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Loss of heterozygosity detected at three short tandem repeat locus commonly used for human DNA identification in a case of paternity testing

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LEGAL MEDICINE 2017年 24卷 7-11页

作者： Zhou, Shiyuan Wang, Haili Wang, Qing K. Wang, Pengyun Wang, Fengyu Xu, Chengqi Henan Prov Res Inst Populat & Family Planning Zhengzhou 450002 Peoples R China Natl Hlth & Family Planning Commiss Key Lab Birthdefects Prevent Zhengzhou 450002 Peoples R China Huazhong Univ Sci & Technol Coll Life Sci & Technol Wuhan 430074 Peoples R China Huazhong Univ Sci & Technol Ctr Human Genome Res Key Lab Mol Biophys Minist Educ Wuhan 430074 Peoples R China Huazhong Univ Sci & Technol Liyuan Hosp Dept Clin Lab Wuhan 430074 Peoples R China

Short tandem repeat (STR) is widely used for DNA profiling in forensic sciences for its stable inheritance. Genomic variations in STR loci may affect the results of the genotyping. In this study, using STR profiling and genome-wide chromosomal microarray assay, we detected the incidence of uniparental disomy or copy -neutral loss of heterozygosity (LOH) in a case of a parental testing, which altered the genotype of three commonly used STR markers including D2S1338, D2S441 and D2S1776. To the best of our knowledge, this is the first time found that LOH affect the genotyping of STR markers commonly used for paternity testing. Our findings demonstrated that the incidence of LOH in the genome may dramatically alter the results of DNA identification, and suggested that genomic structure variation need to be taking into consideration in the DNA identification using STR markers. (C) 2016 Elsevier Ireland Ltd. All rights reserved.

关键词： DNA PATERNITY microarray technology

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Mutation Spectrum of the ABCA4 Gene in a Greek Cohort with Stargardt Disease: Identification of Novel Mutations and Evidence of Three Prevalent Mutated Alleles

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JOURNAL OF OPHTHALMOLOGY 2018年第1期2018卷 10-10页

作者： Smaragda, Kamakari Vassiliki, Kokkinou George, Koutsodontis Polixeni, Stamatiou Christoforos, Giatzakis Anastasios, Anastasakis Minas, Aslanides Ioannis Stavrenia, Koukoula Theoni, Panagiotoglou Ioannis, Datseris Miltiadis, Tsilimbaris K. OMMA Ophthalmol Inst Athens Ophthalm Genet Unit Athens Greece Cretan Ctr Res & Dev Applicat Genet & Mol Biol DNAbiolab Iraklion Crete Greece Athens Eye Hosp Dept Clin Electrophysiol Vis Athens Greece Emmetropia Mediterranean Eye Inst Dept Ophthalmol Iraklion Crete Greece Ophthalm Inst Ophthalmol & Microsurg Thessaloniki Greece Univ Crete Sch Med Dept Ophthalmol Iraklion Greece OMMA Ophthalmol Inst Athens Dept Retinal Disorders Athens Greece

Aim. To evaluate the frequency and pattern of disease-associated mutations of ABCA4 gene among Greek patients with presumed Stargardt disease (STGD1). Materials and Methods. A total of 59 patients were analyzed for ABCA4 mutations using the ABCR400 microarray and PCR-based sequencing of all coding exons and flanking intronic regions. MLPA analysis as well as sequencing of two regions in introns 30 and 36 reported earlier to harbor deep intronic disease-associated variants was used in 4 selected cases. Results. An overall detection rate of at least one mutant allele was achieved in 52 of the 59 patients (88.1%). Direct sequencing improved significantly the complete characterization rate, that is, identification of two mutations compared to the microarray analysis (93.1% versus 50%). In total, 40 distinct potentially disease-causing variants of the ABCA4 gene were detected, including six previously unreported potentially pathogenic variants. Among the disease-causing variants, in this cohort, the most frequent was c.5714+5G>A representing 16.1%, while ***1961Glu and ***541Pro represented 15.2% and 8.5%, respectively. Conclusions. By using a combination of methods, we completely molecularly diagnosed 48 of the 59 patients studied. In addition, we identified six previously unreported, potentially pathogenic ABCA4 mutations.

