Journal articles: 'SNP array genotyping'

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Bianchi, Davide, Lucio Brancadoro, and Gabriella De Lorenzis. "Genetic Diversity and Population Structure in a Vitis spp. Core Collection Investigated by SNP Markers." Diversity 12, no. 3 (March 16, 2020): 103. http://dx.doi.org/10.3390/d12030103.

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Single nucleotide polymorphism (SNP) genotyping arrays are powerful tools to measure the level of genetic polymorphism within a population. The coming of next-generation sequencing technologies led to identifying thousands and millions of SNP loci useful in assessing the genetic diversity. The Vitis genotyping array, containing 18k SNP loci, has been developed and used to detect genetic diversity of Vitis vinifera germplasm. So far, this array was not validated on non-vinifera genotypes used as grapevine rootstocks. In this work, a core collection of 70 grapevine rootstocks, composed of individuals belonging to Vitis species not commonly used in the breeding programs, was genotyped using the 18k SNP genotyping array. SNP results were compared to the established SSR (Simple Sequence Repeat) markers in terms of heterozygosity and genetic structure of the core collection. Genotyping array has proved to be a valuable tool for genotyping of grapevine rootstocks, with more than 90% of SNPs successfully amplified. Structure analysis detected a high degree of admixed genotypes, supported by the complex genetic background of non-vinifera germplasm. Moreover, SNPs clearly differentiated non-vinifera and vinifera germplasm. These results represent a first step in studying the genetic diversity of non-conventional breeding material that will be used to select rootstocks with high tolerance to limiting environmental conditions.

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Fujii, Hiroshi, Takehiko Shimada, Keisuke Nonaka, Masayuki Kita, Takeshi Kuniga, Tomoko Endo, Yoshinori Ikoma, and Mitsuo Omura. "High-throughput genotyping in citrus accessions using an SNP genotyping array." Tree Genetics & Genomes 9, no. 1 (July 5, 2012): 145–53. http://dx.doi.org/10.1007/s11295-012-0542-3.

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Xiao, Yuanyuan, Mark R. Segal, Y. H. Yang, and Ru-Fang Yeh. "A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays." Bioinformatics 23, no. 12 (April 25, 2007): 1459–67. http://dx.doi.org/10.1093/bioinformatics/btm131.

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Straub, T. M., M. D. Quinonez-Diaz, C. O. Valdez, D. R. Call, and D. P. Chandler. "Using DNA microarrays to detect multiple pathogen threats in water." Water Supply 4, no. 2 (April 1, 2004): 107–14. http://dx.doi.org/10.2166/ws.2004.0035.

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We present four studies that illustrate the use of DNA microarrays for the detection and subsequent genotyping of waterborne pathogens. A genotyping array targeting four virulence factor genes in enterohemorrhagic Escherichia coli (EHEC) was tested. The arrays were clearly able to differentiate between E. coli O157:H7 genotypes and E. coli O91:H2. Non-pathogenic E. coli and non-target organisms were not detected on this array. In the second study, an hsp70 gene single nucleotide polymorphism (SNP) array for specific Cryptosporidium parvum detection was constructed to differentiate between principle genotypes. SNPs, and hence differences between genotypes, were easily detected on this type of array. In the third study an array for Helicobacter pylori was tested for simultaneous SNP discrimination and presence or absence of virulence factor genes. Results from this study showed that both SNP discrimination for some conserved genes, and the presence or absence of virulence factor genes was possible. In the fourth study, multiplexing was achieved by direct hybridization and detection of mRNA to the array. For highly expressed genes, visible signal was detected at 312.5 ng of total RNA, indicating that these new methods may have sufficient environmental sensitivity without the need to perform PCR.

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Graham, Natalie, Emily Telfer, Tancred Frickey, Gancho Slavov, Ahmed Ismael, Jaroslav Klápště, and Heidi Dungey. "Development and Validation of a 36K SNP Array for Radiata Pine (Pinus radiata D.Don)." Forests 13, no. 2 (January 24, 2022): 176. http://dx.doi.org/10.3390/f13020176.

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Radiata pine (Pinus radiata D.Don) is one of the world’s most domesticated pines and a key economic species in New Zealand. Thus, the development of genomic resources for radiata pine has been a high priority for both research and commercial breeding. Leveraging off a previously developed exome capture panel, we tested the performance of 438,744 single nucleotide polymorphisms (SNPs) on a screening array (NZPRAD01) and then selected 36,285 SNPs for a final genotyping array (NZPRAD02). These SNPs aligned to 15,372 scaffolds from the Pinus taeda L. v. 1.01e assembly, and 20,039 contigs from the radiata pine transcriptome assembly. The genotyping array was tested on more than 8000 samples, including material from archival progenitors, current breeding trials, nursery material, clonal lines, and material from Australia. Our analyses indicate that the array is performing well, with sample call rates greater than 98% and a sample reproducibility of 99.9%. Genotyping in two linkage mapping families indicated that the SNPs are well distributed across the 12 linkage groups. Using genotypic data from this array, we were also able to differentiate representatives of the five recognized provenances of radiata pine, Año Nuevo, Monterey, Cambria, Cedros and Guadalupe. Furthermore, principal component analysis of genotyped trees revealed clear patterns of population structure, with the primary axis of variation driven by provenance ancestry and the secondary axis reflecting breeding activities. This represents the first commercial use of genomics in a radiata pine breeding program.

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Rauch, A. "Molecular karyotyping using an SNP array for genomewide genotyping." Journal of Medical Genetics 41, no. 12 (December 1, 2004): 916–22. http://dx.doi.org/10.1136/jmg.2004.022855.

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Willet, Cali E., and Bianca Haase. "An updated felCat5 SNP manifest for the Illumina Feline 63k SNP genotyping array." Animal Genetics 45, no. 4 (May 7, 2014): 614–15. http://dx.doi.org/10.1111/age.12169.

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Torkamaneh, Davoud, and Francois Belzile. "Scanning and Filling: Ultra-Dense SNP Genotyping Combining Genotyping-By-Sequencing, SNP Array and Whole-Genome Resequencing Data." PLOS ONE 10, no. 7 (July 10, 2015): e0131533. http://dx.doi.org/10.1371/journal.pone.0131533.

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Vogel, Ivan, Robert C. Blanshard, and Eva R. Hoffmann. "SureTypeSC—a Random Forest and Gaussian mixture predictor of high confidence genotypes in single-cell data." Bioinformatics 35, no. 23 (May 22, 2019): 5055–62. http://dx.doi.org/10.1093/bioinformatics/btz412.

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Abstract Motivation Accurate genotyping of DNA from a single cell is required for applications such as de novo mutation detection, linkage analysis and lineage tracing. However, achieving high precision genotyping in the single-cell environment is challenging due to the errors caused by whole-genome amplification. Two factors make genotyping from single cells using single nucleotide polymorphism (SNP) arrays challenging. The lack of a comprehensive single-cell dataset with a reference genotype and the absence of genotyping tools specifically designed to detect noise from the whole-genome amplification step. Algorithms designed for bulk DNA genotyping cause significant data loss when used for single-cell applications. Results In this study, we have created a resource of 28.7 million SNPs, typed at high confidence from whole-genome amplified DNA from single cells using the Illumina SNP bead array technology. The resource is generated from 104 single cells from two cell lines that are available from the Coriell repository. We used mother–father–proband (trio) information from multiple technical replicates of bulk DNA to establish a high quality reference genotype for the two cell lines on the SNP array. This enabled us to develop SureTypeSC—a two-stage machine learning algorithm that filters a substantial part of the noise, thereby retaining the majority of the high quality SNPs. SureTypeSC also provides a simple statistical output to show the confidence of a particular single-cell genotype using Bayesian statistics. Availability and implementation The implementation of SureTypeSC in Python and sample data are available in the GitHub repository: https://github.com/puko818/SureTypeSC Supplementary information Supplementary data are available at Bioinformatics online.

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Chen, Daniel C., Janna Saarela, Ilpo Nuotio, Anne Jokiaho, Leena Peltonen, and Aarno Palotie. "Comparison of GenFlex Tag Array and Pyrosequencing in SNP Genotyping." Journal of Molecular Diagnostics 5, no. 4 (November 2003): 243–49. http://dx.doi.org/10.1016/s1525-1578(10)60481-3.

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Correll-Tash, Sarah, Laura Conlin, Beth A. Mininger, Brenna Lilley, Michael T. Mennuti, and Beverly S. Emanuel. "The Recurrent t(11;22)(q23;q11.2) Can Occur as a Post-Zygotic Event." Cytogenetic and Genome Research 156, no. 4 (2018): 185–90. http://dx.doi.org/10.1159/000494648.

