Identifying the spectrum of genetic alterations that cooperate with critical oncogenes to promote transformation provides a foundation for understanding the diversity of clinical phenotypes observed in human cancers. Here, we performed integrated analyses to identify genomic alterations that co-occur with oncogenic BRAF in melanoma and abrogate cellular dependence upon this oncogene. We identified concurrent mutational inactivation of the PTEN and RB1 tumor suppressors as a mechanism for loss of BRAF/MEK dependence in melanomas harboring V600EBRAF mutations. RB1 alterations were mutually exclusive with loss of p16INK4A, suggesting that whereas p16INK4A and RB1 may have overlapping roles in preventing tumor formation, tumors with loss of RB1 exhibit diminished dependence upon BRAF signaling for cell proliferation. These findings provide a genetic basis for the heterogeneity of clinical outcomes in patients treated with targeted inhibitors of the mitogen-activated protein kinase pathway. Our results also suggest a need for comprehensive screening for RB1 and PTEN inactivation in patients treated with RAF and MEK-selective inhibitors to determine whether these alterations are associated with diminished clinical benefit in patients whose cancers harbor mutant BRAF.
BRAF; PTEN; RB1; MEK inhibitor; BRAF inhibitor; CDKN2A
Transient hypoxia–ischemia (HI) leads to delayed neuronal death in both mature and immature neurons but the underlying mechanisms are not fully understood. To understand whether the pathogenesis of HI-induced neuronal death is different between mature and immature neurons, we used a rat HI model at postnatal days 7 (P7), 15 (P15), 26 (P26) and 60 (P60) in order to investigate ultrastructural changes and active caspase-3 distribution in HI-injured neurons as a function of developmental age. In P7 pups, despite more than 95% of HI-injured neurons highly expressing active caspase-3, most of these active caspase-3-positive neurons revealed mixed features of apoptosis and necrosis (a chimera type) under electron microscopy (EM). Classical apoptosis was observed only in small populations of HI-injured P7 neurons. Furthermore, in rats older than P7, most HI-injured neurons displayed features of necrotic cell death under EM and, concomitantly, active caspase-3-positive neurons after HI declined dramatically. Classical apoptosis after HI was rarely found in neurons older than P15. In P60 rats, virtually all HI-injured neurons showed the shrinkage necrotic morphology under EM and were negative for active caspase-3. These results strongly suggest that pathogenesis of HI-induced neuronal death is shifting from apoptosis to necrosis during brain development.
neonatal brain; hypoxia–ischemia; neuronal death; brain maturation; RNase protection assay; electron microscopy
Transient cerebral ischemia leads to protein aggregation mainly in neurons destined to undergo delayed neuronal death after ischemia. This study utilized a rat transient cerebral ischemia model to investigate whether ischemic preconditioning is able to alleviate neuronal protein aggregation, thereby protecting neurons from ischemic neuronal damage. Ischemic preconditioning was introduced by a sublethal 3 min period of ischemia followed by 48 h of recovery. Brains from rats with either ischemic preconditioning or sham-surgery were then subjected to a subsequent 7 min period of ischemia followed by 30 min, 4, 24, 48 and 72 h of reperfusion. Protein aggregation and neuronal death were studied by electron and confocal microscopy, as well as by biochemical analyses. Seven minutes of cerebral ischemia alone induced severe protein aggregation after 4 h of reperfusion mainly in CA1 neurons destined to undergo delayed neuronal death (which took place after 72 h of reperfusion). Ischemic preconditioning reduced significantly protein aggregation and virtually eliminated neuronal death in CA1 neurons. Biochemical analyses revealed that ischemic preconditioning decreased accumulation of ubiquitin-conjugated proteins (ubi-proteins) and reduced free ubiquitin depletion after brain ischemia. Furthermore, ischemic preconditioning also reduced redistribution of heat shock cognate protein 70 and Hdj1 from cytosolic fraction to protein aggregate-containing fraction after brain ischemia. These results suggest that ischemic preconditioning decreases protein aggregation after brain ischemia.
