Abstract Our aim was to develop and apply a comprehensive noninvasive prenatal test (NIPT) by using high-coverage targeted next-generation sequencing to estimate fetal fraction, determine fetal sex, and detect trisomy and monogenic disease without parental genotype information. We analyzed 45 pregnancies, 40 mock samples, and eight mother-child pairs to generate 35 simulated datasets. Fetal fraction (FF) was estimated based on analysis of the single nucleotide polymorphism (SNP) allele fraction distribution. A Z-score was calculated for trisomy of chromosome 21 (T21), and fetal sex detection. Monogenic disease detection was performed through variant analysis. Model validation was performed using the simulated datasets. The novel model to estimate FF was robust and accurate (r2= 0.994, p-value < 2.2e-16). For samples with FF > 0.04, T21 detection had 100% sensitivity (95% CI: 63.06 to 100%) and 98.53% specificity (95% CI: 92.08 to 99.96%). Fetal sex was determined with 100% accuracy. We later performed a proof of concept for monogenic disease diagnosis of 5/7 skeletal dysplasia cases. In conclusion, it is feasible to perform a comprehensive NIPT by using only data from high coverage targeted sequencing, which, in addition to detecting trisomies, also make it possible to identify pathogenic variants of the candidate genes for monogenic diseases.
Abstract CHIME syndrome is an extremely rare autosomal recessive multisystemic disorder caused by mutations in PIGL. PIGL is an endoplasmic reticulum localized enzyme that catalyzes the second step of glycosylphosphatidylinositol (GPI) biosynthesis, which plays a role in the anchorage of cell-surface proteins including receptors, enzymes, and adhesion molecules. Germline mutations in other members of GPI and Post GPI Attachment to Proteins (PGAP) family genes have been described and constitute a group of diseases within the congenital disorders of glycosylation. Patients in this group often present alkaline phosphatase serum levels abnormalities and neurological symptoms. We report a CHIME syndrome patient who harbors a missense mutation c.500T > C (p.Leu167Pro) and a large deletion involving the 5’ untranslated region and part of exon 1 of PIGL. In CHIME syndrome, a recurrent missense mutation c.500T > C (p.Leu167Pro) is found in the majority of patients, associated with a null mutation in the other allele, including an overrepresentation of large deletions. The latter are not detected by the standard analysis in sequencing techniques, including next-generation sequencing. Thus, in individuals with a clinical diagnosis of CHIME syndrome in which only one mutation is found, an active search for a large deletion should be sought.
We studied a family presenting 10 individuals affected by autosomal dominant deafness in all frequencies and three individuals affected by high frequency hearing loss. Genomic scanning using the 50k Affymetrix microarray technology yielded a Lod Score of 2.1 in chromosome 14 and a Lod Score of 1.9 in chromosome 22. Mapping refinement using microsatellites placed the chromosome 14 candidate region between markers D14S288 and D14S276 (8.85 cM) and the chromosome 22 near marker D22S283. Exome sequencing identified two candidate variants to explain hearing loss in chromosome 14 [PTGDR - c.G894A:p.R298R and PTGER2 - c.T247G:p.C83G], and one in chromosome 22 [MYH9, c.G2114A:p.R705H]. Pedigree segregation analysis allowed exclusion of the PTGDR and PTGER2 variants as the cause of deafness. However, the MYH9 variant segregated with the phenotype in all affected members, except the three individuals with different phenotype. This gene has been previously described as mutated in autosomal dominant hereditary hearing loss and corresponds to DFNA17. The mutation identified in our study is the same described in the prior report. Thus, although linkage studies suggested a candidate gene in chromosome 14, we concluded that the mutation in chromosome 22 better explains the hearing loss phenotype in the Brazilian family.
Purpose: Evaluate the impact autologous fascial sling (AFS) and tension-free vaginal tape (TVT) procedures on quality-of-life in incontinent women. Materials and Methods: Forty-one women were randomly distributed into two groups. Group G1 (n = 21), underwent AFS and group G2 (n = 20) TVT implant. The clinical follow up was performed at 1, 6, 12 and 36 months. Results: TVT operative time was significantly shorter than AFS. Cure rates were 71% at 1 month, 57% at 6 and 12 months in G1. In G2, cure rates were 75% at 1 month, 70% at 6 months and 65% at 12 months; there was no significant difference between groups. As regards the satisfaction rate, there was no statistical difference between groups. Analysis of quality of life at 36 months revealed that there was no significant difference between groups. Conclusion: Similar results between AFS and TVT, except for operative time were shorter in TVT.