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The AT-rich repeat on chromosome 22q11.2 is known to be involved in the recurrent constitutional t(11;22)(q23;q11.2). Segregation of this translocation has been reported in several hundred families, but a de novo translocation event has been identified in only 8 cases, and everytime the translocation originated in paternal germ-line chromosomes. Further, de novo t(11;22) rearrangements have been detected in the sperm of healthy males, leading to the hypothesis that it occurs somewhere along the meiosis-spermatogenesis pathway. This report describes a woman whose constitutional karyotype revealed mosaicism for the recurrent t(11;22) and the subsequent testing performed to determine the origin of the translocation event. Karyotype analysis, translocation-specific PCR, human identity testing, and a SNP genotyping array were performed to detect mosaicism and/or chimerism. As a result, the SNP genotyping array revealed no evidence for mosaicism in genomic DNA beyond mosaicism for the balanced t(11;22). Human identity testing and the SNP genotyping array ruled out chimerism. PCR of the translocation breakpoint followed by sequencing confirmed that the translocation had occurred at the typical t(11;22) breakpoints. In conclusion, these results indicate that the translocation occurred post-fertilization, providing the first evidence of a de novo t(11;22)(q23;q11.2) occurring in a maternal mitotic environment.

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Bortolin, Susan, Margot Black, Hemanshu Modi, Ihor Boszko, Daniel Kobler, Dan Fieldhouse, Eve Lopes, et al. "Analytical Validation of the Tag-It High-Throughput Microsphere-Based Universal Array Genotyping Platform: Application to the Multiplex Detection of a Panel of Thrombophilia-Associated Single-Nucleotide Polymorphisms." Clinical Chemistry 50, no. 11 (November 1, 2004): 2028–36. http://dx.doi.org/10.1373/clinchem.2004.035071.

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Abstract Background: We have developed a novel, microsphere-based universal array platform referred to as the Tag-It™ platform. This platform is suitable for high-throughput clinical genotyping applications and was used for multiplex analysis of a panel of thrombophilia-associated single-nucleotide polymorphisms (SNPs). Methods: Genomic DNA from 132 patients was amplified by multiplex PCR using 6 primer sets, followed by multiplex allele-specific primer extension using 12 universally tagged genotyping primers. The products were then sorted on the Tag-It array and detected by use of the Luminex xMAP™ system. Genotypes were also determined by sequencing. Results: Empirical validation of the universal array showed that the highest nonspecific signal was 3.7% of the specific signal. Patient genotypes showed 100% concordance with direct DNA sequencing data for 736 SNP determinations. Conclusions: The Tag-It microsphere-based universal array platform is a highly accurate, multiplexed, high-throughput SNP-detection platform.

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Vlachos, Adrianna, Jason Farrar, Eva Atsidaftos, Ellen Muir, Thomas C. Markello, Sharon Singh, Johnson M. Liu, et al. "5q- Syndrome In a Child: Is This Acquired Diamond Blackfan Anemia (DBA)?" Blood 116, no. 21 (November 19, 2010): 4430. http://dx.doi.org/10.1182/blood.v116.21.4430.4430.

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Abstract Abstract 4430 Background: Diamond Blackfan anemia is a rare heritable red cell aplasia which usually presents in infancy but can also be diagnosed in childhood and even adulthood. Mutations or deletions in eleven ribosomal protein (RP) genes, resulting in protein haplo-insufficiency have been reported in about 54% of the patients. The 5q- syndrome is an acquired myelodysplastic syndrome (MDS) characterized by a similar erythroid failure. Another RP gene included in the 5q deleted region, RPS14, has been identified as a causal gene in 5q- MDS but has not been reported in DBA. Purpose: Array Comparative Genomic Hybridization has been used to identify large deletions in patients with DBA. This report demonstrates the use of Single Nucleotide Polymorphism (SNP) genotyping array hybridization to identify a patient, previously thought to have DBA, as having a 5q- deletion consistent with 5q- syndrome. Method: Seventy-five patient samples from the Diamond Blackfan Anemia Registry of North America, a patient database of now 608 patients designed to better understand the biology and epidemiology of DBA, underwent resequencing of 80 RP genes. Approximately 40% of the patients had no identifiable mutation. High resolution SNP array genotyping analysis was done on 23 probands from this cohort who did not have a mutation detected in either the resequencing project and/or the targeted sequencing efforts lead by Gazda and colleagues. Result: An acquired internal deletion on chromosome 5q involving RPS14 was identified in one patient with presumed DBA. The patient presented at 5 years 10 months of age with anemia noted on a routine blood count. The hemoglobin was 8.4 grams/dl, MCV 108.2 fL, and reticulocyte count 0.4%. The eADA was normal. The bone marrow showed decreased cellularity and megaloblastic changes in the erythroid series. There were adequate numbers of megakaryocytes with no hypolobulation. The cytogenetics performed at diagnosis in 1991 were reported as normal. The patient had no significant family history of anemia and was found to have no congenital physical anomalies. A diagnosis of non-classical DBA was presumed and the patient failed a trial of corticosteroids. At present the patient has marrow red cell aplasia and is on a chronic transfusion schedule. SNP array genotyping analysis identified mosaicism in two discrete regions covering ~17.7 Mb on 5q-, with an estimated 63.7% monosomy and 36.3% disomy in this region. The major region extends from 141.1M to 157.2M (hg18), including all of the 5q- syndrome commonly deleted region (CDR) at 5q33 though it excludes the 5q31 CDR associated with AML and more aggressive MDS as well as miR146a, a factor recently postulated to play a role in 5q- MDS. SNP array genotyping from purified peripheral blood populations indicated that lymphocytes were greater than 95% normal, while the myeloid cells were greater than 95% 5q-. CD34+ cells obtained from this patient showed a marked decrease in both myeloid and erythroid colony formation when compared with normal cells. Patient fibroblasts were normal and neither of the parents have any 5q anomalies by SNP array genotyping. Although the deletion was not identified in 1991 at the time of the diagnosis, the 46,XX,der(5)del(5)(q15q22)del(5)(q32q33) deletion was able to be detected on high resolution karyotyping in a post-SNP array genotyping marrow sample. Haploinsufficiency of RPS14 was confirmed by quantitative RT-PCR. Conclusion: Patients with non-classical DBA may have unique acquired 5q deletions with RPS14 haploinsufficiency. A search for other acquired somatic mutations or deletions in patients with DBA, in particular non-classical cases, is underway. SNP array genotyping is an essential diagnostic tool in this search. Disclosures: No relevant conflicts of interest to declare.

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Wijesena, Hiruni R., Gary A. Rohrer, Dan J. Nonneman, Brittney N. Keel, Jessica L. Petersen, Stephen D. Kachman, and Daniel C. Ciobanu. "Evaluation of genotype quality parameters for SowPro90, a new genotyping array for swine1." Journal of Animal Science 97, no. 8 (May 31, 2019): 3262–73. http://dx.doi.org/10.1093/jas/skz185.

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Abstract Understanding early predictors of sow fertility has the potential to improve genomic predictions. A custom SNP array (SowPro90 produced by Affymetrix) was developed to include genetic variants overlapping quantitative trait loci for age at puberty, one of the earliest indicators of sow fertility, as well as variants related to innate and adaptive immunity. The polymorphisms included in the custom genotyping array were identified using multiple genomic approaches including deep genomic and transcriptomic sequencing and genome-wide associations. Animals from research and commercial populations (n = 2,586) were genotyped for 103,476 SNPs included in SowPro90. To assess the quality of data generated, genotype concordance was evaluated between the SowPro90 and Porcine SNP60 BeadArray using a subset of common SNP (n = 44,708) and animals (n = 277). The mean genotype concordance rate per SNP was 98.4%. Differences in distribution of data quality were observed between the platforms indicating the need for platform specific thresholds for quality parameters. The optimal thresholds for SowPro90 (≥97% SNP and ≥93% sample call rate) were obtained by analyzing the data quality distribution and genotype concordance per SNP across platforms. At ≥97% SNP call rate, there were 42,151 SNPs (94.3%) retained with a mean genotype concordance of 98.6% across platforms. Similarly, ≥94% SNPs and ≥85% sample call rates were established as thresholds for Porcine SNP60 BeadArray. At ≥94% SNPs call rate, there were 41,043 SNPs (91.8%) retained with a mean genotype concordance of 98.6% across platforms. Final evaluation of SowPro90 array content (n = 103,476) at ≥97% SNPs and ≥93% sample call rates allowed retention of 89,040 SNPs (86%) for downstream analysis. The findings and strategy for quality control could be helpful in identifying consistent, high-quality genotypes for genomic evaluations, especially when integrating genotype data from different platforms.

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Kranis, Andreas, Almas A. Gheyas, Clarissa Boschiero, Frances Turner, Le Yu, Sarah Smith, Richard Talbot, et al. "Development of a high density 600K SNP genotyping array for chicken." BMC Genomics 14, no. 1 (2013): 59. http://dx.doi.org/10.1186/1471-2164-14-59.

