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We propose a novel analysis procedure for classifying (predicting) human tumor samples based on microarray gene expressions. This procedure involves dimension reduction using Partial Least Squares (PLS) and classification using Logistic Discrimination (LD) and Quadratic Discriminant Analysis (QDA). We compare PLS to the well known dimension reduction method of Principal Components Analysis (PCA). Under many circumstances PLS proves superior; we illustrate a condition when PCA particularly fails to predict well relative to PLS. The proposed methods were applied to five different microarray data sets involving various human tumor samples: (1) normal versus ovarian tumor; (2) Acute Myeloid Leukemia (AML) versus Acute Lymphoblastic Leukemia (ALL); (3) Diffuse Large B-cell Lymphoma (DLBCLL) versus B-cell Chronic Lymphocytic Leukemia (BCLL); (4) normal versus colon tumor; and (5) Non-Small-Cell-Lung-Carcinoma (NSCLC) versus renal samples. Stability of classification results and methods were further assessed by re-randomization studies.

Fragile X-associated tremor/ataxia syndrome (FXTAS) is generally considered to be uncommon in older female carriers of premutation alleles (55-200 CGG repeats) of the fragile X mental retardation 1 (FMR1) gene; however, neither prevalence, nor the nature of the clinical phenotype, has been well characterized in female carriers. In this study, we evaluated 146 female carriers (mean, 42.3 years; range, 20-75 years) with and without core features of FXTAS (tremor; gait ataxia), and 69 age-matched controls (mean, 45.8 years; range, 21-78 years). Compared with controls, carriers with definite or probable FXTAS had greater medical co-morbidity, with increased prevalence of thyroid disease (P ¼ 0.0096), hypertension (P ¼ 0.0020), seizures (P ¼ 0.0077), peripheral neuropathy (P ¼ 0.0040), and fibromyalgia (P ¼ 0.0097), in addition to the typical symptoms of FXTAS-tremor (P < 0.0001) and ataxia (P < 0.0001). The non-FXTAS premutation group had more complaints of chronic muscle pain (P ¼ 0.0097), persistent paraesthesias in extremities (P < 0.0001), and history of tremor (P < 0.0123) than controls. The spectrum of clinical involvement in female carriers with FXTAS is quite broad, encompassing a number of medical co-morbidities as well as the core movement disorder. The remarkable degree of thyroid dysfunction (17% in the non-FXTAS group and 50% in the FXTAS group) warrants consideration of thyroid function studies in all female premutation carriers, particularly those with core features of FXTAS. ß

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BackgroundPopulation screening for FMR1 mutations has been a topic of considerable discussion since the FMR1 gene was identified in 1991. Advances in understanding the molecular basis of fragile X syndrome (FXS) and in genetic testing methods have led to new, less expensive methodology to use for large screening endeavors. A core criterion for newborn screening is an accurate understanding of the public health burden of a disease, considering both disease severity and prevalence rate. This article addresses this need by reporting prevalence rates observed in a pilot newborn screening study for FXS in the US.MethodsBlood spot screening of 14,207 newborns (7,312 males and 6,895 females) was conducted in three birthing hospitals across the United States beginning in November 2008, using a PCR-based approach.ResultsThe prevalence of gray zone alleles was 1:66 females and 1:112 males, while the prevalence of a premutation was 1:209 females and 1:430 males. Differences in prevalence rates were observed among the various ethnic groups; specifically higher frequency for gray zone alleles in males was observed in the White group compared to the Hispanic and African-American groups. One full mutation male was identified (>200 CGG repeats).ConclusionsThe presented pilot study shows that newborn screening in fragile X is technically feasible and provides overall prevalence of the premutation and gray zone alleles in the USA, suggesting that the prevalence of the premutation, particularly in males, is higher than has been previously reported.

Objective:A pilot open label, single dose trial of fenobam, an mGluR5 antagonist, was conducted to provide an initial evaluation of safety and pharmacokinetics in adult males and females with fragile X syndrome (FXS). Methods: Twelve subjects, recruited from two fragile X clinics, received a single oral dose of 50-150 mg of fenobam. Blood for pharmacokinetic testing, vital signs and side effect screening was obtained at baseline and numerous time points for 6 h after dosing. Outcome measures included prepulse inhibition (PPI) and a continuous performance test (CPT) obtained before and after dosing to explore the effects of fenobam on core phenotypic measures of sensory gating, attention and inhibition.Results: There were no significant adverse reactions to fenobam administration. Pharmacokinetic analysis showed that fenobam concentrations were dose dependent but variable, with mean (SEM) peak values of 39.7 (18.4) ng/ml at 180 min after the 150 mg dose. PPI met a response criterion of an improvement of at least 20% over baseline in 6 of 12 individuals (4/6 males and 2/6 females). The CPT did not display improvement with treatment due to ceiling effects. Conclusions: Clinically significant adverse effects were not identified in this study of single dose fenobam across the range of dosages utilised. The positive effects seen in animal models of FXS treated with fenobam or other mGluR5 antagonists, the apparent lack of clinically significant adverse effects, and the potential beneficial clinical effects seen in this pilot trial support further study of the compound in adults with FXS.Fragile X syndrome (FXS) is the most common inherited form of intellectual disability, autism, and learning disability, with a broad range of severity and full mutation gene frequency of 1/2500.1 FXS results from an unstable trinucleotide repeat expansion of .200 CGG repeats (full mutation) in the promoter of the FMR1 (fragile X mental retardation-1) gene 2 which leads to transcriptional silencing of FMR1 and thus, absence or significant reduction of the FMR1 protein (FMRP). 3Because FMR1 is located on the X chromosome, females with a full mutation are more mildly affected than males, due to production of FMRP from the normal FMR1 allele on the non-mutated X chromosome. FMRP is an RNA binding protein which modulates dendritic maturation and synaptic plasticity through mechanisms including inhibition of group 1 metabotropic glutamate receptor (mGluR1 and mGluR5) mediated mRNA translation in dendrites. [4][5][6][7]