brain ischemia; preconditioning; protein aggregation; proteotoxicity; electron microscopy
Focal brain ischemia leads to a slow type of neuronal death in the penumbra that starts several hours after ischemia and continues to mature for days. During this maturation period, blood flow, cellular ATP and ionic homeostasis are gradually recovered in the penumbral region. In striking contrast, protein synthesis is irreversibly inhibited. This study used a rat focal brain ischemia model to investigate whether or not irreversible translational inhibition is due to abnormal aggregation of translational complex components, i.e. the ribosomes and their associated nascent polypeptides, protein synthesis initiation factors and co-translational chaperones. Under electron microscopy, most rosette-shaped polyribosomes were relatively evenly distributed in the cytoplasm of sham-operated control neurons, but clumped into large abnormal aggregates in penumbral neurons subjected to 2 h of focal ischemia followed by 4 h of reperfusion. The abnormal ribosomal protein aggregation lasted until the onset of delayed neuronal death at 24–48 h of reperfusion after ischemia. Biochemical study further suggested that translational complex components, including small ribosomal subunit protein 6 (S6), large subunit protein 28 (L28), eukaryotic initiation factors 2α, 4E and 3g, and co-translational chaperone heat-shock cognate protein 70 (HSC70) and co-chaperone Hdj1, were all irreversibly clumped into large abnormal protein aggregates after ischemia. Translational complex components were also highly ubiquitinated. This study clearly demonstrates that focal ischemia leads to irreversible aggregation of protein synthesis machinery that contributes to neuronal death after focal brain ischemia.
brain ischemia; chaperone; heat-shock cognate protein 70; protein aggregation; protein synthesis; ribosomal proteins; stress granule; ubiquitin
Neuronal repair following injury requires recruitment of large amounts of membranous proteins into synaptic and other cell membranes, which is carried out by the fusion of transport vesicles to their target membranes. A critical molecule responsible for assemblage of membranous proteins is N-ethylmaleimide-sensitive factor (NSF) which is an ATPase. To study whether NSF is involved in ischemic neurological deficits and delayed neuronal death, we investigated alterations of NSF after transient cerebral ischemia by means of biochemical methods, as well as confocal and electron microscopy. We found that transient cerebral ischemia induced depletion of free NSF and concomitantly relocalization of NSF into the Triton X-100-insoluble fraction including postsynaptic densities in CA1 neurons during the postischemic period. The NSF alterations are accompanied by accumulation of large quantities of intracellular vesicles in CA1 neurons that are undergoing delayed neuronal death after transient cerebral ischemia. Therefore, permanent depletion of free NSF and relocalization of NSF into the Triton X-100-insoluble fraction may disable the vesicle fusion machinery necessary for repair of synaptic injury, and ultimately leads to synaptic dysfunction and delayed neuronal death in CA1 neurons after transient cerebral ischemia.
brain ischemia; molecular chaperone; N-ethylmaleimide-sensitive factor; postsynaptic density; electron microscopy
Aberrant activation of Wnt signalling through hypermethylation of Wnt inhibitor genes is involved in several human malignancies, including acute myeloid leukaemia (AML). It remains unclear whether hypermethylation of Wnt inhibitors is associated with molecular gene mutations in the development of AML.
We investigated the association of the promoter hypermethylation of six Wnt inhibitors (Wif-1, SFRP1, SFRR2, SFRP4, SFRP5, and DKK1) with gene aberrations in the leukaemogenesis of 269 AML patients.
In total, 166 patients (61.7%) had hypermethylation of at least one Wnt inhibitor. The majority (68.5%) of patients with Wnt inhibitor hypermethylation had concurrent Class II gene mutations that affect transcription factors or cofactors. There was a close association of Wif-1 hypermethylation with t(15;17) (P=0.0005) and CEBPA mutation (P<0.0001), DKK1 hypermethylation with t(8;21) (P<0.0001) and ASXL1 mutation (P=0.0078), SFRP-1 hypermethylation with t(8;21) (P<0.0001), SFRP-2 hypermethylation with AML1/RUNX1 mutation (P=0.0012), and SFRP-5 hypermethylation with MLL/PTD (P=0.0505). On the other side, hypermethylation of Wnt inhibitors was always negatively associated with NPM1 mutation and FLT3/ITD.