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Bianco, Luca, Alessandro Cestaro, Gareth Linsmith, Hélène Muranty, Caroline Denancé, Anthony Théron, Charles Poncet, et al. "Development and validation of the Axiom®Apple480K SNP genotyping array." Plant Journal 86, no. 1 (April 2016): 62–74. http://dx.doi.org/10.1111/tpj.13145.

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Louis, Yalaukani. "Genotypic Characterisation of Bambara Groundnut (Vigna Subterranea L. Verdc) Germplasm." Biomedical Research and Clinical Trials 1, no. 2 (December 26, 2022): 01–04. http://dx.doi.org/10.31579/2835-7949/006.

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Bambara groundnut (Vigna subterranea (L.) Verdc) is an underexploited crop with the opportunity to address some critical food requirements as it is a high-nutritional alternative food. This study aimed at characterising genetic diversity using Diversity Array Technologies Sequence Low Density (DArTseqLD) Single Nucleotide Polymorphism (SNP) markers in order to identify genomic variation that can be used for crop improvement by plant breeders. One hundred eighty-eight samples were selected for genotyping using DArTseqLD SNP markers. The study generated 1048 DArTseqLD SNP markers. Analysis of molecular variance (AMOVA) revealed 84 % and 13 % variation among and within the Bambara groundnut germplasm respectively, 3 % variation was observed among the populations. Cluster analysis based on genotypic data grouped the 188 samples into 9 clusters. Based genotypic data, it can be concluded that there is a significant degree of genetic diversity in the germplasm genotyped that can be used by plant breeders in crop improvement program.

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Tait, Rich, Ryan Ferretti, Barry Simpson, Jeremy Walker, Jamie Parham, Xiao-Lin Wu, and Stewart Bauck. "34 Present and future of genomic test reporting in the cattle industry." Journal of Animal Science 97, Supplement_2 (July 2019): 19–20. http://dx.doi.org/10.1093/jas/skz122.036.

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Abstract A series of custom low density (LD) SNP genotyping platforms have been created over the years. Recognized by the GeneSeek Genomic Profiler (GGP) nomenclature, these SNP arrays have increased in size as new versions were created, such as: GGP-LD-v1 (n = 8,762), GGP-LD-v2 (n = 20,057), GGP-LD-v3 (n = 26,151), GGP-LD-v4 (n = 30,108), and GGP Bovine 50K (n = 47,843), all of which contained a base of the Illumina Bovine LD array (n = 7,931) and then added SNPs to provide maximum information content (Shannon Entropy) and optimal genomic coverage into target populations without specific restrictions on overlap to historical commercial arrays such as the Illumina Bovine 50K (n = 54,001). Our approach has been to select SNP content which originated on the Illumina Bovine HD array (n = 777,962) or the GGP F250 functional SNP array (n = 221,115). This approach produced GGPs which: 1) have a larger number of SNPs that meet quality control metrics for minor allele frequency and Hardy-Weinberg segregation testing; 2) have superior imputation accuracy to the Illumina HD array in target populations; and 3) have causative SNPs or SNPs in closer LD with causative mutations for functional genomics studies and increased utility across populations. These design features have not always been utilized by users of the GGP portfolio. In some cases, users have imputed from GGP content back to the Illumina Bovine 50K SNP content within their population because that was the earliest process they developed in their evaluation system. This approach ignores the innovation and potential utility designed into the GGP chips for breeders within those organizations. We do not look back to prior SNP arrays for content definition for the purpose of bridging content from current arrays to the past. Instead, our vision is to continue to innovate, on a routine basis, which SNPs we provide to customers, so that their genetic evaluations can continue to evolve and improve into the future.

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Linsky, Ruth Ella, R. Steven Wagner, Reniastoetie Djojoasmoro, Joseph Lorenz, and Biruté M. F. Galdikas. "Cross Species use of Human Microarray Genotyping Technology for Bornean Orangutan (Pongo pygmaeus) SNP Discovery." HAYATI Journal of Biosciences 29, no. 1 (November 30, 2021): 62–75. http://dx.doi.org/10.4308/hjb.29.1.62-75.

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Previous genetic studies of orangutans (Pongo spp.) have relied mainly upon mitochondrial DNA or microsatellite short tandem repeats (STR) for genomic genotyping analysis. Scientists have yet to take advantage of the genetic closeness of the great apes to humans for genomic analysis by using advanced techniques available for human genotyping. To genotype orangutans at Tanjung Puting National Park, we developed a novel combination of a methyl-based magnetic enrichment capture of genomic fecal DNA with genotyping on a human targeted single nucleotide polymorphism (SNP) microarray, and compared this to additional microsatellite (STR) micro-capillary genotyping. We successfully isolated 125 known human genomic SNP loci (0.08% of those targeted) which hybridized orangutan DNA on the human targeted Illumina Infinium QC array. We estimated genetic diversity and relatedness (r) using three estimators for a total of 32 (21 female and 9 male) wild orangutans at the Camp Leakey study site. Average TrioML relatedness within the sample, estimated from our combo SNP/STR dataset, was at a range consistent with half and first cousins (r = .082). All sampled males and females had relatives within the study site indicating we have verified a local, closely related community of wild orangutans at Camp Leakey.

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Ekblom, Robert, Malin Aronsson, Franziska Elsner-Gearing, Malin Johansson, Toby Fountain, and Jens Persson. "Sample identification and pedigree reconstruction in Wolverine (Gulo gulo) using SNP genotyping of non-invasive samples." Conservation Genetics Resources 13, no. 3 (April 22, 2021): 261–74. http://dx.doi.org/10.1007/s12686-021-01208-5.

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AbstractFor conservation genetic studies using non-invasively collected samples, genome-wide data may be hard to acquire. Until now, such studies have instead mostly relied on analyses of traditional genetic markers such as microsatellites (SSRs). Recently, high throughput genotyping of single nucleotide polymorphisms (SNPs) has become available, expanding the use of genomic methods to include non-model species of conservation concern. We have developed a 96-marker SNP array for use in applied conservation monitoring of the Scandinavian wolverine (Gulo gulo) population. By genotyping more than a thousand non-invasively collected samples, we were able to obtain precise estimates of different types of genotyping errors and sample dropout rates. The SNP panel significantly outperforms the SSR markers (and DBY intron markers for sexing) both in terms of precision in genotyping, sex assignment and individual identification, as well as in the proportion of samples successfully genotyped. Furthermore, SNP genotyping offers a simplified laboratory and analysis pipeline with fewer samples needed to be repeatedly genotyped in order to obtain reliable consensus data. In addition, we utilised a unique opportunity to successfully demonstrate the application of SNP genotype data for reconstructing pedigrees in wild populations, by validating the method with samples from wild individuals with known relatedness. By offering a simplified workflow with improved performance, we anticipate this methodology will facilitate the use of non-invasive samples to improve genetic management of many different types of populations that have previously been challenging to survey.

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Bachlava, Eleni, Christopher A. Taylor, Shunxue Tang, John E. Bowers, Jennifer R. Mandel, John M. Burke, and Steven J. Knapp. "SNP Discovery and Development of a High-Density Genotyping Array for Sunflower." PLoS ONE 7, no. 1 (January 4, 2012): e29814. http://dx.doi.org/10.1371/journal.pone.0029814.

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Chen, Haodong, Weibo Xie, Hang He, Huihui Yu, Wei Chen, Jing Li, Renbo Yu, et al. "A High-Density SNP Genotyping Array for Rice Biology and Molecular Breeding." Molecular Plant 7, no. 3 (March 2014): 541–53. http://dx.doi.org/10.1093/mp/sst135.

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Lee, Yun-Gyeong, Namhee Jeong, Ji Hong Kim, Kwanghee Lee, Kil Hyun Kim, Ali Pirani, Bo-Keun Ha, et al. "Development, validation and genetic analysis of a large soybean SNP genotyping array." Plant Journal 81, no. 4 (February 2015): 625–36. http://dx.doi.org/10.1111/tpj.12755.

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Maughan, Peter J., Scott M. Smith, and Joshua A. Raney. "Utilization of Super BAC Pools and Fluidigm Access Array Platform for High-Throughput BAC Clone Identification: Proof of Concept." Journal of Biomedicine and Biotechnology 2012 (2012): 1–7. http://dx.doi.org/10.1155/2012/405940.

