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Biomedical subjects

Li Zhang

Publications and source records attributed to Li Zhang.

At least 55 records · Page 3Linked to original sources

Adaptation for Staphylococcus aureus to hosts via insertion mutation in the accessory gene regulator agrC gene: decreased virulence and enhanced persistence capacity.

UNLABELLED: Staphylococcus aureus is an important human pathogen due to its vast array of virulence factors regulated by multiple regulatory mechanisms, including the accessory gene regulator. In this study, two S. aureus strains were simultaneously isolated from the blood of a febrile patient, belonging to the same clone, designated as 23H with a complete hemolytic phenotype, and 23B, exhibiting an incomplete hemolytic phenotype. The genomic comparison between strains 23B and 23H revealed that 23B had a single adenine base insertion at position 923 in the agrC gene, leading to a functional loss of the encoded AgrC. Experimental findings showed that strain 23B had decreased hemolytic activity, lower cytotoxicity against human alveolar epithelial A549 cells and in the Galleria mellonella model, and a reduced ability to survive intracellularly after infecting macrophages, in comparison to 23H. Conversely, 23B exhibited enhanced biofilm formation, greater adherence to A549 cells, and increased persistence in the face of vancomycin and daptomycin treatment. Transcriptomic analysis revealed that 23B upregulated surface protein-encoding genes while simultaneously reducing the expression levels of virulence factors, highlighting the intricate regulatory adjustments facilitating its persistence and reducing pathogenic potential. ATP assay results indicated that 23B maintained elevated ATP levels during the exponential phase yet exhibited reduced levels in the stationary phase when compared with 23H. Our findings suggested that the mutation in the agrC gene of S. aureus results in diminished virulence but markedly enhances persistence. This mutated strain warrants clinical attention because it may lead to treatment failures and persist in patients. IMPORTANCE: In clinical antimicrobial therapy, bacterial strains often develop resistance to antimicrobial agents. Additionally, mutations in their gene regulatory networks can increase their persistence, especially in immunocompromised patients. This study identified an insertion mutation in the accessory gene regulator, agrC gene, carried by a Staphylococcus aureus strain isolated from the blood of a febrile patient, leading to the functional loss of AgrC. Further research revealed that despite the reduced virulence of the mutated strain, it significantly bolstered the capacity to adapt and endure within the host during prolonged infections. This was evidenced by increased adhesion and biofilm formation capabilities, development of antimicrobial tolerance, and decreased ATP levels linked to persistence. Therefore, monitoring these mutations in S. aureus is crucial clinically, as they can complicate treatment strategies.

Staphylococcus aureus↗

Super Enhanced Purification of Denatured-Refolded Ubiquitinated Proteins by ThUBD Revealed Ubiquitinome Dysfunction in Liver Fibrosis.

Ubiquitination is crucial for maintaining protein homeostasis and plays a vital role in diverse biological processes. Ubiquitinome profiling and quantification are of great scientific significance. Artificial ubiquitin-binding domains (UBDs) have been widely employed to capture ubiquitinated proteins. The success of this enrichment relies on recognizing native spatial structures of ubiquitin and ubiquitin chains by UBDs under native conditions. However, the use of native lysis conditions presents significant challenges, including insufficient protein extraction, heightened activity of deubiquitinating enzymes and proteasomes in removing the ubiquitin signal, and purification of a substantial number of contaminant proteins, all of which undermine the robustness and reproducibility of ubiquitinomics. In this study, we introduced a novel approach that combines denatured-refolded ubiquitinated sample preparation (DRUSP) with a tandem hybrid UBD for ubiquitinomic analysis. The samples were effectively extracted using strongly denatured buffers and subsequently refolded using filters. DRUSP yielded a significantly stronger ubiquitin signal, nearly three times greater than that of the Control method. Then, eight types of ubiquitin chains were quickly and accurately restored; therefore, they were recognized and enriched by tandem hybrid UBD with high efficiency and no biases. Compared with the Control method, DRUSP showed extremely high efficiency in enriching ubiquitinated proteins, improving overall ubiquitin signal enrichment by approximately 10-fold. Moreover, when combined with ubiquitin chain-specific UBDs, DRUSP had also been proven to be a versatile approach. This new method significantly enhanced the stability and reproducibility of ubiquitinomics research. Finally, DRUSP was successfully applied to deep ubiquitinome profiling of early mouse liver fibrosis with increased accuracy, revealing novel insights for liver fibrosis research.

