2009 Vienna - European Society of Human Genetics

Genomics, Genomic technology and Epigenetics
of gene sequence variants and their phenotypic consequences by offering
free support to establish and host Locus-Specific DataBases
(LSDBs). To build, curate and share these gene variant databases, we
have developed the Leiden Open-source Variation Database software
(LOVD, http://www.LOVD.nl). As demonstrated during this presentation,
after installation from CD, this free, open-source, platform-independent
tool builds a basic database following current recommendations
of the Human Genome Variation Society. The database manager
can add any data field desired, e.g. to capture disease-specific phenotype
information, deciding per field the input accepted and whether or
not those data will be available for public display. LOVD supports several
levels of data access (website visitor, submitter, curator, database
manager), searching in and across data columns, custom design of
direct links (to internet, intranet or even local-PC files), data exchange
with central repositories (incl. NCBI, UCSC), automatic mutation nomenclature
error checking using Mutalyzer and data storage on variants
in different genes found in one patient. LOVD allows searching of
data in non-public records, returning the number of hits and the option
to ask for more information. Currently, LOVD is used to curate >260
LSDBs world-wide, with the Leiden server hosting >120 and data collected
for ~60,000 variants from >30,000 patients, the largest series
covering gene variants in relation to neuromuscular disorders.
Funded by the European Community’s Seventh Framework Programme
(FP7/2007-2013) under grant agreement nº 200754 - the
GEN2PHEN project.
P11.066
investigation the methylation status of promoter in JmJD1A of
oligoazoospermia patients
M. Javanmardi 1,2 , M. Noruzinia 3 , H. Abdul-Tehrani 1 , P. Fatehmanesh 3 ;
1 Department of medical biotechnology of Tarbiat modares University, tehran,
Islamic Republic of Iran, 2 Sarem women Hospital, Tehran, Islamic Republic of
Iran, 3 sarem women hospital, tehran, Islamic Republic of Iran.
Introduction:
CpG islands in or near promoter region of many genes are subject
to methylation which can have impact on gene expression. Thus, hypermethylation
of promoter regions are known to be a cause of gene
expression silencing and pathogenic in many genetic disorders. JM-
JD1A is a crucial gene for the final step of spermatogenesis. There
are evidences that this gene directly controls expression of several
genes required for DNA packaging in sperm cells and defects in this
gene could be the cause for some cases of male infertility. In this study
we investigated methylation pattern in JMJD1A promoter region in patients
with unknown infertility.
Methods and materials:
In this study we prepared testicular biopsy from Iranian azoospermic
infertile men for investigation of methylation status of 5´ region of JM-
JD1A gene. Tissue sample of 5 obstructive azoospermic patients were
used as normal controls. MS- PCR (Methylation Specific PCR) was set
up to study methylation status in the promoter region.
Results and discussion:
Patients with non-obstructive azoospermia and infertility showed different
pattern of methylation compared to normal controls. In brief,
100% of controls showed only unmethylated allele. In patient group, 3
patients (10%) showed only methylated allele. 2 patients ( 7%) showed
both methylated and unmethylated alleles. The rest showed only unmethylated
allele. This is the first evidence of involvement of epigenetic
changes in JMJD1A promoter region in male infertility.
P11.067
Identification of functional SNP and putative PPRE sites in
promoter of human malonyl-coA carboxylase gene (mLYcD)
A. K. Lee, T. Kyriakou, S. D. O’Dell;
Nutritional Science Division, London, United Kingdom.
Malonyl-CoA decarboxylase (MCD) catalyses the degradation of malonyl-CoA
to acetyl-CoA. Malonyl-CoA is an intermediate in fatty acid
synthesis and a potent inhibitor of carnitine palmitoyltransferase 1
(CPT1). CPT1 transfers long-chain fatty acyl-CoA (LCFA-CoA) to the
mitochondria for β-oxidation. Reduced activity of MCD would lead to
elevated LCFA-CoA in the hypothalamus, which signals energy surfeit
and leads to inhibition of feeding. We proposed that genetic variation
influencing expression of the MCD gene (MLYCD) could influence body
weight through an effect on energy intake. It has been established that
peroxisomal-proliferator-activated receptor α (PPARα) activates transcription
of rat hepatic MCD via two of the three PPRE sites identified
(PPRE2 and PPRE3). We have identified the putative PPRE sites in
human by alignment with the rat sequence. Promoter deletion analysis
in HepG2 cells with overexpression of PPARα/RXRα (retinoid X receptor
α) showed that PPRE1 and PPRE3 were functional in human. We
also studied the functional impact of the closest single nucleotide polymorphism
(SNP) -379bp C/G (rs880088) to the putative PPRE sites
in HepG2 hepatocytes and GT1-7 hypothalamic neurons in transient
transfection studies. No significant difference in promoter activity was
found between the alleles in HepG2 but the -379 G allele showed 2.1
times greater activity than -379 C allele in GT1-7 cells. Electrophoretic
mobility shift assays (EMSAs) revealed that the -379 G allele binds
to nuclear protein(s) only from GT1-7 cells. In conclusion, the data
suggest the MLYCD -379 C/G polymorphism is a regulatory SNP that
affects promoter activity in GT1-7 cells.
