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Nicola Rizzo

Publications and source records attributed to Nicola Rizzo.

At least 19 recordsLinked to original sources
PubMed2025

Exploiting uniqueness: seed-chain-extend alignment on elastic founder graphs.

SUMMARY: Sequence-to-graph alignment is a central challenge of computational pangenomics. To overcome the theoretical hardness of the problem, state-of-the-art tools use seed-and-extend or seed-chain-extend heuristics to alignment. We implement a complete seed-chain-extend alignment workflow based on indexable elastic founder graphs (iEFGs) that support linear-time exact searches unlike general graphs. We show how to construct iEFGs, find high-quality seeds, chain, and extend them at the scale of a telomere-to-telomere assembled human chromosome. AVAILABILITY AND IMPLEMENTATION: Our sequence-to-graph alignment tool and the scripts to replicate our experiments are available in https://github.com/algbio/SRFAligner.

Software↗
PubMed2006

PLAC1 mRNA levels in maternal blood at induction of labor correlate negatively with induction-delivery interval.

OBJECTIVE: This study was conducted to determine whether, in low risk women having labor induced using prostaglandin gel (dinoprostone gel), there is a relationship between the concentration of mRNA for the PLAC1 gene (a trophoblast-specific gene) in maternal blood and the time elapsed between the first gel administration and spontaneous delivery. STUDY DESIGN: Blood was collected from 49 selected women at 40.2-41.4 weeks' gestation. Total RNA was extracted by means of an ABI Prism 6100 nucleic acid Prep Station and quantitative real-time PCR analysis was performed by use of a PE Applied Biosystems 5700 Sequence Detection System. Sequence data were obtained from the Genebank Sequence Database. To determine the amount of cDNA, the PLAC1 locus was used. RESULTS: Thirty women (61.2%) had a spontaneous delivery. A caesarean section, either for fetal dystocia or fetal distress, was performed in 19 (38.8%). The crude delivery rates of the women who ended up with a spontaneous delivery were 30% at 24 h and 43% at 48 h. Women (n=19) with a blood concentration of logPLAC1 mRNA>or=2.00 displayed a median time to delivery of 23.50h, (95% CI: 13.13-33.87) while those with a logPLAC1 mRNA<2.00 (n=30) had a median time of 54 h. (95% CI: 37.86-70.14; p=0.0043, log-rank test). By means of multivariate analysis, quantitative Bishop score (from 2 to 7) at the time of the first gel administration and logPLAC1 mRNA>or=2.00 were associated with a higher rate of delivery per unit of time with an odds ratio of 1.35 (95% CI: 1.07-1.71) and 3.48 (95% CI: 1.55-7.80), respectively. CONCLUSIONS: In induced term pregnancies, PLAC1 mRNA in maternal blood at the beginning of the treatment correlates with the time elapsed before delivery. This evidence demonstrates that the fetomaternal trafficking of nucleic acids is more consistent when the labor is about to begin.

Adult↗
PubMed2006

Pregnancy outcome after early detection of bacterial vaginosis.

OBJECTIVE: To assess if detecting bacterial vaginosis either in early pregnancy or at midtrimester may predict adverse pregnancy outcome in women at risk for preterm delivery. STUDY DESIGN: 242 pregnant women with a previous preterm delivery were evaluated for bacterial vaginosis either in the first trimester (prior to 10+0 weeks) or in the second one (24-26 weeks). Adverse outcome was intended as miscarriage (< or =25 weeks), or premature delivery (< or =36+6). RESULTS: The risk of adverse pregnancy outcome was significantly increased in women diagnosed at first trimester with bacterial vaginosis (OR: 4.56; 95% CI: 2.54-8.93); the same finding at midtrimester did not increase significantly the risk of preterm delivery. CONCLUSIONS: Early screening for bacterial vaginosis in pregnant women who experienced a preterm delivery may help in predicting the risk of adverse outcome.

Abortion, Spontaneous↗
PubMed2006

Evidence of genetic underexpression in chorionic villi samples of euploid fetuses with increased nuchal translucency at 10-11 weeks' gestation.

