New genomic technologies, PGD/Prenatal Genetics and society

Posted by & filed under Exome sequencing, Part 03: GENERAL THEMES, Part 06: DIAGNOSTIC APPROACHES.

As in every other field of science, the experts in medical genetics should collaborate closely with policy and law-makers to guide the usage of the new technologies. This is particularly important at present time in the context of the advancement of genomic technologies.

A recent article by Farra et al. (retrospective cohort study) published in Clinical Genetics illustrates how pre-implantation genetic testing (PGT) was used in Lebanon from 2007-2007 in the absence of monitoring and regulation. 96.3% of the clinical indications for the 192 PGT cycles performed during the study period were gender selection. The authors conclude that the findings of this study identify some weaknesses “of self-regulated systems in which physicians are the sole gatekeepers of norms and ethics”.

In the context of the current and projected difficulties with interpretation of variants identified by Next Gen panels or Whole Exome Sequencing, WES, developing specific policies as to how the information is used would be very important to guide both the private sector and physicians. One can argue that self-regulated systems can work, as long as there is appropriate representation in the committees making and enforcing the decisions.

Should physicians be involved in discarding embryos or aiding a couple to terminate a pregnancy for gender status? What about for diseases with non-severe phenotype?  Who should define what phenotype is mild or severe?

Should physicians with a VUS (variant of unknown significance) with inadequate evidence for pathogenicity be offering PGT or prenatal testing as per family’s wishes? Who should be deciding if the evidence is adequate?

When trying to answer these questions one definitely needs to factor in that WES may soon become widely used in clinic as a screening genetic test, that multiple such variants will be identified in each family, and that the classification of some variants may change over time.

Reference: The utilization of pre-implantation genetic testing in the absence of governance: a real-time experience (pages 177–180) C. Farra, A. Nassar, T. Arawi, H. Ashkar, C. Monsef and J. Awwad Article first published online: 2 SEP 2013 | DOI: 10.1111/cge.12250

Posted by Yannis Trakadis, MD

Oral treatment for Leber congenital amaurosis

Posted by & filed under Part 29: EYE.

Koenekoop RK et al. Oral 9-cis retinoid for childhood blindness due to Leber congenital amaurosis caused by RPE65 or LRAT mutations: an open-label phase 1b trial. Lancet. 2014 Jul 11. [Epub ahead of print]

Perusek L, Maeda T. Vitamin A derivatives as treatment options for retinal degenerative diseases. Nutrients. 2013 Jul 12;5(7):2646-66.


Koenekoop et al describe a successful open-label, prospective, phase 1b trial for oral synthetic 9-cis-retinyl acetate in the treatment of RPE65 or LRAT-related Leber congenital amaurosis. Mutations in RPE65 or LRAT block the retinoid cycle and cause a deficiency of the visual chromophore 11-cis-retinal; chronic deficiency of 11-cis-retinal leads to photoreceptor degeneration, but this does not seem to occur immediately, thus providing a window of opportunity for treatment (for a clear and interesting review of the visual cycle and the potential of vitamin A derivatives as treatment options, cf. the 2013 review by Perusek and Maeda). In this study, 11-cis-retinal was replaced by 9-cis-retinal in 14 patients with RPE65 or LRAT-related Leber congenital amaurosis; patients were treated orally for seven days. A majority of patients had clinically significant improvement in visual function, with no serious side effects; surprisingly, in six patients, the treatment effect persisted past 12 months post treatment.

This trial suggests that oral 9-cis-retinal may be a promising non-invasive treatment for the forms of Leber congenital amaurosis that are caused by a block in the retinoid cycle secondary to mutations in RPE65 or LRAT (mutations in these two genes account for about 10% of patients). Further studies are, of course, necessary. It would also be interesting to study the effect of treatment in younger patients (the youngest subject in the study was 6 years old); if 9-cis-retinal therapy is truly effective, perhaps more visual function could be salvaged earlier in the course of the disease.

Posted by Alina Levtova, MD

Exome sequencing redefining phenotypes

Posted by & filed under Exome sequencing, Part 06: DIAGNOSTIC APPROACHES, Part 28: NEUROGENETICS, Part 30: MULTISYSTEM INBORN ERRORS OF DEVELOPMENT.

One would intuitively expect that Whole-exome sequencing (WES) will help broaden the phenotypic spectrum of known syndromes since in the past only patients closely matching the described phenotype of a documented genetic syndrome would be tested for the respective diagnosis.

Some recent examples illustrating the direction the field is moving include the publications of Dr. Boycott’s group in Clinical Genetics: Dymetry et al. (2014) describe four patients with an atypical presentation of the genetic diagnoses which were found to explain their epilepsy after WES. Similarly, Nikkel et al. (2014) describe the atypical phenotype of a family with Hunter syndrome.

