Study of the parent-of-origin effect in monogenic diseases with variable age of onset. Application on ATTRv.

In genetic diseases with variable age of onset, an accurate estimation of the survival function for the mutation carriers and also modifying factors effects estimations are important for the management of asymptomatic gene carriers across life. Among the modifying factors, the gender of the parent transmitting the mutation (i.e. the parent-of-origin effect) has been shown to have a significant effect on survival curve estimation on transthyretin familial amyloid polyneuropathy (ATTRv) families. However, as most genotypes are unknown, the parent-of-origin must be calculated through a probability estimated from the pedigree. We propose in this article to extend the method providing mutation carrier survival estimates in order to estimate the parent-of-origin effect. The method is both validated on simulated data and applied to familly samples with ATTRv.

A multicentric study of the disease risks and first manifestations in hereditary transthyretin amyloidosis (ATTRv): insights for an earlier diagnosis.

BACKGROUND: In hereditary transthyretin amyloidosis (ATTRv), early manifestation and age at onset (AO) may vary strikingly. We assessed the disease'risk (penetrance), AO and initial features in ATTRv families to gain insights on the early disease presentation. METHODS: Genealogical information, AO and first disease manifestations were collected in ATTRv families, from Sweden, Italy (Sicily), Spain (Mallorca), France, Turkey, Brazil. Penetrance was computed using a non-parametric survival method. RESULTS: We analysed 258 TTRV30M kindreds and 84 carrying six other variants (TTRT49A, F64L, S77Y, S77F, E89Q, I107V). In ATTRV30M families, the earliest disease risk was found at age 20 years in the Portuguese and Mallorcan families and at age 30-35 years, in the French and Swedish groups. The risks were higher in men and in carriers of maternal descent. In families carrying TTR-nonV30M variants, the earliest disease risk ranged from 30 y-o in TTRT49A to 55 y-o in TTRI107V families. Peripheral neuropathy symptoms were the most frequent initial manifestations. Among patients carrying TTRnonV30M variants, about 25% had an initial cardiac phenotype, one third a mixed phenotype. CONCLUSION: Our work provided solid data on the risks and early features of ATTRv in a spectrum of families to enhance an early diagnosis and treatment.

Regression modelling of interval censored data based on the adaptive ridge procedure.

A new method for the analysis of time to ankylosis complication on a dataset of replanted teeth is proposed. In this context of left-censored, interval-censored and right-censored data, a Cox model with piecewise constant baseline hazard is introduced. Estimation is carried out with the expectation maximisation (EM) algorithm by treating the true event times as unobserved variables. This estimation procedure is shown to produce a block diagonal Hessian matrix of the baseline parameters. Taking advantage of this interesting feature in the EM algorithm, a L 0 penalised likelihood method is implemented in order to automatically determine the number and locations of the cuts of the baseline hazard. This procedure allows to detect specific areas of time where patients are at greater risks for ankylosis. The method can be directly extended to the inclusion of exact observations and to a cure fraction. Theoretical results are obtained which allow to derive statistical inference of the model parameters from asymptotic likelihood theory. Through simulation studies, the penalisation technique is shown to provide a good fit of the baseline hazard and precise estimations of the resulting regression parameters.

Penetrance estimation of Alzheimer disease in SORL1 loss-of-function variant carriers using a family-based strategy and stratification by APOE genotypes.

