferases (HATs) lead to a more relaxed DNA structure, producing more protein.  By inhibiting HDACs with VPA, the DNA packaging balance shifts towards the more relaxed structure and thus genes get activated and proteins produced.  In SMA, the crucial gene is SMN2, a copy gene of the disease-determining gene SMN1.  In healthy individuals, SMN1 is the major source of SMN protein, but SMN2 cannot fully compensate for the loss of SMN1 in SMA patients.  By increasing SMN2 activity, it will produce more SMN protein and ameliorate the condition.

“Avoiding needless VPA treatment of non-responders would have a major effect on healthcare costs and improve quality of life for patients,” Dr. Garbes will say. “Half of the babies born with SMA will die within two years, but the other half can live to twenty or even longer, so this is an important finding for them.   Our findings may also help identify patients who are candidates for VPA treatment in many other diseases of the central nervous system, some of them very common.   

“In the EU, approximately 550 SMA babies are born each year, and there are about 311,000 new cases of epilepsy per year.  It is estimated that, in Europe, migraine affects up to 28% of people at some time in their lives.  We are happy that we may have been able to contribute to the development of personalised medicine for so many people,” he will conclude.

(ends)

Abstract no. CO1.6,
Sunday 13.15 hrs

*A transcriptome-wide microarray profile provides a way of identifying all the genes that are differentially expressed in distinct cell populations or subtypes, allowing the effects of treatment to be monitored.

Note:   When obtaining outside comment, journalists are requested to ensure that their contacts are aware of the embargo on this release.

Notes to editors:  The European Society of Human Genetics uman Geneaims to promote research in basic and applied human and medical genetics, to ensure high standards in clinical practice and to facilitate contacts between all persons who share these aims, particularly those working in Europe.   It currently has about 2000 members from 72 countries.   About 2500 delegates are expected to attend this year's conference.