关键词： GENETICS of retinal degeneration ALLELES GENETIC polymorphisms GLYCOPROTEINS MUTATION (Biology) POLYMERASE chain reaction microarray technology SEQUENCE analysis

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Imputing gene expression to maximize platform compatibility

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BIOINFORMATICS 2017年第4期33卷 522-528页

作者： Zhou, Weizhuang Han, Lichy Altman, Russ B. Stanford Univ Dept Bioengn Stanford CA 94305 USA Stanford Univ Biomed Informat Training Program Stanford CA 94305 USA Stanford Univ Dept Genet Stanford CA 94305 USA

microarray measurements of gene expression constitute a large fraction of publicly shared biological data, and are available in the Gene Expression Omnibus (GEO). Many studies use GEO data to shape hypotheses and improve statistical power. Within GEO, the Affymetrix HG-U133A and HG-U133 Plus 2.0 are the two most commonly used microarray platforms for human samples;the HG-U133 Plus 2.0 platform contains 54 220 probes and the HG-U133A array contains a proper subset (21 722 probes). When different platforms are involved, the subset of common genes is most easily compared. This approach results in the exclusion of substantial measured data and can limit downstream analysis. To predict the expression values for the genes unique to the HG-U133 Plus 2.0 platform, we constructed a series of gene expression inference models based on genes common to both platforms. Our model predicts gene expression values that are within the variability observed in controlled replicate studies and are highly correlated with measured data. Using six previously published studies, we also demonstrate the improved performance of the enlarged feature space generated by our model in downstream analysis.

关键词： GENE expression BIOLOGICAL databases microarray technology GENES INFERENTIAL statistics

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Gene Expression and Pharmacodynamic Changes in 1,760 Systemic Lupus Erythematosus Patients From Two Phase III Trials of BAFF Blockade With Tabalumab

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ARTHRITIS & RHEUMATOLOGY 2017年第3期69卷 643-654页

作者： Hoffman, Robert W. Merrill, Joan T. Alarcon-Riquelme, Marta M. E. Petri, Michelle Dow, Ernst R. Nantz, Eric Nisenbaum, Laura K. Schroeder, Krista M. Komocsar, Wendy J. Perumal, Narayanan B. Linnik, Matthew D. Airey, David C. Liu, Yushi Rocha, Guilherme V. Higgs, Richard E. Eli Lilly & Co Indianapolis IN 46285 USA Oklahoma Med Res Fdn 825 NE 13th St Oklahoma City OK 73104 USA Pfizer Univ Granada Junta Andalucia Granada Spain Johns Hopkins Sch Med Baltimore MD USA

Objective. To characterize baseline gene expression and pharmacodynamically induced changes in whole blood gene expression in 1,760 systemic lupus erythematosus (SLE) patients from 2 phase III, 52-week, randomized, placebo-controlled, double-blind studies in which patients were treated with the BAFF-blocking IgG4 monoclonal antibody tabalumab. Methods. Patient samples were obtained from SLE patients from the ILLUMINATE-1 and ILLUMINATE-2 studies, and control samples were obtained from healthy donors. Blood was collected in Tempus tubes at baseline, week 16, and week 52. RNA was analyzed using Affymetrix Human Transcriptome Array 2.0 and NanoString. Results. At baseline, expression of the interferon (IFN) response gene was elevated in patients compared with controls, with 75% of patients being positive for this IFN response gene signature. There was, however, substantial heterogeneity of IFN response gene expression and complex relationships among gene networks. The IFN response gene signature was a predictor of time to disease flare, independent of anti-double-stranded DNA (anti-dsDNA) antibody and C3 and C4 levels, and overall disease activity. Pharmacodynamically induced changes in gene expression following tabalumab treatment were extensive, occurring predominantly in B cell-related and immunoglobulin genes, and were consistent with other pharmacodynamic changes including anti-dsDNA antibody, C3, and immunoglobulin levels. Conclusion. SLE patients demonstrated increased expression of an IFN response gene signature (75% of patients had an elevated IFN response gene signature) at baseline in ILLUMINATE-1 and ILLUMINATE-2. Substantial heterogeneity of gene expression was detected among individual patients and in gene networks. The IFN response gene signature was an independent risk factor for future disease flares. Pharmacodynamic changes in gene expression were consistent with the mechanism of BAFF blockade by tabalumab.

