[Genome sequencing and personalized medicine: perspectives and limitations]. / Séquençage des génomes et médecine personnalisée: perspectives et limites.

DNA sequencing technologies have advanced at an exponential rate in recent years: the first human genome was sequenced in 2001 after many years of effort by dozens of international laboratories at a cost of tens of millions of dollars, while in 2013 a genome can be sequenced within 24 hours for a few hundred dollars (exome sequencing takes only a few hours). More and more hospital laboratories are acquiring new high-throughput sequencing devices ("next-generation sequencers", NGS), allowing them to analyze tens or hundreds of genes, or even the entire exome. This is having a major impact on medical concepts and practices, especially with respect to genetics and oncology. This ability to search for mutations simultaneously in a large number of genes is finding applications in the diagnosis of Mendelian diseases (including at birth), routine screening for heterozygotes, and pre-conception diagnosis. NGS is now sufficiently sensitive to analyze circulating fetal DNA in maternal blood (cell-free fetal DNA, cffDNA), enabling applications such as non invasive diagnosis of fetal sex (and X-linked diseases), fetal rhesus among rhesus-negative women, trisomy and, in the near future, Mendelian mutations. Data on multifactorial diseases are still preliminary, but it should soon be possible to identify "strong" factors of genetic predisposition that have so far been beyond the scope of genome-wide association studies (GWAS). In the field of constitutional oncogenetics, NGS can also be used for simultaneous analysis of genes involved in " hereditary " cancers (21 breast cancer genes, 6 colon cancer genes, etc.). More generally, NGS can identify all genomic abnormalities (deletions, translocations, mutations) in a given malignant tissue (hemopathy or solid tumor), and has the potential to distinguish between important mutations (those that drive tumor progression) from " bystander " or accessory mutations, and also to identify "druggable" mutations amenable to targeted therapies (e.g. imatinib and Bcr/Abl rearrangement; verumafemib and the BRAF V600E mutation). Systematic sequencing of all the genes involved in drug metabolism and responsiveness will lead to individualized pharmacogenetics. Finally, sequencing of the tumoral and constitutional genomes, identfication of somatic mutations, and detection of pharmacogenetic variants will open up the era of personalized medicine. The first results of these targeted therapeutic indications show a gain in the duration of remission and survival, although the cost-effectiveness of these approaches remains to be determined. Finally, this huge capacity for genome sequencing raises a number of regulatory and ethical issues.

[Intestinal microbiota]. / Le microbiote intestinal.

The human body normally lives in symbiosis with a considerable microscopic environment present on all interfaces with the external environment; it hosts ten times more microbes (microbiota) that it has somatic or germ cells, representing a gene diversity (microbiome) 100-150 times higher than the human genome. These germs are located mainly in the gut, where they represent a mass of about one kilogram. The primary colonization of the gastrointestinal tract depends on the delivery route, the bacterial flora rewarding then depending on the environment, food hygiene, medical treatments. The intestinal microbiota plays an important role in the maturation of the immune system and in different physiological functions: digestion of polysaccharides, glycosaminoglycans and glycoproteins, vitamins biosynthesis, bile salt metabolism of some amino acids and xenobiotics. Quantitative and qualitative changes in the microbiota are observed in a wide range of diseases: obesity, colorectal cancer, liver cancer, inflammatory bowel disease, autoimmune diseases, allergies... pharmacobiotics aim to modify the intestinal microbiota in a therapeutic goal and this by various means: prebiotics, probiotics, antibiotics or fecal transplants. Intestinal flora also plays a direct role in the metabolism of certain drugs and the microbiota should be considered as a predictive parameter of response to some chemotherapies.

[Genetic control of infectious diseases: from Mendel's laws to exome sequencing]. / Le contrôle génétique des maladies infectieuses: des lois de Mendel au séquençage de l'exome.

About one-quarter of deaths worldwide (nearly 13 million per year) are still directly related to infectious diseases. Many new infections have emerged since the end of the 20th century and others will continue to do so. Human beings, like other animals, are not all equal with respect to their susceptibility to infection. Since the 1930s, numerous epidemiological studies have shown that host genetic factors play a major role in susceptibility and resistance to infections. Studies of Mendelian genetics and genetic epidemiology based on association studies, now using high-speed typing of anonymous polymorphic markers, can detect genes or loci that influence an individual's response to a particular germ. Different cases of susceptibility or resistance to viral, bacterial, fungal and parasitic infections will be used to illustrate the importance of genetic factors in the diagnosis of clinical manifestations and their prevention, characterization of host immune responses, and their influence on evolutionary biology. With different phenotypes associated with genetic polymorphisms, and new genomic techniques, the genetics of infectious diseases is entering a new era, raising questions of medical practice, ethics, and public and industrial policies.

