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Journal articles on the topic 'Single nucleotide polymorphism array'

Author: Grafiati

Published: 4 June 2021

Last updated: 4 February 2022

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1

Dutt, Amit, and Rameen Beroukhim. "Single nucleotide polymorphism array analysis of cancer." Current Opinion in Oncology 19, no. 1 (2007): 43–49. http://dx.doi.org/10.1097/cco.0b013e328011a8c1.

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2

Choi, Yong-Sung, Kyung-Sup Lee, and Dae-Hee Park. "Single nucleotide polymorphism (SNP) detection using microelectrode biochip array." Journal of Micromechanics and Microengineering 15, no. 10 (2005): 1938–46. http://dx.doi.org/10.1088/0960-1317/15/10/021.

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3

Spreiz, Ana, Roberta S. Guilherme, Claudio Castellan, et al. "Single-Nucleotide Polymorphism Array-Based Characterization of Ring Chromosome 18." Journal of Pediatrics 163, no. 4 (2013): 1174–78. http://dx.doi.org/10.1016/j.jpeds.2013.06.005.

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4

Gómez-Seguí, Inés, Dolors Sánchez-Izquierdo, Eva Barragán, et al. "Single-Nucleotide Polymorphism Array-Based Karyotyping of Acute Promyelocytic Leukemia." PLoS ONE 9, no. 6 (2014): e100245. http://dx.doi.org/10.1371/journal.pone.0100245.

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5

Zheng, Hai-Tao. "Loss of heterozygosity analyzed by single nucleotide polymorphism array in cancer." World Journal of Gastroenterology 11, no. 43 (2005): 6740. http://dx.doi.org/10.3748/wjg.v11.i43.6740.

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6

Jung, Yun Kyung, Jungkyu Kim, and Richard A. Mathies. "Microfluidic Linear Hydrogel Array for Multiplexed Single Nucleotide Polymorphism (SNP) Detection." Analytical Chemistry 87, no. 6 (2015): 3165–70. http://dx.doi.org/10.1021/ac5048696.

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7

Kagawa, Yasuo, Mami Hiraoka, Yukiko Miyashita-Hatano, et al. "Automated single nucleotide polymorphism typing using bead array in capillary tube." Journal of Bioscience and Bioengineering 110, no. 4 (2010): 505–8. http://dx.doi.org/10.1016/j.jbiosc.2010.05.007.

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8

Hiyama, E., H. Yamaoka, A. Kamimatsuse, et al. "Genomewide single nucleotide polymorphism microarray mapping for prediction of outcome of neuroblastoma patients." Journal of Clinical Oncology 24, no. 18_suppl (2006): 9010. http://dx.doi.org/10.1200/jco.2006.24.18_suppl.9010.

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9010 Background: Neuroblastoma is a biologically and genetically heterogeneous tumor and demonstrates favorable or unfavorable outcomes. However, the number of subgroups in neuroblastoma and natural history of each subgroup remain unclear. In Japan, nation-wide neuroblasotma mass-screening (MS) project had been performed on 6-month-old babies for 20 years that might have detected almost all neuroblastomas including regressing/ maturing tumors developed in this period. We surveyed more than 3,600 neuroblasotma cases including approximately 2,000 MS detecting cases. In this study, we examined ge

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9

Schwartz, Stuart. "Clinical Utility of Single Nucleotide Polymorphism Arrays." Clinics in Laboratory Medicine 31, no. 4 (2011): 581–94. http://dx.doi.org/10.1016/j.cll.2011.09.002.

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10

Creasey, Thomas, Amir Enshaei, Kathryn Watts, et al. "Single Nucleotide Polymorphism Array-Based Signature of Genetic Ploidy Groups in Acute Lymphoblastic Leukemia." Blood 134, Supplement_1 (2019): 1473. http://dx.doi.org/10.1182/blood-2019-122556.