BACKGROUND: Alzheimer disease (AD) is a common complex disorder with a high genetic component. Loss-of-function (LoF) SORL1 variants are one of the strongest AD genetic risk factors. Estimating their age-related penetrance is essential before putative use for genetic counseling or preventive trials. However, relative rarity and co-occurrence with the main AD risk factor, APOE-ε4, make such estimations difficult. METHODS: We proposed to estimate the age-related penetrance of SORL1-LoF variants through a survival framework by estimating the conditional instantaneous risk combining (i) a baseline for non-carriers of SORL1-LoF variants, stratified by APOE-ε4, derived from the Rotterdam study (N = 12,255), and (ii) an age-dependent proportional hazard effect for SORL1-LoF variants estimated from 27 extended pedigrees (including 307 relatives ≥ 40 years old, 45 of them having genotyping information) recruited from the French reference center for young Alzheimer patients. We embedded this model into an expectation-maximization algorithm to accommodate for missing genotypes. To correct for ascertainment bias, proband phenotypes were omitted. Then, we assessed if our penetrance curves were concordant with age distributions of APOE-ε4-stratified SORL1-LoF variant carriers detected among sequencing data of 13,007 cases and 10,182 controls from European and American case-control study consortia. RESULTS: SORL1-LoF variants penetrance curves reached 100% (95% confidence interval [99-100%]) by age 70 among APOE-ε4ε4 carriers only, compared with 56% [40-72%] and 37% [26-51%] in ε4 heterozygous carriers and ε4 non-carriers, respectively. These estimates were fully consistent with observed age distributions of SORL1-LoF variant carriers in case-control study data. CONCLUSIONS: We conclude that SORL1-LoF variants should be interpreted in light of APOE genotypes for future clinical applications.

A nationwide indicator to smooth and normalize heterogeneous SARS-CoV-2 RNA data in wastewater.

Since many infected people experience no or few symptoms, the SARS-CoV-2 epidemic is frequently monitored through massive virus testing of the population, an approach that may be biased and may be difficult to sustain in low-income countries. Since SARS-CoV-2 RNA can be detected in stool samples, quantifying SARS-CoV-2 genome by RT-qPCR in wastewater treatment plants (WWTPs) has been carried out as a complementary tool to monitor virus circulation among human populations. However, measuring SARS-CoV-2 viral load in WWTPs can be affected by many experimental and environmental factors. To circumvent these limits, we propose here a novel indicator, the wastewater indicator (WWI), that partly reduces and corrects the noise associated with the SARS-CoV-2 genome quantification in wastewater (average noise reduction of 19%). All data processing results in an average correlation gain of 18% with the incidence rate. The WWI can take into account the censorship linked to the limit of quantification (LOQ), allows the automatic detection of outliers to be integrated into the smoothing algorithm, estimates the average measurement error committed on the samples and proposes a solution for inter-laboratory normalization in the absence of inter-laboratory assays (ILA). This method has been successfully applied in the context of Obépine, a French national network that has been quantifying SARS-CoV-2 genome in a representative sample of French WWTPs since March 5th 2020. By August 26th, 2021, 168 WWTPs were monitored in the French metropolitan and overseas territories of France. We detail the process of elaboration of this indicator, show that it is strongly correlated to the incidence rate and that the optimal time lag between these two signals is only a few days, making our indicator an efficient complement to the incidence rate. This alternative approach may be especially important to evaluate SARS-CoV-2 dynamics in human populations when the testing rate is low.

Regularized bidimensional estimation of the hazard rate.

In epidemiological or demographic studies, with variable age at onset, a typical quantity of interest is the incidence of a disease (for example the cancer incidence). In these studies, the individuals are usually highly heterogeneous in terms of dates of birth (the cohort) and with respect to the calendar time (the period) and appropriate estimation methods are needed. In this article a new estimation method is presented which extends classical age-period-cohort analysis by allowing interactions between age, period and cohort effects. We introduce a bidimensional regularized estimate of the hazard rate where a penalty is introduced on the likelihood of the model. This penalty can be designed either to smooth the hazard rate or to enforce consecutive values of the hazard to be equal, leading to a parsimonious representation of the hazard rate. In the latter case, we make use of an iterative penalized likelihood scheme to approximate the L0 norm, which makes the computation tractable. The method is evaluated on simulated data and applied on breast cancer survival data from the SEER program.

A timed tally counter for microscopic examination of thick blood smears in malaria studies.