There was distinct association between hypermethylation of individual Wnt inhibitors and specific gene aberrations, especially Class II mutations. The Wnt inhibitor hypermethylation might interact with genetic alterations in the leukaemogenesis.
Wnt pathway inhibitors; methylation; genetic alteration; acute myeloid leukaemia
One approach to circumvent barriers to clinical implementation of pharmacogenetics is to employ pre-prescription genotyping that requires interrogation of multiple pharmacogenetic variants using a high-throughput platform. We compared the performance of the DMET Plus array (1,931 variants in 225 genes) with orthogonal genotyping methods in 220 pediatric patients. A total of 1,692 variants had call rates above 98% and were in Hardy Weinberg equilibrium. Of these, 259 were genotyped by at least one independent method and a total of 19,942 SNP-patient sample pairs were evaluated. The concordance was 99.9% with only 28 genotype discordances observed. For those genes deemed most likely to be clinically relevant (TPMT, CYP2D6, CYP2C19, CYP2C9, VKORC1, DPYD, UGT1A1, and SLCO1B1), a total of 3,799 SNP-patient sample pairs were evaluable and had a concordance of 99.96%. We conclude that the DMET Plus array performs well with primary patient samples when compared to multiple other lower-throughput genotyping methods.
The human ‘pain network’ includes cortical areas which are activated during the response to painful stimuli (termed category 1), or during psychological processes which modulate pain, e.g. distraction (termed category 2). These categories include parts of the parasylvian (PS), medial frontal (MF), and paracentral cortex (S1&M1). We now propose to test the hypothesis that causal interactions both within and between category 1 and category 2 modules occur during attention to a painful stimulus. Event-related causality (ERC) was calculated from local field potentials (LFP) recorded directly from these cortical areas during the response to a painful cutaneous laser stimulus in patients being monitored for epilepsy.
The number of electrodes involved in pairs with significant ERC in category 1 was greater for pre-stimulus versus post-stimulus and for attention versus distraction. This is consistent with our prior evidence that the category 1 ‘pain network’ changes rapidly with time intervals and tasks. In contrast, the interaction between categories was often unchanged or stable across intervals and tasks, particularly in MF.
The proportion of contacts involved in interactions with PS was greater during distraction versus attention while activation was less, which suggests that distraction involves an inhibitory process in PS. Functional interactions between categories were overwhelmingly in the direction from category 2 > 1, particularly for contacts in MF which often had a driver role. These results demonstrate that MF is densely interconnected throughout the ‘pain network’ so that stimulation of MF might be used to disrupt the ‘pain network’ as a therapy for pain.
attention; human; pain; cortex; network; event related. causality
To select an appropriate prognostic model in the treatment of mature T- and natural killer (NK) -cell lymphoma (peripheral T-cell lymphoma (PTCL) and NK-/T-cell lymphoma (NKTCL)) is crucial. This study investigated the usefulness of Ann Arbor staging classification International prognostic index (IPI), prognostic index for T-cell lymphoma (PIT) and International peripheral T-cell lymphoma Project score (IPTCLP). Between 2000 and 2009, 176 patients (122 males) with PTCL and NKTCL were diagnosed and treated from a single institute in Taiwan. The correlation between complete response (CR) rate, 3-year overall survival (OS), early mortality rate and four prognostic models was analyzed. Thirty-one patients received hematopoietic stem cell transplantation (HSCT) and were analyzed separately. Three-year OS rate was 34.7%, and anaplastic large-cell lymphoma harbored better outcome than others. IPI score had the lowest Akaike information criterion value (1081.197) and was the best score in predicting OS and early mortality (P=0.009). Ann Arbor stage classification can predict CR rate more precisely (P=0.006). OS was significantly better in patients who received HSCT, even in patients with unfavorable features compared with chemotherapy alone. All prognostic models were useful to evaluate the outcome of patients with PTCL and NKTCL but IPI score did best in predicting OS in PTCL and PIT score in NKTCL. This study also supported the role of HSCT in patients with high-risk or refractory PTCL or NKTCL.