Animals↗

Microenvironmental genomic alterations and clinicopathological behavior in head and neck squamous cell carcinoma.

CONTEXT: Carcinogens associated with head and neck squamous cell carcinoma (SCC) genesis should inflict genomic alterations not only on the epithelium but also the mesenchyme of the aerodigestive tract. Therefore, the apparently nonmalignant stroma surrounding the tumor epithelium can acquire genomic alterations and contribute to cancer initiation and progression. OBJECTIVES: To determine compartment-specific loci of loss of heterozygosity or allelic imbalance (LOH/AI) and to identify which genomic alterations restricted to the stroma cell population contribute to aggressiveness of head and neck SCC disease. DESIGN, SETTING, AND PATIENTS: Tumor epithelium and surrounding stroma were isolated from 122 US patients with oral cavity and oropharyngeal or hypopharyngeal SCC and subjected to whole-genome LOH/AI analysis using 366 microsatellite markers. Samples, collected between 2001 and 2004, were pulled and transferred in batches of 10 to 30 between 2002 and 2005. Laser capture microdissection DNA extraction and technical genotyping occurred on a rolling model between 2002 and November 2005. MAIN OUTCOME MEASURES: Compartment-specific frequency and distribution of LOH/AI were determined, and hot spots of genomic alterations identified. Compartment-specific LOH/AI events were correlated with presenting clinicopathologic characteristics. RESULTS: Tumor-associated stroma of head and neck SCC from smokers were found to have a high degree of genomic alterations. A correlation between tumor aggressiveness could be found for a specific set of 5 loci. Three stroma-specific loci (D4S2417, D3S360, and D19555) were associated with tumor size (pT) and regional nodal metastases (pN). Furthermore, 2 epithelial-specific LOH/AI hot spots were positively correlated with pN status and clinical stage. CONCLUSIONS: Stroma-specific genetic alterations are associated with smoking-related head and neck SCC genesis. These findings suggest novel prognostic or diagnostic biomarkers and identify potential new molecular targets for therapeutic and preventive intervention.

Aged↗

Glutathione and glutathione-linked enzymes in normal human aortic smooth muscle cells: chemical inducibility and protection against reactive oxygen and nitrogen species-induced injury.

Substantial evidence suggests a crucial role for glutathione (GSH) and GSH-linked enzymes in protecting against oxidative vascular disorders. However, studies on the chemical inducibility of these antioxidant defenses and their protective effects on oxidant injury in normal human vascular cells are currently lacking. Accordingly, this study was undertaken to investigate the inducibility of GSH, glutathione reductase (GR), glutathione peroxidase (GPx), and glutathione S-transferase (GST) by the chemoprotective agent, 3H-1,2-dithiole-3-thione (D3T) in cultured normal human aortic smooth muscle cells (HASMCs). HASMCs expressed measurable levels/activities of GSH, GR, GPx, and GST. Incubation of HASMCs with low micromolar concentrations of D3T resulted in a marked elevation in total cellular GSH content and GR activity. The protein and mRNA expression of gamma-glutamylcysteine ligase (GCL) and GR were also upregulated by D3T. In addition, D3T caused significant increases in mitochondrial GSH content and GR activity. In contrast, neither cellular GPx nor GST activity was altered after D3T treatment. Pretreatment of HASMCs with D3T afforded remarkable protection against reactive oxygen and nitrogen species (ROS/RNS)-mediated cell injury. Depletion of cellular GSH by pretreatment with buthionine sulfoximine (BSO), an inhibitor of GSH biosynthesis led to marked potentiation of the ROS/RNS-induced cell injury. Moreover, co-treatment of HASMCs with BSO was found to completely abolish the D3T-mediated GSH elevation, and remarkably reverse D3T cytoprotection against the ROS/RNS-elicited injury. Taken together, this study demonstrates that both GSH/GCL and GR in normal HASMCs are inducible by D3T, and that upregulation of GSH biosynthesis appears to be the predominant mechanism underlying D3T-mediated cytoprotection against ROS/RNS-elicited injury to human vascular smooth muscle cells.

Antineoplastic Agents↗

Protective effects of exercise and phosphoinositide 3-kinase(p110alpha) signaling in dilated and hypertrophic cardiomyopathy.