BACKGROUND: Despite many technological advances for malaria parasite detection (e.g. high resolution image acquisition), microscopic reading of thick blood smear (TBS) remains the gold standard. Even though available in low technology environment, the microscopy of TBS is slow and time consuming. Moreover microscopy may induce errors at many levels and has no quality control. METHODS: A electronic extension of the mechanical tally counter is proposed. In addition to the counting process it includes the process of counting itself that relies on the time elapsed between two successive pressures of the counting button leading to a timed tally counter (TTC). The microscopist performs the reading with the specific instruction starting by counting, in each high power fields, leucocytes first and then parasites. The time-stamp of all pressures of counting buttons are recorded along with the nature of the count. The data are recorded internally in CSV format and are exportable. The detection of HPFs locations and leukocyte/parasite counts per HPFs is performed through a hidden semi-Markov model (with outliers) allowing both to take into account the known distribution of leukocyte per HPFs (using a negative binomial distribution) and the pauses and hesitation of the microscopist during the reading. Parameters are estimated via the expectation-maximization algorithm. Hyper-parameters are calibrated using expert annotations. Forward/backward recursions are used to obtain the HPFs locations. RESULTS: This approach provides richer data at no extra cost. It has been demonstrated that the method can derive parasites per HPF, leukocytes per HPF, and parasite/leukocyte ratio with robust non-parametric confidence intervals. Moreover a direct digital data entry leads to a less expensive process and decreased time-consuming and error-prone manual data entry. Lastly the TTC allows detecting possible protocol break during reading and prevents the risk of fraud. DISCUSSION AND CONCLUSION: Introducing a programmed digital device in the data acquisition of TBS reading gives the opportunity to develop easily new (possible adaptive) reading protocols that will be easily followed by the reader since they will be embedded directly in the device. With the TTC the reader only has to read HPFs, counting leukocytes first and parasites second, and the counter will beep when the protocol is completed.

New data on the genetic profile and penetrance of hereditary Val30Met transthyretin amyloidosis in Sweden.

INTRODUCTION: Hereditary transthyretin (ATTRv) amyloidosis is of autosomal dominant transmission, caused by a spectrum of mutations in the transthyretin (TTR) gene. The ATTRV30M (p.Val50Met) is the most frequent substitution in Europe. Northern Sweden is a known cluster for ATTRV30M amyloidosis patients due to high prevalence of the mutation rate, with homozygous cases. First symptoms occur generally during the 6th decade. Previous studies reported low penetrance in this area and possible anticipation in families. In order to refine our knowledge of the genetic aspects, penetrance and factors that influence the disease's risk, we performed a comprehensive study of ATTRV30M families in Sweden. METHODS: To assess anticipation, well-established age at onset (AO) was compared in all informative parent-offspring pairs and in subgroups, after excluding ascertainment biases. Penetrance was estimated using a non-parametric method that enables to study covariates' effect on the disease's risk. RESULTS: We analysed 114 ATTRV30M Swedish families, including 12 homozygous individuals. Among 131 parent-offspring pairs, we found an average anticipation of 11.7 [Standard Deviation (SD) =10.03] years, higher in case of maternal transmission (mean ± SD = 13.7 ± 8.4 years), compared to paternal transmission (mean ± SD = 7.9 ± 11.5 years, p < .003). Anticipation remained significant, after exclusion of ascertainment biases. In heterozygous ATTRV30M kindred, penetrance was low, estimated below 10% [95% confidence interval (CI) = 6-10] at 40 years-old, increasing to 71% [95% CI= 65-76] at age 90 years. The risk was found to be higher in male patients (p < .01) and in case of maternal transmission (p < .01), reflecting a parent of origin effect. We observed no difference of penetrance according the geographical origin. Finally, the disease risk was similar in heterozygous and homozygous ATTRV30M amyloidosis individuals. CONCLUSIONS: Our study provides new data on the genetics of ATTRV30M families in Sweden, including the occurrence of anticipation and on penetrance. Both are increased in case of maternal inheritance and in male patients. Overall, gender seems to be a factor that substantially modulates the AO of the disease, in this area. Clinically, these findings are of importance to guide the management of sibships and the monitoring of mutation carriers.

Genetic, structural, and functional characterization of POLE polymerase proofreading variants allows cancer risk prediction.

