Processing and analyzing multiple genomes alignments with MafFilter

As the number of available genome sequences from both closely related species and individuals withinspecies increased, theoretical and methodological convergences between the fields of phylogenomics andpopulation genomics emerged. Population genomics typically focuses on the analysis of variants, whilephylogenomics heavily relies on genome alignments. However, these are playing an increasingly importantrole in studies at the population level. Multiple genome alignments of individuals are used when structuralvariation is of primary interest and when genome architecture permits to assemblede novogenomesequences. Here I describe MafFilter, a command-line-driven program allowing to process genome align-ments in the Multiple Alignment Format (MAF). Using concrete examples based on publicly availabledatasets, I demonstrate how MafFilter can be used to develop efficient and reproducible pipelines withquality assurance for downstream analyses. I further show how MafFilter can be used to perform both basicand advanced population genomic analyses in order to infer the patterns of nucleotide diversity alonggenomes

Genetic analyses in a variant of Mayer-Rokitansky-Kuster-Hauser syndrome (MURCS association).

Item does not contain fulltextMayer-Rokitansky-Kuster-Hauser (MRKH) syndrome is characterized by the congenital absence of uterus and upper part of the vagina as a result of Mullerian duct agenesis. The combination of MRKH syndrome with renal anomalies and cervicothoracic dysplasia is known as MURCS association (Mullerian aplasia, Renal anomalies, and Cervicothoracic Somite dysplasia). The etiology remains poorly understood. We delineate this disease by reporting on a 16-year-old patient showing the cardinal features of MURCS association accompanied by a persistent left superior vena cava and atrial septal defect, orofacial clefting, and mild reduction deformities of the left hand. Fluorescence in situ hybridization did not show major deletions or duplications of the DiGeorge/VCFS (velocardiofacial syndrome) region at chromosome 22q11.1 as well as the TBX5/TBX3 region at 12q24.1. In addition, sequencing of the TP63L (p63) gene, residing at 3q27, remained normal in the presented patient. Thus, we provide further evidence for the genetic heterogeneity of MURCS association

Cell transformation and activation of pp60c-src by overexpression of a protein tyrosine phosphatase

Nature3596393336-339NATU