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Bacterial artificial chromosome (BAC) libraries are critical for identifying full-length genomic sequences, correlating genetic and physical maps, and comparative genomics. Here we describe the utilization of the Fluidigm access array genotyping system in conjunction with KASPar genotyping technology to identify individual BAC clones corresponding to specific single-nucleotide polymorphisms (SNPs) from an Amplicon Express seven-plate super pooledAmaranthus hypochondriacusBAC library. Ninety-six SNP loci, spanning the length ofA. hypochondriacuslinkage groups 1, 2, and 15, were simultaneously tested for clone identification from four BAC super pools, corresponding to 28 384-well plates, using a single Fluidigm integrated fluidic chip (IFC). Forty-six percent of the SNPs were associated with a single unambiguous identified BAC clone. PCR amplification and next-generation sequencing of individual BAC clones confirmed the IFC clone identification. Utilization of the Fluidigm Dynamic array platform allowed for the simultaneous PCR screening of 10,752 BAC pools for 96 SNP tag sites in less than three hours at a cost of~$0.05per reaction.

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Vlachos, Adrianna, Jason Farrar, Eva Atsidaftos, Ellen Muir, Thomas C. Markello, Sharon Singh, Johnson M. Liu, et al. "5q- Myelodysplastic Syndrome, In One of 23 Children Lacking a Known Ribosomal Gene Mutation, Masquerading as Diamond Blackfan Anemia (DBA) and Responding to Lenalidomide." Blood 116, no. 21 (November 19, 2010): LBA—2—LBA—2. http://dx.doi.org/10.1182/blood.v116.21.lba-2.lba-2.

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Abstract Abstract LBA-2 Background: 5q- myelodysplastic syndrome is a rare, acquired macrocytic anemia with a female predominance. The bone marrow is characterized by a paucity of erythroid precursors with relatively normal leukocyte and platelet counts and no excess blasts. The mean age at diagnosis is approximately 70 years. The phenotype of 5q deletion has been shown to result from haploinsufficiency of the RPS14 gene. Historically red blood cell transfusions have been the primary treatment; however lenalidomide has recently been effective in ameliorating the anemia with a response rate of 67%. DBA is a rare heritable red cell aplasia which usually presents in infancy. It too is characterized by a bone marrow deficient in erythroid precursors. Mutations or deletions in eleven ribosomal protein (RP) genes, resulting in protein haploinsufficiency, have been reported in 50–60% of patients. To date RPS14 mutations have not been identified in DBA patients. Array Comparative Genomic Hybridization (CGH) has been used to identify large deletions in patients with DBA, but a more sensitive approach was hypothesized to identify additional deletions. Purpose: To address the question of whether chromosomal deletions could be the underlying defect in patients with DBA who did not have mutations in the known RP genes, Single Nucleotide Polymorphism (SNP) genotyping array hybridization was utilized. Methods: Seventy-five patient samples from the DBA Registry (DBAR) underwent resequencing of 80 RP genes. Approximately 40% of the patients had no identifiable mutation. High resolution SNP array genotyping analysis was done on 23 probands who did not have a mutation detected by resequencing. Results: An acquired internal deletion on chromosome 5q involving RPS14 was identified in one of 23 patients with presumed DBA. The patient presented with anemia at 5 10/12 years of age. The hemoglobin was 8.4 g/dl, MCV 108.2 fL, and reticulocyte count 0.4%. The erythrocyte adenosine deaminase (eADA) activity, elevated in 85% of DBA patients, was normal. The bone marrow showed decreased cellularity and megaloblastoid changes in the erythroid series. There were adequate numbers of megakaryocytes with no hypolobulation. Cytogenetics performed at diagnosis in 1991 appeared normal. The patient had no significant family history or congenital anomalies. A diagnosis of non-classical DBA was made. The patient failed a trial of corticosteroids and had remained transfusion-dependent for 19 years. No RP gene mutation was identified by sequencing. SNP array genotyping analysis identified mosaicism in two discrete regions covering ∼17.7 Mb on 5q-, with an estimated 63.7% monosomy and 36.3% disomy in this region. The major region extends from 141.1M to 157.2M (hg18), including all of the 5q- syndrome commonly deleted region (CDR) at 5q33, though it excludes the 5q31 CDR, miR146a, as well as Cdc25C and PPP2Acα, factors for which haploinsufficient expression has previously been suggested to be important in response to lenalidomide. SNP array genotyping from purified populations indicated that lymphocytes were >95% normal, while the myeloid cells were >95% 5q-. CD34+ cells showed a marked decrease in both myeloid and erythroid colony formation. Patient fibroblasts were normal and neither of the parents have 5q abnormalities by SNP analysis. Although the deletion was not identified in 1991, the 46,XX,der(5)del(5)(q15q22)del(5)(q32q33) deletion was detected on high resolution karyotyping in a post-SNP array genotyping marrow sample. Haploinsufficiency of RPS14 was confirmed by quantitative RT-PCR. After a trial of lenalidomide, complicated by Grade 4 neutropenia and Grade 3 thrombocytopenia, the patient has a reticulocyte count of 7.4% (from a previous baseline of <0.2%) and has achieved a hemoglobin of 11.1 gm/dl without transfusion support. Conclusions: Patients with non-classical DBA, who also have no congenital anomalies and normal eADA activity, may have somatically acquired 5q deletions with RPS14 haploinsufficiency. The DBAR is presently performing SNP array genotyping on other DBA patients who fit these criteria. These data suggest that haploinsufficiency of Cdc25C and PPP2Acα are not required for an erythroid response to lenolidamide. Reclassification of non-classical DBA patients as 5q- MDS offers them a potential treatment option with lenalidomide. Disclosures: No relevant conflicts of interest to declare.

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Banos, G., and M. P. Coffey. "Linkage disequilibrium in two divergent genetic groups of dairy cows using a high-density map of Single Nucleotide Polymorphisms." Proceedings of the British Society of Animal Science 2009 (April 2009): 43. http://dx.doi.org/10.1017/s1752756200028829.

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A 50K bovine DNA array allows large scale genotyping of dairy cattle for around 50 thousand markers (Single Nucleotide Polymorphisms -SNP). This development opens the door to genomic prediction and selection, and also facilitates gene detection, mapping and association studies. Any such application requires knowledge of the Linkage Disequilibrium (LD) state of the markers. The objective of this work was to examine the LD in two divergent genetic lines of dairy cows genotyped with the 50K bovine DNA array.

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Selmer, Kaja K., Kristin Brandal, Ole K. Olstad, Bård Birkenes, Dag E. Undlien, and Thore Egeland. "Genome-wide Linkage Analysis with Clustered SNP Markers." Journal of Biomolecular Screening 14, no. 1 (November 21, 2008): 92–96. http://dx.doi.org/10.1177/1087057108327327.

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Single nucleotide polymorphisms (SNPs) have recently replaced microsatellites as the genetic markers of choice in linkage analysis, primarily because they are more abundant and the genotypes more amenable for automatic calling. One of the most recently launched linkage mapping sets (LMS) is the Applied Biosystems Human LMS 4K, which is a genome-wide linkage set based on the SNPlex™ technology and the use of clustered SNPs. In this article the authors report on their experience with this set and the associated genotyping software GeneMapper® version 4.0, which they have used for linkage analyses in 17 moderate to large families with assumed monogenic disease. For comparison of methods, they also performed a genome-wide linkage analysis in 1 of the 17 families using the Affymetrix GeneChip® Human Mapping 10K 2.0 array. The conclusion is that both methods performed technically well, with high call rates and comparable and low rates of Mendelian inconsistencies. However, genotyping is less automated in GeneMapper® version 4.0 than in the Affymetrix software and thus more time consuming. ( Journal of Biomolecular Screening 2009:92-96)

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Mason, Annaliese S., Erin E. Higgins, Rod J. Snowdon, Jacqueline Batley, Anna Stein, Christian Werner, and Isobel A. P. Parkin. "A user guide to the Brassica 60K Illumina Infinium™ SNP genotyping array." Theoretical and Applied Genetics 130, no. 4 (February 20, 2017): 621–33. http://dx.doi.org/10.1007/s00122-016-2849-1.

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Dash, S., A. Singh, A. K. Bhatia, S. Jayakumar, A. Sharma, S. Singh, I. Ganguly, and S. P. Dixit. "Evaluation of Bovine High-Density SNP Genotyping Array in Indigenous Dairy Cattle Breeds." Animal Biotechnology 29, no. 2 (June 21, 2017): 129–35. http://dx.doi.org/10.1080/10495398.2017.1329150.

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Gondro, Cedric, Laercio R. Porto-Neto, and Seung Hwan Lee. "snpqc- an R pipeline for quality control of Illumina SNP genotyping array data." Animal Genetics 45, no. 5 (July 18, 2014): 758–61. http://dx.doi.org/10.1111/age.12198.

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Sanada, Masashi, Yasuhito Nannya, Kumi Nakazaki, Go Yamamoto, Lili Wang, Noriko Hosoya, Akira Hangaishi, Mineo Kurokawa, Shigeru Chiba, and Seishi Ogawa. "Genome-Wide Analysis of Copy Number Analysis of Myelodysplastic Syndromes Using High-Density SNP-Genotyping Microarrays." Blood 106, no. 11 (November 16, 2005): 3420. http://dx.doi.org/10.1182/blood.v106.11.3420.3420.