PURPOSE: Polymerase proofreading-associated polyposis is a dominantly inherited colorectal cancer syndrome caused by exonuclease domain missense variants in the DNA polymerases POLE and POLD1. Manifestations may also include malignancies at extracolonic sites. Cancer risks in this syndrome are not yet accurately quantified. METHODS: We sequenced POLE and POLD1 exonuclease domains in 354 individuals with early/familial colorectal cancer (CRC) or adenomatous polyposis. We assessed the pathogenicity of POLE variants with yeast fluctuation assays and structural modeling. We estimated the penetrance function for each cancer site in variant carriers with a previously published nonparametric method based on survival analysis approach, able to manage unknown genotypes. RESULTS: Pathogenic POLE exonuclease domain variants P286L, M294R, P324L, N363K, D368N, L424V, K425R, and P436S were found in ten families. The estimated cumulative risk of CRC at 30, 50, and 70 years was 11.1% (95% confidence interval [CI]: 4.2-17.5), 48.5% (33.2-60.3), and 74% (51.6-86.1). Cumulative risk of glioblastoma was 18.7% (3.2-25.8) at 70 years. Variants interfering with DNA binding (P286L and N363K) had a significantly higher mutagenic effect than variants disrupting ion metal coordination at the exonuclease site. CONCLUSION: The risk estimates derived from this study provide a rational basis on which to provide genetic counseling to POLE variant carriers.

Long-term consequences of one anastomosis gastric bypass on esogastric mucosa in a preclinical rat model.

Although bariatric surgery is proven to sustain weight loss in morbidly obese patients, long-term adverse effects have yet to be fully characterized. This study compared the long-term consequences of two common forms of bariatric surgery: one-anastomosis gastric bypass (OAGB) and Roux-en-Y Gastric Bypass (RYGB) in a preclinical rat model. We evaluated the influence of biliopancreatic limb (BPL) length, malabsorption, and bile acid (BA) reflux on esogastric mucosa. After 30 weeks of follow-up, Wistar rats operated on RYGB, OAGB with a short BPL (15 cm, OAGB-15), or a long BPL (35 cm, OAGB-35), and unoperated rats exhibit no cases of esogastric cancer, metaplasia, dysplasia, or Barrett's esophagus. Compared to RYGB, OAGB-35 rats presented higher rate of esophagitis, fundic gastritis and perianastomotic foveolar hyperplasia. OAGB-35 rats also revealed the greatest weight loss and malabsorption. On the contrary, BA concentrations were the highest in the residual gastric pouch of OAGB-15 rats. Yet, no association could be established between the esogastric lesions and malabsorption, weight loss, or gastric bile acid concentrations. In conclusion, RYGB results in a better long-term outcome than OAGB, as chronic signs of biliary reflux or reactional gastritis were reported post-OAGB even after reducing the BPL length in a preclinical rat model.

Plasmodium falciparum merozoite surface antigen-specific cytophilic IgG and control of malaria infection in a Beninese birth cohort.

BACKGROUND: Substantial evidence indicates that cytophilic IgG responses to Plasmodium falciparum merozoite antigens play a role in protection from malaria. The specific targets mediating immunity remain unclear. Evaluating antibody responses in infants naturally-exposed to malaria will allow to better understand the establishment of anti-malarial immunity and to contribute to a vaccine development by identifying the most appropriate merozoite candidate antigens. METHODS: The study was based on parasitological and clinical active follow-up of infants from birth to 18 months of age conducted in the Tori Bossito area of southern Benin. For 399 infants, plasma levels of cytophilic IgG antibodies with specificity for five asexual stage malaria vaccine candidate antigens were determined by ELISA in infants' peripheral blood at 6, 9, 12 and 15 months of age. Multivariate mixed logistic model was used to investigate the association between antibody levels and anti-malarial protection in the trimester following the IgG quantification. Moreover, the concentrations of merozoite antigen-specific IgG were compared between a group of infants apparently able to control asymptomatic malaria infection (CAIG) and a group of infants with no control of malaria infection (Control group (NCIG)). Protective effect of antibodies was also assessed after 15 months of malaria exposure with a Cox regression model adjusted on environmental risk. RESULTS: Cytophilic IgG responses to AMA1, MSP1, MSP2-3D7, MSP2-FC27, MSP3 and GLURP R2 were associated with increasing malarial infection risk in univariate analysis. The multivariate mixed model showed that IgG1 and IgG3 to AMA1 were associated with an increased risk of malarial infection. However infants from CAIG (n = 53) had significantly higher AMA1-, MSP2-FC27-, MSP3-specific IgG1 and AMA1-, MSP1-, MSP2-FC27-, MSP3 and GLURP-R2-specific IgG3 than those from NCIG (n = 183). The latter IgG responses were not associated with protection against clinical malaria in the whole cohort when protective effect is assessed after 15 months of malaria exposition. CONCLUSION: In this cohort, merozoite antigen-specific cytophilic IgG levels represent a marker of malaria exposure in infants from 6 to 18 months of age. However, infants with resolution of asymptomatic infection (CAIG) seem to have acquired naturally immunity against P. falciparum. This observation is encouraging in the context of the development of multitarget P. falciparum vaccines.