T-cell lymphoma; prognostic score; hematopoietic stem cell transplantation; Asian population
The current model of fear conditioning suggests that it is mediated through modules involving the amygdala (AMY), hippocampus (HIP), and frontal lobe (FL). We now test the hypothesis that habituation and acquisition stages of a fear conditioning protocol are characterized by different event-related causal interactions (ERC) within and between these modules. The protocol employed the painful cutaneous laser as the unconditioned stimulus and ERC was estimated by analysis of local field potentials recorded through electrodes implanted for investigation of epilepsy.
During the pre-stimulus interval of the habituation stage FL>AMY ERC interactions were common. For comparison, in the post-stimulus interval of the habituation stage only a subdivision of the FL (dorsal lateral prefrontal cortex, dlPFC) still exerted the FL>AMY ERC interaction (dlFC>AMY). For a further comparison, during the poststimulus interval of the acquisition stage the dlPFC>AMY interaction persisted and an AMY>FL interaction appeared.
In addition to these ERC interactions between modules, the results also show ERC interactions within modules. During the post-stimulus interval HIP>HIP ERC interactions were more common during acquisition, and deep hippocampal contacts exerted causal interactions upon superficial contacts, possibly explained by connectivity between the perihippocampal gyrus and the hippocampus. During the prestimulus interval of the habituation stage AMY>AMY ERC interactions were commonly found, while interactions between the deep and superficial amygdala (indirect pathway) were independent of intervals and stages. These results suggest that the network subserving fear includes distributed or widespread modules, some of which are themselves `local networks'. ERC interactions between and within modules can be either static or change dynamically across intervals or stages of fear conditioning.
Pain; Fear; Network; Human; Laser; Local Field Potentials
Transient cerebral ischemia leads to irreversible translational inhibition which has been considered as a hallmark of delayed neuronal death after ischemia. This study utilized a rat transient cerebral ischemia model to investigate whether irreversible translational inhibition is due to abnormal aggregation of translational complex, i.e. the ribosomes and their associated nascent polypeptides, initiation factors, translational chaperones and degradation enzymes after ischemia. Translational complex aggregation was studied by electron microscopy, as well as by biochemical analyses. A duration of 15 or 20 min of cerebral ischemia induced severe translational complex aggregation starting from 30 min of reperfusion and lasting until the onset of delayed neuronal death at 48 h of reperfusion. Under electron microscopy, most rosette-shaped polyribosomes were relatively evenly distributed in the cytoplasm of sham-operated control neurons. After ischemia, most ribosomes were clumped into large abnormal aggregates in neurons destined to die. Translational complex components consisting of small ribosomal subunit protein 6, large subunit protein 28, eukaryotic initiation factor-3η, co-translational chaperone heat shock cognate protein 70 and co-chaperone HSP40-Hdj1, as well as co-translational ubiquitin ligase c-terminus of hsp70-interacting protein were all irreversibly clumped into large abnormal protein aggregates after ischemia. Translational components were also highly ubiquitinated. To our knowledge, irreversible aggregation of translational components has not been reported after brain ischemia. This study clearly indicates that ischemia damages co-translational chaperone and degradation machinery, resulting in irreversible destruction of protein synthesis machinery by protein aggregation after ischemia.
brain ischemia; protein aggregation; co-translational folding; protein synthesis; ribosomal proteins; CHIP-; HSC70-; Hdj1-HSP40-; eIF-3η
To report the long-term follow-up (more than 10 years) of three patients who have undergone polypseudophakia phacoemulsification cataract surgery.
A case series of three patients and four procedures. Two poly-methyl-methacrylate (PMMA) intraocular lenses (IOLs) were placed within the capsular bag (P359UV, Storz, Tuttlingen, Germany). No complications occurred peri-operatively. A full ophthalmological examination was performed at 10-year follow-up, looking for decentration, tilt, and complications of interlenticular opacification (ILO) between the IOLs.
Inferior ILO with Elschnig pearls was observed in only one case, and was likely to be visually insignificant. No ILO was observed in the other three eyes. In one patient, the piggyback IOL had been displaced 1–2 mm nasally, but there was no tilt of the IOLs, with the haptics remaining well aligned. There was no displacement or tilt of the piggyback IOL in the other three cases. Corneal endothelial cell count (SP-2000P, Topcon, Tokyo, Japan) was above 1000 cell/mm2 in all cases.