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Abstract Myelodysplastic syndromes (MDS) are clonal disorders of hematopoietic progenitors characterized by impaired blood cell production due to ineffective hematopoiesis and high propensity to acute myeloid leukemias. One of the prominent features of MDS is the high frequency of unbalanced chromosomal abnormalities that result in genetic imbalances and copy number alterations. Although the chromosomal segments involved in these abnormalities are thought to contain relevant genes to the pathogenesis of MDS, conventional analyses including FISH have failed to identify critical regions small enough to pinpoint their target genes. Affymetrix® GeneChip® 100K/500K mapping arrays were originally developed for large-scale genotyping of more than 100,000/500,000 SNPs in two separate arrays, but the quantitative nature of the preparative whole-genome amplification and array hybridization thereafter also allows for accurate copy number estimate of the genome using these platforms at the resolutions of 21.3 kb and 5.4 kb with 116,204 and 520,000 oligonucleotide probes, respectively. Here we developed robust algorithms (CNAG) for copy number detection using 100K and/or 500K arrays and analyzed 88 MDS samples on these platforms in order to identify relevant genes for development of MDS. With these huge numbers of uniformly distributed SNP probes, numerous copy number alterations were sensitively detected in cases with MDS with more numbers of abnormalities found in advanced diseases (RAEB and RAEB-t). In addition to large-scale alterations of various chromosomal segments previously reported in these syndromes, a number of small cryptic chromosomal abnormalities were identified that would escape conventional cytogenetic analysis or array CGH analysis. Minimum overlapping deletions in 5q, 7q, 12p, 13q, and 20q were precisely defined, although no pinpoint homozygous deletions were detected within these regions. A common 20q deletion spans a 400 kb segment harboring five transcriptomes and the common 12p deletion defines a 1.3 Mb region that contains the ETV6 gene. Other common overlapping abnormalities include deletions in 21q22, 17q13, and gains of 11q25. Genome-wide analysis of copy number changes using high-density oligonucleotide arrays provides valuable information about genetic abnormalities in MDS.

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Jankowska, Anna M., Bartlomiej P. Przychodzen, Lukasz P. Gondek, and Jaroslaw P. Maciejewski. "SNP Arrays Facilitate Genotyping of Non-Synonymous SNP in MDS To Identify Disease Susceptibility Loci." Blood 110, no. 11 (November 16, 2007): 2421. http://dx.doi.org/10.1182/blood.v110.11.2421.2421.

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Abstract Myelodysplastic syndrome (MDS) is a clonal premalignant disease of hematopoietic stem cells characterized by cytopenias and predilection to acute myeloid leukemia (AML). While various exogenous factors (exemplified by chemotherapy-related MDS) constitute known risks for the development of MDS, it is possible that despite long latency, complex genetic traits contribute to MDS susceptibility. Such heritable factors include genes involving DNA repair, apoptosis, senescence, carcinogen catabolism and immune surveillance. Previously, disease association studies were mainly empiric and relied on rational selection of a very limited number of polymorphisms. Recent advances of SNP-array (SNP-A) technology allow for screening of a large number of SNPs. While some SNP-A utilize haplotype tags, custom arrays may specifically target known non-synonymous SNPs. We hypothesized that application of SNP-A genotyping may facilitate identification of potentially pathogenic SNPs. Such a screening approach is a hypothesis forming tool and our study is the first application of this technique to MDS. We have used the 13.9K non-synonymous Genotyping BeadChip (Illumina); DNA from 151 MDS patients (low risk: N=79, advanced: N=51, CMML1/2: N=21) and 99 controls (120 historical controls). In total, ∼2.4 mil genotypes were obtained. Genotype calls were computed and analyzed with Exemplar software. In the initial training Bonferroni correction was not applied. Instead as a hypothesis-forming approach we have ranked all SNPs according to their p value (automated analysis of multiplexed statistical evidence) and case/control ratio. We focused our search on the 100 highest ranking SNPs with a control frequency <5%. Globally, in the whole group 49 SNPs showed a p value of <.001, 75 SNPs present in ≤1% of controls and were found in >5% of cases. For example, the AA (rs3219484) variant of MUTYH, a gene involved in oxidative DNA repair was found in 19% of MDS vs. 2.6% of controls (p=9×10−8). To limit the impact of heterogeneity, subgroups of MDS were also analyzed separately. Among many interesting SNPs found, the AG genotype of (rs8192297) ANPEP was associated with RARS (35% vs. 15% in controls; p=.007). Similarly, the GA form of rs3730947 in DNA repair gene LIG1 was found in 11% of RARS patients (p=.00045), though it was absent in other MDS subtypes and controls. Similar, “enrichment” was observed in patients with CMML1/2, showing e.g., heterozygosity of WDR35 (rs1060742), ALPK2 (rs3809975) at the frequency of 45% and 30% (13% and 4% of controls; p=.0006, p=.0001). In sum, our study constitutes the first application of SNP-A genotyping to study susceptibility loci in MDS.

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Li, Ming, Yalu Wen, and Wenjiang Fu. "A Single-Array-Based Method for Detecting Copy Number Variants Using Affymetrix High Density SNP Arrays and its Application to Breast Cancer." Cancer Informatics 13s4 (January 2014): CIN.S15203. http://dx.doi.org/10.4137/cin.s15203.

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Cumulative evidence has shown that structural variations, due to insertions, deletions, and inversions of DNA, may contribute considerably to the development of complex human diseases, such as breast cancer. High-throughput genotyping technologies, such as Affymetrix high density single-nucleotide polymorphism (SNP) arrays, have produced large amounts of genetic data for genome-wide SNP genotype calling and copy number estimation. Meanwhile, there is a great need for accurate and efficient statistical methods to detect copy number variants. In this article, we introduce a hidden-Markov-model (HMM)-based method, referred to as the PICR-CNV, for copy number inference. The proposed method first estimates copy number abundance for each single SNP on a single array based on the raw fluorescence values, and then standardizes the estimated copy number abundance to achieve equal footing among multiple arrays. This method requires no between-array normalization, and thus, maintains data integrity and independence of samples among individual subjects. In addition to our efforts to apply new statistical technology to raw fluorescence values, the HMM has been applied to the standardized copy number abundance in order to reduce experimental noise. Through simulations, we show our refined method is able to infer copy number variants accurately. Application of the proposed method to a breast cancer dataset helps to identify genomic regions significantly associated with the disease.

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Stephens, Alex J., Flavia Huygens, John Inman-Bamber, Erin P. Price, Graeme R. Nimmo, Jacqueline Schooneveldt, Wendy Munckhof, and Philip M. Giffard. "Methicillin-resistant Staphylococcus aureus genotyping using a small set of polymorphisms." Journal of Medical Microbiology 55, no. 1 (January 1, 2006): 43–51. http://dx.doi.org/10.1099/jmm.0.46157-0.

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The aim of this study was to identify a set of genetic polymorphisms that efficiently divides methicillin-resistant Staphylococcus aureus (MRSA) strains into groups consistent with the population structure. The rationale was that such polymorphisms could underpin rapid real-time PCR or low-density array-based methods for monitoring MRSA dissemination in a cost-effective manner. Previously, the authors devised a computerized method for identifying sets of single nucleotide polymorphisms (SNPs) with high resolving power that are defined by multilocus sequence typing (MLST) databases, and also developed a real-time PCR method for interrogating a seven-member SNP set for genotyping S. aureus. Here, it is shown that these seven SNPs efficiently resolve the major MRSA lineages and define 27 genotypes. The SNP-based genotypes are consistent with the MRSA population structure as defined by eburst analysis. The capacity of binary markers to improve resolution was tested using 107 diverse MRSA isolates of Australian origin that encompass nine SNP-based genotypes. The addition of the virulence-associated genes cna, pvl and bbp/sdrE, and the integrated plasmids pT181, pI258 and pUB110, resolved the nine SNP-based genotypes into 21 combinatorial genotypes. Subtyping of the SCCmec locus revealed new SCCmec types and increased the number of combinatorial genotypes to 24. It was concluded that these polymorphisms provide a facile means of assigning MRSA isolates into well-recognized lineages.

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Klitø, Niels G. F., Qihua Tan, Mette Nyegaard, Klaus Brusgaard, Mads Thomassen, Charlotte Skouboe, Jesper Dahlgaard, and Torben A. Kruse. "Arrayed Primer Extension in the “Array of Arrays” Format: A Rational Approach for Microarray-Based SNP Genotyping." Genetic Testing 11, no. 2 (June 2007): 160–66. http://dx.doi.org/10.1089/gte.2007.9998.

