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

The GnRH system : importance for precocious puberty in children

We discuss here the secular early onset of puberty in children, the central mechanisms of puberty as well as the clinical aspects of central precocious puberty in children. How to suspect it, how to explore it and how to treat it are the main topics of this articleAprès avoir rappelé les mécanismes centraux de la puberté, nous nous focalisons sur les aspects cliniques de la puberté précoce centrale chez l’enfant. Comment la suspecter, comment l’explorer, comment la traiter : voilà les points qui sont développés dans cet articl

Etude de la fertilité chez 190 patients présentant une hyperplasie congénitale des surrénales à révélation tardive par déficit en 21-hydroxylase

Une étude rétrospective de la fertilité a été réalisée chez 190 patientes (161 cas-index et 29 cas familiaux) atteintes d une HCS tardive par déficit en 21-DF suivies depuis 1978. Ces patientes ont consulté majoritairement pour un hirsutisme (71,6%); 53% d entre elles présentaient des troubles du cycle, et 11% ont consulté pour infertilité. L étude du gène CYP21 réalisée chez 141 patientes a révélé que 2/3 des patientes présentaient au moins une mutation sévère. Parmi ces femmes, 95 ont désiré une grossesse. 187 grossesses et 141 naissances ont été obtenues respectivement chez 85 et 82 d entre elles. 57% des grossesses ont été spontanées, 83% des grossesses ont été obtenues en moins d un an. Un traitement glucocorticoïde a été utilisé pour 41% des grossesses et apparaît suffisant pour normaliser le taux d androgènes et rétablir des cycles réguliers chez la majorité des patientes. En deuxième intention, l association à un traitement par citrate de clomifène chez ces patientes dont un certain nombre présentent un phénotype d ovaires polykystiques apparaît indiquée. Le taux de fausse couches (FCS), parmi les grossesses survenues sans traitement glucocorticoïde (23%) est significativement supérieur au taux de FCS lors de grossesses survenues sous traitement glucocorticoïde (6,6%). L effet d autres facteurs de risques de FCS en dehors d un antécédent d infertilité n apparaît pas en étude multivariée. L incidence de la naissance d un enfant atteint d une forme classique de la maladie est estimée à 1,5% dans notre cohorte. Dès lors, il est indispensable d explorer le conjoint des patientes porteuses d une mutation sévère afin de prévoir le risque de forme précoce chez leurs enfants.PARIS6-Bibl.Pitié-Salpêtrie (751132101) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

Prevalence of Dysmenorrhea in Adolescents in France: Results of a Large Cross-Sectional Study

International audienceBACKGROUNDS: Dysmenorrhea is the most common gynecological complaint in young women but is overlooked by recent studies. Our objective was to evaluate the prevalence of dysmenorrhea in adolescents in France and its impact on daily living. METHODS: It was a cross-sectional study conducted between April-May 2019, in eight randomly selected high schools in France. Participants were randomly selected post-menarche girl pupils 15-19 years who completed a 50-item questionnaire. Dysmenorrhea severity was assessed with the Numerical Rating Scale (NRS) and Verbal Multidimensional Scoring System Scale (VMSS). RESULTS: Questionnaires from 953 girls were analyzed (mean age: 16.9 years). The prevalence of dysmenorrhea was 92.9 % with 8.9 % describing their pain as severe. Impact on quality of life was significant: 43.3% reported school absences because of dysmenorrhea, 74.9% difficulties in attending classes and 77.2% difficulties in sports activities. Risk factors of severe dysmenorrhea in multivariate analysis were heavy menstrual bleeding (OR 2.02, 95%CI [1.12; 3.63] p=0.0192), early menarche (OR 0.68, 95%CI [0.57; 0.81] p<0.0001), chronic pelvic pain (OR 2.60, 95%CI [1.10; 6.11] p=0.0274), BMI (BMI<18, OR 1.94, 95%CI [1.03; 3.66] p=0.0335). Of the 50.4% who had consulted a physician, 45.4% had seen a general practitioner. Among the girls who had not consulted, 55.1% reported that menstruation was a "woman’s burden". CONCLUSIONS: Dysmenorrhea is highly prevalent in adolescents in France and has a real impact on daily living with social repercussions. As such, it should be treated as a public health problem with educational and information campaigns targeting the girls themselves, their families and healthcare professionals