Physical activity protects against cardiovascular disease, and physiological cardiac hypertrophy associated with regular exercise is usually beneficial, in marked contrast to pathological hypertrophy associated with disease. The p110alpha isoform of phosphoinositide 3-kinase (PI3K) plays a critical role in the induction of exercise-induced hypertrophy. Whether it or other genes activated in the athlete's heart might have an impact on cardiac function and survival in a setting of heart failure is unknown. To examine whether progressive exercise training and PI3K(p110alpha) activity affect survival and/or cardiac function in two models of heart disease, we subjected a transgenic mouse model of dilated cardiomyopathy (DCM) to swim training, genetically crossed cardiac-specific transgenic mice with increased or decreased PI3K(p110alpha) activity to the DCM model, and subjected PI3K(p110alpha) transgenics to acute pressure overload (ascending aortic constriction). Life-span, cardiac function, and molecular markers of pathological hypertrophy were examined. Exercise training and increased cardiac PI3K(p110alpha) activity prolonged survival in the DCM model by 15-20%. In contrast, reduced PI3K(p110alpha) activity drastically shortened lifespan by approximately 50%. Increased PI3K(p110alpha) activity had a favorable effect on cardiac function and fibrosis in the pressure-overload model and attenuated pathological growth. PI3K(p110alpha) signaling negatively regulated G protein-coupled receptor stimulated extracellular responsive kinase and Akt (via PI3K, p110gamma) activation in isolated cardiomyocytes. These findings suggest that exercise and enhanced PI3K(p110alpha) activity delay or prevent progression of heart disease, and that supraphysiologic activity can be beneficial. Identification of genes important for hypertrophy in the athlete's heart could offer new strategies for treating heart failure.

Animals↗

Bi-ventricular circulatory support with the Abiomed AB5000 system in a patient with idiopathic refractory ventricular fibrillation.

A 45-year-old man had life-threatening recurrent idiopathic ventricular fibrillation and persistent cardiogenic shock develop. The episodes of ventricular fibrillation were refractory to aggressive medical management; therefore an Abiomed AB5000 bi-ventricular support system was implanted for arrhythmia control. The device was able to maintain hemodynamic stability during the following 2 weeks. The patient was discharged from the hospital with fully recovered cardiac function.

Heart-Assist Devices↗

Nanorobotic spot welding: controlled metal deposition with attogram precision from copper-filled carbon nanotubes.

With the continuing development of bottom-up nanotechnology fabrication processes, spot welding can play a role similar to its macro counterpart for the interconnection of nano building blocks for the assembly of nanoelectronics and nanoelectromechanical systems (NEMS). Spot welding using single-crystalline copper-filled carbon nanotubes (CNTs) is investigated experimentally using nanorobotic manipulation inside a transmission electron microscope (TEM). Controlled melting and flowing of copper inside nanotube shells are realized by applying bias voltages between 1.5 and 2.5 V. The average mass flow rate of the copper was found to be 120 ag/s according to TEM video imaging (measured visually at approximately 11.6 nm/s through the CNT). Successful soldering of a copper-filled CNT onto another CNT shows promise for nano spot welding and thermal dip-pen lithography.

Copper↗

Lysosomal membranes from beige mice contain higher than normal levels of endoplasmic reticulum proteins.

Chediak-Higashi syndrome is characterized by dysfunctional giant organelles of common origin, that is, lysosomes, melanosomes, and platelet dense bodies. Its defective gene LYST encodes a large molecular weight protein whose function is unknown. The Beige mouse also defective in Lyst is a good model of the human disease. Purified lysosomes from Beige and normal black mouse livers were used to carry out a proteomics study. Two-dimensional gel electrophoretic separation of soluble lysosomal proteins of Beige and normal mice revealed no major differences. The cleavable isotope-coded affinity tag (cICAT) technique was used to compare the composition of Beige and normal lysosomal membrane proteins. While the levels of common proteins, that is, Lamp1, Lamp2, and Niemann-Pick type C1, were decreased in Beige mice, there was an increase in the levels of endoplasmic reticulum (ER) resident proteins, for example, cytochrome P450, NADPH-cytochrome P450 oxidoreductase, and flavin-containing monooxygenase. Confocal microscopy confirmed that another ER protein, calnexin, colocalizes with Lamp1 on membranes of giant lysosomes from fibroblasts of Chediak-Higashi syndrome patient. Our results suggest that LYST may play a role in either preventing inappropriate incorporation of proteins into the lysosomal membrane or in membrane recycling/maturation.

Animals↗

Estimating optimal parameters for MRF stereo from a single image pair.