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Lü, Yan, Yulin Jiang, Xiya Zhou, Na Hao, Guizhen Lü, Xiangxue Guo, Ruidong Guo, et al. "Evaluation and Analysis of Absence of Homozygosity (AOH) Using Chromosome Analysis by Medium Coverage Whole Genome Sequencing (CMA-seq) in Prenatal Diagnosis." Diagnostics 13, no. 3 (February 2, 2023): 560. http://dx.doi.org/10.3390/diagnostics13030560.

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Objective: Absence of homozygosity (AOH) is a genetic characteristic known to cause human diseases mainly through autosomal recessive or imprinting mechanisms. The importance and necessity of accurate AOH detection has become more clinically significant in recent years. However, it remains a challenging task for sequencing-based methods thus far. Methods: In this study, we developed and optimized a new bioinformatic algorithm based on the assessment of minimum sequencing coverage, optimal bin size, the Z-score threshold of four types of allele count and the frequency for accurate genotyping using 28 AOH negative samples, and redefined the AOH detection cutoff value. We showed the performance of chromosome analysis by five-fold coverage whole genome sequencing (CMA-seq) for AOH identification in 27 typical prenatal/postnatal AOH positive samples, which were previously confirmed by chromosomal microarray analysis with single nucleotide polymorphism array (CMA/SNP array). Results: The blinded study indicated that for all three forms of AOH, including whole genomic AOH, single chromosomal AOH and segmental AOH, and all kinds of sample types, including chorionic villus sampling, amniotic fluid, cord blood, peripheral blood and abortive tissue, CMA-seq showed equivalent detection power to that of routine CMA/SNP arrays (750K). The subtle difference between the two methods is that CMA-seq is prone to detect small inconsecutive AOHs, while CMA/SNP array reports it as a whole. Conclusion: Based on our newly developed bioinformatic algorithm, it is feasible to detect clinically significant AOH using CMA-seq in prenatal diagnosis.

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Lamb, Harrison J., Ben J. Hayes, Imtiaz A. S. Randhawa, Loan T. Nguyen, and Elizabeth M. Ross. "Genomic prediction using low-coverage portable Nanopore sequencing." PLOS ONE 16, no. 12 (December 15, 2021): e0261274. http://dx.doi.org/10.1371/journal.pone.0261274.

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Most traits in livestock, crops and humans are polygenic, that is, a large number of loci contribute to genetic variation. Effects at these loci lie along a continuum ranging from common low-effect to rare high-effect variants that cumulatively contribute to the overall phenotype. Statistical methods to calculate the effect of these loci have been developed and can be used to predict phenotypes in new individuals. In agriculture, these methods are used to select superior individuals using genomic breeding values; in humans these methods are used to quantitatively measure an individual’s disease risk, termed polygenic risk scores. Both fields typically use SNP array genotypes for the analysis. Recently, genotyping-by-sequencing has become popular, due to lower cost and greater genome coverage (including structural variants). Oxford Nanopore Technologies’ (ONT) portable sequencers have the potential to combine the benefits genotyping-by-sequencing with portability and decreased turn-around time. This introduces the potential for in-house clinical genetic disease risk screening in humans or calculating genomic breeding values on-farm in agriculture. Here we demonstrate the potential of the later by calculating genomic breeding values for four traits in cattle using low-coverage ONT sequence data and comparing these breeding values to breeding values calculated from SNP arrays. At sequencing coverages between 2X and 4X the correlation between ONT breeding values and SNP array-based breeding values was > 0.92 when imputation was used and > 0.88 when no imputation was used. With an average sequencing coverage of 0.5x the correlation between the two methods was between 0.85 and 0.92 using imputation, depending on the trait. This suggests that ONT sequencing has potential for in clinic or on-farm genomic prediction, however, further work to validate these findings in a larger population still remains.

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Scionti, Francesca, Maria Di Martino, Licia Pensabene, Valentina Bruni, and Daniela Concolino. "The Cytoscan HD Array in the Diagnosis of Neurodevelopmental Disorders." High-Throughput 7, no. 3 (September 14, 2018): 28. http://dx.doi.org/10.3390/ht7030028.

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Submicroscopic chromosomal copy number variations (CNVs), such as deletions and duplications, account for about 15–20% of patients affected with developmental delay, intellectual disability, multiple congenital anomalies, and autism spectrum disorder. Most of CNVs are de novo or inherited rearrangements with clinical relevance, but there are also rare inherited imbalances with unknown significance that make difficult the clinical management and genetic counselling. Chromosomal microarrays analysis (CMA) are recognized as the first-line test for CNV detection and are now routinely used in the clinical diagnostic laboratory. The recent use of CMA platforms that combine classic copy number analysis with single-nucleotide polymorphism (SNP) genotyping has increased the diagnostic yields. Here we discuss the application of the Cytoscan high-density (HD) SNP-array for the detection of CNVs. We provide an overview of molecular analyses involved in identifying pathogenic CNVs and highlight important guidelines to establish pathogenicity of CNV.

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Ballesta, Paulina, David Bush, Fabyano Fonseca Silva, and Freddy Mora. "Genomic Predictions Using Low-Density SNP Markers, Pedigree and GWAS Information: A Case Study with the Non-Model Species Eucalyptus cladocalyx." Plants 9, no. 1 (January 13, 2020): 99. http://dx.doi.org/10.3390/plants9010099.

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High-throughput genotyping techniques have enabled large-scale genomic analysis to precisely predict complex traits in many plant species. However, not all species can be well represented in commercial SNP (single nucleotide polymorphism) arrays. In this study, a high-density SNP array (60 K) developed for commercial Eucalyptus was used to genotype a breeding population of Eucalyptus cladocalyx, yielding only ~3.9 K informative SNPs. Traditional Bayesian genomic models were investigated to predict flowering, stem quality and growth traits by considering the following effects: (i) polygenic background and all informative markers (GS model) and (ii) polygenic background, QTL-genotype effects (determined by GWAS) and SNP markers that were not associated with any trait (GSq model). The estimates of pedigree-based heritability and genomic heritability varied from 0.08 to 0.34 and 0.002 to 0.5, respectively, whereas the predictive ability varied from 0.19 (GS) and 0.45 (GSq). The GSq approach outperformed GS models in terms of predictive ability when the proportion of the variance explained by the significant marker-trait associations was higher than those explained by the polygenic background and non-significant markers. This approach can be particularly useful for plant/tree species poorly represented in the high-density SNP arrays, developed for economically important species, or when high-density marker panels are not available.

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Chu, Y., C. C. Holbrook, T. G. Isleib, M. Burow, A. K. Culbreath, B. Tillman, J. Chen, J. Clevenger, and P. Ozias-Akins. "Phenotyping and genotyping parents of sixteen recombinant inbred peanut populations." Peanut Science 45, no. 1 (January 1, 2018): 1–11. http://dx.doi.org/10.3146/ps17-17.1.

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ABSTRACT In peanut (Arachis hypogaea L.), most agronomically important traits such as yield, disease resistance, and pod and kernel characteristics are quantitatively inherited. Phenotypic selection of these traits in peanut breeding programs can be augmented by marker-assisted selection. However, reliable associations between unambiguous genetic markers and phenotypic traits have to be established by genetic mapping prior to early generation marker-assisted selection. Previously, a nested association mapping (NAM) population of 16 recombinant inbred line populations (RILs) consisting 4870 lines was established. In order to facilitate effective mapping of such a large genetic resource, the first objective of the current study was to phenotype the parental lines for yield, pod traits, field maturity, germination, plant morphology, salt tolerance and resistance to tomato spotted wilt virus (TSWV) and late leaf spot (LLS). For most measured traits, more than one parental combination demonstrated statistically significant variation which can be further quantified and mapped in the respective RIL populations. The second objective of this study was to genotype the parental lines using the Arachis Axiom SNP arrays to reveal the marker density of the mapping populations. The Version 1 array identified 1,000 to 4,000 SNPs among the population parents and the number of SNPs doubled on the Version 2 array. Further phenotyping and genotyping of the NAM populations will allow the construction of high density genetic maps containing quantitative trait loci.

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Duval, Henri, Eva Coindre, Sebastian E. Ramos-Onsins, Konstantinos G. Alexiou, Maria J. Rubio Cabetas, Pedro J. Martínez-García, Michelle Wirthensohn, Amit Dhingra, Anna Samarina, and Pere Arús. "Development and Evaluation of an AxiomTM 60K SNP Array for Almond (Prunus dulcis)." Plants 12, no. 2 (January 5, 2023): 242. http://dx.doi.org/10.3390/plants12020242.