With the introduction of foldable IOLs, the piggyback IOL is usually placed in the sulcus, but we have shown good long-term stability and minimal complications of dual PMMA IOLs placed within the bag.
polypseudophakia; piggyback; intraocular lens; cataract; phacoemulsification; PMMA
One approach to the study of disordered spatial attention is to carry out tests of extinction, in which stimuli are detected on the left when they are presented on the left alone, but not when both sides are stimulated simultaneously in a dual simultaneous stimulation (DSS) protocol. Extinction has been documented for multiple sensory modalities, but not for thermal pain stimuli, to our knowledge. We now test the hypothesis that subjects with visual spatial neglect (hemi-neglect) will have alterations in thermal pain sensation which are related to abnormal spatial attention. The results demonstrate that thermal pain extinction of hot and cold pain stimuli occurs in a proportion of subjects with hemi-neglect. In the subjects with visual spatial hemi-neglect but without thermal pain extinction, the sensation of the thermal pain stimulus on the affected (left) side was not extinguished but was often localized to the unaffected (right) side, and the submodality of the stimulus (cold or hot) was often misidentified. Ratios indicating the magnitude of extinction, mislocalization and misidentification were significantly larger on the left side of subjects with visual spatial neglect than in healthy controls or in controls with stroke but without hemineglect. The proportion of subjects with thermal pain extinction, mislocalization, or misidentification was significantly higher in subjects with hemi-neglect than those in either control group. These results demonstrate that disordered attention exerts a powerful effect upon the perception of both the location and the quality of thermal pain stimuli.
Neglect; Attention; Human; Thermal pain; Mislocalization; Misidentification
Cauda equina syndrome (CES) is a rare manifestation in patients with long-standing ankylosing spondylitis (AS). We report a 57-year-old male patient with a 30-year history of AS who developed CES in the past 4 years. The CT and MRI examinations showed unique appearances of dural ectasia, multiple dorsal dural diverticula, erosion of the vertebral posterior elements, tethering of the conus medullaris to the dorsal aspect of the spinal canal and adhesion of the nerve roots of the cauda equina to the wall of the dural sac. A large dural defect was found at surgery. De-adhesion of the tethered conus medullaris was performed but without significant clinical improvement. The possible aetiologies of CES and dural ectasia in patients with chronic AS are discussed and the literature is reviewed.
Adult-onset hypothyroidism induces a variety of impairments on hippocampus- dependent neurocognitive functioningin which many synaptic proteins in hippocampus neurons are involved. Here, we observed the effect of adult-onset hypothyroidism on the expression of syntaxin-1 and munc-18 in the dorsal hippocampus and whether the altered proteins could be restored by levothyroxine (T4) treatment. All rats were separated into 4 groups randomly: hypothyroid group, 5 µg T4 /100 g body weight (BW) treated group, 20 µg T4/100 g BW treated group and control group. The radioimmunoassay kits were applied to assay the levels of serum T3 and T4, and the levels of syntaxin-1 and munc-18 in hippocampus were assessed by immunohistochemistry and Western blot. Both analysis corroborated that syntaxin-1 in the hypothyroid group was significantly higher. Munc-18 was lower in four layers of CA3 and dentate gyrus by immunohistochemistry. After two weeks of treatment with 5 µg T4/100 g BW for hypothyroidism, syntaxin-1 levels were completely restored, whereas the recovery of munc-18 only located in two of the four impaired layers. Twenty µg T4/100 g BW treatment normalized munc-18 levels. These data suggested that adult-onset hypothyroidism induced increment of syntaxin-1 and decrement of munc-18 in the dorsal hippocampus, which could be restored by T4 treatment. Larger dosage of T4 caused more effective restorations.
hypothyroidism; levothyroxine (T4); munc-18; syntaxin-1; hippocampus.