This paper presents a novel approach for estimating the parameters for MRF-based stereo algorithms. This approach is based on a new formulation of stereo as a maximum a posterior (MAP) problem in which both a disparity map and MRF parameters are estimated from the stereo pair itself. We present an iterative algorithm for the MAP estimation that alternates between estimating the parameters while fixing the disparity map and estimating the disparity map while fixing the parameters. The estimated parameters include robust truncation thresholds for both data and neighborhood terms, as well as a regularization weight. The regularization weight can be either a constant for the whole image or spatially-varying, depending on local intensity gradients. In the latter case, the weights for intensity gradients are also estimated. Our approach works as a wrapper for existing stereo algorithms based on graph cuts or belief propagation, automatically tuning their parameters to improve performance without requiring the stereo code to be modified. Experiments demonstrate that our approach moves a baseline belief propagation stereo algorithm up six slots in the Middlebury rankings.

Algorithms↗

[Internal target volume definition using four-dimensional CT and dosimetric evaluation for hepatocellular carcinoma].

BACKGROUND & OBJECTIVE: Accurate definition of target volume is difficult in three-dimensional conformal radiotherapy (3D CRT) for liver tumors because of the wide moving extent of tumors with respiration. This study was to define individualized internal target volume (ITV) using four-dimensional computed tomography (4D-CT), and compare planning target volumes (PTVs) and dose distribution of 3D planning with 4D planning for hepatocellular carcinoma (HCC). METHODS: Seven primary HCC patients received 4D-CT scanning. Gross tumor volumes (GTVs) and clinical target volumes (CTVs) were contoured on all 10 respiratory phases of CT images. The 3D and 4D treatment plans were made for each patient using different PTVs, namely, PTV-3D derived from a single CTV plus conventional margins; PTV-4D derived from ITV-4D which encompassing all 10 CTVs plus setup margins (SM). The two plans were designed at the 20% respiratory phase CT images using 3D treatment planning system and compared with respect to PTVs, dose distribution to normal tissues, normal tissue complication probability. The prescription dose and design of irradiating fields were identical for both plans. RESULTS: The average PTV was (417.6+/-197.7) cm(3) in 3D plan and (331.9+/-183.1) cm(3) in 4D plan, decreased by 20.50% (12.60%-34.40%). PTV coverage and dose uniformity were similar in the 2 plans. 4D plans spared more normal liver, kidney, stomach, and small intestine than 3D plans, especially for the liver. The V30 and V40 of the liver were lower in 4D plans than in 3D plans (33.59% vs. 38.77%, 22.62% vs. 27.32%); the mean dose to normal liver was decreased from 24.13 Gy to 21.5 Gy; liver complication probability was decreased from 21.57% to 15.86%. Without increasing the normal tissue complication probability, the prescription dose was higher in 4D plans than in 3D plans [(54.86+/-2.79) Gy vs. (50.57+/-1.51) Gy], increased by 9.72% (4%-16%). CONCLUSIONS: The 3D plans have pitfalls of geometric miss or over coverage of target volume. The 4D plans can accurately definite target volume to spare more normal tissues and make dose escalation as compared with 3D CRT.

Adult↗

Angiogenesis and improved cerebral blood flow in the ischemic boundary area detected by MRI after administration of sildenafil to rats with embolic stroke.

To dynamically investigate the long-term response of an ischemic lesion in rat brain to the administration of sildenafil, male Wistar rats subjected to embolic stroke were treated with sildenafil (n=11) or saline (n=10) at a dose of 10 mg/kg administered subcutaneously 24-h after stroke and daily for an additional 6 days. Magnetic resonance images were acquired and functional performance was measured in all animals at 1 day, 2 days and weekly for 6 weeks post-stroke. All rats were sacrificed 6 weeks after stroke and endothelial barrier antigen immunostaining was employed for morphological analysis and quantification of cerebral vessels. Map-ISODATA was computed from T(1), T(2) and T(1sat) maps. ISODATA derived tissue signatures characterize the degree of ischemic injury. Based on the map-ISODATA calculated at 6 weeks, the ischemic lesion for each animal was divided into two specific regions, the ischemic boundary and ischemic core. The temporal profiles of cerebral blood flow (CBF) and tissue signature were retrospectively tracked in these two regions and were compared with histological evaluation and functional outcome. After 1 week of sildenafil treatment, the ischemic lesion exhibited two significantly different regions, with higher CBF level and correspondingly, lower tissue signature value in the boundary region than in the core region. Sildenafil treatment did not significantly reduce the lesion size, but did enhance angiogenesis. Functional performance was significantly increased after sildenafil treatment compared with the control group. Administration of sildenafil to rats with embolic stroke enhances angiogenesis and selectively increases the CBF level in the ischemic boundary, and improves neurological functional recovery compared to saline-treated rats.