Pelo crescente aumento da importância econômica e perante a escassez de informações técnicas para o cultivo da chicória (Cichorium endivia L.), objetivou-se com o presente trabalho avaliar o comportamento de duas cultivares em três ambientes de cultivo, no período de 11/09/04 a 04/12/04, em Ponta Grossa (PR). Os tratamentos foram arranjados em parcela subdividida, constituindo-se a parcela em ambientes de cultivo (túnel baixo, agrotêxtil branco e ambiente natural) e a subparcela em cultivares (AF-254 e Marina). O delineamento experimental foi o de blocos casualizados, com quatro repetições. As mudas foram produzidas sob ambiente protegido, em bandejas de poliestireno, com o substrato Plantmax e transplantadas aos 39 dias da semeadura. Após o transplante, foram instalados o túnel baixo coberto com polietileno e o agrotêxtil branco de 17 g.m-2. Na colheita, foram avaliados a ocorrência de tipburn, número de folhas por planta e massa fresca da planta. Observou-se que os maiores valores de temperaturas máximas e mínimas foram encontrados sob agrotêxtil, até 20 dias após o transplante e, posteriormente, com o desenvolvimento das plantas, os valores ficaram muito próximos entre os três ambientes. O ambiente que propiciou maior rendimento em massa fresca da cabeça foi o túnel baixo. Dentre cultivares, AF-254 apresentou melhor desempenho que Marina, tendo superioridade na massa fresca, embora tenha apresentado maior suscetibilidade a tipburn, quando em ambiente protegido.
Considering the increasing of economical importance on endive and the need of studies on this crop, the present work aimed to evaluate the behaviour of two endive cultivars (Cichorium endivia L.) under differents ambients during the period from 11/09/04 to 04/12/04, in Ponta Grossa, Paraná State. The experimental outline was a randomized block with the treatments arranged in a split plot, with four replications, being the plots represented by crop ambients (low tunnel of polyetylene, polypropylene as floating cover and natural ambient), and two cultivars (AF-254 and Marina). Endive seedlings were produced under protected cultivation, on polyestyrene trays with 200 cells, with the substrate Plantmax®. The seedlings were tranplanted at open field, 39 days after sowing. After seedling transplanting, the low tunnel was installed and also the white polypropylene with 17 g.m-2. At plant harvest, it was evaluated the number of leaves, head fresh weight and the incidence of Tipburn. The highest values of maximum and minimum temperature were observed under polypropylene till 20 days after transplant. According to the plants development the values of temperature became very close among the ambients. The highest head fresh weight was obtained at ambient of low tunnel. Between cultivars, AF-254 showed better performance than Marina, being superior on head fresh weight, although the first cultivar was more suscetible to Tipburn under protected cultivation.
A Lippia alba (Verbenaceae) é um arbusto produtor de óleo essencial com importantes atividades biológicas, farmacológicas e aromatizantes. Visando o cultivo sustentado de uma nova espécie com potencial econômico, os objetivos deste trabalho foram avaliar o desempenho da L. alba para massa de folha fresca (MF), massa de folha seca (MS), sintomas de vírus (SV - Cucumber mosaic virus, CMV), rendimento de óleo essencial (RE) e composição química do óleo (CQ), e avaliar a estabilidade e adaptabilidade fenotípica para o caráter MS. Dez genótipos pertencentes a quatro grupos químicos foram testados em seis experimentos instalados no estado de São Paulo, Brasil, com delineamento em blocos ao acaso e duas plantas por parcela. Em Monte Alegre do Sul e Pindorama, foi utilizado espaçamento de 2,0 x 0,4 x 1,6 m e em Campinas, foram instalados quatro experimentos 1,0 x 0,4 x 0,6 m sob condições distintas de adubação e irrigação. O efeito de genótipo foi significativo para todas as características avaliadas, revelando elevada produtividade de folhas do IAC-16 (citral), RE Yamamoto et al. superior dos quimiotipos linalol e limoneno/carvona e susceptibilidade deste último ao CMV. As oscilações no desempenho dos genótipos nos diferentes experimentos foram de baixa magnitude para os caracteres fitoquímicos (RE e CQ) e nenhuma variação qualitativa foi observada para CQ. Os genótipos IAC-2 (linalol) e IAC-13 (limoneno/carvona) apresentaram-se estáveis para MS e com ampla adaptabilidade, e são recomendados para o início do cultivo da espécie. A presente pesquisa fornece subsídios também para o início de programas de melhoramento genético em L. alba.