Computationally Stable Estimation Procedure for the Multivariate Linear Mixed-Effect Model and Application to Malaria Public Health Problem.

In this paper, we provide the ML (Maximum Likelihood) and the REML (REstricted ML) criteria for consistently estimating multivariate linear mixed-effects models with arbitrary correlation structure between the random effects across dimensions, but independent (and possibly heteroscedastic) residuals. By factorizing the random effects covariance matrix, we provide an explicit expression of the profiled deviance through a reparameterization of the model. This strategy can be viewed as the generalization of the estimation procedure used by Douglas Bates and his co-authors in the context of the fitting of one-dimensional linear mixed-effects models. Beside its robustness regarding the starting points, the approach enables a numerically consistent estimate of the random effects covariance matrix while classical alternatives such as the EM algorithm are usually non-consistent. In a simulation study, we compare the estimates obtained from the present method with the EM algorithm-based estimates. We finally apply the method to a study of an immune response to Malaria in Benin.

Detecting latent exposure in genome-wide association studies using a breakpoint model for logistic regression.

Detecting gene-environment (G × E) interactions in the context of genome-wide association studies (GWAS) is a challenging problem since standard methods generally present a lack of power. An additional difficulty arises from the fact that the causal exposure is seldom observed and only a proxy of this exposure is observed. This leads to an additional drop in terms of power and it explains the failure of standard methods in detecting interactions, even very strong ones. In this article, we consider the latent exposure as a source of heterogeneity and we propose a new powerful method, named "Breakpoint Model for Logistic Regression" (BMLR), based on a breakpoint model, in order to detect G × E interactions when causal exposure is unobserved. First, the BMLR method is compared to the ordered-subset analysis for case-control method, which has been developed for the same purpose, through simulations. This highlights the ability of BMLR to detect the heterogeneity, and therefore, to detect interaction with latent exposure. Finally, the BMLR method is compared to standard methods, such as Plink, to perform a GWAS on a published realistic benchmark.

Non-parametric estimation of survival in age-dependent genetic disease and application to the transthyretin-related hereditary amyloidosis.

In genetic diseases with variable age of onset, survival function estimation for the mutation carriers as well as estimation of the modifying factors effects are essential to provide individual risk assessment, both for mutation carriers management and prevention strategies. In practice, this survival function is classically estimated from pedigrees data where most genotypes are unobserved. In this article, we present a unifying Expectation-Maximization (EM) framework combining probabilistic computations in Bayesian networks with standard statistical survival procedures in order to provide mutation carrier survival estimates. The proposed approach allows to obtain previously published parametric estimates (e.g. Weibull survival) as particular cases as well as more general Kaplan-Meier non-parametric estimates, which is the main contribution. Note that covariates can also be taken into account using a proportional hazard model. The whole methodology is both validated on simulated data and applied to family samples with transthyretin-related hereditary amyloidosis (a rare autosomal dominant disease with highly variable age of onset), showing very promising results.

SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information.