OBJECTIVE: To retrospectively investigate whether the genetic profile from chorionic villous sampling (CVS) found in euploid fetuses with increased NT differs from matched controls. STUDY DESIGN: We employed cDNA microarray technology to characterize and compare the gene expression profile of chorionic villous tissues (which encompass the trophoblast and inner mesenchymal core) belonging to four singleton male fetuses with increased NT at 10-11 weeks' gestation. A pool of four normal chorionic villous tissues belonging to four respective fetuses, matched for gestational age and gender, was used as controls. RESULTS: In euploid fetuses, we found several underexpressed genes, possibly involved in mechanisms associated with the abnormal NT thickness. All these genes are likely to belong to the mesenchymal core of the villus that originates from the extraembryonic mesoderm, and thus might be closely representative of the embryonic genetic profile. They include: (1) genes of embryonic development and differentiation such as Endothelin 3 (EDN3) and secreted frizzled-related protein 4 (SFRP4); (2) genes of the extracellular matrix (ECM) metabolism such as tissue inhibitor of metalloproteinase1 (TIMP1), and disintegrin-like and matrix metalloproteinase (MMP) (reprolysin type) with thrombospondin type 1 Motif or ADAMTS2, exostoses (multiple)-like 1 (EXTL1), heparan sulfate (HS) 6-O-sulfotransferase 1 or HS6ST1, fibronectin 1 (FN1) and Integrin Alpha 10 (ITGA10) involved in HS and proteoglycan bio-synthesis, ECM synthesis and cell-matrix adhesion; (3) genes involved in vessel formation and differentiation such as angiogenic factor (VG5Q), and in blood pressure control and muscle contraction, like Endothelin 3 or EDN3 and sarcolemma associated protein (SLMAP). Such lower expressions of the villous tissues might be related to an immature genetic profile of the embryo development as well as abnormal regulation of ECM bio-synthesis and/or improper vessel growth and blood pressure control. Also, the results partially support the theories proposed for NT enlargement such as altered composition of ECM and abnormal/delayed development of the circulatory system. CONCLUSIONS: Abnormal extraembryonic genetic expression is found at 10-11 weeks' gestation in euploid fetuses with increased NT. If both extra- and intraembryonic mesoderms express the same genetic alterations, then microarray analyses on CVS could be used to screen several mesoderm-derivate anomalies.

Case-Control Studies↗
PubMed2006

Total activin A in maternal blood as a marker of preterm delivery in low-risk asymptomatic patients.

OBJECTIVES: To retrospectively evaluate whether increased serum levels of total activin A (t-activin A) are found in women who subsequently experience preterm delivery (PTD). METHODS: Data on maternal serum t-activin A concentrations were available from a total of 84 singleton pregnant women and included 14 PTD pregnancies, each matched for gestational age and length of freezer storage, with 5 control pregnancies having term delivery (TD). Analyte values were expressed as multiple(s) of the control median. RESULTS: The median t-activin A for controls and cases was 1.00 +/- 0.45 and 1.27 +/- 0.53 MoM, respectively. Univariate analysis of the MoM values was performed using the Kaplan-Meier algorithm. Differences in the rate of delivery using a t-activin A MoM cut-off of > or = 1 SD (equivalent to 1.26 MoM) were analysed using the log rank test. The cumulative rate of PTD (< 37 weeks) was significantly higher for women with t-activin A concentrations > or = 1.26 MoM than those with t-activin A concentrations below this cut-off (40% vs.. 10%, p-value = 0.0218 log rank test). CONCLUSIONS: T-activin A concentration is higher in women who will develop PTD in a low-risk population. T-activin A values are inversely proportional to the time elapsed from blood test to delivery. Prospective studies would determine the precise discriminability of this marker for PTD and the best week for performing the blood test, allowing for a proper calculation of the detection rate and a positive predictive value.

Activins↗
PubMed2006

Quantitative distribution of a panel of circulating mRNA in preeclampsia versus controls.

OBJECTIVE: The aim of this study was to evaluate whether the quantitative distribution of a panel of circulating mRNAs from maternal whole blood of normal pregnancies is statistically different from those complicated with preeclampsia (PE) with or without intrauterine growth restriction (IUGR). METHODS: Maternal whole blood of six subjects with mild or severe PE with or without IUGR and 30 matched controls (1:5 match for gestational age) were retrospectively examined for circulating mRNA markers. Seven specific mRNA markers were identified and chosen based on previous microarray mRNA expressions performed on placental tissue from normal and PE patients. They were human placental lactogen (hPL), inhibin A, KISS-1, pregnancy-associated plasma protein-A (PAPP-A), plasminogen activator inhibitor type 1 (PAI-1), selectin-P and vascular endothelial growth factor receptor (VEGFR), which were therefore quantified for statistical purposes. RESULTS: Median gestational age was 229 (178-283) and 232 (194-262) days for controls and cases respectively. All mRNA markers but PAPP-A, showed statistically different median values. They were hPL, inhibin A, KISS-1, PAI-1, Selectin-P, and VEGFR. Inhibin A, Selectin-P and VEGFR showed higher values than expected for controls. Instead, hPL, KISS-1 and PAI-1 values of PE patients were lower than those of controls. Selectin-P was the marker with the most aberrant difference, followed by VEGFR and KISS-1. CONCLUSION: This preliminary analysis revealed that the median values of a panel of mRNAs from the maternal blood of PE patients were different from those of the same gestational age control group at the third trimester. If prospective studies at the second trimester could detect a related marker sufficiently able to discriminate between affected and unaffected patients and thus detect the disease before its clinical onset, then a screening project using a panel of mRNAs would be feasible.