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Acute lymphoblastic leukemia (ALL) is characterised by a number of recurrent chromosomal abnormalities which inform prognosis. Low hypodiploidy (HoTr) and high hyperdiploidy (HeH) are genetic subgroups associated with large non-random ploidy shifts, specifically 30-39 chromosomes and 51-65 chromosomes respectively. HoTr ALL often presents with a near triploid karyotype of 60-78 chromosomes through chromosomal endoreduplication without cytokinesis. This presents a diagnostic challenge in distinguishing this poor risk entity from good risk HeH ALL. To date, classification of such challenging cas

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11

Turuspekov, Yerlan, Joerg Plieske, Martin Ganal, Eduard Akhunov, and Saule Abugalieva. "Phylogenetic analysis of wheat cultivars in Kazakhstan based on the wheat 90 K single nucleotide polymorphism array." Plant Genetic Resources 15, no. 1 (2015): 29–35. http://dx.doi.org/10.1017/s1479262115000325.

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The recent introduction of Illumina single nucleotide polymorphism (SNP) arrays is an important step towards comprehensive genome-wide studies of genetic diversity in wheat. In this study, 90 cultivars of hexaploid spring wheat growing in Kazakhstan were genotyped using the high-density wheat 90 K Illumina SNP array. The analysis allowed the identification of 30,288 polymorphic SNPs. A subset of 3541 high-quality SNPs were used for a comparison of 690 wheat accessions representing landraces and varieties, including those from Asia, Australia, Canada, Europe, Kazakhstan, USA and other parts of

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12

Hiyama, Eiso, Hiroaki Yamaoka, Arata Kamimatsuse, et al. "Single nucleotide polymorphism array analysis to predict clinical outcome in neuroblastoma patients." Journal of Pediatric Surgery 41, no. 12 (2006): 2032–36. http://dx.doi.org/10.1016/j.jpedsurg.2006.08.002.

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13

Khoshfetrat, Seyyed Mehdi, Mitra Ranjbari, Mohsen Shayan, Masoud A. Mehrgardi, and Abolfazl Kiani. "Wireless Electrochemiluminescence Bipolar Electrode Array for Visualized Genotyping of Single Nucleotide Polymorphism." Analytical Chemistry 87, no. 16 (2015): 8123–31. http://dx.doi.org/10.1021/acs.analchem.5b02515.

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14

Sato-Otsubo, Aiko, Masashi Sanada, and Seishi Ogawa. "Single-Nucleotide Polymorphism Array Karyotyping in Clinical Practice: Where, When, and How?" Seminars in Oncology 39, no. 1 (2012): 13–25. http://dx.doi.org/10.1053/j.seminoncol.2011.11.010.

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15

Hirschhorn, J. N., P. Sklar, K. Lindblad-Toh, et al. "SBE-TAGS: An array-based method for efficient single-nucleotide polymorphism genotyping." Proceedings of the National Academy of Sciences 97, no. 22 (2000): 12164–69. http://dx.doi.org/10.1073/pnas.210394597.

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16

Debela, A. M., S. Thorimbert, B. Hasenknopf, C. K. O'Sullivan, and M. Ortiz. "Electrochemical primer extension for the detection of single nucleotide polymorphisms in the cardiomyopathy associated MYH7 gene." Chemical Communications 52, no. 4 (2016): 757–59. http://dx.doi.org/10.1039/c5cc07762a.

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17

Heinrichs, Stefan, Cheng Li, and A. Thomas Look. "SNP array analysis in hematologic malignancies: avoiding false discoveries." Blood 115, no. 21 (2010): 4157–61. http://dx.doi.org/10.1182/blood-2009-11-203182.

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Comprehensive analysis of the cancer genome has become a standard approach to identifying new disease loci, and ultimately will guide therapeutic decisions. A key technology in this effort, single nucleotide polymorphism arrays, has been applied in hematologic malignancies to detect deletions, amplifications, and loss of heterozygosity (LOH) at high resolution. An inherent challenge of such studies lies in correctly distinguishing somatically acquired, cancer-specific lesions from patient-specific inherited copy number variations or segments of homozygosity. Failure to include appropriate norm

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18

Walther, Charles, Jenny Nilsson, Fredrik Vult von Steyern, et al. "Cytogenetic and single nucleotide polymorphism array findings in soft tissue tumors in infants." Cancer Genetics 206, no. 7-8 (2013): 299–303. http://dx.doi.org/10.1016/j.cancergen.2013.06.004.