Animals↗

Computer-based QSARs for predicting mixture toxicity of benzene and its derivatives.

During the past decades, the Quantitative structure-activity relationships (QSARs) have been proven to be reliable tools when little or no empirical data are available in medicinal chemistry, biochemistry, toxicology, and environmental sciences. However, only few studies that quantitatively predict mixtures toxicity have been reported. In this study, the QASR models for the binary mixtures toxicity of 12 benzene and its derivatives, including eight non-polar-narcotic compounds and four polar narcotic compounds were developed, without reference to exact toxicity mechanisms of single compounds. All parameters for the QSAR studies were defined on the basis of quantum mechanical calculations and these parameters were selected by the stepwise procedure. The results of this study provided a simple means of predicting the binary mixtures toxicity from the chemical structure.

Benzene↗

Many quality measurements, but few quality measures assessing the quality of breast cancer care in women: a systematic review.

BACKGROUND: Breast cancer in women is increasingly frequent, and care is complex, onerous and expensive, all of which lend urgency to improvements in care. Quality measurement is essential to monitor effectiveness and to guide improvements in healthcare. METHODS: Ten databases, including Medline, were searched electronically to identify measures assessing the quality of breast cancer care in women (diagnosis, treatment, followup, documentation of care). Eligible studies measured adherence to standards of breast cancer care in women diagnosed with, or in treatment for, any histological type of adenocarcinoma of the breast. Reference lists of studies, review articles, web sites, and files of experts were searched manually. Evidence appraisal entailed dual independent assessments of data (e.g., indicators used in quality measurement). The extent of each quality indicator's scientific validation as a measure was assessed. The American Society of Clinical Oncology (ASCO) was asked to contribute quality measures under development. RESULTS: Sixty relevant reports identified 58 studies with 143 indicators assessing adherence to quality breast cancer care. A paucity of validated indicators (n = 12), most of which assessed quality of life, only permitted a qualitative data synthesis. Most quality indicators evaluated processes of care. CONCLUSION: While some studies revealed patterns of under-use of care, all adherence data require confirmation using validated quality measures. ASCO's current development of a set of quality measures relating to breast cancer care may hold the key to conducting definitive studies.

Breast Neoplasms↗

Free energy of DNA duplex formation on short oligonucleotide microarrays.

DNA/DNA duplex formation is the basic mechanism that is used in genome tiling arrays and SNP arrays manufactured by Affymetrix. However, detailed knowledge of the physical process is still lacking. In this study, we show a free energy analysis of DNA/DNA duplex formation these arrays based on the positional-dependent nearest-neighbor (PDNN) model, which was developed previously for describing DNA/RNA duplex formation on expression microarrays. Our results showed that the two ends of a probe contribute less to the stability of the duplexes and that there is a microarray surface effect on binding affinities. We also showed that free energy cost of a single mismatch depends on the bases adjacent to the mismatch site and obtained a comprehensive table of the cost of a single mismatch under all possible combination of adjacent bases. The mismatch costs were found to be correlated with those determined in aqueous solution. We further demonstrate that the DNA copy number estimated from the SNP array correlates negatively with the target length; this is presumably caused by inefficient PCR amplification for long fragments. These results provide important insights into the molecular mechanisms of microarray technology and have implications for microarray design and the interpretation of observed data.

Base Pair Mismatch↗

Homologous peptide of connective tissue growth factor ameliorates epithelial to mesenchymal transition of tubular epithelial cells.

The hallmark of failing renal transplants is tubular atrophy and interstitial fibrosis. The cytokine connective tissue growth factor (CTGF or CCN2) plays an important role in epithelial-mesenchymal transition (EMT) of tubular epithelial cells (TECs). A unique domain within CTGF (IRTPKISKPIKFELSG) which binds to its potential receptor integrin alpha v beta3 has been identified. This study was carried out to further characterize a synthetic hexadeca-peptide (P2) homologous to this domain and to determine its effect on CTGF-mediated solid phase cell adhesion, EMT induction and fibrogenesis in rat renal NRK-52E cells. Results showed that both P2 and recombinant CTGF bound to NRK-52E cells. Unlike CTGF, P2 had little effect on EMT induction including cytoskeleton remodeling and expression of alpha-smooth muscle actin (alpha-SMA) and E-cadherin, nor did it have effect on fibrogenic induction including alternation of extracellular matrix (ECM) proteins, collagen type I and IV at gene and protein levels. All data showed that P2 bound preferably on the surface of NRK-52E cells and inhibited the effect of CTGF on EMT induction and cell fibrogenesis, probably by occupying the binding sites of CTGF within its potential receptors. Therefore, P2 may be used as a potential anti-fibrotic agent.