[The biology of aging]. / Biologie du vieillissement.

Although aging is unavoidable, its course can be influenced by various factors, as illustrated by the increase in life expectancy associated with improvements in hygiene and with the general reduction in morbidity. Longevity has also been altered experimentally in some animal species. Aging follows a period of growth and reproduction. Death may occur when the immortality of the germinal line has been ensured. In other cases it results from gradual cellular deterioration. Four principal molecular and cellular processes have been studied in experimental models (mainly mice, worms and fruit flies):--inhibition of the insulin/IGF-1 axis increases life expectancy by allowing a transcription factor (DAF-16 in C. elegans, FoXo in mice) to enter the nucleus, where it stimulates the expression of genes encoding survival-promoting proteins; one such inhibitor is Klotho protein;--the detrimental effects of highly toxic reactive oxygen species, mainly produced in the mitochondria, are partly controlled by scavenging molecules and enzymes. Their accumulation leads to DNA, lipid and protein changes, resulting in cell dysfunction;--the telomeres situated at the ends of each chromosome get shorter with time because of inadequate telomerase activity, and this appears to be associated with diminished longevity;--autophagia within lysosomes destroys altered proteins and thereby maintains cell homeostasis. However, this activity diminishes with time, resulting in the accumulation of toxic metabolites in the cell, dysfunction of the endoplasmic reticulum and mitochondria, and increased apoptosis. Studies of genetically mediated aging disorders have revealed the importance of lamins (intermediate nuclear filaments). For example, a mutation that prevents the protein lamin A from maturing is the cause of progeria, a disease associated with an acceleration of most aging processes and with premature death. There is no single biological marker of aging. In contrast, a combination of Nt-proBNP, troponin I, C-reactive protein and cystatin may be useful, as increased levels are a risk factor for atheroma and cardiovascular diseases, both of which are associated with aging. The different organs age in different ways: vessel walls become rigid due to protein glycation and develop atheroma; the heart is invaded by fibrosis; the brain suffers from neurofibrillar degeneration and senile plaques (responsible for Alzheimer's disease); the retina undergoes macular degeneration; renal function declines in parallel with the fall in the glomerular filtration rate due to a gradual decrease in the nephron pool; and immune defenses become less effective due to the functional degradation of B and T lymphocytes and thymus involution. Reproduction is a special case: despite the increase in human longevity, the chronology of the reproductive cycle and the age of menopause onset have not changed. The frequency of cancers increases with age, due to the increase in somatic mutations and the decline in immune defenses. Drug therapy must be adapted to age, owing to age-related changes in pharmacology. Physical exercise and dietary measures are currently the only known ways of slowing the aging process.

Five distinct biological processes and 14 differentially expressed genes characterize TEL/AML1-positive leukemia.

BACKGROUND: The t(12;21)(p13;q22) translocation is found in 20 to 25% of cases of childhood B-lineage acute lymphoblastic leukemia (B-ALL). This rearrangement results in the fusion of ETV6 (TEL) and RUNX1 (AML1) genes and defines a relatively uniform category, although only some patients suffer very late relapse. TEL/AML1-positive patients are thus an interesting subgroup to study, and such studies should elucidate the biological processes underlying TEL/AML1 pathogenesis. We report an analysis of gene expression in 60 children with B-lineage ALL using Agilent whole genome oligo-chips (44K-G4112A) and/or real time RT-PCR. RESULTS: We compared the leukemia cell gene expression profiles of 16 TEL/AML1-positive ALL patients to those of 44 TEL/AML1-negative patients, whose blast cells did not contain any additional recurrent translocation. Microarray analyses of 26 samples allowed the identification of genes differentially expressed between the TEL/AML1-positive and negative ALL groups. Gene enrichment analysis defined five enriched GO categories: cell differentiation, cell proliferation, apoptosis, cell motility and response to wounding, associated with 14 genes -RUNX1, TCFL5, TNFRSF7, CBFA2T3, CD9, SCARB1, TP53INP1, ACVR1C, PIK3C3, EGFL7, SEMA6A, CTGF, LSP1, TFPI - highlighting the biology of the TEL/AML1 sub-group. These results were first confirmed by the analysis of an additional microarray data-set (7 patient samples) and second by real-time RT-PCR quantification and clustering using an independent set (27 patient samples). Over-expression of RUNX1 (AML1) was further investigated and in one third of the patients correlated with cytogenetic findings. CONCLUSION: Gene expression analyses of leukemia cells from 60 children with TEL/AML1-positive and -negative B-lineage ALL led to the identification of five biological processes, associated with 14 validated genes characterizing and highlighting the biology of the TEL/AML1-positive ALL sub-group.