Biomarkers↗
PubMed2006

PLAC1 mRNA in maternal blood correlates with Doppler waveform in uterine arteries in normal pregnancies at the second and third trimester.

Doppler analysis of the uterine arteries is currently used for pre-eclampsia (PE) screening. PLAC1 is a trophoblast-specific gene, and it is known that in normal pregnancies, trophoblastic cells are released into the maternal circulation, where specific trophoblastic mRNA can be detected. In PE, as in women who eventually develop PE, an abnormal passage of fetal and placental cells is also present. In this study, we aimed to verify whether, in normal pregnancies, Doppler waveform of the uterine arteries correlates with PLAC1 mRNA concentrations. Thirteen cases of normal pregnancies at 37 weeks' gestation (23-41) were enrolled in the study. PLAC1 mRNA was extracted from 2 mL of blood by ABI PRISM 6100 nucleic acid Prep Station (Applied Biosystems, Foster City, CA) and quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) analysis was performed by a PE 5700 Sequence detection system. Bulk RNA from normal placental tissue was used as the reference curve, and the amount of PLAC1 mRNA in the study samples was then expressed as the "relative amount" of weight of placental tissue (ng/mL). The uterine arterial mean resistance index (RI) and presence/absence of a dicrote waveform were calculated by using a 5 MHz transabdominal probe (Tecnos, ESAOTE) at the uterine cervico-corporal junction. Doppler measurement was performed on the same day as blood collection. The median of the means of uterine arterial RI was 0.52 (0.39-0.68). RI of uterine arteries and PLAC1 mRNA were significantly correlated in a log-linear regression (R(2) = 0.483, P = 0.024). Our data support that in normal pregnancy, the passage of trophoblast material into the maternal circulation is correlated with the quantitative measurement of uterine hemodynamics.

Arteries↗
PubMed2006

Time profile of appearance and disappearance of circulating placenta-derived mRNA in maternal plasma.

BACKGROUND: Fetal RNA of placental origin has been detected in the plasma of pregnant women, but the timing of the first appearance and the detailed kinetics of postdelivery clearance of such circulating RNA have not been studied. METHODS: To address the timing of the first appearance of circulating placental RNA, we collected serial maternal blood samples from 47 women who had conceived by assisted reproductive procedures. To address the postdelivery clearance kinetics, we collected serial postdelivery blood samples from 6 pregnant women who had delivered by cesarean section. Placenta-derived transcripts were sought by real-time quantitative reverse transcription-PCR. RESULTS: The earliest gestational age at which human placental lactogen and human chorionic gonadotropin beta-subunit mRNAs were detectable in a proportion of the pregnant women was the 4th week of gestation. The postdelivery study indicated that the median apparent half-life for the clearance of human placental lactogen mRNA was 14 min. CONCLUSIONS: Placenta-derived mRNA can be found in maternal plasma from very early on in gestation, suggesting a possible role for early noninvasive prenatal diagnosis or monitoring. The rapid kinetics of circulating placental mRNA suggest that its plasma concentrations may be used to monitor recent physiologic or pathologic events.

Female↗
PubMed2005

High levels of fetal cell-free DNA in maternal serum: a risk factor for spontaneous preterm delivery.