In this paper, we describe SAFlex (Structural Alphabet Flexibility), an extension of an existing structural alphabet (HMM-SA), to better explore increasing protein three dimensional structure information by encoding conformations of proteins in case of missing residues or uncertainties. An SA aims to reduce three dimensional conformations of proteins as well as their analysis and comparison complexity by simplifying any conformation in a series of structural letters. Our methodology presents several novelties. Firstly, it can account for the encoding uncertainty by providing a wide range of encoding options: the maximum a posteriori, the marginal posterior distribution, and the effective number of letters at each given position. Secondly, our new algorithm deals with the missing data in the protein structure files (concerning more than 75% of the proteins from the Protein Data Bank) in a rigorous probabilistic framework. Thirdly, SAFlex is able to encode and to build a consensus encoding from different replicates of a single protein such as several homomer chains. This allows localizing structural differences between different chains and detecting structural variability, which is essential for protein flexibility identification. These improvements are illustrated on different proteins, such as the crystal structure of an eukaryotic small heat shock protein. They are promising to explore increasing protein redundancy data and obtain useful quantification of their flexibility.

Prognostic and diagnostic value of elevated serum concentration of procalcitonin in patients with suspected heart failure. A review and meta-analysis.

PURPOSE: The diagnostic and prognostic significance of procalcitonin remains uncertain in HF patients. We reviewed and performed a meta-analysis of studies that measured PCT in HF patients, with or without infection. MATERIALS AND METHODS: We identified seven studies (9514 patients, 5810 with diagnoses of HF) eligible for our analysis, out of 247 examined. We estimated the serum PCT concentrations in patients with and without HF and/or infection and examined the mortality rates of patients with versus without elevated serum PCT concentrations. RESULTS: The mean age of the study samples ranged between 58 and 81 years, the men proportion between 47% and 66%, the follow-up duration between 22 and 180 days. The median PCT concentration in patients with HF and concomitant infections tended to be higher (0.26 ng/l [0.06, 0.46]) than in patients with HF alone (0.10 ng/l [0.08, 0.12]; p = 0.059). The mortality of patients suffering from HF and whose serum PCT concentrations were elevated was significantly higher than that of patients suffering from HF whose PCT concentrations were normal at 30 (2.66 [1.74, 4.05]), 90 (2.12 [1.59, 2.83]) and 180 days (2.06 [1.13, 3.78]). CONCLUSIONS: In patients with HF, an elevated serum PCT concentration predicted the short-term risk of death.

Is Placental Malaria a Long-term Risk Factor for Mild Malaria Attack in Infancy? Revisiting a Paradigm.

Background: Children born to mothers with placental malaria (PM) have been described as more susceptible to the occurrence of a first malaria infection. However, whether or not these children remain more at risk during infancy has never been explored. We aimed to determine if children born to mothers with PM are more susceptible to malaria and remain at higher risk between birth and 18 months. Methods: Five hundred fifty children were followed up weekly with control of temperature and, if >37.5°C, both a rapid diagnostic test for malaria and a thick blood smear were performed. Taking into account environmental risk of infection, the relationship between occurrences of malaria attacks from birth to 18 months was modeled using Cox models for recurrent events. Results: PM is not associated with an overall susceptibility to malaria but only with the delay of occurrence of the first malaria attack. Children born from mothers with PM tend to have an increased risk for the first malaria attack (hazard ratio [HR] = 1.33; P = .048) but not for subsequent ones (HR = 0.9; P = .46). Children who experienced 1 malaria attack were strongly at risk to develop subsequent infections independent of placental infection and environmental exposure. Conclusions: These results are consistent with the existence of an individual susceptibility to malaria unrelated to PM. From a public health point of view, protecting children born to infected placenta remains a priority, but seems insufficient to account for other frail children for whom a biomarker of frailty needs to be found.

A change-point model for detecting heterogeneity in ordered survival responses.

In this article, we suggest a new statistical approach considering survival heterogeneity as a breakpoint model in an ordered sequence of time-to-event variables. The survival responses need to be ordered according to a numerical covariate. Our estimation method will aim at detecting heterogeneity that could arise through the ordering covariate. We formally introduce our model as a constrained Hidden Markov Model, where the hidden states are the unknown segmentation (breakpoint locations) and the observed states are the survival responses. We derive an efficient Expectation-Maximization framework for maximizing the likelihood of this model for a wide range of baseline hazard forms (parametrics or nonparametric). The posterior distribution of the breakpoints is also derived, and the selection of the number of segments using penalized likelihood criterion is discussed. The performance of our survival breakpoint model is finally illustrated on a diabetes dataset where the observed survival times are ordered according to the calendar time of disease onset.