The spin current, orbit angular momentum current and total angular momentum current in a tensor form have been universally defined according to the quantum electrodynamics. Their conservation quantities and the continuity equations have been discussed in different cases. Non-relativistic approximation forms are deduced in order to explain their physical meanings, and to analyze some experimental results. The spin current of helical edge states in HgTe/CdTe quantum wells is calculated to demonstrate the properties of the spin current of the two dimensional quantum spin-Hall system. A generalized spin-orbit coupling term in the semiconducting media is deduced based on the theory of the electrodynamics in the moving media. It is recommended to use the effective total angular momentum current instead of the pure spin current to describe the distribution of polarization and the transport properties in spintronics.
The pathways by which painful stimuli are signaled within the human medial temporal lobe are unknown. Rodent studies have shown that nociceptive inputs are transmitted from the brainstem or thalamus through one of two pathways to the central nucleus of the amygdala. The indirect pathway projects from the basal and lateral nuclei of the amygdala to the central nucleus, while the direct pathway projects directly to the central nucleus. We now test the hypothesis that the human ventral amygdala (putative basal and lateral nuclei) exerts a causal influence upon the dorsal amygdala (putative central nucleus), during the application of a painful laser stimulus.
Local field potentials (LFPs) were recorded from depth electrode contacts implanted in the medial temporal lobe for the treatment of epilepsy, and causal influences were analyzed by Granger causality (GRC). This analysis indicates that the dorsal amygdala exerts a pre-stimulus causal influence upon the hippocampus, consistent with an attention-related response to the painful laser. Within the amygdala, the analysis indicates that the ventral contacts exert a causal influence upon dorsal contacts, consistent with the human (putative) indirect pathway. Potentials evoked by the laser (LEPs) were not recorded in the ventral nuclei, but were recorded at dorsal amygdala contacts which were not preferentially those receiving causal influences from the ventral contacts. Therefore, it seems likely that the putative indirect pathway is associated with causal influences from the ventral to the dorsal amygdala, and is distinct from the human (putative) indirect pathway which mediates LEPs in the dorsal amygdala.
human; pain; amygdala; hippocampus; causality; fear conditioning
Our previous studies show that attention to painful cutaneous laser stimuli is associated with functional connectivity between human primary somatosensory cortex (SI), parasylvian cortex (PS), and medial frontal cortex (MF), which may constitute a pain network. However, the direction of functional connections within this network is unknown. We now test the hypothesis that activity recorded from the SI has a driver role, and a causal influence, with respect to activity recorded from PS and MF during attention to a laser. Local field potentials (LFP) were recorded from subdural grid electrodes implanted for the treatment of epilepsy. We estimated causal influences by using the Granger causality (GRC), which was computed while subjects performed either an attention task (counting laser stimuli) or a distraction task (reading for comprehension). Before the laser stimuli, directed attention to the painful stimulus (counting) consistently increased the number of GRC pairs both within the SI cortex and from SI upon PS (SI > PS). After the laser stimulus, attention to a painful stimulus increased the number of GRC pairs from SI > PS, and SI > MF, and within the SI area. LFP at some electrode sites (critical sites) exerted GRC influences upon signals at multiple widespread electrodes, both in other cortical areas and within the area where the critical site was located. Critical sites may bind these areas together into a pain network, and disruption of that network by stimulation at critical sites might be used to treat pain.
Attention; Human; Pain; Somatic sensory cortex; Network; Event-related; Laser evoked; potentials
FTO harbours the strongest known obesity-susceptibility locus in Europeans. While there is growing evidence for a role for FTO in obesity risk in Asians, its association with type 2 diabetes, independently of BMI, remains inconsistent. To test whether there is an association of the FTO locus with obesity and type 2 diabetes, we conducted a meta-analysis of 32 populations including 96,551 East and South Asians.
All studies published on the association between FTO-rs9939609 (or proxy [r2 > 0.98]) and BMI, obesity or type 2 diabetes in East or South Asians were invited. Each study group analysed their data according to a standardised analysis plan. Association with type 2 diabetes was also adjusted for BMI. Random-effects meta-analyses were performed to pool all effect sizes.