关键词： CHI-squared test FISHER exact test FLOW cytometry GENE expression MONOCLONAL antibodies FINANCING of research SYSTEMIC lupus erythematosus RANDOMIZED controlled trials BLIND experiment DATA analysis software microarray technology DESCRIPTIVE statistics

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Adjuvant Therapy Using Mistletoe Containing Drugs Boosts the T-Cell-Mediated Killing of Glioma Cells and Prolongs the Survival of Glioma Bearing Mice

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EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2018年第1期2018卷 p1-12页

作者： Schoetterl, Sonja Huber, Stephan M. Lentzen, Hans Mittelbronn, Michel Naumann, Ulrike Univ Tubingen Hertie Inst Clin Brain Res Mol Neurooncol Otfried Muller Str 27 D-72076 Tubingen Germany Univ Tubingen Ctr Neurol Otfried Muller Str 27 D-72076 Tubingen Germany Univ Tubingen Dept Radiat Oncol Hoppe Seyler Str 3 D-72076 Tubingen Germany MELEMA Pharma GmbH Hamburg Germany Luxembourg Ctr Neuropathol LCNP 1 Rue Louis Rech L-3555 Dudelange Luxembourg LIH NORLUX Neurooncol Lab 84 Rue Val Fleuri L-1526 Luxembourg Luxembourg Goethe Univ Frankfurt Neurol Inst Edinger Inst Heinrich Hoffmann Str 7 D-60528 Frankfurt Germany Dudelange LNS Lab Natl Sante 1 Rue Louis Rech L-3555 Dudelange Luxembourg Univ Luxembourg LCSB 7 Ave Hauts Fourneaux L-4362 Esch Sur Alzette Luxembourg

Viscum album L. extracts (VE) are applied as complementary cancer therapeutics for more than one century. Extracts contain several compounds like mistletoe lectins (ML) 1-3 and viscotoxins, but also several minor ingredients. Since ML-1 has been described as one of the main active components harboring antitumor activity, purified native or recombinant ML-1 has been also used in clinical trials in the last years. The present study examined and compared the immunoboosting effects of three ML-1 containing drugs (the extract ISCADOR Qu, the recombinant ML-1 Aviscumine, and purified native ML-1) in the context of the T-cell mediated killing of glioma cells. Additionally we examined the possible underlying T-cell stimulating mechanisms. Using cocultures of immune and glioma cells, a PCR-based microarray, quantitative RT-PCR, and an antibody-based array to measure cytokines in blood serum, immunosupporting effects were determined. A highly aggressive, orthotopic, immunocompetent syngeneic mouse glioma model was used to determine the survival of mice treated with ISCADOR Qu alone or in combination with tumor irradiation and temozolomide (TMZ). Treatment of glioblastoma (GBM) cells with ISCADOR Qu that contains a high ML concentration, but also viscotoxins and other compounds, as well as with Aviscumine or native ML-1, enhanced the expansion of cancer cell-specific T-cells as well as T-cell-mediated tumor cell lysis, but to a different degree. In GBM cells all three ML-1-containing preparations modulated the expression of immune response associated genes. In vivo, subcutaneous ISCADOR Qu injections at increasing concentration induced cytokine release in immunocompetent VM/Dkmice. Finally, ISCADOR Qu, if applied in combination with tumor irradiation and TMZ, further prolonged the survival of glioma mice. Our findings indicate that ML-1 containing drugs enhance anti-GBM immune responses and work in synergy with radiochemotherapy. Therefore, adjuvant mistletoe therapy should be