OBJECTIVE: This study was conducted to determine whether there is a relationship between the concentration of fetal cell-free DNA in maternal serum and the duration of pregnancy in women who are at high risk for preterm delivery because of either preterm labor or preterm premature rupture of the membranes. STUDY DESIGN: Sera were collected and frozen from 71 women with a male fetus. Maternal serum fetal cell-free DNA concentration was measured with the use of real-time polymerase chain reaction amplification of DYS1. Fetal cell-free DNA concentrations were converted to multiples of the median. The following groups were studied: group 1: women with preterm labor and intact membranes who were delivered at > or = 36 weeks of gestation (n = 21); group 2: women with preterm labor who were delivered at <36 weeks of gestation (n = 29); and group 3: women with preterm premature rupture of the membranes in labor (n = 20) or not in labor (n = 1) who were delivered prematurely (<36 weeks of gestation). Kaplan-Meier and Cox regression analyses were used to analyze the relationship between fetal cell-free DNA concentrations and the likelihood of preterm delivery. RESULTS: A cut-off value for fetal cell-free DNA of 1.82 multiples of the median was chosen for analysis. The cumulative rate of early preterm delivery (<30 weeks of gestation) was significantly higher for women with fetal cell-free DNA concentrations of > or = 1.82 multiples of the median than those with fetal cell-free DNA concentrations below this cut-off (45% [95% CI, 36%-74%] vs 18% [95% CI, 11%-25%]; P = .008]. The cumulative rate of preterm delivery (<36 weeks of gestation) was also significantly higher at > or = 1.82 multiples of the median (73% [95% CI, 52%-93%] vs 66% [95% CI, 54%-79%]; P = .02). After adjustment for covariates, Cox analysis showed that fetal cell-free DNA at > or = 1.82 multiples of the mechanisms of disease that are associated with a mean hazard rate of delivery of 1.57 (P = .005). CONCLUSION: High concentrations of fetal cell-free DNA in maternal serum are associated with an increased risk of spontaneous preterm delivery. This observation may have implications for the understanding of the mechanisms of disease that is associated with preterm labor.

Cross-Sectional Studies↗
PubMed2005

Ultrasound screening for congenital pyelectasis in term pregnancies.

The purpose of this study was to compare the role of antenatal ultrasound screening for congenital pyelectasis at term with postnatal screening. An ultrasonographic prospective study of 231 fetuses of low-risk pregnancies was performed, evaluating the renal pelvis at term (38 to 42 weeks gestation) and after birth (first and third months of life). Cut-off points used were 9 mm antenatally, and 10 and 12 mm, respectively postnatally, all in an anteroposterior view. A sensitivity of 20% and a specificity of 93.4% was obtained when comparing the antenatal versus the third-month scan, whereas when we compared the sonograms from the first versus the third month of life, we found a sensitivity of 60% and a specificity of 89.7%, with a positive predictive value of 14.7% in the first case and 25% in the second case. A p value < 0.001 was obtained when comparing the sensitivities; a p value of 0.2 was reported when comparing the specificities. Data on a comparative screening of the renal pelvis measured antenatally at term and postnatally do not exist. Although it is extremely feasible, the measurement of the fetal renal pelvis during the routine ultrasound scan at term of gestation seems of no benefit in terms of sensitivity and positive predictive values in identifying infants affected by congenital pyelectasis. Because of the low values of sensitivity obtained in our study, a screening program for the renal pelvis dilation both in fetuses and newborns cannot be recommended.

Female↗
PubMed2004

Delivery and immigration: the experience of an Italian hospital.

OBJECTIVE: We studied mode of delivery and prevalence of complications in pregnant women from the western world (WW) and immigrant mothers from non European Union (non-EU) countries at a third level Italian Obstetric Department. STUDY DESIGN: The study was population based and used data from the local Birth Registry at the University of Bologna. A 1:1 case control was performed by matching 510 single live births from immigrant mothers (non-EU) during the period 1997-2001 with 510 controls in chronological order (WW). Data were matched by age and parity. RESULTS: No differences between the two groups were noted as concerns preterm delivery, percentage of infants transferred to neonatal intensive care unit, perinatal mortality, caesarean section rate, episiotomies, instrumental deliveries and post-partum complications. Significant differences were noted in the rate of elective caesarean section (which was higher in the WW women: P < 0.01) and in the rate of vaginal lacerations and neonatal malformations (which was higher in the non-EU group: P < 0.05). CONCLUSIONS: There was no substantial variation in the mode of delivery between non-EU immigrants and western women; only the rate of elective caesarean section was significantly higher in the WW group. A higher rate of vaginal lacerations and neonatal malformations was found in the non-EU group. In our experience the standard of medical care is achievable regardless of ethnic group.

Case-Control Studies↗
PubMed2004

Cell-free fetal DNA (SRY locus) concentration in maternal plasma is directly correlated to the time elapsed from the onset of preeclampsia to the collection of blood.

