KRAS Mutational Regression Is Associated With Oligo-Metastatic Status and Good Prognosis in Metastatic Colorectal Cancer.

Background: We previously reported that loss of mutations ("regressive" mutational trajectories) from primary tumors to metastases associated with the oligo-metastatic status in colorectal cancer (CRC). The present study was undertaken in order to analyze the mutational trajectories of in a well-characterized cohort of CRC patients who developed poly- or oligo-metastatic disease.

Material And Methods: Patients were treated and followed-up according to European Society of Medical Oncology guidelines.

Interpreting Genetic Variants in Titin in Patients With Muscle Disorders.

Importance: Mutations in the titin gene (TTN) cause a wide spectrum of genetic diseases. The interpretation of the numerous rare variants identified in TTN is a difficult challenge given its large size.

Objective: To identify genetic variants in titin in a cohort of patients with muscle disorders.

Clinical and Genetic Evaluation of a Cohort of Pediatric Patients with Severe Inherited Retinal Dystrophies.

We performed a clinical and genetic characterization of a pediatric cohort of patients with inherited retinal dystrophy (IRD) to identify the most suitable cases for gene therapy. The cohort comprised 43 patients, aged between 2 and 18 years, with severe isolated IRD at the time of presentation. The ophthalmological characterization also included assessment of the photoreceptor layer integrity in the macular region (ellipsoid zone (EZ) band).

Next-Generation Sequencing Approaches to Define the Role of the Autophagy Lysosomal Pathway in Human Disease: The Example of LysoPlex.

Next-Generation Sequencing (NGS) technologies have deeply changed the throughput of genetic testing allowing analyzing millions of DNA fragments in parallel. One key application is the understanding of genetically heterogeneous and complex diseases where 50-100 different genes may converge to control the same pathways. These disorders cannot be studied using traditional approaches, based on gene-by-gene Sanger sequencing.

Mutations in the PCYT1A gene are responsible for isolated forms of retinal dystrophy.

Mutations in the PCYT1A gene have been recently linked to two different phenotypes: one characterized by spondylometaphyseal dysplasia and cone-rod dystrophy (SMD-CRD) and the other by congenital lipodystrophy, severe fatty liver disease, and reduced HDL cholesterol without any retinal or skeletal involvement. Here, we identified, by next generation sequencing, sequence variants affecting function in the PCYT1A gene in three young patients with isolated retinal dystrophy from two different Italian families. A thorough clinical evaluation of the patients, with whole skeleton X-ray, metabolic assessment and liver ultrasound failed to reveal signs of skeletal dysplasia, metabolic and hepatic alterations.

The italian limb girdle muscular dystrophy registry: Relative frequency, clinical features, and differential diagnosis.

Introduction: Limb girdle muscular dystrophies (LGMDs) are characterized by high molecular heterogeneity, clinical overlap, and a paucity of specific biomarkers. Their molecular definition is fundamental for prognostic and therapeutic purposes.

Methods: We created an Italian LGMD registry that included 370 molecularly defined patients.

The genetic basis of undiagnosed muscular dystrophies and myopathies: Results from 504 patients.

Objective: To apply next-generation sequencing (NGS) for the investigation of the genetic basis of undiagnosed muscular dystrophies and myopathies in a very large cohort of patients.

Methods: We applied an NGS-based platform named MotorPlex to our diagnostic workflow to test muscle disease genes with a high sensitivity and specificity for small DNA variants. We analyzed 504 undiagnosed patients mostly referred as being affected by limb-girdle muscular dystrophy or congenital myopathy.

[Next Generation Sequencing and ADPKD].

Autosomal Dominant Polycistic Kidney Disease (ADPKD) is the most common inherited genetic disorder in the word, caused by mutations in PKD1 gene in 85% of cases and PKD 2 gene in the remaining 15%. Although diagnosis is usually based on ultrasound, MRI and CT scans, in some cases genetic testing is necessary, for example, in patients with atypical phenotype or with a negative family history, or in cases of donation from relatives. The presence of pseudogenes in PKD1, the size of the gene, the costs of the Sanger sequencing and genetic heterogeneity underlying kidney disease make genetic analysis particularly difficult to be performed.