[Personal identification with biometric and genetic methods]. / Identification des personnes par des analyses biométriques et génétiques.

The need for personal identification is growing in many avenues of society. To "identify" a person is to establish a link between his or her observed characteristics and those previously stored in a database. To "authenticate" is to decide whether or not someone is the person he or she claims to be. These two objectives can now be achieved by analysing biometric data and genetic prints. All biometric techniques proceed in several stages: acquisition of an image or physical parameters, encoding them with a mathematical model, comparing the results of this model with those contained in the database, and calculating the error risk. These techniques must be usable worldwide and must examine specific and permanent personal data. The most widely used are facial recognition, digital prints (flexion folds and dermatoglyphs, that offer the advantage of leaving marks), and the surface and texture of the iris. Other biometric techniques analyse behaviours such as walking, signing, typing, or speaking. Implanted radio-transmitters are another means of identification. All these systems are evaluated on the basis of the same parameters, namely the false rejection rate, the false acceptance rate, and the failure-to-enrol rate. The uses of biometrics are increasing and diversifying, and now include national and international identification systems, control of access to protected sites, criminal and victim identification, and transaction security. Genetic methods can identify individuals almost infallibly, based on short tandem repeats of 2-5 nucleotides, or microsatellites. The most recent kits analyze 11-16 independent autosomal markers. Mitochondrial DNA and Y chromosome DNA can also be analyzed. These genetic tests are currently used to identify suspected criminals or their victims from biological samples, and to establish paternity. Personal identification raises many ethical questions, however, such as when to create and how to use a database while preserving personal freedom? How to control access to genetic data? Do genetic polymorphisms delineate different human races? To what extent should different databases be interconnected? and What limits should be placed on individual files available on the web and on radiofrequency identification by implanted chips? A balance must be struck between the need to ensure the security of persons and transactions and the need to protect individual freedom and privacy.

[Generalized neonatal screening based on laboratory tests]. / Le dépistage neonatal généralisé par des tests d'analyse biologique.

Implementation of a generalized screening program for neonatal diseases must obey precise rules. The disease must be severe, recognizable at an early stage, amenable to an effective treatment, detectable with a non expensive and widely applicable test; it must also be a significant public health problem. Subjects with positive results must be offered immediate treatment or prevention. All screening programs must be regularly evaluated. In France, since 1978, a national screening program has been organized by a private association ("Association française pour le dépistage et la prévention des handicaps de l'enfant") and supervised by the "Caisse nationale d'assurance maladie" and "Direction Générale de la Sante". Five diseases are now included in the screening program: phenylketonuria, hypothyroidism, congenital adrenal hyperplasia, cystic fibrosis and sickle cell disease (the latter only in at-risk newborns). Toxoplasmosis is a particular problem because only the children of mothers who were not tested during the pregnancy or who seroconverted are screened. Neonatal screening for phenylketonuria and hypothyrodism is unanimously recommended. Screening for congenital adrenal hyperplasia is approved in most countries. Cases of sickle cell disease and cystic fibrosis are more complex because--not all children who carry the mutations develop severe forms;--there is no curative treatment;--parents may become anxious, even though the phenotype is sometimes mild or even asymptomatic. Supporters of screening stress the benefits of early diagnosis (which extends the life expectancy of these children, particularly in the case of sickle cell disease), the fact that it opens up the possibility of prenatal screening of future pregnancies, and the utility of informing heterozygous carriers identified by familial screening. Neonatal screening for other diseases is under discussion. Indeed, technical advances such as tandem mass spectrometry make it possible to detect about 50 diseases in a single run. In addition to issues of cost and organization, any increase in the number of screened diseases will raise ethical problems, such as how to inform parents of an incurable disease, a late-onset disease, or an entirely asymptomatic disorder. It is unanimously agreed that only Mendelian diseases should be screened for (excluding genetic polymorphisms). Analysis of the present situation suggests the following changes:--guidelines for choosing new diseases for neonatal screening should be updated;--all new screening programs should be tested locally before nationwide implementation;--an evaluation committee of paediatricians and epidemiologists should be created, and the children's long-term outcome should be studied;--the conditions in which heterozygous carriers are informed after familial investigations need to be precisely defined;--blood samples should be banked for epidemiological studies.