These are exciting findings and demonstrate how useful WES can be at a clinical level. However, as the field advances, one also needs to keep in mind that the expansion of the phenotypes will yield increasingly more cases where concluding whether a mutation in a gene associated with a specific syndrome is the explanation for the patient’s phenotype is more difficult. Multiple findings in different genes may be perceived to possibly explain the phenotype independently.  This is already true when using Next Gen sequencing panels.

Making use of different levels of phenotypic information (e.g. metabolomics, transcriptomics, proteomics) in clinic and a network-based approach may prove helpful to this end.


Whole-exome sequencing expands the phenotype of Hunter syndrome. Nikkel et al. Clin Genet. 2014 Aug;86(2):172-6. PMID: 23844659

Whole-exome sequencing broadens the phenotypic spectrum of rare pediatric epilepsy: Aretrospective study. Dyment DA, et al. Clin Genet. 2014 Jul 21. doi: 10.1111/cge.12464. [Epub ahead of print]

Posted by Yannis Trakadis, MD

Sodium pyruvate for the treatment of disorders of oxidative phosphorylation

Posted by & filed under Part 10: DISORDERS OF MITOCHONDRIAL FUNCTION.

Fujii T, Nozaki F, Saito K, Hayashi A, Nishigaki Y, Murayama K, Tanaka M, Koga Y, Hiejima I, Kumada T. Efficacy of pyruvate therapy in patients with mitochondrial disease: a semi-quantitative clinical evaluation study. Mol Genet Metab. 2014 Jun;112(2):133-8. 

Tanaka M, Nishigaki Y, Fuku N, Ibi T, Sahashi K, Koga Y. Therapeutic potential of pyruvate therapy for mitochondrial diseases. Mitochondrion2007 Dec;7(6):399-401.


In 2007, Tanaka et al formulated the elegant and exciting theory that pyruvate may be helpful in mitochondrial diseases with an elevated lactate/pyruvate ratio by regenerating NAD+ and thus promoting energy production through glycolysis, by activating pyruvate dehydrogenase and by non-enzymatically removing hydrogen peroxide. In Fujii et al’s recent study, four severely affected patients with disorders of oxidative phosphorylation were treated with sodium pyruvate; three showed some improvement, and the effect was maintained for two years in one. The authors found that blood lactate and lactate/pyruvate ratios were not informative for the purpose of monitoring therapy.

The use of sodium pyruvate as a potential treatment for disorders of oxidative phosphorylation certainly merits further study, perhaps in a placebo-controlled trial with less severely affected patients, in whom treatments effect might be more apparent.


Posted by Alina Levtova, MD


Interplay between nature and nurture in reading achievement

Posted by & filed under Part 03: GENERAL THEMES.

Plomin R, Shakeshaft NG, McMillan A, Trzaskowski M. NatureNurture, and Expertise. Intelligence. 2014 Jul;45:46-59.

In a cross-sectional twin study, Plomin et al explore the genetic and environmental underpinnings of reading expertise, defined as performance above the 95th percentile on a comprehensive reading test at age 12. They find that more than half of the difference in performance between expert and ordinary readers can be tied to genetic factors; that expert reading performance forms a continuum with ordinary performance, and appears to be influenced by genetic and environmental factors to the same degree; and that shared family and school environment per se only accounts for a fifth of the difference between expert and ordinary readers.

Apart from the perhaps predictable but nonetheless valuable experimental findings, the article is very much worth reading for the sake of the detailed and nuanced discussion of the interplay between genetics, environment, and individual achievement.

Posted by Alina Levtova, MD

Recombinant alkaline phosphatase improves bone growth, mineralization and strength in mouse models of neurofibromatosis type-1

Posted by & filed under Part 04: CANCER.

Neurofibromatosis type-1 (NF1) can present with focal skeletal dysplasias that remain extremely difficult to treat. Elefteriou and colleagues report that ablation of Nf1 in bone-forming cells results in accumulation of pyrophosphate (PPi), a strong inhibitor of hydroxyapatite formation, and that a chronic extracellular signal–regulated kinase (ERK)-dependent increase in expression of genes promoting PPi synthesis and extracellular transport, namely Enpp1 and Ank, causes this phenotype. Nf1 ablation also prevents bone morphogenic protein-2–induced osteoprogenitor differentiation and, consequently, expression of alkaline phosphatase (ALP) and PPi breakdown, further contributing to PPi accumulation. The short stature and impaired bone mineralization in mice lacking Nf1 in osteochondroprogenitors or osteoblasts can be corrected by asfotase-alpha, a recombinant form of ALP used in hypophosphatasia. This study highlights the role of neurofibromin as an important regulator of bone mineralization and suggests that altered PPi homeostasis contributes to the skeletal dysplasia related to NF1 and that some of the NF1 skeletal manifestations could be prevented pharmacologically.

Posted by Nicola Brunetti-Pierri, MD

Wilson Disease Protein ATP7B Utilizes Lysosomal Exocytosis to Maintain Copper Homeostasis

Posted by & filed under Part 14: METALS.