关键词： GLIOMAS GLIOMA treatment TEMOZOLOMIDE ANIMAL experimentation CELL lines COMBINED modality therapy CYTOKINES GENE expression IMMUNE response IMMUNOCOMPETENT cells MICE NEUROGLIA POLYMERASE chain reaction RADIOTHERAPY SURVIVAL T cells VISCUM microarray technology IN vivo studies CHEMORADIOTHERAPY PROGNOSIS THERAPEUTICS

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Improving cross-study prediction through addon batch effect adjustment or addon normalization

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BIOINFORMATICS 2017年第3期33卷 397-404页

作者： Hornung, Roman Causeur, David Bernau, Christoph Boulesteix, Anne-Laure Univ Munich Dept Med Informat Biometry & Epidemiol D-81377 Munich Germany Agrocampus Ouest Dept Appl Math F-35042 Rennes France Leibniz Supercomp Ctr D-85748 Garching Germany

Motivation: To date most medical tests derived by applying classification methods to highdimensional molecular data are hardly used in clinical practice. This is partly because the prediction error resulting when applying them to external data is usually much higher than internal error as evaluated through within-study validation procedures. We suggest the use of addon normalization and addon batch effect removal techniques in this context to reduce systematic differences between external data and the original dataset with the aim to improve prediction performance. Results: We evaluate the impact of addon normalization and seven batch effect removal methods on cross-study prediction performance for several common classifiers using a large collection of microarray gene expression datasets, showing that some of these techniques reduce prediction error.

关键词： HIGH-dimensional model representation OUTCOME assessment (Medical care) GENE expression microarray technology COMPUTATIONAL biology BIOINFORMATICS

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Genome-Wide Association Meta-Analysis Reveals Novel Juvenile Idiopathic Arthritis Susceptibility Loci

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ARTHRITIS & RHEUMATOLOGY 2017年第11期69卷 2222-2232页

作者： McIntosh, Laura A. Marion, Miranda C. Sudman, Marc Comeau, Mary E. Becker, Mara L. Bohnsack, John F. Fingerlin, Tasha E. Griffin, Thomas A. Haas, J. Peter Lovell, Daniel J. Maier, Lisa A. Nigrovic, Peter A. Prahalad, Sampath Punaro, Marilynn Rose, Carlos D. Wallace, Carol A. Wise, Carol A. Moncrieffe, Halima Howard, Timothy D. Langefeld, Carl D. Thompson, Susan D. Cincinnati Childrens Hosp Med Ctr Cincinnati OH 45229 USA Univ Cincinnati Cincinnati OH 45221 USA Wake Forest Univ Sch Med Winston Salem NC 27109 USA Childrens Mercy Kansas City Kansas City MO USA Univ Utah Salt Lake City UT USA Natl Jewish Hlth Denver CO USA Univ Colorado Denver CO 80202 USA Levine Childrens Specialty Ctr Charlotte NC USA German Ctr Pediat & Adolescent Rheumatol Garmisch Partenkirchen Germany Boston Childrens Hosp Boston MA USA Brigham & Womens Hosp 75 Francis St Boston MA 02115 USA Harvard Med Sch Boston MA USA Emory Univ Sch Med Atlanta GA USA Texas Scottish Rite Hosp Children Dallas TX 75219 USA UT Southwestern Med Ctr Dallas TX USA DuPont Childrens Hosp Wilmington DE USA Seattle Childrens Hosp & Res Inst Seattle WA USA Texas Scottish Rite Hosp Children McDermott Ctr Human Growth & Dev Dallas TX 75219 USA