Actins↗

Antipsychotic clozapine inhibits the function of alpha7-nicotinic acetylcholine receptors.

The effects of the antipsychotic clozapine on the function of the cloned alpha(7) subunit of the nicotinic acetylcholine (nACh) receptor expressed in Xenopus oocytes was investigated by using the two-electrode voltage-clamp technique. Clozapine reversibly inhibited nicotine (10 microM)-induced currents in a concentration-dependent manner (300 nM to 90 microM), with an IC(50) value of 3.2+/-0.4 microM. The effect of clozapine was not dependent on the membrane potential. Clozapine did not affect the activity of endogenous Ca(2+)-dependent Cl(-) channels since the inhibition by clozapine was unaltered by the intracellularly injected Ca(2+) chelator BAPTA and perfusion with Ca(2+)-free bathing solution containing 2mM Ba(2+). Clozapine decreased the maximal nicotine-induced responses without significantly affecting its potency, indicating that it acts as a noncompetitive antagonist on alpha(7)-nACh receptors. In hippocampal slices, the whole-cell recordings from CA1 pyramidal neurons indicated that the increases in the frequency and amplitudes of the GABA-mediated spontaneous inhibitory postsynaptic currents induced by bath application of 2 mM choline, a specific agonist for alpha(7)-nACh receptors, were abolished after 10 min application of 5 microM clozapine. In conclusion, these results demonstrate that clozapine inhibits the function of alpha(7)-nACh receptors expressed in Xenopus oocytes and in hippocampal neurons.

Animals↗

Neural basis of cultural influence on self-representation.

Culture affects the psychological structure of self and results in two distinct types of self-representation (Western independent self and East Asian interdependent self). However, the neural basis of culture-self interaction remains unknown. We used fMRI to measured brain activity from Western and Chinese subjects who judged personal trait adjectives regarding self, mother or a public person. We found that the medial prefrontal cortex (MPFC) and anterior cingulate cortex (ACC) showed stronger activation in self- than other-judgment conditions for both Chinese and Western subjects. However, relative to other-judgments, mother-judgments activated MPFC in Chinese but not in Western subjects. Our findings suggest that Chinese individuals use MPFC to represent both the self and the mother whereas Westerners use MPFC to represent exclusively the self, providing neuroimaging evidence that culture shapes the functional anatomy of self-representation.

Adult↗

X-APL: an improved family-based test of association in the presence of linkage for the X chromosome.

Family-based association methods have been developed primarily for autosomal markers. The X-linked sibling transmission/disequilibrium test (XS-TDT) and the reconstruction-combined TDT for X-chromosome markers (XRC-TDT) are the first association-based methods for testing markers on the X chromosome in family data sets. These are valid tests of association in family triads or discordant sib pairs but are not theoretically valid in multiplex families when linkage is present. Recently, XPDT and XMCPDT, modified versions of the pedigree disequilibrium test (PDT), were proposed. Like the PDT, XPDT compares genotype transmissions from parents to affected offspring or genotypes of discordant siblings; however, the XPDT can have low power if there are many missing parental genotypes. XMCPDT uses a Monte Carlo sampling approach to infer missing parental genotypes on the basis of true or estimated population allele frequencies. Although the XMCPDT was shown to be more powerful than the XPDT, variability in the statistic due to the use of an estimate of allele frequency is not properly accounted for. Here, we present a novel family-based test of association, X-APL, a modification of the test for association in the presence of linkage (APL) test. Like the APL, X-APL can use singleton or multiplex families and properly infers missing parental genotypes in linkage regions by considering identity-by-descent parameters for affected siblings. Sampling variability of parameter estimates is accounted for through a bootstrap procedure. X-APL can test individual marker loci or X-chromosome haplotypes. To allow for different penetrances in males and females, separate sex-specific tests are provided. Using simulated data, we demonstrated validity and showed that the X-APL is more powerful than alternative tests. To show its utility and to discuss interpretation in real-data analysis, we also applied the X-APL to candidate-gene data in a sample of families with Parkinson disease.

Chromosomes, Human, X↗