Lysoplex: An efficient toolkit to detect DNA sequence variations in the autophagy-lysosomal pathway.

The autophagy-lysosomal pathway (ALP) regulates cell homeostasis and plays a crucial role in human diseases, such as lysosomal storage disorders (LSDs) and common neurodegenerative diseases. Therefore, the identification of DNA sequence variations in genes involved in this pathway and their association with human diseases would have a significant impact on health. To this aim, we developed Lysoplex, a targeted next-generation sequencing (NGS) approach, which allowed us to obtain a uniform and accurate coding sequence coverage of a comprehensive set of 891 genes involved in lysosomal, endocytic, and autophagic pathways.

Are all the previously reported genetic variants in limb girdle muscular dystrophy genes pathogenic?

Hundreds of variants in autosomal genes associated with the limb girdle muscular dystrophies (LGMDs) have been reported as being causative. However, in most cases the proof of pathogenicity derives from their non-occurrence in hundreds of healthy controls and/or from segregation studies in small families. The limited statistics of the genetic variations in the general population may hamper a correct interpretation of the effect of variants on the protein.

Next generation sequencing on patients with LGMD and nonspecific myopathies: Findings associated with ANO5 mutations.

We studied 786 undiagnosed patients with LGMD or nonspecific myopathic features to investigate the role of ANO5 mutations in limb-girdle muscular dystrophies (LGMDs) and in nonspecific myopathies using the next generation sequencing (NGS) approach. In 160 LGMD patients, we first sequenced hotspot exons 5 and 20 and then sequenced the remaining part of the coding region. Another 626 patients, recruited using broader inclusion criteria, were directly analyzed by targeted NGS.

MotorPlex provides accurate variant detection across large muscle genes both in single myopathic patients and in pools of DNA samples.

Mutations in ~100 genes cause muscle diseases with complex and often unexplained genotype/phenotype correlations. Next-generation sequencing studies identify a greater-than-expected number of genetic variations in the human genome. This suggests that existing clinical monogenic testing systematically miss very relevant information.

Prediction of rare single-nucleotide causative mutations for muscular diseases in pooled next-generation sequencing experiments.

Next-generation sequencing (NGS) is a new approach for biomedical research, useful for the diagnosis of genetic diseases in extremely heterogeneous conditions. In this work, we describe how data generated by high-throughput NGS experiments can be analyzed to find single nucleotide polymorphisms (SNPs) in DNA samples of patients affected by neuromuscular disorders. In particular, we consider untagged pooled NGS data, where DNA samples of different individuals are combined in a single experiment, still providing information with an uncertainty limited to only two patients.

Familial exudative vitreoretinopathy caused by a homozygous mutation in TSPAN12 in a cystic fibrosis infant.

Familial exudative vitreoretinopathy (FEVR) is a genetic disease affecting the vascularization of the peripheral retina. The clinical manifestations are very heterogeneous, ranging from mildly affected patients, who could present no visual defects, to severe conditions which can also cause complete blindness at birth or in the first decade. FEVR can be inherited in all the three genetic forms: dominant, recessive and X-linked.

Familial trisomy 6p in mother and daughter.

Several patients with partial trisomy 6p resulting from parental balanced translocations or from a de novo duplication or insertion have already been described. Here, we report on the first case of familial pure trisomy 6p as a result of interstitial tandem duplication. The patient, an 11-year-old female, presented with mild dysmorphic features, moderate intellectual disability with behavioral disturbances, immunodeficiency, and epilepsy.

Enhancer chip: detecting human copy number variations in regulatory elements.

Critical functional properties are embedded in the non-coding portion of the human genome. Recent successful studies have shown that variations in distant-acting gene enhancer sequences can contribute to disease. In fact, various disorders, such as thalassaemias, preaxial polydactyly or susceptibility to Hirschsprung's disease, may be the result of rearrangements of enhancer elements.