Experience of a multidisciplinary task force with exome sequencing for Mendelian disorders.

BACKGROUND: In order to optimally integrate the use of high-throughput sequencing (HTS) as a tool in clinical diagnostics of likely monogenic disorders, we have created a multidisciplinary "Genome Clinic Task Force" at the University Hospitals of Geneva, which is composed of clinical and molecular geneticists, bioinformaticians, technicians, bioethicists, and a coordinator. METHODS AND RESULTS: We have implemented whole exome sequencing (WES) with subsequent targeted bioinformatics analysis of gene lists for specific disorders. Clinical cases of heterogeneous Mendelian disorders that could potentially benefit from HTS are presented and discussed during the sessions of the task force. Debate concerning the interpretation of identified variants and the content of the final report constitutes a major part of the task force's work. Furthermore, issues related to bioethics, genetic counseling, quality control, and reimbursement are also addressed. CONCLUSIONS: This multidisciplinary task force has enabled us to create a platform for regular exchanges between all involved experts in order to deal with the multiple complex issues related to HTS in clinical practice and to continuously improve the diagnostic use of HTS. In addition, this task force was instrumental to formally approve the reimbursement of HTS for molecular diagnosis of Mendelian disorders in Switzerland.

[Trophoblastic diseases: a multidisciplinary approach, a first Swiss center]. / Maladies trophobtastiques: une prise en charge pluridisciplinaire, un premier centre suisse.

Trophoblastic diseases are rare and complex. The Center for trophoblastic diseases, the first in Switzerland, was founded in Geneva in January 2009 to formalize the collaboration between obstetricians-gynecologists, pathologists, geneticists, radiologists and oncologists. At the physician's request and with patient consent, an integrative diagnosis is proposed after centralized review of the histological slides, anti-p57KIP2 immunohistochemistry, and ploidy analysis by QF-PCR (Quantitative fluorescent polymerase chain reaction). The referring physician receives treatment and beta-hCG dosage recommendations. This pluridisciplinary diagnostic and therapeutic approach allows optimal surveillance and treatment of patients.

Increased methylation of glucocorticoid receptor gene (NR3C1) in adults with a history of childhood maltreatment: a link with the severity and type of trauma.

Childhood maltreatment, through epigenetic modification of the glucocorticoid receptor gene (NR3C1), influences the hypothalamic-pituitary-adrenal axis (HPA axis). We investigated whether childhood maltreatment and its severity were associated with increased methylation of the exon 1(F) NR3C1 promoter, in 101 borderline personality disorder (BPD) and 99 major depressive disorder (MDD) subjects with, respectively, a high and low rate of childhood maltreatment, and 15 MDD subjects with comorbid post-traumatic stress disorder (PTSD). Childhood sexual abuse, its severity and the number of type of maltreatments positively correlated with NR3C1 methylation (P=6.16 × 10(-8), 5.18 × 10(-7) and 1.25 × 10(-9), respectively). In BPD, repetition of abuses and sexual abuse with penetration correlated with a higher methylation percentage. Peripheral blood might therefore serve as a proxy for environmental effects on epigenetic processes. These findings suggest that early life events may permanently impact on the HPA axis though epigenetic modifications of the NR3C1. This is a mechanism by which childhood maltreatment may lead to adulthood psychopathology.

Specific language impairment as the prominent feature in a patient with a low-level trisomy 21 mosaicism.

BACKGROUND: The extent and severity of the disabilities is variable among individuals with Down syndrome, although generally characterized by a range of physical and intellectual conditions, including language impairment. Whether the language deficit is due to the intellectual disability (ID) or associated to the supernumerary or portion of chromosome 21 is still debated. METHODS: Karyotyping was performed on blood lymphocyte and skin fibroblasts. Fluorescence in situ hybridization analysis was performed on cultured lymphocytes and buccal smear cells. RESULTS: The trisomy 21 (T21) mosaicism was characterized by 0.7-10% of mosaic cells in the different tissues, in a 14-year-old girl presenting an intellectual development within the normal range and specific language impairment (SLI) as the only prominent feature. CONCLUSION: This case illustrates the wide range of phenotypical abnormalities possibly associated with T21 mosaicism. We propose that SLI is indeed a phenotypic trait specific to Down syndrome rather than subsequent to the ID most often associated to the syndrome.

Six cases of cryptic subtelomeric translocations in four families: the use of subtelomeric FISH probes as a diagnostic tool.

Finding the diagnosis in children with mental retardation and a normal karyotype, whether or not associated with dysmorphic features, is important for defining an eventual syndrome and for genetic counselling of the families. Telomeric re-arrangements may be a common and underestimated-to-date cause of non-syndromic mental retardation. Using a FISH-based approach combining subtelomeric probes, we report the detection of 4 cases of cryptic translocations t(2;10)(p25.3;q26.3), t(4;17)(p16.2;q25), t(4;20)(p16.2;q13) and t(5;7)(p15.3;q36) associated with MR and dysmorphic features. We discuss the usefulness of subtelomeric FISH in children with unexplained delayed psychomotor development, when the genetic cause remains unknown and the karyotype is normal.