Objective. Juvenile idiopathic arthritis (JIA) is the most common childhood rheumatic disease and has a strong genomic component. To date, JIA genetic association studies have had limited sample sizes, used heterogeneous patient populations, or included only candidate regions. The aim of this study was to identify new associations between JIA patients with oligoarticular disease and those with IgM rheumatoid factor (RF)-negative polyarticular disease, which are clinically similar and the most prevalent JIA disease subtypes. Methods. Three cohorts comprising 2,751 patients with oligoarticular or RF-negative polyarticular JIA were genotyped using the Affymetrix Genome-Wide SNP Array 6.0 or the Illumina HumanCoreExome-12+ Array. Overall, 15,886 local and out-of-study controls, typed on these platforms or the Illumina HumanOmni2.5, were used for association analyses. High-quality single-nucleotide polymorphisms (SNPs) were used for imputation to 1000 Genomes prior to SNP association analysis. Results. Meta-analysis showed evidence of association (P < 1 x 10(-6)) at 9 regions: PRR9_LOR (P = 5.12 x 10(-8)), ILDR1_CD86 (P = 6.73 x 10(-8)), WDFY4 (P = 1.79 x 10(-7)), PTH1R (P = 1.87 x 10(-7)), RNF215 (P = 3.09 x 10(-7)), AHI1_LINC00271 (P = 3.48 x 10(-7)), JAK1 (P = 4.18 x 10(-7)), LINC00951 (P = 5.80 x 10(-7)), and HBP1 (P = 7.29 x 10(-7)). Of these, PRR9_LOR, ILDR1_CD86, RNF215, LINC00951, and HBP1 were shown, for the first time, to be autoimmune disease susceptibility loci. Furthermore, associated SNPs included cis expression quantitative trait loci for WDFY4, CCDC12, MTP18, SF3A1, AHI1, COG5, HBP1, and GPR22. Conclusion. This study provides evidence of both unique JIA risk loci and risk loci overlapping between JIA and other autoimmune diseases. These newly associated SNPs are shown to influence gene expression, and their bounding regions tie into molecular pathways of immunologic relevance. Thus, they likely represent regions that contribute to the pathology of oligoar

关键词： AUTOIMMUNE diseases RHEUMATOID arthritis in children DISEASE susceptibility GENE expression GENETIC polymorphisms HUMAN genome LONGITUDINAL method META-analysis PROBABILITY theory EVIDENCE-based medicine microarray technology GENOTYPE RISK factors GENETIC aspects

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Meta-analytic principal component analysis in integrative omics application

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BIOINFORMATICS 2018年第8期34卷 1321-1328页

作者： Kim, SungHwan Kang, Dongwan Huo, Zhiguang Park, Yongseok Tseng, George C. Keimyung Univ Dept Stat Daegu 42601 South Korea Lawrence Berkeley Natl Lab Genom Div Berkeley CA 94720 USA Univ Pittsburgh Dept Biostat Pittsburgh PA 15261 USA Univ Pittsburgh Dept Computat & Syst Biol Pittsburgh PA 15213 USA

Motivation: With the prevalent usage of microarray and massively parallel sequencing, numerous high-throughput omics datasets have become available in the public domain. Integrating abundant information among omics datasets is critical to elucidate biological mechanisms. Due to the highdimensional nature of the data, methods such as principal component analysis (PCA) have been widely applied, aiming at effective dimension reduction and exploratory visualization. Results: In this article, we combine multiple omics datasets of identical or similar biological hypothesis and introduce two variations of meta-analytic framework of PCA, namely MetaPCA. Regularization is further incorporated to facilitate sparse feature selection in MetaPCA. We apply MetaPCA and sparse MetaPCA to simulations, three transcriptomic meta-analysis studies in yeast cell cycle, prostate cancer, mouse metabolism and a TCGA pan-cancer methylation study. The result shows improved accuracy, robustness and exploratory visualization of the proposed framework.