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19

Frühmesser, Anne, Peter H. Vogt, Jutta Zimmer, et al. "Single nucleotide polymorphism array analysis in men with idiopathic azoospermia or oligoasthenozoospermia syndrome." Fertility and Sterility 100, no. 1 (2013): 81–87. http://dx.doi.org/10.1016/j.fertnstert.2013.03.016.

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20

Creasey, Thomas, Amir Enshaei, Karin Nebral, et al. "Single nucleotide polymorphism array‐based signature of low hypodiploidy in acute lymphoblastic leukemia." Genes, Chromosomes and Cancer 60, no. 9 (2021): 604–15. http://dx.doi.org/10.1002/gcc.22956.

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21

Tai, Yu-Tzu, Cheng Li, Rory Coffey, et al. "Chromosomal Deletions and Amplifications in Multiple Myeloma Detected by 500K Single Nucleotide Polymorphism Array Analysis." Blood 106, no. 11 (2005): 1551. http://dx.doi.org/10.1182/blood.v106.11.1551.1551.

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Abstract Genetic aberrations, such as deletions and amplifications are among the major pathogenetic mechanisms underlying malignant transformation and progression. Analysis of chromosomal aberrations is particularly important as amplifications of oncogenes and deletions of tumor suppressor genes are major steps in the “multi-hit” process of tumorigenesis. Genome-wide molecular analyses, such as loss of heterozygosity (LOH) profiling and comparative genomic hybridization (CGH) have significantly enhanced our ability to detect chromosomal aberrations in cancer cells and assess their role in tumo

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22

Straub, Timothy M., Don S. Daly, Sharon Wunshel, Paul A. Rochelle, Ricardo DeLeon, and Darrell P. Chandler. "Genotyping Cryptosporidium parvum with an hsp70 Single-Nucleotide Polymorphism Microarray." Applied and Environmental Microbiology 68, no. 4 (2002): 1817–26. http://dx.doi.org/10.1128/aem.68.4.1817-1826.2002.

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ABSTRACT We investigated the application of an oligonucleotide microarray to (i) specifically detect Cryptosporidium spp., (ii) differentiate between closely related C. parvum isolates and Cryptosporidium species, and (iii) differentiate between principle genotypes known to infect humans. A microarray of 68 capture probes targeting seven single-nucleotide polymorphisms (SNPs) within a 190-bp region of the hsp70 gene of Cryptosporidium parvum was constructed. Labeled hsp70 targets were generated by PCR with biotin- or Cy3-labeled primers. Hybridization conditions were optimized for hybridizatio

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23

Gleeson, Grainne, Annemarie Larkin, Noel Horgan, and Susan Kennedy. "Evaluation of Chromogenic In Situ Hybridization for the Determination of Monosomy 3 in Uveal Melanoma." Archives of Pathology & Laboratory Medicine 138, no. 5 (2014): 664–70. http://dx.doi.org/10.5858/arpa.2012-0747-oa.

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Context.—Loss of 1 copy of chromosome 3 is considered a significant indicator of metastatic dissemination in uveal melanoma. Fresh or paraffin-embedded tumor tissue is most commonly used for current cytogenetic techniques for determining chromosome 3 status in uveal melanoma and often requires referral to an external specialist laboratory for analysis. Objectives.—To assess the chromogenic in situ hybridization assay for detecting chromosome 3 alterations using frozen tumor imprints and to compare the results obtained with those obtained by standard fluorescence in situ hybridization or single

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24

Stegelmann, F., L. Bullinger, M. Griesshammer, et al. "High-resolution single-nucleotide polymorphism array-profiling in myeloproliferative neoplasms identifies novel genomic aberrations." Haematologica 95, no. 4 (2009): 666–69. http://dx.doi.org/10.3324/haematol.2009.013623.

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25

Dirse, Vaidas, Egle Gineikiene, Tadas Zvirblis, Ruta Bertasiute, Kajsa Paulsson, and Laimonas Griskevicius. "Single nucleotide polymorphism array analysis of clonal evolution in younger adult acute lymphoblastic leukemia." Leukemia & Lymphoma 57, no. 11 (2016): 2716–19. http://dx.doi.org/10.3109/10428194.2016.1160081.