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A high-density single nucleotide polymorphism (SNP) array is essential to enable faster progress in plant breeding for new cultivar development. In this regard, we have developed an Axiom 60K almond SNP array by resequencing 81 almond accessions. For the validation of the array, a set of 210 accessions were genotyped and 82.8% of the SNPs were classified in the best recommended SNPs. The rate of missing data was between 0.4% and 2.7% for the almond accessions and less than 15.5% for the few peach and wild accessions, suggesting that this array can be used for peach and interspecific peach × almond genetic studies. The values of the two SNPs linked to the RMja (nematode resistance) and SK (bitterness) genes were consistent. We also genotyped 49 hybrids from an almond F2 progeny and could build a genetic map with a set of 1159 SNPs. Error rates, less than 1%, were evaluated by comparing replicates and by detection of departures from Mendelian inheritance in the F2 progeny. This almond array is commercially available and should be a cost-effective genotyping tool useful in the search for new genes and quantitative traits loci (QTL) involved in the control of agronomic traits.

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Nugent, Cameron M., Jong S. Leong, Kris A. Christensen, Eric B. Rondeau, Matthew K. Brachmann, Anne A. Easton, Christine L. Ouellet-Fagg, et al. "Design and characterization of an 87k SNP genotyping array for Arctic charr (Salvelinus alpinus)." PLOS ONE 14, no. 4 (April 5, 2019): e0215008. http://dx.doi.org/10.1371/journal.pone.0215008.

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Kwong, Qi Bin, Chee Keng Teh, Ai Ling Ong, Huey Ying Heng, Heng Leng Lee, Mohaimi Mohamed, Joel Zi-Bin Low, et al. "Development and Validation of a High-Density SNP Genotyping Array for African Oil Palm." Molecular Plant 9, no. 8 (August 2016): 1132–41. http://dx.doi.org/10.1016/j.molp.2016.04.010.

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Massa, Alicia N., Marina Bressano, Juan H. Soave, Mario I. Buteler, Guillermo Seijo, Victor S. Sobolev, Valerie A. Orner, et al. "Genotyping tools and resources to assess peanut germplasm: smut-resistant landraces as a case study." PeerJ 9 (January 29, 2021): e10581. http://dx.doi.org/10.7717/peerj.10581.

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Peanut smut caused by Thecaphora frezii is a severe fungal disease currently endemic to Argentina and Brazil. The identification of smut resistant germplasm is crucial in view of the potential risk of a global spread. In a recent study, we reported new sources of smut resistance and demonstrated its introgression into elite peanut cultivars. Here, we revisited one of these sources (line I0322) to verify its presence in the U.S. peanut germplasm collection and to identify single nucleotide polymorphisms (SNPs) potentially associated with resistance. Five accessions of Arachis hypogaea subsp. fastigiata from the U.S. peanut collection, along with the resistant source and derived inbred lines were genotyped with a 48K SNP peanut array. A recently developed SNP genotyping platform called RNase H2 enzyme-based amplification (rhAmp) was further applied to validate selected SNPs in a larger number of individuals per accession. More than 14,000 SNPs and nine rhAmp assays confirmed the presence of a germplasm in the U.S. peanut collection that is 98.6% identical (P < 0.01, bootstrap t-test) to the resistant line I0322. We report this germplasm with accompanying genetic information, genotyping data, and diagnostic SNP markers.

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Yu, Yuan, Chunxian Chen, Ming Huang, Qibin Yu, Dongliang Du, Matthew R. Mattia, and Frederick G. Gmitter. "Genetic Diversity and Population Structure Analysis of Citrus Germplasm with Single Nucleotide Polymorphism Markers." Journal of the American Society for Horticultural Science 143, no. 6 (November 2018): 399–408. http://dx.doi.org/10.21273/jashs04394-18.

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Citrus (Citrus sp.) germplasm collections are a valuable resource for citrus genetic breeding studies, and further utilization of the resource requires knowledge of their genotypic and phylogenetic relationships. Diverse citrus accessions, including citron (Citrus medica), mandarin (Citrus reticulata), pummelo (Citrus maxima), papeda (Papeda sp.), trifoliate orange (Poncirus trifoliata), kumquat (Fortunella sp.), and related species, have been housed at the Florida Citrus Arboretum, Winter Haven, FL, but the accessions in the collection have not been genotyped. In this study, a collection of 80 citrus accessions were genotyped using 1536 sweet orange–derived single nucleotide polymorphism (SNP) markers, to determine their SNP fingerprints and to assess genetic diversity, population structure, and phylogenetic relationships, and thereby to test the efficiency of using the single genotype-derived SNP chip with relatively low cost for these analyses. Phylogenetic relationships among the 80 accessions were determined by multivariate analysis. A model-based clustering program detected five basic groups and revealed that C. maxima introgressions varied among mandarin cultivars and segregated in mandarin F1 progeny. In addition, reciprocal differences in C. maxima contributions were observed among citranges (Citrus sinensis × P. trifoliata vs. P. trifoliata × C. sinensis) and may be caused by the influence of cytoplasmic DNA and its effect on selection of cultivars. Inferred admixture structures of many secondary citrus species and important cultivars were confirmed or revealed, including ‘Bergamot’ sour orange (Citrus aurantium), ‘Kinkoji’ (C. reticulata × Citrus paradisi), ‘Hyuganatsu’ orange (Citrus tamurana), and palestine sweet lime (Citrus aurantifolia). The relatively inexpensive SNP array used in this study generated informative genotyping data and led to good consensus and correlations with previously published observations based on whole genome sequencing (WGS) data. The genotyping data and the phylogenetic results may facilitate further exploitation of interesting genotypes in the collection and additional understanding of phylogenetic relationships in citrus.

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Teumer, Alexander, Florian D. Ernst, Anja Wiechert, Katharina Uhr, Matthias Nauck, Astrid Petersmann, Henry Völzke, Uwe Völker, and Georg Homuth. "Comparison of genotyping using pooled DNA samples (allelotyping) and individual genotyping using the affymetrix genome-wide human SNP array 6.0." BMC Genomics 14, no. 1 (2013): 506. http://dx.doi.org/10.1186/1471-2164-14-506.

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Gondek, Lukasz P., Hemant Ishwaran, Andrew Jeffrey Dunbar, Christine L. O’Keefe, Michael A. McDevitt, Denise Batista, Mikkael A. Sekeres, Ghulam J. Mufti, and Jaroslaw Maciejewski. "Array-Based Karyotyping and Genotyping Demonstrates a Non Random Selection of Allelic Variants of Genes in Clones with 5q31 Deletion Mutants." Blood 112, no. 11 (November 16, 2008): 2057. http://dx.doi.org/10.1182/blood.v112.11.2057.2057.

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Abstract Interstitial deletion of chromosome 5 has been frequently reported in acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) pointing towards the pathogenic role of this region in phenotype and clonal evolution. To investigate the frequency of 5q LOH and better delineate the commonly deleted region (CDR) we applied metaphase cytogenetics (MC) and performed array-based interphase cytogenetics on DNA using high-density 250K SNP-array (SNP-A) in malignant myeloid disorders. SNP-A analysis was performed using Affymetrix 250K SNP-array on a subset of 250 patients and 118 controls. SNP-A data were analyzed using CNAG v.3.0. Using SNP-A-based karyotyping 5q abnormalities were identified in 42/250 patients vs. 29/250 by MC (17% vs. 11%, primarily as a result of resolving uninformative MC). By SNP-A, previously cryptic lesions other than 5q deletions were identified in 71% of the patients (30/42) and included e.g., upd(1)(p35.1pter), upd(17)(p13.1pter), del(7)(q21.3q36.2). In 2 patients somatic UPD5q was found. In 6 other patients 5q micro-deletions of chromosome 5 were detected likely representing CNVs. Subsequently, we undertook an SNP-A-based definition of the CDR covering approximately 1.92MB and positioned within previously reported regions. This region spans approximately from base pair 137,528,564-139,451,907 and several candidate tumor suppressor genes including those already reported e.g., CTNNA1 and EGR1 as well as CDC25, ETF1 to name a few. As mutations in any of the genes in CDR on 5q were not found, the malignant phenotype can result either from haploinsufficiency or hemizygozity for a pathogenic allele occurring otherwise in heterozygous or major allele in homozygous constellation. Previously, underexpression of RPS14 was demonstrated to be responsible for dysplastic features in 5q- syndrome, but haploinsufficiency of this gene does not explain the clonal evolution and malignant properties of clones with del5q. Utilizing another advantage of SNP-A, the ability to assign genotypes, we also performed analysis of the allele distribution within newly defined CRD on 5q31. We genotyped 987 SNPs located in the common area of LOH (5q31) to determine whether for certain loci allelic distribution in the hemizygous deletion mutant is skewed to one or the other allele (when the original diploid constellation is heterozygous). For the purpose of this study we hypothesized that informative alleles must display a very low frequency in homozygous constellation in controls. To test if the distribution of remaining alleles (and the inherent change of genotype) in the deleted region on 5q is random or skewed towards one allelic variant we applied a multinomial test statistics. Because of the discrete nature of the problem, p-values were calculated by selecting the minimum of the left or right tail of the event spectrum. This value was computed without approximation by using the exact form of the binomial distribution. We used the smaller of the two p-values from the two binomial models as our reported p-value. SNPs present in ARHGAP26 locus appeared to be most significantly skewed (p<.004 for 3 SNP loci within gene: rs2028268, rs3776227, rs17100139). For the alleles located in this gene one would expect that 14% of patient will be hemizygous for minor and 96% for major allele respectively. However, we have observed that 57% of clones showed minor constellation. ARHGAP26 and its function as a tumor suppressor may indicate involvement in the pathology and disease progression. In sum, we demonstrated that a combined genotypic and cytogenetic analysis is possible using SNP-A to investigate areas of LOH for the presence of genotypes which may convey selection advantage.

