Estimation of Trait-Model Parameters in a MOD Score Linkage Analysis

Background/Aims: Theoretically, the trait-model parameters (disease allele frequency and penetrance function) can be estimated without bias in a MOD score linkage analysis. We aimed to practically evaluate the MOD score approach regarding its ability to provide unbiased trait-model parameters for various pedigree-type and trait-model scenarios. We further investigated the ability of the MOD score approach to detect imprinting using affected sib pairs (ASPs) and affected half-sib pairs (AHSPs) when all parental genotypes are missing. Methods: Simulated pedigree data were analyzed using the GENEHUNTER-MODSCORE software package. Parameter estimation performance in terms of bias and variability was evaluated with regard to trait-model type and pedigree complexity. Results: Generally, parameters were estimated with lower bias and variability with increasing pedigree complexity, especially for recessive and over-dominant models. However, dominant and additive models could hardly be distinguished even when using 3-generation pedigrees. Imprinting could clearly be detected for mixtures of mainly ASPs and only few AHSPs with the common parent of the imprinted sex, even though no parental genotypes were available. Conclusion: Our results provide guidance to researchers regarding the possibility to estimate trait-model parameters by a MOD score analysis, including the degree of imprinting, with certain types of pedigrees. (C) 2017 The Author(s) Published by S. Karger AG, Base

Methoden und Algorithmen der Kopplungsanalyse bei quantitativen Phänotypen

Motivation: Krankheiten beim Menschen werden zu einem großen Teil durch geneti- sche Varianten beeinflusst oder verursacht. Um den Krankheitsmechanismus zu ver- stehen und um Patienten ursächlich behandeln zu können, ist ein erster Schritt, die genetische Variante im menschlichen Genom zu lokali Methoden um ein mächtiges Verfahren zur genetischen Kartierung quantitativer Phänotypen erweitert. Da genehunter-qmod auf dem Lander-Green-Algorithmus basiert, können viele Marker gleichzeitig in die Kopplungsanalyse einbezogen werden. Darum eignet sich genehunter-qmod gut für die Anwendung in Genkartierungs- projekten mit diallelischen SNP-Markern, die weniger informativ sind als Mikrosatelliten und daher in größerer Zahl in die Analyse eingehen müssen. genehunter-qmod ist nicht kommerzielle Software und im Internet unter http://www.helmholtz-muenchen.de/genepi/downloads frei erhältlich

Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives

Simulations of close relatives and identical by descent (IBD) segments are common in genetic studies, yet most past efforts have utilized sex averaged genetic maps and ignored crossover interference, thus omitting features known to affect the breakpoints of IBD segments. We developed Ped-sim, a method for simulating relatives that can utilize either sex-specific or sex averaged genetic maps and also either a model of crossover interference or the traditional Poisson model for inter-crossover distances. To characterize the impact of previously ignored mechanisms, we simulated data for all four combinations of these factors. We found that modeling crossover interference decreases the standard deviation of pairwise IBD proportions by 10.4% on average in full siblings through second cousins. By contrast, sex-specific maps increase this standard deviation by 4.2% on average, and also impact the number of segments relatives share. Most notably, using sex-specific maps, the number of segments half-siblings share is bimodal; and when combined with interference modeling, the probability that sixth cousins have non-zero IBD sharing ranges from 9.0 to 13.1%, depending on the sexes of the individuals through which they are related. We present new analytical results for the distributions of IBD segments under these models and show they match results from simulations. Finally, we compared IBD sharing rates between simulated and real relatives and find that the combination of sex-specific maps and interference modeling most accurately captures IBD rates in real data. Ped-sim is open source and available from https://github.com/williamslab/ped-sim

Selected Works in Bioinformatics

This book consists of nine chapters covering a variety of bioinformatics subjects, ranging from database resources for protein allergens, unravelling genetic determinants of complex disorders, characterization and prediction of regulatory motifs, computational methods for identifying the best classifiers and key disease genes in large-scale transcriptomic and proteomic experiments, functional characterization of inherently unfolded proteins/regions, protein interaction networks and flexible protein-protein docking. The computational algorithms are in general presented in a way that is accessible to advanced undergraduate students, graduate students and researchers in molecular biology and genetics. The book should also serve as stepping stones for mathematicians, biostatisticians, and computational scientists to cross their academic boundaries into the dynamic and ever-expanding field of bioinformatics

T-plastin, a cytoskeletal protein with important function in axonal growth, acts as a modifier of spinal muscular atrophy