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26

Palti, Y., G. Gao, S. Liu, et al. "The development and characterization of a 57K single nucleotide polymorphism array for rainbow trout." Molecular Ecology Resources 15, no. 3 (2014): 662–72. http://dx.doi.org/10.1111/1755-0998.12337.

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27

Wang, Yunhong, Sue Miller, Diane Roulston, Dale Bixby, and Lina Shao. "Genome-Wide Single-Nucleotide Polymorphism Array Analysis Improves Prognostication of Acute Lymphoblastic Leukemia/Lymphoma." Journal of Molecular Diagnostics 18, no. 4 (2016): 595–603. http://dx.doi.org/10.1016/j.jmoldx.2016.03.004.

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28

Conlin, Laura K., Brian D. Thiel, Carsten G. Bonnemann, et al. "Mechanisms of mosaicism, chimerism and uniparental disomy identified by single nucleotide polymorphism array analysis." Human Molecular Genetics 19, no. 7 (2010): 1263–75. http://dx.doi.org/10.1093/hmg/ddq003.

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29

Lips, EH, EJ de Graaf, RAEM Tollenaar, et al. "Single nucleotide polymorphism array analysis of chromosomal instability patterns discriminates rectal adenomas from carcinomas." Journal of Pathology 212, no. 3 (2007): 269–77. http://dx.doi.org/10.1002/path.2180.

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30

Nishimura, Riki, Junko Takita, Aiko Sato‐Otsubo, et al. "Characterization of genetic lesions in rhabdomyosarcoma using a high‐density single nucleotide polymorphism array." Cancer Science 104, no. 7 (2013): 856–64. http://dx.doi.org/10.1111/cas.12173.

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31

Ronchi, Cristina L., Silviu Sbiera, Ellen Leich, et al. "Single Nucleotide Polymorphism Array Profiling of Adrenocortical Tumors - Evidence for an Adenoma Carcinoma Sequence?" PLoS ONE 8, no. 9 (2013): e73959. http://dx.doi.org/10.1371/journal.pone.0073959.

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32

Cai, Meiying, Na Lin, Linjuan Su, et al. "Prenatal diagnosis of 22q11.2 copy number abnormalities in fetuses via single nucleotide polymorphism array." Molecular Biology Reports 47, no. 10 (2020): 7529–35. http://dx.doi.org/10.1007/s11033-020-05815-7.

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Abstract The q11.2 region on chromosome 22 contains numerous low-copy repeats that lead to deleted or duplicated regions in the chromosome, thereby resulting in different syndromes characterized by intellectual disabilities or congenital anomalies. The association between patient phenotypes and 22q11.2 copy number abnormalities has been previously described in postnatal cases; however, these features have not been systematically evaluated in prenatal cases because of limitations in phenotypic identification in prenatal testing. In this study, we investigated the detection rate of 22q11.2 copy

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33

Jankowska, Anna M., Hideki Makishima, Ramon V. Tiu, et al. "Mutational spectrum analysis of chronic myelomonocytic leukemia includes genes associated with epigenetic regulation: UTX, EZH2, and DNMT3A." Blood 118, no. 14 (2011): 3932–41. http://dx.doi.org/10.1182/blood-2010-10-311019.

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Abstract Chronic myelomonocytic leukemia (CMML), a myelodysplastic/myeloproliferative neoplasm, is characterized by monocytic proliferation, dysplasia, and progression to acute myeloid leukemia. CMML has been associated with somatic mutations in diverse recently identified genes. We analyzed 72 well-characterized patients with CMML (N = 52) and CMML-derived acute myeloid leukemia (N = 20) for recurrent chromosomal abnormalities with the use of routine cytogenetics and single nucleotide polymorphism arrays along with comprehensive mutational screening. Cytogenetic aberrations were present in 46

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34

Visani, Giuseppe, Alessandro Isidori, Maria Rosaria Sapienza, et al. "Identification of Novel Cryptic Chromosomal Abnormalities in Primary Myelofibrosis by Single-Nucleotide Polymorphism Oligonucleotide Microarray." Blood 114, no. 22 (2009): 1890. http://dx.doi.org/10.1182/blood.v114.22.1890.1890.