The role of DMDs in the maintenance of epigenetic states.

An important aspect of genome reprogramming is the establishment and maintenance of gamete-specific DNA methylation patterns that distinguish the parental alleles of imprinted genes. Disrupting the accurate transmission of genomic imprints by interfering with these methylation patterns causes severe defects in fetal growth and development. The inheritance of sex-specific DNA methylation patterns from both parents is thus a fundamental molecular definition of genomic imprinting. The other cardinal aspect is the regulation of imprinted gene expression over a long genomic distance, spanning a few clustered imprinted genes. There is converging experimental evidence that differentially methylated domains (DMDs), located in non-coding regions of imprinted genes, are involved in both processes. As such, DMDs are the imprinting backbone upon which the fundamental processes of sex-specific methylation and imprinted gene expression are built.

[A conflict within the genome, the battle of the sexes?]. / Empreinte génomique, la bataille des sexes?

It is estimated that 100 to 200 genes in the human genome are imprinted. These are expressed only from one parental allele, although having the same DNA sequence. Several of the known imprinted genes have been shown to be involved in fetal and placental growth, and imprinting defects can lead to embryonic, developmental defects as well as cancer. This mechanism of gene regulation probably emerged 150 million years ago in mammals. The reasons for the appearance and maintenance of this phenomenon throughout evolution are still controversial.

Parenteral nutrition practices in hospital pharmacies in Switzerland, France, and Belgium.

OBJECTIVE: Important changes in administering total parenteral nutrition (PN) admixtures have occurred over the past decade. This study describes hospital pharmacists' practices in France (F), Switzerland (CH), and Belgium (B). METHODS: From the responses received using a standardized questionnaire, (n = 378) we determined the origin, types of container used, and choice of PN formula (standard versus tailor-made) and the type of quality control and the existence of nutrition support teams. RESULTS: The mean response rates were 55.6% (CH), 30.5% (F), and 24.5% (B). Standard formulas were used mainly for adult patients (CH, 86%; F, 79%; B, 86%), whereas approximately 50% of tailor-made PN bags were used for children. Single-compartment or multicompartment bags or glass bottles contained standard formulas. Most standard formulas were provided by industry, apart from (B), where 50% of PN solutions were compounded by hospital pharmacies. Single-compartment bags contained generally tailor-made formulas produced exclusively by hospital pharmacies in (CH) and (B), whereas 33% were provided by industry in (F). Quality controls were mostly visual and occurred in 75% to 95% of hospitals. Nutrition support teams were present in 32% to 45% of hospitals. CONCLUSION: The choice, origin, and type of container used for PN formulas were highly variable among countries. However, the use of standard formulas in bags was predominant in (CH) and (B). The function of nutrition support teams was similar in (F), (CH), and (B).

Genomic interactions with disease and nutrition.

The putative influence of genomic factors on the responsiveness to nutrient intake is a newly developed field of research. As well, there is growing interest for determining the interactions between nutrient, inflammation and aging and the possible impact on lifespan and disease development. Inflammation adversely affects health in many diseases with an inflammatory basis, such as atherosclerosis, obesity and type 2 diabetes mellitus. The metabolic effects of inflammation are mediated by pro-inflammatory cytokines. Metabolic effects include insulin insensitivity, hyperlipidemia, muscle protein loss and oxidant stress. Aging is also characterized by an increase in inflammatory stress and contains some of the hallmarks of inflammatory disease. It is also a phase of life when inflammatory diseases rise in incidence. Evidence is accumulating that the individual level of cytokine production is influenced by single nucleotide polymorphisms (SNPs) in cytokine genes. The combination of SNPs might control the relative level of inflammatory stress following inflammatory stimuli and diseases. These genomic characteristics might therefore influence lifespan, morbidity and mortality in diseases with an infectious or inflammatory basis.Recent studies indicate that genotypic factors may influence the effectiveness of such immunonutrients as anti-oxidants and n-3 polyunsaturated fatty acids. A better understanding of this aspect of nutrient gene interactions and of the genomic factors which influence the intensity of inflammation in disease will help in the targeting of nutritional therapy.

Genetics and nutrition.

The understanding of the role of nutrients on DNA stability, repair and on the different gene expression processes recently became more prominent in nutritional science. Nutrients and the genomics interact at two levels. Nutrients can induce gene expression thereby altering individual phenotype. Conversely single nucleotide polymorphisms, in a range of genes important in inflammation and lipid metabolism, alter the bioactivity of important metabolic pathways and mediators and influence the ability of nutrients to interact with them. The study on single effects of nutrients on the individual's phenotype as well as the serial analyses of gene expression patterns in response to specific nutrients will help us to understand how metabolic homeostasis is maintained. Considering that there is wide variation in the ability of nutritional factors to modulate the expression of detrimental or protective proteins at an individual level, the concept of diet-medication could be developed in the light of a better understanding of nutrient-gene interactions. In this way, 'good responders' and 'poor responders' to diet therapy can be identified. Furthermore, as several vitamins participate in DNA protection and genomic stabilisation, diet-linked therapies could become part of cancer prevention and other treatments with relevant consequences for human health.