RNA sequencing reveals the differential expression profiles of RNA in metastatic triple negative breast cancer and identifies SHISA3 as an efficient tumor suppressor gene

International audienceBreast cancer metastasis is the second leading cause of female mortality worldwide. Because of the heterogeneity within the group, metastatic biomarkers for triple-negative breast cancer (TNBC) providing predictive and prognosis values are urgently needed. Using RNA-Seq, we analyzed the transcriptome profiles of two groups of TNBCs tumors with or without distant metastasis. Whole transcriptome sequencing identified a set of genes implicated in TNBC metastasis with major roles in cell-cell adhesion, immune-modulation, and Wnt/β-catenin pathways. We further selected the SHISA3 gene and studied its biological significance through a series of in vitro and in vivo experiments. SHISA3 is a tumor suppressor gene, involved in several types of cancer. However, little is known concerning the role of SHISA3 in TNBC. Our in vitro and in vivo studies demonstrate that overexpression of SHISA3 inhibits TNBCs cell proliferation, metastasis and colony formation, and TNBC growth in xenografts. Mechanistically, SHISA3 inhibits TNBCs development and growth via downregulation of the epithelial-mesenchymal transition. Taken together, these results identified SHISA3 as a novel tumor suppressor gene in TNBC and suggest that SHISA3 could serve as a therapeutic target for TNBC patients

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

Detection Rate and Spectrum of Pathogenic Variations in a Cohort of 83 Patients with Suspected Hereditary Risk of Kidney Cancer

International audienceHereditary predisposition to cancer affects about 3–5% of renal cancers. Testing criteria have been proposed in France for genetic testing of non-syndromic renal cancer. Our study explores the detection rates associated with our testing criteria. Using a comprehensive gene panel including 8 genes related to renal cancer and 50 genes related to hereditary predisposition to other cancers, we evaluated the detection rate of pathogenic variants in a cohort of 83 patients with suspected renal cancer predisposition. The detection rate was 7.2% for the renal cancer genes, which was 2.41-fold higher than the estimated 3% proportion of unselected kidney cases with inherited risk. Pathogenic variants in renal cancer genes were observed in 44.5% of syndromic cases, and in 2.7% of non-syndromic cases. Incidental findings were observed in CHEK2, MSH2, MUTYH and WRN. CHEK2 was associated with renal cancer (OR at 7.14; 95% CI 1.74–29.6; p < 0.003) in our study in comparison to the gnomAD control population. The detection rate in renal cancer genes was low in non-syndromic cases. Additional causal mechanisms are probably involved, and further research is required to find them. A study of the management of renal cancer risk for CHEK2 pathogenic variant carriers is needed

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

International audienc

Analysis of 11 candidate genes in 849 adult patients with suspected hereditary cancer predisposition

International audienceHereditary predisposition to cancer concerns between 5% and 10% of cancers. The main genes involved in the most frequent syndromes (hereditary breast and ovarian cancer syndrome, hereditary nonpolyposis colorectal cancer syndrome) were identified in the 1990s. Exploration of their functional pathways then identified novel genes for hereditary predisposition to cancer, and candidate genes whose involvement remains unclear. To determine the contribution of truncating variants in 11 candidate genes (BARD1, FAM175A, FANCM, MLH3, MRE11A, PMS1, RAD50, RAD51, RAD51B, RINT1, and XRCC2) to cancer predisposition in a population of interest, panel sequencing was performed in 849 patients with a suspected hereditary predisposition to cancer for whom a diagnostic panel of 38 genes identified no causal mutation. Sixteen truncating variants were found in FANCM (n = 7), RINT1 (n = 4), RAD50 (n = 2), BARD1, PMS1, and RAD51B. FANCM (adjusted P-value: .03) and RINT1 (adjusted P-value: 0.04) were significantly associated with hereditary breast and ovarian cancer. However, further studies are required to determinate the risk of cancer, including the segregation of the variants in the families of our cases. No mutation was identified in RAD51, MRE11A, FAM175A, XRCC2, or MLH3. The involvement of these genes in the hereditary predisposition to cancer cannot be ruled out, although if it exists it is rare or does not seem to involve truncating variants