Novel intragenic deletion within the FXN gene in a patient with typical phenotype of Friedreich ataxia: may be more prevalent than we think?

Background Friedreich ataxia is the most common inherited ataxia in Europe and is mainly caused by biallelic pathogenic expansions of the GAA trinucleotide repeat in intron 1 of the FXN gene that lead to a decrease in frataxin protein levels. Rarely, affected individuals carry either a large intragenic deletion or whole-gene deletion of FXN on one allele and a full-penetrance expanded GAA repeat on the other allele.Case presentation We report here a patient that presented the typical clinical features of FRDA and genetic analysis of FXN intron 1 led to the assumption that the patient carried the common biallelic expansion. Subsequently, parental sample testing led to the identification of a novel intragenic deletion involving the 5'UTR upstream region and exons 1 and 2 of the FXN gene by MLPA.Conclusions With this case, we want to raise awareness about the potentially higher prevalence of intragenic deletions and underline the essential role of parental sample testing in providing accurate genetic counselling

The Reproductive Journey in the Genomic Era: From Preconception to Childhood

It is estimated that around 10–15% of the population have problems achieving a pregnancy. Assisted reproduction techniques implemented and enforced by personalized genomic medicine have paved the way for millions of infertile patients to become parents. Nevertheless, having a baby is just the first challenge to overcome in the reproductive journey, the most important is to obtain a healthy baby free of any genetic condition that can be prevented. Prevention of congenital anomalies throughout the lifespan of the patient must be a global health priority. Congenital disorders can be defined as structural or functional anomalies that occur during intrauterine life and can be identified prenatally, at birth, or sometimes may only be detected later during childhood. It is considered a frequent group of disorders, affecting 3–6% of the population, and one of the leading causes of morbidity and mortality. Congenital anomalies can represent up to 30–50% of infant mortality in developed countries. Genetics plays a substantial role in the pathogenesis of congenital anomalies. This becomes especially important in some ethnic communities or populations where the incidence and levels of consanguinity are higher. The impact of genetic disorders during childhood is high, representing 20–30% of all infant deaths and 11.1% of pediatric hospital admissions. With these data, obtaining a precise genetic diagnosis is one of the main aspects of a preventive medicine approach in developed countries. The field of reproductive health has changed dramatically from traditional non-molecular visual microscope-based techniques (i.e., fluorescence in situ hybridization (FISH) or G-banding karyotype), to the latest molecular high-throughput techniques such as next-generation sequencing (NGS). Genome-wide technologies are applied along the different stages of the reproductive health lifecycle from preconception carrier screening and pre-implantation genetic testing, to prenatal and postnatal testing. The aim of this paper is to assess the new horizon opened by technologies such as next-generation sequencing (NGS), in new strategies, as a genomic precision diagnostic tool to understand the mechanisms underlying genetic conditions during the “reproductive journey”

A cheap and simple method for sample tracking for illumina TruSightOne clinical Exomes

In high throughput clinical genetics environments it is crucial to keep track of samples and have methods to double check that results from the lab are correct and belongs to the original sample. There are such methods available commercially but are expensive and based in genotyping methodology so extra processing is needed. We have developed a new method for double checking sample integrity during the NGS pipeline. We have created a plasmid that contains the sequences for a region of a distal 3'UTR captured by the TSO probes that is not used in clinical reports and added synthetic unique barcodes in the middle of the sequence. Plasmids are added to the DNA before starting the NGS pipeline and the unique part of the sequences of the plasmids captured by the TSO sequencing allows us to obtain the ID of the sample and check the identity. We have create a software and test data for automatic deployment of this procedure in any exome capture sequencing facility