Pregnancy outcome of 30 fetuses with cystic hygroma diagnosed during the first 15 weeks of gestation.

The goal of the study was to assess the prognostic value of ultrasound finding of fetal cystic hygromas. Thirty cases of septated cystic hygromas were diagnosed at 10-15 weeks gestation by transabdominal ultrasound and followed through pregnancy. The rate of abnormal karyotype was found to be 61% and the global rate of unfavorable outcome, independently of karyotype result, as high as 96%. These data suggest that cautious genetic counselling should be offered when such cystic hygromas are noticed during the first 15 weeks of gestation, even with a normal karyotype.

A case of (X;15) translocation diagnosed as a paracentric inversion of Xp: diagnostic revision with FISH.

In 1990 we reported the case of a 17 years old girl with growth retardation, overweight and primary amenorrhea, presenting a de novo chromosomal rearrangement cytogenetically characterized as a paracentric inversion of the short arm of X chromosome. The FISH analyses that were recently performed, revealed that in fact our patient presented a case of unbalanced translocation, 46,X, t(X;15)(p11.2; q15).

Frequency of replication/transcription errors in (A)/(T) runs of human genes.

To estimate the error rate of the gene expression machinery and its possible age-related increase, we compared the occurrence of polymerase errors during replication and transcription in (A)/(T) runs, in DNA and RNA of young and old individuals and of early- and late-passage cultured fibroblasts. We analyzed three human genes: TPRD, TGFBR2, and ATRX containing stretches of (A)8, (A)10, and (T)13, respectively. The error rate was determined by sequencing 100 cloned PCR or RT-PCR fragments from each DNA and RNA sample. The error rates in replication and transcription increased with the stretch length. The pooled error rates for genomic DNA were: TPRD (A)8, TGFBR2 (A)10, and ATRX (T)13: 1%+/-0.41, 15.8%+/-1.3, and 31.3%+/-2.9, while those for RNA were: 3.8%+/-0.5, 19.3%+/-2.1, and 54.3%+/-1.8, respectively. The deletions of one nucleotide were the most frequent errors. In the replication analysis, a significant difference was found in old versus young individuals for the ATRX (T)13. In the transcription analysis, significantly higher error rates were obtained in old versus young individuals for the TPRD (A)8 and TGFBR2 (A)10. For these genes, the error rate in RNA isolated from fibroblasts was significantly higher than that in blood. The data show a trend of age-related increase in replication/transcription errors; however further studies are necessary to confirm this hypothesis, since the sample size is small. This imperfect fidelity of the gene expression process may explain the evolutionary disadvantage of nucleotide repeats within coding sequences, and that these repeats are targets for mutations in human diseases.

Suicide attempts and the tryptophan hydroxylase gene.

Tryptophan hydroxylase (TPH) is the rate-limiting enzyme of serotonin synthesis. In this case-control study, we investigated whether the TPH gene was a susceptibility factor for suicidal behavior. Seven polymorphisms spanning the entire gene were studied in a case-control study including 231 individuals who had attempted suicide and 281 controls. Significant associations were found between variants in introns 7, 8 and 9 (chi(2) = 11.2, df = 1, P< 0.0008 for the allele distribution; these loci are in complete linkage disequilibrium) and in the 3' noncoding region (chi(2) = 30.94, P = 0.0014) and suicide attempt. The association was strongest for subjects who had attempted suicide by violent means and who had a history of major depression. No significant association was observed between suicide attempts and polymorphisms in the promoter, intron 1 and intron 3. The results presented here, and those of previous studies, suggest that a genetic variant of the 3' part of the TPH gene may be a susceptibility factor for a phenotype combining suicidal behavior, mood disorder and impulsive aggression.

Familial t(6;21)(p21.1;p13) translocation associated with male-only sterility.

A 38-year-old male with primary infertility was referred for cytogenetic investigation. Karyotype analysis revealed a 46,XY,t(6;21)(p21.1;pl3) translocation. The Ag-nucleolar organizer regions (NORs) banding technique demonstrated that the 21p NORs were retained in the derivative and actively transcribed. Family studies showed that three brothers, two sisters and their mother carried the t(6;21). All carrier males suffered from primary infertility with severe oligoasthenoteratospermia or azoospermia, whereas at least two of the three carrier women were fertile. The region of the translocation breakpoint was narrowed down cytogenetically and by fluorescence in situ hybridisation as 21p13 and 6p21.1. Southern blot analysis showed that the gene ZNF165, which maps to this region and which is specifically expressed in the testis, was not disrupted by the translocation. However, studies performed on testicular biopsy showed spermatocyte meiosis anomalies. We discuss the possible mechanisms by which the translocation might affect meiosis in spermatogenesis and lead to infertility.