A shifting level model algorithm that identifies aberrations in array-CGH data.

Array comparative genomic hybridization (aCGH) is a microarray technology that allows one to detect and map genomic alterations. The goal of aCGH analysis is to identify the boundaries of the regions where the number of DNA copies changes (breakpoint identification) and then to label each region as loss, neutral, or gain (calling). In this paper, we introduce a new algorithm, based on the shifting level model (SLM), with the aim of locating regions with different means of the log(2) ratio in genomic profiles obtained from aCGH data. We combine the SLM algorithm with the CGHcall calling procedure and compare their performances with 5 state-of-the-art methods. When dealing with synthetic data, our method outperforms the other 5 algorithms in detecting the change in the number of DNA copies in the most challenging situations. For real aCGH data, SLM is able to locate all the cytogenetically mapped aberrations giving a smaller number of false-positive breakpoints than the compared methods. The application of the SLM algorithm is not limited to aCGH data. Our approach can also be used for the analysis of several emerging experimental strategies such as high-resolution tiling array.

372 kb microdeletion in 18q12.3 causing SETBP1 haploinsufficiency associated with mild mental retardation and expressive speech impairment.

Several cases of interstitial deletion encompassing band 18q12.3 are described in patients with mild dysmorphic features, mental retardation and impairment of expressive language. The critical deleted region contains SETBP1 gene (SET binding protein 1). Missense heterozygous mutations in this gene cause Schinzel-Giedion syndrome (SGS, MIM#269150), characterized by profound mental retardation and multiple congenital malformations. Recently, a 18q12.3 microdeletion causing SETBP1 haploinsufficiency has been described in two patients that show expressive speech impairment, moderate developmental delay and peculiar facial features. The phenotype of individual with partial chromosome 18q deletions does not resemble SGS. The deletion defines a critical region in which SETBP1 is the major candidate gene for expressive speech defect. We describe an additional patient with the smallest 18q12.3 microdeletion never reported that causes the disruption of SETBP1. The patient shows mild mental retardation and expressive speech impairment with striking discrepancy between expressive and receptive language skills. He is able to communicate using gestures and mimic expression of face and body with surprising efficacy. The significant phenotypic overlap between this patient and the cases previously reported enforce the hypothesis that SETBP1 haploinsufficiency may have a role in expressive language development.

Nicolaides-Baraitser syndrome: two new cases with autism spectrum disorder.

Nicolaides-Baraitser syndrome is a rare clinical condition characterized by mental retardation with impairment of expressive language, short stature, microcephaly, sparse hair, typical facial dysmorphisms, and interphalangeal joint swellings. To date 24 cases have been reported, most of them being sporadic. The genetic background of Nicolaides-Baraitser syndrome is unclear in terms of cause and mode of inheritance, one of the more probable explanations is de novo mutation of a dominant gene. Some reported patients presented autistic features, although in none of these patients was the diagnosis of autism spectrum disorder formally made. We describe two unrelated patients with clinical features suggesting Nicolaides-Baraitser syndrome and, in addition, autism spectrum disorder is defined by the presence of the three cardinal core features: qualitative impairments in social, communicative, and behavioral development.