Alternating Hemiplegia of Childhood: Retrospective Genetic Study and Genotype-Phenotype Correlations in 187 Subjects from the US AHCF Registry.

Mutations in ATP1A3 cause Alternating Hemiplegia of Childhood (AHC) by disrupting function of the neuronal Na+/K+ ATPase. Published studies to date indicate 2 recurrent mutations, D801N and E815K, and a more severe phenotype in the E815K cohort. We performed mutation analysis and retrospective genotype-phenotype correlations in all eligible patients with AHC enrolled in the US AHC Foundation registry from 1997-2012.

Temporal profiling of cytokine-induced genes in pancreatic β-cells by meta-analysis and network inference.

Type 1 Diabetes (T1D) is an autoimmune disease where local release of cytokines such as IL-1β and IFN-γ contributes to β-cell apoptosis. To identify relevant genes regulating this process we performed a meta-analysis of 8 datasets of β-cell gene expression after exposure to IL-1β and IFN-γ. Two of these datasets are novel and contain time-series expressions in human islet cells and rat INS-1E cells.

Diseases as network perturbations.

The tremendous amount of the data obtained from the study of complex biological systems changes our view on the pathogenesis of human diseases. Instead of looking at individual components of biological processes, we focus our attention more on the interaction and dynamics of biological systems. A network representation and analysis of the physiology and pathophysiology of biological systems is an effective way to study their complex behavior.

HIV medical care provider practices for reducing high-risk sexual behavior: results of a qualitative study.

A first step in ensuring that HIV-infected persons practice the safer sexual behaviors that reduce disease transmission is to make certain that they receive accurate information about the relationship between sexual risk behaviors and HIV transmission. Health care providers can play a pivotal role in preventing secondary transmission of HIV; federal agencies and professional guidelines encourage providers to counsel HIV-infected patients about safer sex practices and transmission risks, particularly since the health care encounter may be the only time that HIV-infected persons receive information about prevention and risk reduction interventions. Yet research indicates that these opportunities are often missed.

Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008).

The main conclusion is that systems biology approaches can indeed advance cancer research, having already proved successful in a very wide variety of cancer-related areas, and are likely to prove superior to many current research strategies. Major points include: Systems biology and computational approaches can make important contributions to research and development in key clinical aspects of cancer and of cancer treatment, and should be developed for understanding and application to diagnosis, biomarkers, cancer progression, drug development and treatment strategies. Development of new measurement technologies is central to successful systems approaches, and should be strongly encouraged.

Dense genome-wide SNP linkage scan in 301 hereditary prostate cancer families identifies multiple regions with suggestive evidence for linkage.

The search for susceptibility loci in hereditary prostate cancer (HPC) has proven challenging due to genetic and disease heterogeneity. Multiple risk loci have been identified to date, however few loci have been replicated across independent linkage studies. In addition, most previous analyses have been hampered by the relatively poor information content provided by microsatellite scans.

A personal journey of discovery: developing technology and changing biology.

This autobiographical article describes my experiences in developing chemically based, biological technologies for deciphering biological information: DNA, RNA, proteins, interactions, and networks. The instruments developed include protein and DNA sequencers and synthesizers, as well as ink-jet technology for synthesizing DNA chips. Diverse new strategies for doing biology also arose from novel applications of these instruments.

Identification and characterization of novel SNPs in CHEK2 in Ashkenazi Jewish men with prostate cancer.

Checkpoint kinase 2 (CHEK2) is a protein involved in arresting cell cycle in response to DNA damage. To investigate whether it plays an important role in the development of prostate cancer (PRCA) in the Ashkenazi Jewish (AJ) population, we sequenced CHEK2 in 75 AJ individuals with prostate, breast, or no cancer (n=25 each). We identified seven coding SNPs (five are novel) that changed the amino-acid sequence, resulting in R3W, E394F, Y424H, S428F, D438Y, P509S, and P509L.

Genome-wide linkage scan of prostate cancer Gleason score and confirmation of chromosome 19q.

Despite evidence that prostate cancer has a genetic etiology, it has been extremely difficult to confirm genetic linkage results across studies, emphasizing the large extent of genetic heterogeneity associated with this disease. Because prostate cancer is common--approximately one in six men will be diagnosed with prostate cancer in their life--genetic linkage studies are likely plagued by phenocopies (i.e.

Genomic scan of 12 hereditary prostate cancer families having an occurrence of pancreas cancer.

Background: Prostate cancer is a genetically heterogeneous disease. Using the occurrence of other cancers in hereditary prostate cancer (HPC) families is a promising strategy for developing genetically homogeneous data sets that can enhance the ability to identify susceptibility loci using linkage analysis.

Methods: Twelve HPC families with the co-occurrence of adenocarcinoma of the pancreas were selected from the Prostate Cancer Genetic Research Study (PROGRESS).

Prostate cancer and genetic susceptibility: a genome scan incorporating disease aggressiveness.

Background: Prostate cancer is a heterogeneous disease, both genetically and phenotypically. Linkage studies attempting to map genes for hereditary prostate cancer (HPC) have proved challenging, and one potential problem contributing to this challenge is the variability in disease phenotypes.

Methods: We collected clinical data on 784 affected men with prostate cancer from 248 HPC families for whom a genomic screen was performed.

Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.

A crucial aim upon the completion of the human genome is the verification and functional annotation of all predicted genes and their protein products. Here we describe the mapping of peptides derived from accurate interpretations of protein tandem mass spectrometry (MS) data to eukaryotic genomes and the generation of an expandable resource for integration of data from many diverse proteomics experiments. Furthermore, we demonstrate that peptide identifications obtained from high-throughput proteomics can be integrated on a large scale with the human genome.

Patterns of Internet use by persons with spinal cord injuries and relationship to health-related quality of life.

Objectives: To examine patterns of computer and Internet use among persons with spinal cord injuries (SCI) and to assess the relationship between Internet use and health-related quality of life (HRQOL).

Design: Cross-sectional survey design.

Setting: National Model Spinal Cord Injury Systems.

POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer.

DNA arrays are valuable tools in molecular biology laboratories. Their rapid acceptance was aided by the release of plans for a pin-spotting microarrayer by researchers at Stanford. Inkjet microarraying is a flexible, complementary technique that allows the synthesis of arrays of any oligonucleotide sequences de novo.

Oligogenic segregation analysis of hereditary prostate cancer pedigrees: evidence for multiple loci affecting age at onset.

Previous studies have suggested strong evidence for a hereditary component to prostate cancer (PC) susceptibility. Here, we analyze 3,796 individuals in 263 PC families recruited as part of the ongoing Prostate Cancer Genetic Research Study (PROGRESS). We use Markov chain Monte Carlo (MCMC) oligogenic segregation analysis to estimate the number of quantitative trait loci (QTLs) and their contribution to the variance in age at onset of hereditary PC (HPC).

Oligonucleotide arrays for high-throughput SNPs detection in the MHC class I genes: HLA-B as a model system.

A simple and efficient oligonucleotide array was developed to identify single nucleotide polymorphisms (SNPs) encoded within the highly polymorphic human major histocompatibility complex (MHC) using HLA-B as a model system. A total of 137 probes were designed to represent all known polymorphisms encoded in exons 2 and 3. PCR products were amplified from human genomic DNA and allowed to hybridize with the oligonucleotide array.