关键词： microarray technology MULTIPLE correspondence analysis (Statistics) INFORMATION visualization META-analysis DATA integration (Computer science)

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StrandScript: evaluation of Illumina genotyping array design and strand correction

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BIOINFORMATICS 2017年第15期33卷 2399-2401页

作者： Wang, Jing Samuels, David C. Shyr, Yu Guo, Yan Vanderbilt Univ Med Ctr Dept Biomed Informat Nashville TN 37232 USA Vanderbilt Univ Dept Mol Physiol & Biophys Nashville TN 37232 USA Vanderbilt Univ Med Ctr Dept Biostat Nashville TN 37232 USA

After the introduction of high-throughput sequencing, genotyping arrays continue to be a viable source for conducting large-scale genetic studies. Currently, Illumina is one of the largest genotyping array manufacturers. One technical issue that has always plagued the post-processing of Illumina genotyping array data is the strand definition. Against convention, Illumina uses their own definition of strand, which is inconsistent with the standard reference forward and reverse definition. This issue has been a major obstacle in the consistency of reporting, meta-analysis and correct interpretation of phenotype association results. To date, the strand issue has not been adequately addressed, prompting us to develop StrandScript, a tool that can convert all genotyping data generated from Illumina genotyping arrays to the reference forward strand. StrandScript works independently of the Illumina array version and is future proof for newer Illumina array designs. Furthermore, StrandScript can examine an Illumina genotyping array manifest file and can detect all problematic SNPs, including SNPs with wrong RS ID and SNPs with mismatched probe sequences. Here, we introduce StrandScript's design and development, and demonstrate its effectiveness using real genotyping data.

关键词： GENOTYPE ARRAY processing SINGLE nucleotide polymorphisms microarray technology

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Meta-analytic framework for liquid association

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BIOINFORMATICS 2017年第14期33卷 2140-2147页

作者： Wang, Lin Liu, Silvia Ding, Ying Yuan, Shin-sheng Ho, Yen-Yi Tseng, George C. Capital Univ Econ & Business Sch Stat Beijing 100070 Peoples R China Univ Pittsburgh Grad Sch Publ Hlth Dept Biostat Pittsburgh PA 15261 USA Univ Pittsburgh Sch Med Dept Computat & Syst Biol Pittsburgh PA 15213 USA Acad Sinica Inst Stat Sci Taipei 115 Taiwan Univ South Carolina Coll Arts & Sci Dept Stat Columbia SC 29208 USA

Motivation: Although coexpression analysis via pair-wise expression correlation is popularly used to elucidate gene-gene interactions at the whole-genome scale, many complicated multi-gene regulations require more advanced detection methods. Liquid association (LA) is a powerful tool to detect the dynamic correlation of two gene variables depending on the expression level of a third variable (LA scouting gene). LA detection from single transcriptomic study, however, is often unstable and not generalizable due to cohort bias, biological variation and limited sample size. With the rapid development of microarray and NGS technology, LA analysis combining multiple gene expression studies can provide more accurate and stable results. Results: In this article, we proposed two meta-analytic approaches for LA analysis (MetaLA and MetaMLA) to combine multiple transcriptomic studies. To compensate demanding computing, we also proposed a two-step fast screening algorithm for more efficient genome-wide screening: boot-strap filtering and sign filtering. We applied the methods to five Saccharomyces cerevisiae datasets related to environmental changes. The fast screening algorithm reduced 98% of running time. When compared with single study analysis, MetaLA and MetaMLA provided stronger detection signal and more consistent and stable results. The top triplets are highly enriched in fundamental biological processes related to environmental changes. Our method can help biologists understand underlying regulatory mechanisms under different environmental exposure or disease states.

关键词： BIOLOGICAL variation statistics microarray technology GENE expression GLOBAL environmental change DISEASES

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