Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

Risks from transgenic crops

No abstract available

Supplementary Material for: Gamma Knife Radiosurgery in the Treatment of Tumor-Related Facial Pain

<i>Background:</i> Intracranial neoplasms can cause pain similar to trigeminal neuralgia. Literature regarding radiosurgery for this is limited. We present a retrospective review of patients with tumor-related facial pain from benign lesions treated with gamma knife radiosurgery (GKRS) at Wake Forest University. <i>Objectives: </i>The primary objectives were to determine long-term pain relief and predictive factors for pain alleviation. <i>Methods:</i> We reviewed 515 patients treated with GKRS for benign meningioma, vestibular schwannoma or trigeminal schwannoma between August 1999 and August 2010. Twenty-one eligible patients had tumor-related facial pain prior to GKRS. The median marginal tumor dose was 12 Gy. Long-term pain relief data were obtained by chart review and telephone interview. <i>Results:</i> The median follow-up for symptom evaluation was 3.8 years. Seventeen of 21 patients (81%) experienced a Barrow Neurological Institute (BNI) score of I–III at 6 months following GKRS. Kaplan-Meier estimates of freedom from BNI IV–V relapse were 66% at 1 year and 53% at 2 years. No pain relapses occurred after 2 years. <i>Conclusion:</i> GKRS of benign lesions is a noninvasive option for patients with tumor-related facial pain. Pain relief is modest, with the majority of pain relapses occurring within 2 years and approximately one half of patients maintaining relief beyond 2 years

Dissociating state and item components of recognition memory using fMRI

Cognitive functions such as memory retrieval involve a combination of state- and item-related processes. State-related processes are sustained throughout a task (e.g., "retrieval mode" associated with ongoing goals), whereas item-related processes are transient and allied to individual stimuli (e.g., "retrieval success" associated with the recovery of information from memory). The present study employed a mixed "blocked and event-related" experimental design to identify neural mechanisms that support state- and item-related processes during a recognition memory task. Subjects alternated between blocks of fixation and recognition memory (discriminating between old and new words). Critically, event-related procedures were embedded within the recognition blocks, including the jittering of sequential trials. This design ensures that the temporal profiles of state- and item-related activity differ and consequently renders them separable; without this procedure item-related activity would summate to produce a state-like response. Results suggest three classes of brain region support recognition memory, exhibiting: (1) predominantly transient activity (including regions in medial parietal, lateral parietal, and anterior left frontal cortex) reflecting item-related processing associated with "retrieval success," (2) predominantly sustained activity (including decreased activity in bilateral parahippocampal cortex) reflecting state-related processing associated with "retrieval mode," (3) concurrent sustained and transient activity (including regions in left middle frontal gyrus, bilateral frontal operculum, and medial frontal gyrus), reflecting a combination of state- and item-related processing. The present findings support the idea that recognition memory tasks are dependent upon a combination of state- and item-related processes that have dissociable neural correlates identifiable using fMRI. Moreover, the mixed "blocked and event-related" design employed here provides a general procedure for separating state- and item-related processes