Copper is an essential metal but its overload causes Wilson disease, a disorder due to mutations in copper transporter ATP7B. To remove excess copper into the bile, ATP7B traffics toward canalicular area of hepatocytes. However, the trafficking mechanisms of ATP7B remain elusive. Polishchuk and colleagues show that, in response to elevated copper, ATP7B moves from the Golgi to lysosomes and imports metal into their lumen. ATP7B enables lysosomes to undergo exocytosis through the interaction with p62 subunit of dynactin that allows lysosome translocation toward the canalicular pole of hepatocytes. Activation of lysosomal exocytosis stimulates copper clearance from the hepatocytes and rescues the most frequent Wilson-disease-causing ATP7B mutant to the appropriate functional site. This findings indicate that lysosomes serve as an important intermediate in ATP7B trafficking, whereas lysosomal exocytosis operates as an integral process in copper excretion and hence can be targeted for therapeutic approaches to combat Wilson disease.

Posted by Nicola Brunetti-Pierri, MD

Sapropterin dihydrochloride in maternal phenylketonuria

Posted by & filed under Part 08: AMINO ACIDS, Treatment.

Feillet F et al. Use of sapropterin dihydrochloride in maternal phenylketonuria. A European experience of eight cases. J Inherit Metab Dis. 2014 May 1. [Epub ahead of print] Feillet et al describe the use of sapropterin dihydrochloride during pregnancy in eight cases of maternal phenylketonuria. Seven of eight patients (who were known to be responsive to sapropterin dihydrochloride) had normal pregnancies and gave birth to healthy newborns; no complications attributable to the medication were seen, and metabolic control seems to have been facilitated by the treatment. The eighth had a catastrophic outcome (Potter syndrome and neonatal death) due to a late diagnosis of pregnancy, with uncontrolled phenylalanine levels in the first trimester and phenylalanine embryopathy. These observations suggest that sapropterin dihydrochloride is safe and effective in pregnant patients previously determined to be responsive to it. As the unfortunate eighth case study illustrates, the stakes in this clinical situation are high; if the same favourable profile is borne out by larger studies, sapropterin dihydrochloride will be an extremely useful tool for metabolic control in pregnant responsive patients. Posted by Alina Levtova, MD

Pyridoxine responsiveness in PNPO deficiency

Posted by & filed under Part 17: VITAMINS, Part 28: NEUROGENETICS.

Plecko B, Paul K, Mills P, et al. (2014) Pyridoxine responsiveness in novel mutations of the PNPO gene. Neurology 82(16): 1425-1433.

Pyridoxal 5’-phosphate dependent epilepsy due to pyridox(am)ine 5’-phosphate oxidase deficiency is a newly discovered treatable cause of neonatal epileptic encephalopathy, clinically resembling pyridoxine-dependent epilepsy due to antiquitin deficiency  (Mills, Surtees et al. 2005). PNPO converts pyridoxine 5’-phosphate and pyridoxamine 5’-phosphate into pyridoxal 5’-phosphate (PLP; the only active form of vitamin B6). In keeping with this mechanism, most of the initially described patients with PNPO deficiency did not respond to pyridoxine, but did respond to PLP. This has been thought to provide a clinical means of discriminating between antiquitin deficiency and PNPO deficiency.

Recent studies, however, have suggested a more complex picture. For instance, Plecko et al performed PNPO gene analysis on a cohort of 31 patients presenting with pyridoxine-responsive seizures, but in whom antiquitin deficiency has been ruled out, and identified deleterious PNPO mutations in 9 living patients from 7 unrelated families. Surprisingly, two of these patients reacted poorly (with status epilepticus) to being switched from pyridoxine to PLP treatment.

These findings suggest that pyridoxine responsiveness in PNPO deficiency may be more common than initially thought, perhaps due to residual enzyme function being maximised by increased substrate; further studies are also needed to gain a more nuanced view of the molecular pathophysiology of the disorder, and in particular to explain some pyridoxine-responsive patients’ deterioration when switched to PLP.

Posted by Alina Levtova, MD

Valproic acid and hepatotoxicity

Posted by & filed under Part 10: DISORDERS OF MITOCHONDRIAL FUNCTION.

It is well known that in some individuals, administration of valproic acid leads to hepatotoxicity. The causes for this are not completely understood, though mutations in POLG are a well known risk factor. In a fibroblast model, Luis et al (JIMD, (2014) 37 353-357) found that Valproyl-CoA inhibited the activities of both GTP- and ATP-specific succinate:CoA ligases to a significant degree. Possibly this leads to impaired energy metabolism due to abnormal Krebs cycle flux. The authors also postulate that inhibition of ATP-specific succinate:CoA ligase might disturb nucleoside diphosphate kinase activity leading to an imbalance of mitochondrial nucleotides and therefore mitochondrial DNA depletion. This theory does provide an explanation as to why POLG mutations are a particular susceptibility factor for valproate toxicity.

Hilary Vernon, MD PhD