[Human iron metabolism]. / Le métabolisme du fer chez l'homme.

Iron, associated with proteins and enzymes, mainly as heminic groups and Fe/S clusters, is essential for oxygen transport and many other biological functions. Systemic iron homeostasis is essentially a closed system. There is no regulated mechanism of iron excretion, for example through the liver or kidneys: iron losses occur only through bleeding and by shedding of mucosal and skin cells. These losses are compensated for by intestinal absorption. In contrast, iron absorption is tightly regulated. Three recently identified proteins, named HFE, hepcidin and hemojuvelin, play an important role in this regulation. About 20 other proteins have been shown to play a part in iron metabolism, often through studies of genetic diseases in humans or other animals. Mitochondria play a major role in iron metabolism.

[Genetics of hereditary iron overload]. / Génétique des surcharges martiales primitives.

The classification of hereditary abnormalities of iron metabolism was recently expanded and diversified. Genetic hemochromatosis now corresponds to six diseases, namely classical hemochromatosis HFE 1; juvenile hemochromatosis HFE 2 due to mutations in an unidentified gene on chromosome 1; hemochromatosis HFE 3 due to mutations in the transferrin receptor 2 (TfR2); hemochromatosis HFE 4 caused by a mutation in the H subunit of ferritin; and hemochromatosis HFE 6 whose gene is hepcidine (HAMP). Systemic iron overload is also associated with aceruloplasminemia, atransferrinemia and the "Gracile" syndrome caused by mutations in BCS1L. The genes responsible for neonatal and African forms of iron overload are unknown. Other genetic diseases are due to localized iron overload: Friedreich's ataxia results from the expansion of triple nucleotide repeats within the frataxin (FRDA) gene; two forms of X-linked sideroblastic anemia are due to mutations within the delta aminolevulinate synthetase (ALAS 2) or ABC-7 genes; Hallervorden-Spatz syndrome is caused by a pantothenate kinase 2 gene (PANK-2) defect; neuroferritinopathies; and hyperferritinemia--cataract syndrome due to a mutation within the L-ferritin gene. In addition to this wide range of genetic abnormalities, two other features characterize these iron disorders: 1) most are transmitted by an autosomal recessive mechanism, but some, including hemochromatosis type 4, have dominant transmission; and 2) most correspond to cytosolic iron accumulation while some, like Friedreich's ataxia, are disorders of mitochondrial metabolism.

[Should we support large-scale screening for genetic haemochromatosis in France?]. / Faut-il promouvoir le dépistage systématique de l'hémochromatose génétique en France?

Genetic hemochromatosis meets the principal World Health Organization criteria for diseases warranting systematic population screening. Indeed, it is a frequent, late-onset, severe disease that is easy to diagnose and cure. However, its penetrance is much lower than thought prior to the discovery of the HFE1 gene, whose C282 Y mutation is responsible for more than 95% of cases with phenotypic expression. Moreover, several questions remain to be answered, notably concerning practical modalities [genotypic or phenotypic screening? at what age?, etc.], the risk of genetic discrimination, and cost-effectiveness. Current recommendations should include [i] broad information of the general population and GPs on early symptoms, [ii] transferrin saturation assay in all patients with symptoms compatible with hemochromatosis and, when elevated, genetic testing, the cost of which should be covered by public health insurance, [iii] both phenotypic and genotypic screening of all proband families, and [iv] implementation of regional and national pilot studies aimed at assessing disease penetrance and the acceptability and cost-effectiveness of large-scale screening.