jviz webcomponents: a foundation js framework for clinical NGS bioinformatics

<div><p>At Medical Genomics Visualization group (MGviz) we recently have developed fully integrated QC and data análisis procedures that creates automatic NGS clinical reports for clinicians to review. We provide integrated and summarized quality control measures with threshold based in all the previous runs that allow detecting any kind of bias or sample performance problems and any kind of sample swap. Also we provide very intuitive interactive tools that help prioritize and select the variants of interest related to the patients phenotype from our NGS gene panels and other common products like TruSightOne from Illumina or whole exome capture from Agilent.</p><br>We have also developed a full suit of open source tools in python, R and MEAN stack for creating clinical bioinformatics as a service from sample tracking and variant annotation to interactive selection tools, reannotation and automatic clinical reports generation. All this is bases in our own modern js library for interactive bioinformatic visualization: jviz (https://github.com/jviz).<br></div

MGvizCE:Clinical exome QC and analytics

<p></p> <p> </p><p>NGS facilities dedicated for clinical genomics need high QC standards, and they need continuously keeping track of their experiments and their metrics. As part of the Medical Genomics Visualization toolset (MGviz) we have developed an interactive software suit with R-Shiny and Python (Bokeh, crossfilter, flask and ReportLab) for automatic reports of QC for the whole NGS experiments in clinical diagnostics labs. The tool allows comparison of the current experiment with historic data to see the performance of the sequencher, checking different metrics for coverage and variations, warning for large copy number regions In addition it remembers decisions over annotations, helps in variant prioritization, segregation and finding compound heterozygotes and make automatic historical reports of pathogenic variants informed by the lab.</p

Earlier relapse detection after allogeneic haematopoietic stem cell transplantation by chimerism assays: Digital PCR versus quantitative real-time PCR of insertion/deletion polymorphisms.

BackgroundThe analysis of molecular haematopoietic chimerisms (HC) has become a well-established method to monitor the transplant evolution and to assess the risk of relapse after allogeneic stem cells transplantation (allo-STC). Different techniques and molecular markers are being used for chimerism surveillance after transplantation, including quantitative real-time PCR (qPCR) and the recently developed digital PCR (dPCR). This study aims to compare the sensitivity and accuracy of both methods to quantify HC and predict early relapse.MethodologyHC was evaluated using custom PCR systems for the specific detection of the Y-chromosome, null alleles and insertion-deletion polymorphisms. A total of 281 samples from 28 adult patients who underwent an allo-SCT were studied. Increasing mixed chimerism was detected prior to relapse in 100% of patients (18 relapses).ResultsCompared with conventional qPCR amplification, dPCR predicted relapse with a median anticipation period of 63 days versus 45.5 days by qPCR. Overall, 56% of the relapses were predicted earlier with dPCR whereas 38% of the relapses where detected simultaneously using both techniques and only in 1 case, relapse was predicted earlier with qPCR.ConclusionsIn conclusion, chimerism determination by dPCR constitutes a suitable technique for the follow-up of patients with haematological pathologies after allo-STC, showing greater sensitivity to predict an early relapse

Correction: Earlier relapse detection after allogeneic haematopoietic stem cell transplantation by chimerism assays: Digital PCR versus quantitative real-time PCR of insertion/deletion polymorphisms.

[This corrects the article DOI: 10.1371/journal.pone.0212708.]

Functional assessment of variants in the TSC1 and TSC2 genes identified in individuals with Tuberous Sclerosis Complex

The effects of missense changes and small in-frame deletions and insertions on protein function are not easy to predict, and the identification of such variants in individuals at risk of a genetic disease can complicate genetic counselling. One option is to perform functional tests to assess whether the variants affect protein function. We have used this strategy to characterize variants identified in the TSC1 and TSC2 genes in individuals with, or suspected of having, Tuberous Sclerosis Complex (TSC). Here we present an overview of our functional studies on 45 TSC1 and 107 TSC2 variants. Using a standardized protocol we classified 16 TSC1 variants and 70 TSC2 variants as pathogenic. In addition we identified eight putative splice site mutations (five TSC1 and three TSC2). The remaining 24 TSC1 and 34 TSC2 variants were classified as probably neutral