The FTO-rs9939609 minor allele increased risk of obesity by 1.25-fold/allele (p = 9.0 × 10−19), overweight by 1.13-fold/allele (p = 1.0 × 10−11) and type 2 diabetes by 1.15-fold/allele (p = 5.5 × 10−8). The association with type 2 diabetes was attenuated after adjustment for BMI (OR 1.10-fold/allele, p = 6.6 × 10−5). The FTO-rs9939609 minor allele increased BMI by 0.26 kg/m2 per allele (p = 2.8 × 10−17), WHR by 0.003/allele (p = 1.2 × 10−6), and body fat percentage by 0.31%/allele (p = 0.0005). Associations were similar using dominant models. While the minor allele is less common in East Asians (12–20%) than South Asians (30–33%), the effect of FTO variation on obesity-related traits and type 2 diabetes was similar in the two populations.
FTO is associated with increased risk of obesity and type 2 diabetes, with effect sizes similar in East and South Asians and similar to those observed in Europeans. Furthermore, FTO is also associated with type 2 diabetes independently of BMI.
Electronic supplementary material
The online version of this article (doi:10.1007/s00125-011-2370-7) contains peer-reviewed but unedited supplementary material, which is available to authorised users.
Asians; FTO; Meta-analysis; Obesity; Type 2 diabetes
The discriminatory power of post-genotyping analyses, such as kinship or clustering analysis, is dependent on the amount of genetic information obtained from the DNA fragment/genotyping analysis. The number of microsatellite loci amplified in one multiplex is limited by the number of dyes and overlapping loci boundaries; requiring researchers to amplify replicate samples with 2 or more multiplexes in order to obtain a genotype for 12–15 loci. AFLP is another method that is limited by the number of dyes, often requiring multiple amplifications of replicate samples to obtain more complete results. Traditionally, researchers export the genotyping results into a spread sheet, manually combine the results for each individual and then import into a third software package for post-genotyping analysis. GeneMarker is highly accurate, user-friendly genotyping software that allows all of these steps to be done in one software package, avoiding potential errors from data transfer to different programs and decreasing the amount of time needed to process the results. The Merge Project tool automatically combines the results from replicate samples processed with different primer sets. Replicate animal (diploid) DNA samples were amplified with three different multiplexes, each multiplex provided information on 4–6 loci. The kinship analysis using the merged results provided a 1017 increase in statistical power with a range of 108 when 5 loci were used versus 1025 when 15 loci were used to determine potential relationship levels with identity by descent calculations. These same sample sets were used in clustering analysis to diagram dendrograms. The dendrogram based on a single multiplex resulted in three branches at a given Euclidian distance. In comparison, the dendrogram that was constructed using the merged results had eight branches at the same Euclidian distance.
Depending on the macromolecule size and configuration, migration rates through capillary electrophoresis vary greatly. Internal size standards for capillary electrophoresis of the same macromolecule may not be readily available. The Macromolecule Tool in GeneMarker® aids with analysis of macromolecule fragments without an internal lane size standard. Methods included importing raw data files to the software and physically identifying reference peaks in the samples known to have the same size. The program uses this information to calibrate from one capillary to another. Characteristics of the aligned data (such as relative size, peak height, peak area, peak ratios) were exported in an excel sheet. Ninety six raw data files from 4 dye capillary electrophoresis were analyzed. Peak height, height ratio, area, area ratio, and relative sizes were determined for all samples. These values can be used to determine characteristics such as number and relative size of degradation products or other macromolecules, such as DNA binding carbohydrates commonly functioning in gene regulation.
RNA sequencing is a powerful tool for interrogating the entire transcriptome at once. It allows identification of novel isoforms including gene fusions and alternative splicing- and expression level analysis across several orders of magnitude. NextGENe's new RNA-seq application can be used to analyze data from any of the three main 2nd generation sequencing systems including Roche GS FLX™ and FLX Titanium, Illumina Genome Analyzers, and Applied Biosystems SOLiD™ Systems. Variant detection, expression level analysis, and isoform identification are all performed in one analysis. The tool employs a hybrid approach, combining the use of an exon junction reference sequence with the de novo detection of exons. This allows discovery of previously un-annotated genes in addition to highly accurate alignment to known transcripts. All detected transcripts are reported in addition to the information provided by NextGENe's variant and expression reports. Results are shown in the NextGENe Viewer which provides a high level of visualization for review and editing.