P11.068
Loss of paternal methylation affecting the MEG locus located
on chromosome 14q32.2 imprinted region in a girl with maternal
upd-like phenotype
B. Demeer 1 , G. Morin 1 , R. Gouron 2 , L. Razafimanantsoa 3 , S. Kanafani 4 , J.
Andrieux 5 , H. Copin 4 , L. Cusisset 6 , M. Mathieu 1 ;
1 Department of Medical Genetics, University Hospital, Amiens, France, 2 Department
of Orthopaedics, University Hospital, Amiens, France, 3 Pediatric Department,
Beauvais, France, 4 Department of Cytogenetics, University Hospital,
Amiens, France, 5 Department of Molecular Genetics, University Hospital, Lille,
France, 6 Department of Molecular Genetics, Cochin-Saint Vincent de Paul
Hospital, Paris, France.
We report the case of a 8-year old girl seen in the orthopaedic department
for scoliosis. She is the third child of non consanguinous healthy
parents. She was born after an uneventful pregnancy (BW : 2.330kg,
BH : 47.5cm, BHC : 32 cm, Apgar score 10,10). Neonatal feeding difficulties
and moderate axial hypotonia were noted. Motor milestones
and speech were delayed. From the age of 2 years, she began to
put on weight and developed obesity. At 8 years 2/12, parameters are
38.4kg (+4SD), 136.5cm (+2.2SD), BMI 20.6; Tanner stages : S1A1P2.
She presents a 40° dorsal scoliosis, rather short hands and feet, no
dysmorphic facial features and no mental retardation. Cerebral MRI
was normal. Karyotype is 46, XX, ish15q11-13(SNRPNx2), and Array-
CGH did not detect any microdeletion or microduplication.
As maternal uniparental disomy for chromosome 14 (maternal UPD
14) was suspected, microsatellite studies and methylation analysis of
Maternally Expressed Gene 3 (MEG3) located in the 14q32.2 region
were performed. Maternal UPD 14 was excluded by showing biparental
inheritance of microsatellite markers. Methylation of the MEG3
locus showed loss of paternal methylation with normal profil methylation
of both parents.
Yet very few patients with exclusively maternal methylation profil of
the MEG3 locus have been described, but notably clinical features
seemed to be grossly similar in epimutation patients and maternal
UPD 14 patients.
P11.069
Both translation start sites in the human MCT gene are used to
produce two mct8 protein isoforms in vitro
E. C. H. Friesema1 , S. Kersseboom1 , T. Wood2 , C. E. Schwartz2 , T. J. Visser1 ;
1 2 Erasmus University Medical Center, Rotterdam, The Netherlands, Greenwood
Genetic Center, Greenwood, SC, United States.
Mutations in MCT8 (SLC16A2) are associated with severe X-linked
psychomotor retardation and elevated serum T3 levels, also known as
Allan-Herndon-Dudley syndrome. MCT8 is an important thyroid hormone
transporter, especially in the brain. In contrast to the mouse, the
human MCT8 gene contains two possible translation start sites (TLSs),
giving rise to proteins of 613 (MCT8L) or 539 (MCT8S) amino acids.
Studies in human liver revealed the presence of mRNA species containing
both TLSs. Also, we described last year a patient with an insertion
of 2 amino acids (p.G41_S42 dup) located between the two TLSs
in MCT8. In addition to short MCT8 cDNA containing only the 2nd TLS,
we cloned long MCT8 cDNA with both TLSs, inserted the G41_S42 duplication
or mutated the second TLS (M75A, M75L) to prevent the synthesis
of MCT8S. Western blotting showed that transfection with long
MCT8 cDNA results in bands of 61 and 69 kDa, representing MCT8S