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Takita, Junko, Motohiro Kato, Fumihiko Nakamura, Yuyan Chen, Go Yamamoto, Yasuhito Nannya, Masashi Sanada, et al. "High-Resolution Analyses of Genetic and Epigenetic Aberrations in Infant Leukemia with MLL Rearrangement." Blood 110, no. 11 (November 16, 2007): 4238. http://dx.doi.org/10.1182/blood.v110.11.4238.4238.

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Abstract MLL rearrangement-positive leukemia is one of the most aggressive types of leukemia. It is diagnosed predominantly in infants and typically shows a multilineage phenotype. Since current chemotherapy fails in more than 50% of infantile leukemia with MLL rearrangement, a better understanding of biological features of the disease is importantly in order to develop more specific and successful treatment strategies. Thus, to explore both genetic and epigenetic lesions associated with MLL rearrangement-positive infantile leukemia, we performed genome-wide analyses of copy number alterations/allelic imbalances as well as methylation analysis using Affymetrix GeneChip SNP genotyping microarrays and promoter tiling array combined with methylated DNA immunoprecipitation (MeDIP). Combined with newly developed algorithm, CNAG/AsCNAR, SNP array analysis enables accurate copy number analysis at extremely high resolutions. In addition, by sensing subtle distortions in allele-specific signals caused by allelic imbalance using anonymous controls, sensitive detection of LOH is enabled with accurate determination of allele-specific copy numbers even in the face of up to 70–80% normal cell contamination. In total, 25 specimens from MLL rearrangement-positive leukemia were analyzed using high-density SNP-genotyping microarrays (Affymetrix GeneChip 100K/500K arrays). While unbalanced translocation involving chromosome 11q23 is the most frequent genetic alterations, uniparental disomy of 17q is also common genetic alterations in MLL rearrangement-positive leukemia. A number of other genetic changes were also identified but these were mostly found in a single case. On the other hand, epigenetic abnormalities have been implicated in MLL rearrangement-positive leukemia, because MLL is known to be involved in epigenetic regulations. In our assay, fragmented genomic DNA from leukemia specimens was immunoprecipitated with anti-methylcytosine antibody (MeDIP). The immunoprecipitated DNA was amplified by PCR and subjected to hybridization to the promoter tiling array, in which regulatory regions of more than 25,000 genes are tiled by 6.5 millions of oligonucleotide probes to enable sensitive detection of target sequences. This tiling array covers approximate 59% of CpG islands in the human genomes. In addition to the previously described genes, such as FHIT and HOX family, a number of tumor specific methylated sites were identified in the leukemic cells and which were subsequently verified by bisulfate sequencing. These results indicated that high-resolution analyses of genetic and epigenetic aberrations using microarray techniques are powerful and useful for detection of new findings in the pathogenesis of infant leukemia with MLL rearrangement.

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Gadi, Inder K., Peter Papenhausen, Stuart Schwartz, and James Tepperberg. "A Novel Look at MDS Patients: Utilization and Effectiveness of a SNP Microarray for the Detection of Both Copy Number and Copy Neutral Changes." Blood 116, no. 21 (November 19, 2010): 4846. http://dx.doi.org/10.1182/blood.v116.21.4846.4846.

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Abstract Abstract 4846 Myelodysplastic syndrome (MDS), includes a variety of hematological dysplasias that can be divided into high grade or low grade disease. Individuals with high grade MDS have an increased chance of having their disease progress to Acute Myelogenous Leukemia. Both standard chromosomal analysis and fluorescence in-situ hybridization (FISH) are utilized to detect abnormal clones aiding in the diagnosis and prognosis of the patient. FISH probes can be used to detect a deletion of 5q, 7q and 20p as well as trisomy 8 in frequently used routinely panels. Both standard cytogenetic analysis and FISH analysis can detect abnormalities in approximately 35–40% of MDS patients. The promise of microarray analysis of MDS clones is the 100x resolution power compared to routine chromosome analysis in identifying clonal genetic alterations and the comprehensive genomic coverage compared to the limited targets in routine FISH analysis. In order to validate microarray analysis and verify its usefulness for studying CLL, we have examined 27 patients, including both normal (19) and abnormal (8) patients using the Affymetrix SNP 6.0 microarray. The studies have indicated a number of interesting and important findings including: (1) Of the 19 normal cases, 7 clinically significant abnormalities were detected by the array analysis (37%), indicative of the usefulness of SNP array analysis rather than FISH; (2) The remaining 8 cases had at least one abnormality which was detected by either cytogenetics or FISH. Six of these cases (75%) showed additional abnormalities by the array analysis; (3) There were a number of potentially important oncogene deletions identified by the array analysis, including: miRNA 15–16, RUNX1, NFAT5, TET2, IGK, BCL2, MYC, PTCH1 and ETV6; (4) The utilization of a genotyping array proved to be extremely valuable since there were five cases (18.5%) with UPD. [UPD1, UPD4, UPD12, UPD17 and UPD 22]. The majority of these were segmental except chromosome 22 and were detected in the patients that already demonstrated abnormalities; (5) The array could detect every abnormality detected by FISH that was present in at least 14.5% of the cells. These studies clearly show the importance of utilizing genotyping array analysis to study patients with MDS through both 100x improved resolution over cytogenetics as well as offering the capability to identify “silent” clonal evolution based copy neutral changes. In particular, the high percent of abnormalities detected in patients considered normal by FISH and chromosome analysis is extremely important for establishing a true genetic basis for the MDS. The large percent of copy neutral changes detected by the genotyping array is intriguing and likely to be proven important for the prognosis of the patient. Additionally, the array has been very useful in better clarifying abnormalities seen by cytogenetic analysis that cannot be fully delineated. The high success rates are likely to include blood sample analysis, so that marrow aspirate may not be mandatory. Based on our referral pattern- using SNP microarray allows for better diagnostic information in 46% of cases. Disclosures: No relevant conflicts of interest to declare.

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Calvo, Jorge H., Magdalena Serrano, Flavie Tortereau, Pilar Sarto, Laura P. Iguacel, María A. Jiménez, José Folch, José L. Alabart, Stéphane Fabre, and Belén Lahoz. "Development of a SNP parentage assignment panel in some North-Eastern Spanish meat sheep breeds." Spanish Journal of Agricultural Research 18, no. 4 (October 27, 2020): e0406. http://dx.doi.org/10.5424/sjar/2020184-16805.

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Aim of study: To validate two existing single nucleotide polymorphism (SNP) panels for parentage assignment in sheep, and develop a cost effective genotyping system to use in some North-Eastern Spanish meat sheep populations for accurate pedigree assignment.Area of study: SpainMaterial and methods: Nine sheep breeds were sampled: Rasa Aragonesa (n=38), Navarra (n=39), Ansotana (n=41), Xisqueta (n=41), Churra Tensina (n=38), Maellana (39), Roya Bilbilitana (n=24), Ojinegra (n=36) and Cartera (n=39), and these animals were genotyped with the Illumina OvineSNP50 BeadChip array. Genotypes were extracted from the sets of 249 SNPs and 163 SNPs for parentage assignment designed in France and North America, respectively. Validation of a selected cost-effective genotyping panel of 158 SNPs from the French panel were performed by Kompetitive allele specific PCR (KASP). Additionally, some functional SNPs (n=15) were also genotyped.Main results: The set of 249 SNPs for parentage assignment showed better diversity, probability of identity, and exclusion probabilities than the set of 163 SNPs. The average minor allele frequency for the set of 249, 163 and 158 SNPs were 0.41 + 0.01, 0.39 + 0.01 and 0.42 + 0.01, respectively. The parentage assignment rate was highly dependent to the percentage of putative sires genotyped.Research highlights: The described method is a cost-effective genotyping system combining the genotyping of SNPs for the parentage assignment with some functional SNPs, which was successfully used in some Spanish meat sheep breeds.

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Journal articles on the topic 'SNP array genotyping'

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