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Abstract Abstract 1890 Poster Board I-913 Background. Primary myelofibrosis (PMF) is a clonal myeloproliferative neoplasm (MPN) characterised by a proliferation of predominantly megakaryocytes and granulocytes in bone marrow that in fully developed disease is replaced by fibrous tissue. At molecular level, no specific defect has been identified yet. Cytogenetic abnormalities occur in up to 30% of patients, the commonest including del(13)(q12-22), der(6)t(1;6)(q21-23;p21.3), del (20q), and partial trisomy 1q. In addition, approximately 50% of patients with PMF exhibit a single, recurrent, somat

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35

Nagano, Yasuhiko, Do Ha Kim, Li Zhang, et al. "Allelic alterations in pancreatic endocrine tumors identified by genome-wide single nucleotide polymorphism analysis." Endocrine-Related Cancer 14, no. 2 (2007): 483–92. http://dx.doi.org/10.1677/erc-06-0090.

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Pancreatic endocrine tumors (PETs) are uncommon and the genetic alterations in these indolent tumors are not well characterized. Chromosomal imbalances are frequent in tumors but PETs have not been studied by high-density single nucleotide polymorphism (SNP) array. We used genome-wide high-density SNP array analysis to detect copy number alterations using matched tumor and non-neoplastic tissue samples from 15 patients with PETs. In our study, whole or partial loss of chromosomes 1, 3, 11, 22 was present in 40, 47, 53, 40% of tumors respectively, and gain of chromosomes 5, 7, 12, 14, 17, and 2

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36

Huh, Jungwon, Yeung Chul Mun, Wha Soon Chung, and Chu Myong Seong. "Ring Chromosome 5 in Acute Myeloid Leukemia Defined by Whole-genome Single Nucleotide Polymorphism Array." Annals of Laboratory Medicine 32, no. 4 (2012): 307–11. http://dx.doi.org/10.3343/alm.2012.32.4.307.

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37

Zarzour, Peter, Lies Boelen, Fabio Luciani, et al. "Single nucleotide polymorphism array profiling identifies distinct chromosomal aberration patterns across colorectal adenomas and carcinomas." Genes, Chromosomes and Cancer 54, no. 5 (2015): 303–14. http://dx.doi.org/10.1002/gcc.22243.

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38

Zhang, HuiMin, WeiQiang Liu, Min Chen, ZhiHua Li, XiaoFang Sun, and ChenHong Wang. "Implementation of a High-Resolution Single-Nucleotide Polymorphism Array in Analyzing the Products of Conception." Genetic Testing and Molecular Biomarkers 20, no. 7 (2016): 352–58. http://dx.doi.org/10.1089/gtmb.2016.0035.

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39

Jasmine, F., H. Ahsan, I. L. Andrulis, E. M. John, J. Chang-Claude, and M. G. Kibriya. "Whole-Genome Amplification Enables Accurate Genotyping for Microarray-Based High-Density Single Nucleotide Polymorphism Array." Cancer Epidemiology Biomarkers & Prevention 17, no. 12 (2008): 3499–508. http://dx.doi.org/10.1158/1055-9965.epi-08-0482.

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40

Harrison, Blair E., Rowan J. Bunch, Russell McCulloch, et al. "The structure of a cattle stud determined using a medium density single nucleotide polymorphism array." Animal Production Science 52, no. 10 (2012): 890. http://dx.doi.org/10.1071/an11267.

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Genetic progress depends on accurate knowledge of the genetic composition of a population or herd including level of inbreeding and parentage. However, in many circumstances, such as at an individual property level, the relationships between animals may be unknown, or at best, only partly known. In this study, we used DNA from 938 animals and genotypes from ~54 000 single nucleotide polymorphisms (SNP) to determine the genetic structure of a stud from Central Queensland. Animals on the study were bred using multi-sire mating in mobs of composite tropically adapted cattle of the Senepol, Belmon

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41

Purdie, Karin J., Catherine A. Harwood, Abha Gulati, et al. "Single Nucleotide Polymorphism Array Analysis Defines a Specific Genetic Fingerprint for Well-Differentiated Cutaneous SCCs." Journal of Investigative Dermatology 129, no. 6 (2009): 1562–68. http://dx.doi.org/10.1038/jid.2008.408.

