Removing noise from pyrosequenced amplicons

Background In many environmental genomics applications a homologous region of DNA from a diverse sample is first amplified by PCR and then sequenced. The next generation sequencing technology, 454 pyrosequencing, has allowed much larger read numbers from PCR amplicons than ever before. This has revolutionised the study of microbial diversity as it is now possible to sequence a substantial fraction of the 16S rRNA genes in a community. However, there is a growing realisation that because of the large read numbers and the lack of consensus sequences it is vital to distinguish noise from true sequence diversity in this data. Otherwise this leads to inflated estimates of the number of types or operational taxonomic units (OTUs) present. Three sources of error are important: sequencing error, PCR single base substitutions and PCR chimeras. We present AmpliconNoise, a development of the PyroNoise algorithm that is capable of separately removing 454 sequencing errors and PCR single base errors. We also introduce a novel chimera removal program, Perseus, that exploits the sequence abundances associated with pyrosequencing data. We use data sets where samples of known diversity have been amplified and sequenced to quantify the effect of each of the sources of error on OTU inflation and to validate these algorithms

ASPECT TDM ET IRM DES RADIONECROSES CEREBRALES CHEZ 28 PATIENTS IRRADIES POUR UNE TUMEUR ORL (CORRELATION DE L'IMAGERIE AVEC LA RADIOTHERAPIE)

PARIS-BIUM (751062103) / SudocCentre Technique Livre Ens. Sup. (774682301) / SudocSudocFranceF

Tristan L'Hermite, "héritier" et "précurseur"

PARIS3-BU (751052102) / SudocSudocFranceF

Etude de matériaux ferromagnétiques doux à forte aimantation et à résistivité élevée pour les radio-fréquences (applications aux inductances spirales planaires sur silicium pour réduire la surface occupée)

La miniaturisation des circuits RF impose une réduction de la taille des inductances spirales. L'idée d'utiliser des écrans magnétiques pour augmenter la densité d'inductance surfacique est connue mais sa concrétisation bute sur les limites des matériaux de l'état de l'art. Nous avons pour cela développé un matériau doux uniaxial à forte aimantation et à forte résistivité de composition FeHfN(O). A suivi la fabrication des inductances montrant, en particulier, la possibilité de réaliser un caractère bidirectionnel aux éléments magnétiques sur la base d'un dépôt unique, ce qui est particulièrement avantageux. Ensuite, les perspectives à cette réalisation ont été élargies par la simulation à d'autres configurations. Le principe du redimensionnement à inductance et facteur de qualité constants a été validé bien qu'il existe une limitation intrinsèque sur Q avec les spirales dont la cause s'est avérée indépendante du facteur de qualité du matériau lui même.The RF circuit miniaturization imposes a RF spiral inductor down-sizing. It is well known that the use of magnetic core allows increasing the inductor density per unit area but realisation of such a component reaches the limitations of state of the art materials. We have developed an uniaxial soft magnetic material with a high magnetization and a high resistivity and composed of FeHfN(O). Then, we have realized bi-directional ferromagnetic inductors with only a single deposition which is very advantageous. Next, other ferromagnetic inductor configurations have been simulated in order to broaden the application fields. Finally, it has been proven that the reason for the intrinsic limitation on Q with the spiral inductor is independent of the magnetic material quality factor.LIMOGES-BU Sciences (870852109) / SudocSudocFranceF

Proposal of new candidate genes of predisposition to serous ovarian cancer using whole-exome-sequencing of 16 patients with a familial form

International audienceHigh grade serous ovarian cancer 9th type of cancer 5th cause of death Late diagnostic and poor prognosis 15-20% of familial cancers : 2 Sporadic cancers Familial cancers 15-20% BRCA1/2 Unknown genes 50-85% MMR/RAD5

Early Onset Multiple Primary Tumors in Atypical Presentation of Cowden Syndrome Identified by Whole-Exome-Sequencing

International audienceA family with an aggregation of rare early onset multiple primary tumors has been managed in our oncogenetics department: the proband developed four early onset carcinomas between ages 31 and 33 years, including acral melanoma, bilateral clear cell renal carcinoma (RC), and follicular variant of papillary thyroid carcinoma. The proband's parent developed orbital lymphoma and small intestine mucosa-associated lymphoid tissue (MALT) lymphoma between 40 and 50 years old. Whole-exome-sequencing (WES) of the nuclear family (proband, parents, and sibling) identified in the proband a de novo deleterious heterozygous mutation c.1003C > T (p.Arg335∗) in the phosphatase and tensin homolog (PTEN) gene. Furthermore, WES allowed analysis of the nuclear family's genetic background, and identified deleterious variants in two candidate modifier genes: CEACAM1 and MIB2. CEACAM1, a tumor suppressor gene, presents loss of expression in clear cell RC and is involved in proliferation of B cells. It could explain in part the phenotype of proband's parent and the occurrence of clear cell RC in the proband. Deleterious mutations in the MIB2 gene are associated with melanoma invasion, and could explain the occurrence of melanoma in the proband. Cowden syndrome is a hereditary autosomal dominant disorder associated with increased risk of muco-cutaneous features, hamartomatous tumors, and cancer. This atypical presentation, including absence of muco-cutaneous lesions, four primary early onset tumors and bilateral clear cell RC, has not been described before. This encourages including the PTEN gene in panel testing in the context of early onset RC, whatever the histological subtype. Further studies are required to determine the implication of CEACAM1 and MIB2 in the severity of Cowden syndrome in our proband and occurrence of early onset MALT lymphoma in a parent

Is BRCA2 involved in early onset colorectal cancer risk?

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Feedback of extended panel sequencing in 1530 patients referred for suspicion of hereditary predisposition to adult cancers

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Salmonella detoxifying enzymes are sufficient to cope with the host oxidative burst.

International audienceThe oxidative burst produced by the NADPH oxidase (Phox) is an essential weapon used by host cells to eradicate engulfed pathogens. In Salmonella typhimurium, oxidative stress resistance has been previously proposed to be mediated by the pathogenicity island 2 type III secretion system (T3SS-2), periplasmic superoxide dismutases and cytoplasmic catalases/peroxidases. Here, we fused an OxyR-dependent promoter to the gfp to build the ahpC-gfp transcriptional fusion. This reporter was used to monitor hydrogen peroxide levels as sensed by Salmonella during the course of an infection. We showed that the expression of this fusion was under the exclusive control of reactive oxygen species produced by the host. The ahpC-gfp expression was noticeably modified in the absence of bacterial periplasmic superoxide dismutases or cytoplasmic catalases/peroxidases. Surprisingly, inactivation of the T3SS-2 had no effect on the ahpC-gfp expression. All together, these results led to a model in which Salmonella resistance relies on its arsenal of detoxifying enzymes to cope with Phox-mediated oxidative stress