Spinal muscular atrophy (SMA) is a common inherited disorder characterized by neurodegeneration of α-motor neurons. SMA is caused by mutation and/or deletion of the SMN1 gene that encodes the survival of motor neuron protein (SMN). Homozygous SMN1 deletion in unaffected persons is a rare event suggesting that the SMA phenotype is modified by other factors. The microarray expression analysis of the SMA discordant families revealed for the first time, a transcript that encodes for a cytoskeletal protein, namely T-plastin, to be the most up-regulated gene in asymptomatic vs. symptomatic SMN1-deleted sibs. A closer look to a possible involvement of T-plastin in SMA pathophysiology revealed exciting observations. First, T-plastin was found to be expressed at high levels in spinal cord and muscle of fetal and adult tissues by semi-quantitative PCR, an observation that provides a strong evidence for T-plastin implication in neuronal differentiation and neuromuscular maturation. Moreover, T-plastin associates with SMN as shown by Co-IP experiments, but this interaction, as demonstrated by in vitro binding assay, is mediated by another so far unknown protein. Second, T-plastin and SMN were found by immunofluorescence to co-localize along the axons, at branch points and at the growth cones in neurite-like extensions in differentiated PC12 cells. Interestingly, the T-plastin protein amount was found to be up-regulated in differentiated PC12 cells under NGF stimulation, an observation that might propose a possible function for T-plastin as substrate for signalling molecules. Moreover, under NGF stimulation, the affinity of T-plastin for SMN increased up to 50% suggesting that a transient complex might occur during neuronal differentiation that contributes to a specific role during this biological process. Third, the effect of T-plastin loss/overexpression in differentiated PC12 cells (cells presenting either shorter neurites when T-plastin was depleted or longer neurites when T-plastin was overexpressed) hints to a perturbation in the axon growth, guidance (and perhaps branching) due to the involvement of T-plastin in F-actin filament formation and stabilization. Interestingly, by in vitro experiments it has been observed that in differentiated PC12 cells expressing low amount of SMN protein, but overexpressing T-plastin, the length of the neurites was rescued at least in part by higher T-plastin levels. This suggests that a higher amount of T-plastin protein might help the growth cone structures to reach their target (the muscle in case of motor neurons). While all analyzed unaffected SMN1-deleted sibs expressed T-plastin in both peripheral blood and EBV-transformed lymphoblastoid cell lines, only 6.5% of the control population expressed T-plastin. In classical SMA patients, T-plastin was highly expressed in 5.9%, medium in 7.4% and very weak in 13.4%. Finally, 8% patients without SMN1 mutations expressed T-plastin. These data suggest that T-plastin expression in leukocytes happens as a rare event in humans and its expression in blood significantly correlates with an SMA protection. Nevertheless, not all blood-T-plastin-expressing SMN1-deleted individuals are SMA protected, which suggest a potential differential regulation in the spinal cord.The answer to the question by which mechanism T-plastin is expressed in unaffected sibs with homozygous absence of SMN1 gene or in control population and classical SMA patients, was not found. No correlation between the T-plastin expression and any mutation or DNA variation in the T-plastin coding region, promoter, 3'UTR or intron 1 was observed. Moreover, epigenetic analysis of the T-plastin regulatory region (promoter-first exon-first intron) revealed no differences in DNA modification level. These observations together with the haplotype analysis of two blocks described within the T-plastin genomic region in both SMA discordant families and control population, strongly suggest that likely a trans- rather than a cis-acting factor is responsible for the differential expression between SMA discordant sibs or between SMA discordant families and control population. In hope to find additional modifying genes or factors that are able to regulate T-plastin expression, a genome-wide scan analysis was performed in 42 SMA discordant families. Regions on chromosomes 3q, 7p, 16p and 22q, respectively, are suggestive for linkage and require further investigations, however, none of these reached a significant LOD score. Taken together, the discovery of the T-plastin protein as a modulator of the SMA phenotype provides the opportunity to identify novel regulatory mechanisms that may act specifically in motor neurons from asymptomatic sibs with SMN1 homozygous deletion

Linkage analysis using sex-specific recombination fractions with GENEHUNTER-MODSCORE