Lippia alba (Verbenaceae) is a shrub whose essential oil has important biological, pharmacological, and aromatizing properties. To reach the sustained cultivation of new species with economic potential, the present study aimed to evaluate L. alba performance for fresh leaf matter (FM), leaf dry matter (DM), virus symptoms (VS - Cucumber mosaic virus, CMV), oil yield (OY), and oil chemical composition (OC), and to evaluate DM stability and adaptability. Ten genotypes of four chemical groups (chemotypes) were evaluated in six experiments designed as randomized blocks with two plants per plot, over the whole State of São Paulo, Brazil. A 2.0 x 0.4 x 1.6 m spacing was used in Monte Alegre do Sul and Pindorama, while a 1.0 x 0.4 x 0.6 m spacing was used in Campinas, where four experiments were established under different irrigation and fertilization conditions. The genotype effect was significant (p < 0.05) for all traits evaluated, with high leaf productivity of IAC-16 (citral chemotype), best OY means in the linalool and limonene/carvone chemotypes, and susceptibility of the latter chemotype to CMV. The genotype performance oscillations in the six environments were significant for FM and DM, and despite their significance for phytochemical traits (OY and OC), they were of low magnitude. No qualitative variation was detected for OC. The IAC-2 (linalool) and IAC-13 (limonene/carvone) genotypes showed high stability and wide adaptability, and are recommended to establish initial cultivations of this species. This research also indicated genetic sources to start Lippia alba genetic breeding programs.
O experimento foi realizado na UEPG, Ponta Grossa, PR. Estudou-se o efeito da proteção com 'não tecido' de polipropileno sobre o desenvolvimento, a qualidade e a produção de três cultivares de alface, transplantadas no inverno de 1998. O delineamento experimental foi inteiramente casualizado, distribuído segundo esquema fatorial 3x2 (cultivares x sistema de cultivo), com 5 repetições. As cultivares utilizadas foram Tainá, Elisa e Verônica, cultivadas sob a proteção do 'não tecido' de polipropileno (PP) e em ambiente natural (AN). O uso do 'não tecido' como proteção de plantas de alface resultou em maior peso de matéria fresca de cabeça para todas as cultivares estudadas quando comparado ao AN. Verificou-se, para as cultivares Tainá e Verônica, incremento do índice de área foliar, com conseqüente aumento da biomassa das plantas produzidas sob o 'não tecido'. A cultivar Elisa apresentou limbo foliar com aspecto de estiolamento, perdendo a turgidez rapidamente após a colheita. Possivelmente, os níveis de radiação sob PP foram inferiores ao ponto de saturação fotossintética para a cv. Elisa. Recomenda-se o uso do 'não tecido' para as cultivares Verônica e Tainá, no inverno, para a região de Ponta Grossa, por apresentarem cabeças com ótima qualidade e peso comercial.
A field experiment was carried out in ''Capão da Onça'' School Farm, at the Universidade Estadual de Ponta Grossa in Brazil. The effect of the protection of an spunbonded polypropylene non woven fabric on the development, quality and yield of three lettuce cultivars, transplanted during the winter of 1998 was studied. The experimental design was of complete randomized blocks, displayed in a factorial scheme 3x2 (cultivars x crop system), with five replications. The cultivars were Tainá, Elisa and Verônica growing under non woven polypropylene protection (PP) and environmental conditions (EC). Greater head fresh weight was observed on woven protected plants. Increased leaf area index (LAI) was observed for 'Tainá' and 'Verônica', with consequent increase of biomass in row cover plants. 'Elisa' showed etiolate leafs, that lost rapidly the turgidity after harvesting. It is possible that the radiation levels under PP were bellow of the saturated photosynthetic point for cv. Elisa. The use the non woven protection for cv. Verônica and cv. Tainá, during winter season of Ponta Grossa's region is recommended, due to the fact that these plants presented heads with excellent quality and commercial weight.