Cerebral palsy (CP) represents a group of non-progressive clinically heterogeneous disorders that are characterized by motor impairment and early age of onset, frequently accompanied by co-morbidities. The cause of CP has historically been attributed to environmental stressors resulting in brain damage. While genetic risk factors are also implicated, guidelines for diagnostic assessment of CP d...

Argyrophilic grain disease (AGD) is a progressive neurodegenerative disease of the human brain that has never been associated to a particular gene locus. In the present study, we report the results of a CNV investigation in 29 individuals whose anatomopathologic investigation of the brain showed AGD. Rare CNVs were identified in six patients (21%), in particular a 40 kb deletion at 17p13.2 enco...

In recent years, cancer genome sequencing and other high-throughput studies of cancer genomes have generated many notable discoveries. In this review, novel genomic alteration mechanisms, such as chromothripsis (chromosomal crisis) and kataegis (mutation storms), and their implications for cancer are discussed. Genomic alterations spur cancer genome evolution. Thus, the relationship between can...

This document guides the reader through the use of the seqCNA package. The aim of the package is to process high-throughput sequencing copy number data coming from tumoural samples, departing from SAM or BAM aligned reads up to the final stage of calling the copy numbers. It includes, among other features, an integrated summarization method, several filters based on a range of genomic and read-...

In order to identify somatic focal copy number aberrations (CNAs) in cancer specimens and to distinguish them from germ-line copy number variations (CNVs), we developed the software package FocalCall. FocalCall enables user-defined size cutoffs to recognize focal aberrations and builds on established array comparative genomic hybridization segmentation and calling algorithms. To distinguish CNA...

Motivated by DNA copy number variation (CNV) analysis based on high-density single nucleotide polymorphism (SNP) data, we consider the problem of detecting and identifying sparse short segments in a long one-dimensional sequence of data with additive Gaussian white noise, where the number, length and location of the segments are unknown. We present a statistical characterization of the identifi...

The availability of high-density single nucleotide polymorphism (SNP) microarrays in recent years has proven to be a great step forward in the context of global analysis of genomic abnormalities in disease. SNP arrays offer great robustness, high resolution and the possibility to detect a variety of different genomic copy number variations such as submicroscopic deletions, amplifications, loss ...

UNLABELLED CNVDetector is a program for locating copy number variations (CNVs) in a single genome. CNVDetector has several merits: (i) it can deal with the array comparative genomic hybridization data even if the noise is not normally distributed; (ii) it has a linear time kernel; (iii) its parameters can be easily selected; (iv) it evaluates the statistical significance for each CNV calling. ...

In humans, copy number variations (CNVs) are a common source of phenotypic diversity and disease susceptibility. Facioscapulohumeral muscular dystrophy (FSHD) is an important genetic disease caused by CNVs. It is an autosomal-dominant myopathy caused by a reduction in the copy number of the D4Z4 macrosatellite repeat located at chromosome 4q35. Interestingly, the reduction of D4Z4 copy number i...

Human genetic variation is represented by the genetic differences both within and among populations, and most genetic variants do not cause overt diseases but contribute to disease susceptibility and influence drug response. During the last century, various genetic variants, such as copy number variations (CNVs), have been associated with diverse human disorders. Here, we review studies on the ...