OBJECTIVE: To determine (1) if fetal DNA (fDNA) in the maternal circulation in women affected by preeclampsia correlates with the time elapsed from the onset of symptoms to the time of blood collection, and (2) if the inclusion of this variable improves the discrimination between affected and unaffected patients by using fDNA distributions. METHODS: Plasma were collected from 34 women at 33.7 +/- 3.9 weeks' gestation, affected by preeclampsia, and bearing a single male fetus. fDNA was extracted from 1.5-mL plasma samples, and the SRY and beta-globin gene were analyzed by real-time quantitative PCR. MoMs (multiple of the control median) were calculated by using a log equation of 102 normal cases. Log MoMs were then plotted against the time elapsed from onset of symptoms to blood collection (expressed in days) by means of a log-linear regression. Adjusted MoMs were then calculated. ROC curves were used to test the discrimination obtained by using adjusted MoMs. RESULTS: The median MoMs of controls and preeclamptic patients were 1.00 +/- 1.53 and 2.62 +/- 2.70 respectively. By plotting log MoM fDNA against the time elapsed from onset of symptoms to blood collection, we found a significant positive correlation, (p-value < 0.001, R2 = 0.55, F = 38.97, from 1 to 50 days). The adjusted median fDNA MoM was 2.66 +/- 2.50. Areas under the curves, as estimated by ROC curves, were 76.7 for unadjusted and 85.5 for adjusted MoMs respectively (p-value = 0.02). CONCLUSIONS: The effect of a further covariate showed that (1) fDNA passage from trophoblasts to maternal circulation for unit of time is proportional to the duration of the damage and that (2) increased discrimination can be obtained in comparison to normal subjects.

Area Under Curve↗
PubMed2003

Cell-free fetal DNA concentration in plasma of patients with abnormal uterine artery Doppler waveform and intrauterine growth restriction--a pilot study.

OBJECTIVE: To evaluate if an increased amount of fetal DNA concentration can be found in women screened positive for intrauterine growth restriction because of abnormal uterine artery Doppler waveforms. METHODS: We enrolled eight pregnant women (each bearing a male fetus), with the evidence of abnormal uterine artery Doppler waveforms, and 16 control patients for a case-control study matched for gestational age (1 : 2). Uterine artery Doppler was carried out at 20 to 35 weeks' gestation (median 29). The mean uterine artery resistance index (RI) was subsequently calculated, and a value >0.6 was considered positive for the clinical features of pre-eclampsia. The SRY locus was used to determine the amount of male fetal DNA in the maternal plasma at the time of Doppler analysis. RESULTS: Two controls (normal Doppler) were excluded from the final analysis because they had a pre-term delivery. One case (abnormal Doppler) had evidence of intrauterine growth restriction at the time of enrolment. In four out of eight cases (abnormal Doppler), intrauterine growth restriction was subsequently observed. Multiples of median (MoM) conversion of the fetal DNA values showed an increase of 1.81 times in the cases when compared to the controls. An increase of 2.16 times was instead observed for the cases with a growth-restricted fetus (5 cases out of 8) in comparison with the controls (14 cases). CONCLUSIONS: In subjects positive to uterine artery Doppler velocimetry analysis (Doppler analysis for pre-eclampsia screening), the fetal DNA concentration is higher than expected, in the absence of any other clinical feature. Since the increase in fetal DNA seems to be related to the presence or to the future development of intrauterine growth restriction, this paper suggests a possible integration between ultrasound and molecular markers for predicting the disease in some cases.

Adult↗
PubMed2002

Testing normality of fetal DNA concentration in maternal plasma at 10-12 completed weeks' gestation: a preliminary approach to a new marker for genetic screening.

OBJECTIVES: To test the distribution of fetal DNA in maternal plasma expressed as gen/eq in a population of normal pregnancies. METHODS: Peripheral blood samples were obtained from 63 women (85% > or =35 years of age at delivery) bearing a euploid male fetus. Each patient underwent chorionic villus sampling (CVS) for karyotype analysis and/or beta thalassemia screening. Ultrasound scanning was used to determine gestational age. At 10-12 weeks' gestation, a peripheral blood sample was collected followed by CVS. To detect the Y chromosome specific sequences (SRY) quantitative polymerase chain reaction (PCR) analysis was used. Normal distribution of the data was tested by means of the Kolmogorov-Smirnov (KS) test. A Symmetry test (reliability p>0.05) was used to evaluate the reliability of the median. RESULTS: Only after natural logarithmic transformation did the data display a normal distribution. The median value of fetal DNA was 23.3 gen/eq (range 2.08-195), interquartile range 18.57-45.4. A Pearson test showed a significant correlation between gestational age and fetal DNA concentration (r=0.25, p=0.045). CONCLUSION: The present finding is a preliminary step towards a possible integration of fetal DNA with other variables (biochemical and/or ultrasound). It may serve to improve the discrimination of the screening for genetic diseases in the first trimester. Because of the relatively high dispersion, adjustments for possible covariates would appear to be necessary in further studies.

Chorionic Villi Sampling↗