Motivation: Sex-specific marker maps have become increasingly available. We have implemented the usage of sex-specific recombi-nation frequencies in the GENEHUNTER-MODSCORE program that performs multipoint linkage analysis. Furthermore, we have devised a consistent method to choose the combinations of male and female genetic positions at which linkage scores should be calculated. Marker coordinates can be read automatically from publicly available genetic maps. Results: In a MOD-score analysis of the COGA dataset provided for Genetic Analysis Workshop 14, the highest linkage peak on chro-mosome 1 further increases when using sex-specific maps, while some smaller peaks are decreased. Simulations confirm that the MOD score can be biased when a sex-averaged instead of the cor-rect sex-specific map is employed. This shows that an adequate modeling of the female:male ratio of genetic distances is important, especially for complex traits

Estudio genético de distrofias hereditarias de retina: Desarrollo de una estrategia combinada para el diagnóstico de las formas recesivas y esporádicas de retinosis pigmentaria

La Retinosis Pigmentaria Autosómica Recesiva (RPAR) constituye una de las causas más importantes de ceguera en nuestra sociedad. Se caracteriza por la degeneración progresiva de las células fotorreceptoras de la retina, y los pacientes generalmente presentan ceguera nocturna, seguida de constricción del campo visual periférico. Esta enfermedad conlleva un alto coste social y humano, pues aún no existe un tratamiento eficaz. En conjunto, afecta aproximadamente a 1 de cada 3000 personas en todo el mundo. Hasta la fecha, se han localizado al menos 55 genes asociados a RPAR. Sin embargo, las mutaciones de estos genes sólo causan algo más del 50% de los casos familiares. Esto hace pensar en la existencia de un elevado número de genes potencialmente implicados en la RPAR aún por descubrir. El diagnóstico de la RPAR se ha basado tradicionalmente en el estudio genético directo mediante secuenciación Sanger de aquellos genes conocidos. Este abordaje requiere un enorme gasto de tiempo, personal y reactivos. En un principio, éste fue el único abordaje práctico, facilitado por el número reducido de genes conocidos. Al comienzo de este trabajo, se seguía realizando el diagnóstico de la misma forma, y la sobrecarga impuesta por el incesante incremento de los genes conocidos se vería compensada por la incorporación de nuevas herramientas tecnológicas y nuevas estrategias de estudio. Gracias al uso del abordaje propuesto, que combina estudios genéticos indirectos (análisis de cosegregación y de homozigosidad), y estudios genéticos directos posteriores (secuenciación Sanger) orientados por los estudios indirectos previos, se ha constatado que es posible reducir el tiempo necesario para caracterizar genéticamente a cada familia, pues el estudio de unos pocos marcadores genéticos muy cercanos a los genes asociados a RPAR, permite descartar más del 50% de estos genes en la mayoría de las familias con más de 1 afecto, y el análisis de homozigosidad permite priorizar aquellos genes no descartados para un cribado mutacional posterior. Este análisis de homozigosidad puede ser fundamental para los casos esporádicos (RPES), que merecen una consideración especial, ya que constituyen alrededor del 30% de los casos de RPAR. Los casos esporádicos son aquellos en los que existe un caso único reconocido en la familia con la patología ocular. Entre las causas infrecuentes de RPES podrían estar: mutaciones dominantes de novo o de muy baja penetrancia; mosaicismo somático; tri-alelismo; o herencia digénica. Sin embargo, la mayoría de las veces, estos casos representan herencia autosómica recesiva causada por mutaciones en genes frecuentes, en los que a veces las mutaciones aparecen en homozigosis a causa de una consanguinidad conocida o encubierta. Debido a ello, resulta de gran ayuda el estudio de homozigosisdad. Para el estudio genético indirecto, se usan dos tipos de marcadores: STRs y SNPs; y para analizar los datos provenientes de ambas plataformas de genotipado, se desarrolló un programa bioinformático para el análisis automático de los datos, que permitió realizar un estudio de segregación familiar automático, descartando aquellos genes que no cosegreguen con la enfermedad, en cada familia analizada. Asimismo, dicho programa detecta la existencia de homocigosidad en todos los marcadores ligados a un gen, en todos los miembros afectados de una misma familia, alertando al usuario de una posible región de homocigosidad en el locus de un determinado gen. Gracias a este abordaje, se logra descartar más del 50% de los genes en familias con más de 1 afecto, y tras estudios genéticos directos posteriores, se ha llegado a caracterizar a familias RPAR y RPES con una tasa de éxito de hasta el 17,52%. Finalmente, las alertas de homocigosidad obtenidas con STRs, son muy específicas, pero poco sensibles a la hora de predecir una variante patogénica en homocigosis, pudiendo obtener falsos negativos; mientras que las alertas de homocigosidad obtenidas con SNPs, son más sensibles y menos específicas que con STRs, para el mismo cometid