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42

Roth, Jacquelyn J., Mariarita Santi, Lucy B. Rorke-Adams, et al. "Diagnostic application of high resolution single nucleotide polymorphism array analysis for children with brain tumors." Cancer Genetics 207, no. 4 (2014): 111–23. http://dx.doi.org/10.1016/j.cancergen.2014.03.002.

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43

Miyachi, Hirotaka, Kazunori Ikebukuro, Kazuyoshi Yano, Hiroyuki Aburatani, and Isao Karube. "Single nucleotide polymorphism typing on DNA array with hydrophobic surface fabricated by plasma-polymerization technique." Biosensors and Bioelectronics 20, no. 2 (2004): 184–89. http://dx.doi.org/10.1016/j.bios.2004.02.022.

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44

Prakash, Siddharth, Dongchuan Guo, Cheryl L. Maslen, Michael Silberbach, Dianna Milewicz, and Carolyn A. Bondy. "Single-nucleotide polymorphism array genotyping is equivalent to metaphase cytogenetics for diagnosis of Turner syndrome." Genetics in Medicine 16, no. 1 (2013): 53–59. http://dx.doi.org/10.1038/gim.2013.77.

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45

Takahashi, Hiroki, Yoshihiko Usui, Shunichiro Ueda, et al. "Genome-Wide Analysis of Ocular Adnexal Lymphoproliferative Disorders Using High-Resolution Single Nucleotide Polymorphism Array." Investigative Opthalmology & Visual Science 56, no. 6 (2015): 4156. http://dx.doi.org/10.1167/iovs.15-16382.

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46

Armstrong, Barbara, Michael Stewart, and Abhijit Mazumder. "Suspension arrays for high throughput, multiplexed single nucleotide polymorphism genotyping." Cytometry 40, no. 2 (2000): 102–8. http://dx.doi.org/10.1002/(sici)1097-0320(20000601)40:2<102::aid-cyto3>3.0.co;2-4.

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47

Wang, Jun, Min Lin, Andrew Crenshaw, et al. "High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays." BMC Genomics 10, no. 1 (2009): 561. http://dx.doi.org/10.1186/1471-2164-10-561.

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48

da Silva, Fernanda Borges, and Fabiola Traina. "Metaphase cytogenetics and single nucleotide polymorphism arrays in myeloid malignancies." Revista Brasileira de Hematologia e Hemoterapia 37, no. 2 (2015): 71–72. http://dx.doi.org/10.1016/j.bjhh.2015.01.007.

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49

Szuhai, Károly, and Maarten Vermeer. "Microarray Techniques to Analyze Copy-Number Alterations in Genomic DNA: Array Comparative Genomic Hybridization and Single-Nucleotide Polymorphism Array." Journal of Investigative Dermatology 135, no. 10 (2015): 1–5. http://dx.doi.org/10.1038/jid.2015.308.

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50

Ow, T. J., K. Upadhyay, T. J. Belbin, M. B. Prystowsky, H. Ostrer, and R. V. Smith. "Bioinformatics in otolaryngology research. Part two: other high-throughput platforms in genomics and epigenetics." Journal of Laryngology & Otology 128, no. 11 (2014): 942–47. http://dx.doi.org/10.1017/s0022215114002011.

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AbstractObjectives:This second segment of the two-part review summarises several modern high-throughput methods in genomics, epigenetics and molecular biology. Many principles from nucleotide sequencing and transcriptomics can be applied to other high-throughput molecular biology techniques. Specifically, this manuscript reviews: array comparative genome hybridisation; single nucleotide polymorphism arrays; microarray technology, used to study epigenetics; and methodology applied in proteomics. Finally, the review describes current methods for the integration of multiple molecular biology plat

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